``` r
interacting_miRNAs_high0.5 <- unique(high0.5_cor_bind_FA$miRNA) %>% na.omit
results_high0.5_cor_targets <- NULL  # initialize empty df

for(miRNA in interacting_miRNAs_high0.5) {
  
  # Run topGO enrichment function
  miRNA_results <- miRNA_topGO_FE(miRNA, high0.5_cor_bind_FA)
  
  # Only keep results if not empty
  if (nrow(miRNA_results) > 0) {
    
    # Add the miRNA source column
    miRNA_results$miRNA <- miRNA

    # Bind to the accumulating results data frame
    results_high0.5_cor_targets <- rbind(results_high0.5_cor_targets, miRNA_results)
  }
}
```

```
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 34 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(3 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(6 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(14 eliminated genes)
```

```
## 
## 	 Level 5:	5 nodes to be scored	(16 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(16 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(211 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(672 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(778 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 38 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 8:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	5 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	5 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 5:	7 nodes to be scored	(160 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(166 eliminated genes)
```

```
## 
## 	 Level 3:	7 nodes to be scored	(472 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(1024 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1779 eliminated genes)
```

```
##        GO.ID                                               Term Annotated
## 1 GO:0006598                        polyamine catabolic process         3
## 2 GO:0001745                         compound eye morphogenesis         3
## 3 GO:0000014 single-stranded DNA endodeoxyribonuclease activity         3
## 4 GO:0005290     L-histidine transmembrane transporter activity         9
##   Significant Expected Fisher               type
## 1           1     0.00 0.0042 Biological.Process
## 2           1     0.00 0.0042 Biological.Process
## 3           1     0.01 0.0065 Molecular.Function
## 4           1     0.02 0.0193 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 42 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 15:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 14:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 13:	1 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 11:	3 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 10:	3 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 9:	5 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(72 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(125 eliminated genes)
```

```
## 
## 	 Level 4:	4 nodes to be scored	(138 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(209 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(239 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(246 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 57 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	5 nodes to be scored	(371 eliminated genes)
```

```
## 
## 	 Level 6:	9 nodes to be scored	(409 eliminated genes)
```

```
## 
## 	 Level 5:	12 nodes to be scored	(561 eliminated genes)
```

```
## 
## 	 Level 4:	10 nodes to be scored	(640 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(1150 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(1518 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2039 eliminated genes)
```

```
##        GO.ID                                             Term Annotated
## 1 GO:0001658 branching involved in ureteric bud morphogenesis         4
## 2 GO:0001945                         lymph vessel development         5
## 3 GO:0004252               serine-type endopeptidase activity        53
## 4 GO:0005201      extracellular matrix structural constituent        17
## 5 GO:0004771                         sterol esterase activity         5
##   Significant Expected Fisher               type
## 1           1     0.01 0.0057 Biological.Process
## 2           1     0.01 0.0071 Biological.Process
## 3           3     0.25 0.0016 Molecular.Function
## 4           2     0.08 0.0026 Molecular.Function
## 5           1     0.02 0.0232 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 70 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	2 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(52 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(55 eliminated genes)
```

```
## 
## 	 Level 6:	10 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 5:	14 nodes to be scored	(178 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(211 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(339 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(586 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(765 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 37 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(522 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(611 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(1263 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1841 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0001895                   retina homeostasis         2           1
## 2 GO:0004013      adenosylhomocysteinase activity         1           1
## 3 GO:0005524                          ATP binding       263           5
## 4 GO:0009034               tryptophanase activity         2           1
## 5 GO:0003964 RNA-directed DNA polymerase activity       122           3
##   Expected Fisher               type
## 1     0.01 0.0085 Biological.Process
## 2     0.00 0.0047 Molecular.Function
## 3     1.23 0.0050 Molecular.Function
## 4     0.01 0.0093 Molecular.Function
## 5     0.57 0.0171 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 73 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	2 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(52 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(55 eliminated genes)
```

```
## 
## 	 Level 6:	10 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 5:	15 nodes to be scored	(178 eliminated genes)
```

```
## 
## 	 Level 4:	12 nodes to be scored	(211 eliminated genes)
```

```
## 
## 	 Level 3:	12 nodes to be scored	(359 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(605 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(827 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 36 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(524 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(613 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(768 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1594 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0001895                   retina homeostasis         2           1
## 2 GO:0005524                          ATP binding       263           6
## 3 GO:0003964 RNA-directed DNA polymerase activity       122           4
## 4 GO:0009034               tryptophanase activity         2           1
## 5 GO:0004322                 ferroxidase activity         3           1
## 6 GO:0000287                magnesium ion binding        56           2
##   Expected Fisher               type
## 1     0.01 0.0099 Biological.Process
## 2     1.42 0.0016 Molecular.Function
## 3     0.66 0.0033 Molecular.Function
## 4     0.01 0.0108 Molecular.Function
## 5     0.02 0.0161 Molecular.Function
## 6     0.30 0.0355 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 70 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	2 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(52 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(55 eliminated genes)
```

```
## 
## 	 Level 6:	10 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 5:	14 nodes to be scored	(178 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(211 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(339 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(586 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(765 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 36 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	5 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(458 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(613 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(1265 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1594 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0001895                   retina homeostasis         2           1
## 2 GO:0009034               tryptophanase activity         2           1
## 3 GO:0004322                 ferroxidase activity         3           1
## 4 GO:0003964 RNA-directed DNA polymerase activity       122           3
## 5 GO:0005524                          ATP binding       263           4
## 6 GO:0000287                magnesium ion binding        56           2
##   Expected Fisher               type
## 1     0.01 0.0085 Biological.Process
## 2     0.01 0.0086 Molecular.Function
## 3     0.01 0.0129 Molecular.Function
## 4     0.53 0.0136 Molecular.Function
## 5     1.14 0.0211 Molecular.Function
## 6     0.24 0.0232 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 24 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	1 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(37 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(40 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(137 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(148 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(217 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(235 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(246 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 40 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	5 nodes to be scored	(270 eliminated genes)
```

```
## 
## 	 Level 5:	8 nodes to be scored	(400 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(534 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(1182 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(1465 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1794 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0002040               sprouting angiogenesis        12           1
## 2 GO:0001701       in utero embryonic development        15           1
## 3 GO:0004382             GDP phosphatase activity         3           1
## 4 GO:0003964 RNA-directed DNA polymerase activity       122           3
##   Expected Fisher               type
## 1     0.03  0.025 Biological.Process
## 2     0.03  0.032 Biological.Process
## 3     0.01  0.013 Molecular.Function
## 4     0.53  0.014 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 23 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 4:	4 nodes to be scored	(29 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(181 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(471 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(532 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## Warning in getSigGroups(object, test.stat): No enrichment can pe performed -
## there are no feasible GO terms!
```

```
##        GO.ID                                          Term Annotated
## 1 GO:0006511 ubiquitin-dependent protein catabolic process         7
##   Significant Expected Fisher               type
## 1           1        0  0.005 Biological.Process
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 115 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	4 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	7 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 8:	7 nodes to be scored	(154 eliminated genes)
```

```
## 
## 	 Level 7:	9 nodes to be scored	(161 eliminated genes)
```

```
## 
## 	 Level 6:	15 nodes to be scored	(254 eliminated genes)
```

```
## 
## 	 Level 5:	22 nodes to be scored	(378 eliminated genes)
```

```
## 
## 	 Level 4:	22 nodes to be scored	(437 eliminated genes)
```

```
## 
## 	 Level 3:	16 nodes to be scored	(830 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(1032 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1257 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 93 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	17 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	19 nodes to be scored	(540 eliminated genes)
```

```
## 
## 	 Level 4:	22 nodes to be scored	(797 eliminated genes)
```

```
## 
## 	 Level 3:	17 nodes to be scored	(1386 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(1734 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2475 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0006598                            polyamine catabolic process         3
## 2  GO:0001676                long-chain fatty acid metabolic process         3
## 3  GO:0001822                                     kidney development        65
## 4  GO:0003777                             microtubule motor activity        16
## 5  GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) ...         1
## 6  GO:0004494                      methylmalonyl-CoA mutase activity         1
## 7  GO:0005080                               protein kinase C binding         1
## 8  GO:0004190                   aspartic-type endopeptidase activity         2
## 9  GO:0005319                             lipid transporter activity         3
## 10 GO:0000016                                       lactase activity         4
##    Significant Expected Fisher               type
## 1            1     0.01 0.0130 Biological.Process
## 2            1     0.01 0.0130 Biological.Process
## 3            2     0.28 0.0280 Biological.Process
## 4            2     0.14 0.0087 Molecular.Function
## 5            1     0.01 0.0090 Molecular.Function
## 6            1     0.01 0.0090 Molecular.Function
## 7            1     0.01 0.0090 Molecular.Function
## 8            1     0.02 0.0179 Molecular.Function
## 9            1     0.03 0.0268 Molecular.Function
## 10           1     0.04 0.0356 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 115 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 14:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 13:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	3 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 11:	4 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 10:	5 nodes to be scored	(203 eliminated genes)
```

```
## 
## 	 Level 9:	6 nodes to be scored	(205 eliminated genes)
```

```
## 
## 	 Level 8:	6 nodes to be scored	(207 eliminated genes)
```

```
## 
## 	 Level 7:	8 nodes to be scored	(211 eliminated genes)
```

```
## 
## 	 Level 6:	17 nodes to be scored	(257 eliminated genes)
```

```
## 
## 	 Level 5:	25 nodes to be scored	(285 eliminated genes)
```

```
## 
## 	 Level 4:	18 nodes to be scored	(369 eliminated genes)
```

```
## 
## 	 Level 3:	12 nodes to be scored	(527 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(962 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1103 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 113 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	4 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	6 nodes to be scored	(100 eliminated genes)
```

```
## 
## 	 Level 7:	17 nodes to be scored	(396 eliminated genes)
```

```
## 
## 	 Level 6:	22 nodes to be scored	(421 eliminated genes)
```

```
## 
## 	 Level 5:	25 nodes to be scored	(544 eliminated genes)
```

```
## 
## 	 Level 4:	20 nodes to be scored	(668 eliminated genes)
```

```
## 
## 	 Level 3:	12 nodes to be scored	(1272 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(1724 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2146 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0000349 generation of catalytic spliceosome for first trans...         1
## 2  GO:0001825                                   blastocyst formation         1
## 3  GO:0000050                                             urea cycle         2
## 4  GO:0002790                                      peptide secretion         2
## 5  GO:0001734         mRNA (N6-adenosine)-methyltransferase activity         1
## 6  GO:0004777 succinate-semialdehyde dehydrogenase (NAD+) activit...         1
## 7  GO:0004067                                  asparaginase activity         1
## 8  GO:0004035                          alkaline phosphatase activity         1
## 9  GO:0004408                     holocytochrome-c synthase activity         1
## 10 GO:0008137               NADH dehydrogenase (ubiquinone) activity         1
## 11 GO:0004748 ribonucleoside-diphosphate reductase activity, thio...         1
## 12 GO:0004325                                ferrochelatase activity         1
## 13 GO:0004176                       ATP-dependent peptidase activity         2
## 14 GO:0003730                                    mRNA 3'-UTR binding         2
## 15 GO:0003824                                     catalytic activity      1042
##    Significant Expected Fisher               type
## 1            1     0.00 0.0043 Biological.Process
## 2            1     0.00 0.0043 Biological.Process
## 3            1     0.01 0.0085 Biological.Process
## 4            1     0.01 0.0085 Biological.Process
## 5            1     0.01 0.0100 Molecular.Function
## 6            1     0.01 0.0100 Molecular.Function
## 7            1     0.01 0.0100 Molecular.Function
## 8            1     0.01 0.0100 Molecular.Function
## 9            1     0.01 0.0100 Molecular.Function
## 10           1     0.01 0.0100 Molecular.Function
## 11           1     0.01 0.0100 Molecular.Function
## 12           1     0.01 0.0100 Molecular.Function
## 13           1     0.02 0.0200 Molecular.Function
## 14           1     0.02 0.0200 Molecular.Function
## 15          17    10.51 0.0280 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 332 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	4 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	7 nodes to be scored	(155 eliminated genes)
```

```
## 
## 	 Level 10:	9 nodes to be scored	(206 eliminated genes)
```

```
## 
## 	 Level 9:	21 nodes to be scored	(219 eliminated genes)
```

```
## 
## 	 Level 8:	27 nodes to be scored	(260 eliminated genes)
```

```
## 
## 	 Level 7:	40 nodes to be scored	(345 eliminated genes)
```

```
## 
## 	 Level 6:	60 nodes to be scored	(478 eliminated genes)
```

```
## 
## 	 Level 5:	66 nodes to be scored	(753 eliminated genes)
```

```
## 
## 	 Level 4:	50 nodes to be scored	(905 eliminated genes)
```

```
## 
## 	 Level 3:	34 nodes to be scored	(1097 eliminated genes)
```

```
## 
## 	 Level 2:	11 nodes to be scored	(1271 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1374 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 173 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	9 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 8:	12 nodes to be scored	(42 eliminated genes)
```

```
## 
## 	 Level 7:	19 nodes to be scored	(454 eliminated genes)
```

```
## 
## 	 Level 6:	34 nodes to be scored	(555 eliminated genes)
```

```
## 
## 	 Level 5:	36 nodes to be scored	(799 eliminated genes)
```

```
## 
## 	 Level 4:	29 nodes to be scored	(1180 eliminated genes)
```

```
## 
## 	 Level 3:	23 nodes to be scored	(1922 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(2171 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2543 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0002674     negative regulation of acute inflammatory response         4
## 2  GO:0001960 negative regulation of cytokine-mediated signaling ...         1
## 3  GO:0001967                                      suckling behavior         1
## 4  GO:0000183                         rDNA heterochromatin formation         1
## 5  GO:0000184 nuclear-transcribed mRNA catabolic process, nonsens...        10
## 6  GO:0001409 guanine nucleotide transmembrane transporter activi...        30
## 7  GO:0003682                                      chromatin binding        13
## 8  GO:0003723                                            RNA binding       128
## 9  GO:0004143                         diacylglycerol kinase activity         1
## 10 GO:0004441       inositol-1,4-bisphosphate 1-phosphatase activity         1
## 11 GO:0005289 high-affinity L-arginine transmembrane transporter ...         1
## 12 GO:0004568                                     chitinase activity         1
## 13 GO:0004033                    aldo-keto reductase (NADP) activity         1
## 14 GO:0003676                                   nucleic acid binding       497
##    Significant Expected Fisher               type
## 1            2     0.15 0.0076 Biological.Process
## 2            1     0.04 0.0369 Biological.Process
## 3            1     0.04 0.0369 Biological.Process
## 4            1     0.04 0.0369 Biological.Process
## 5            2     0.37 0.0496 Biological.Process
## 6            5     1.08 0.0038 Molecular.Function
## 7            3     0.47 0.0100 Molecular.Function
## 8           10     4.61 0.0154 Molecular.Function
## 9            1     0.04 0.0360 Molecular.Function
## 10           1     0.04 0.0360 Molecular.Function
## 11           1     0.04 0.0360 Molecular.Function
## 12           1     0.04 0.0360 Molecular.Function
## 13           1     0.04 0.0360 Molecular.Function
## 14          25    17.90 0.0412 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 117 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	4 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 7:	9 nodes to be scored	(145 eliminated genes)
```

```
## 
## 	 Level 6:	20 nodes to be scored	(169 eliminated genes)
```

```
## 
## 	 Level 5:	25 nodes to be scored	(406 eliminated genes)
```

```
## 
## 	 Level 4:	21 nodes to be scored	(480 eliminated genes)
```

```
## 
## 	 Level 3:	17 nodes to be scored	(647 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(944 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1211 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 55 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	8 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	7 nodes to be scored	(277 eliminated genes)
```

```
## 
## 	 Level 5:	10 nodes to be scored	(463 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(471 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(842 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(1256 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1714 eliminated genes)
```

```
##        GO.ID                        Term Annotated Significant Expected Fisher
## 1 GO:0001755 neural crest cell migration         2           1     0.01 0.0110
## 2 GO:0000165                MAPK cascade        35           2     0.20 0.0150
## 3 GO:0004017   adenylate kinase activity         1           1     0.01 0.0061
## 4 GO:0005524                 ATP binding       263           5     1.61 0.0175
##                 type
## 1 Biological.Process
## 2 Biological.Process
## 3 Molecular.Function
## 4 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 24 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 7:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(154 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(170 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(215 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(408 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(514 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 46 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	6 nodes to be scored	(265 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(269 eliminated genes)
```

```
## 
## 	 Level 5:	8 nodes to be scored	(461 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(498 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(744 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(1278 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1816 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000165                                           MAPK cascade        35
## 2 GO:0005524                                            ATP binding       263
## 3 GO:0004698            calcium-dependent protein kinase C activity         2
## 4 GO:0000900 mRNA regulatory element binding translation repress...         3
## 5 GO:0001640 adenylate cyclase inhibiting G protein-coupled glut...         9
##   Significant Expected   Fisher               type
## 1           4     0.15 4.60e-06 Biological.Process
## 2           5     0.95 1.20e-03 Molecular.Function
## 3           1     0.01 7.20e-03 Molecular.Function
## 4           1     0.01 1.08e-02 Molecular.Function
## 5           1     0.03 3.20e-02 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 96 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 15:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 14:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 13:	1 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 11:	4 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 10:	4 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 9:	8 nodes to be scored	(16 eliminated genes)
```

```
## 
## 	 Level 8:	8 nodes to be scored	(16 eliminated genes)
```

```
## 
## 	 Level 7:	13 nodes to be scored	(19 eliminated genes)
```

```
## 
## 	 Level 6:	12 nodes to be scored	(89 eliminated genes)
```

```
## 
## 	 Level 5:	17 nodes to be scored	(293 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(314 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(433 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(616 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(907 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 50 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	7 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 5:	14 nodes to be scored	(166 eliminated genes)
```

```
## 
## 	 Level 4:	10 nodes to be scored	(244 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(1003 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(1352 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2097 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0001945                               lymph vessel development         5
## 2 GO:0003333                     amino acid transmembrane transport         2
## 3 GO:0001658       branching involved in ureteric bud morphogenesis         4
## 4 GO:0001889                                      liver development         8
## 5 GO:0004252                     serine-type endopeptidase activity        53
## 6 GO:0046982                    protein heterodimerization activity         1
## 7 GO:0004771                               sterol esterase activity         5
## 8 GO:0001640 adenylate cyclase inhibiting G protein-coupled glut...         9
## 9 GO:0005302          L-tyrosine transmembrane transporter activity         9
##   Significant Expected  Fisher               type
## 1           2     0.03 0.00028 Biological.Process
## 2           1     0.01 0.01131 Biological.Process
## 3           1     0.02 0.02251 Biological.Process
## 4           1     0.05 0.04458 Biological.Process
## 5           3     0.29 0.00250 Molecular.Function
## 6           1     0.01 0.00540 Molecular.Function
## 7           1     0.03 0.02670 Molecular.Function
## 8           1     0.05 0.04770 Molecular.Function
## 9           1     0.05 0.04770 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 42 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	4 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 6:	5 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 5:	5 nodes to be scored	(21 eliminated genes)
```

```
## 
## 	 Level 4:	9 nodes to be scored	(36 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(321 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(457 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(603 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 38 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 4:	9 nodes to be scored	(399 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(485 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(1152 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1737 eliminated genes)
```

```
##        GO.ID                                       Term Annotated Significant
## 1 GO:0015969 guanosine tetraphosphate metabolic process         9           1
## 2 GO:0019700      organic phosphonate catabolic process        12           1
## 3 GO:0001666                        response to hypoxia        14           1
## 4 GO:0005178                           integrin binding         4           1
## 5 GO:0003964       RNA-directed DNA polymerase activity       122           2
##   Expected Fisher               type
## 1     0.02  0.019 Biological.Process
## 2     0.03  0.025 Biological.Process
## 3     0.03  0.029 Biological.Process
## 4     0.01  0.011 Molecular.Function
## 5     0.35  0.045 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 141 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	6 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 8:	9 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 7:	15 nodes to be scored	(166 eliminated genes)
```

```
## 
## 	 Level 6:	22 nodes to be scored	(271 eliminated genes)
```

```
## 
## 	 Level 5:	28 nodes to be scored	(518 eliminated genes)
```

```
## 
## 	 Level 4:	23 nodes to be scored	(588 eliminated genes)
```

```
## 
## 	 Level 3:	20 nodes to be scored	(886 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(1058 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1251 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 108 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	7 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	7 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 7:	14 nodes to be scored	(457 eliminated genes)
```

```
## 
## 	 Level 6:	18 nodes to be scored	(545 eliminated genes)
```

```
## 
## 	 Level 5:	21 nodes to be scored	(750 eliminated genes)
```

```
## 
## 	 Level 4:	19 nodes to be scored	(957 eliminated genes)
```

```
## 
## 	 Level 3:	14 nodes to be scored	(1639 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(2052 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2306 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0002674     negative regulation of acute inflammatory response         4
## 2 GO:0002221         pattern recognition receptor signaling pathway        11
## 3 GO:0000165                                           MAPK cascade        35
## 4 GO:0001818             negative regulation of cytokine production        18
## 5 GO:0001640 adenylate cyclase inhibiting G protein-coupled glut...         9
## 6 GO:0004143                         diacylglycerol kinase activity         1
## 7 GO:0005524                                            ATP binding       263
## 8 GO:0032450                     maltose alpha-glucosidase activity         2
## 9 GO:0000026                 alpha-1,2-mannosyltransferase activity         3
##   Significant Expected   Fisher               type
## 1           3     0.05 8.20e-06 Biological.Process
## 2           2     0.15 8.80e-03 Biological.Process
## 3           3     0.47 1.03e-02 Biological.Process
## 4           2     0.24 2.31e-02 Biological.Process
## 5           2     0.13 6.50e-03 Molecular.Function
## 6           1     0.01 1.40e-02 Molecular.Function
## 7           8     3.69 2.67e-02 Molecular.Function
## 8           1     0.03 2.79e-02 Molecular.Function
## 9           1     0.04 4.16e-02 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 245 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	7 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	10 nodes to be scored	(203 eliminated genes)
```

```
## 
## 	 Level 9:	17 nodes to be scored	(222 eliminated genes)
```

```
## 
## 	 Level 8:	22 nodes to be scored	(271 eliminated genes)
```

```
## 
## 	 Level 7:	26 nodes to be scored	(339 eliminated genes)
```

```
## 
## 	 Level 6:	38 nodes to be scored	(412 eliminated genes)
```

```
## 
## 	 Level 5:	49 nodes to be scored	(503 eliminated genes)
```

```
## 
## 	 Level 4:	36 nodes to be scored	(615 eliminated genes)
```

```
## 
## 	 Level 3:	27 nodes to be scored	(1009 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(1217 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1346 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 126 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 12:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	3 nodes to be scored	(3 eliminated genes)
```

```
## 
## 	 Level 9:	8 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 8:	9 nodes to be scored	(145 eliminated genes)
```

```
## 
## 	 Level 7:	12 nodes to be scored	(460 eliminated genes)
```

```
## 
## 	 Level 6:	21 nodes to be scored	(486 eliminated genes)
```

```
## 
## 	 Level 5:	22 nodes to be scored	(704 eliminated genes)
```

```
## 
## 	 Level 4:	20 nodes to be scored	(949 eliminated genes)
```

```
## 
## 	 Level 3:	19 nodes to be scored	(1684 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(1935 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2389 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0000184 nuclear-transcribed mRNA catabolic process, nonsens...        10
## 2  GO:0006513                             protein monoubiquitination         1
## 3  GO:0001771                        immunological synapse formation         1
## 4  GO:0000183                         rDNA heterochromatin formation         1
## 5  GO:0002181                                cytoplasmic translation        21
## 6  GO:0000027                       ribosomal large subunit assembly         2
## 7  GO:0001409 guanine nucleotide transmembrane transporter activi...        30
## 8  GO:0003951                                   NAD+ kinase activity         1
## 9  GO:0004017                              adenylate kinase activity         1
## 10 GO:0005085             guanyl-nucleotide exchange factor activity        12
## 11 GO:0003964                   RNA-directed DNA polymerase activity       122
## 12 GO:0003727                            single-stranded RNA binding         2
## 13 GO:0003676                                   nucleic acid binding       497
##    Significant Expected  Fisher               type
## 1            3     0.20 0.00077 Biological.Process
## 2            1     0.02 0.01984 Biological.Process
## 3            1     0.02 0.01984 Biological.Process
## 4            1     0.02 0.01984 Biological.Process
## 5            3     0.42 0.02812 Biological.Process
## 6            1     0.04 0.03931 Biological.Process
## 7            3     0.56 0.01800 Molecular.Function
## 8            1     0.02 0.01900 Molecular.Function
## 9            1     0.02 0.01900 Molecular.Function
## 10           2     0.22 0.02000 Molecular.Function
## 11           6     2.29 0.02500 Molecular.Function
## 12           1     0.04 0.03700 Molecular.Function
## 13          14     9.31 0.03800 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 380 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 14:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 13:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	5 nodes to be scored	(2 eliminated genes)
```

```
## 
## 	 Level 11:	12 nodes to be scored	(143 eliminated genes)
```

```
## 
## 	 Level 10:	20 nodes to be scored	(211 eliminated genes)
```

```
## 
## 	 Level 9:	32 nodes to be scored	(249 eliminated genes)
```

```
## 
## 	 Level 8:	34 nodes to be scored	(342 eliminated genes)
```

```
## 
## 	 Level 7:	48 nodes to be scored	(418 eliminated genes)
```

```
## 
## 	 Level 6:	67 nodes to be scored	(550 eliminated genes)
```

```
## 
## 	 Level 5:	66 nodes to be scored	(765 eliminated genes)
```

```
## 
## 	 Level 4:	48 nodes to be scored	(915 eliminated genes)
```

```
## 
## 	 Level 3:	34 nodes to be scored	(1123 eliminated genes)
```

```
## 
## 	 Level 2:	10 nodes to be scored	(1278 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1396 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 163 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 12:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	3 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 9:	10 nodes to be scored	(10 eliminated genes)
```

```
## 
## 	 Level 8:	12 nodes to be scored	(44 eliminated genes)
```

```
## 
## 	 Level 7:	19 nodes to be scored	(356 eliminated genes)
```

```
## 
## 	 Level 6:	26 nodes to be scored	(375 eliminated genes)
```

```
## 
## 	 Level 5:	32 nodes to be scored	(579 eliminated genes)
```

```
## 
## 	 Level 4:	28 nodes to be scored	(847 eliminated genes)
```

```
## 
## 	 Level 3:	20 nodes to be scored	(1747 eliminated genes)
```

```
## 
## 	 Level 2:	9 nodes to be scored	(1998 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2568 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0001933         negative regulation of protein phosphorylation         5
## 2  GO:0001782                                     B cell homeostasis         7
## 3  GO:0001764                                       neuron migration         8
## 4  GO:0001731         formation of translation preinitiation complex         1
## 5  GO:0001960 negative regulation of cytokine-mediated signaling ...         1
## 6  GO:0001556                                      oocyte maturation         1
## 7  GO:0002092        positive regulation of receptor internalization         1
## 8  GO:0002026           regulation of the force of heart contraction         1
## 9  GO:0000038           very long-chain fatty acid metabolic process         9
## 10 GO:0005524                                            ATP binding       263
## 11 GO:0004197                   cysteine-type endopeptidase activity        18
## 12 GO:0004715 non-membrane spanning protein tyrosine kinase activ...         6
## 13 GO:0005436                    sodium:phosphate symporter activity         1
## 14 GO:0015175 neutral amino acid transmembrane transporter activi...         1
## 15 GO:0005220 inositol 1,4,5-trisphosphate-sensitive calcium-rele...         1
## 16 GO:0004745                     NAD-retinol dehydrogenase activity         1
## 17 GO:0003874           6-pyruvoyltetrahydropterin synthase activity         1
## 18 GO:0004862       cAMP-dependent protein kinase inhibitor activity         1
## 19 GO:0003989                        acetyl-CoA carboxylase activity         1
## 20 GO:0004423                         iduronate-2-sulfatase activity         1
## 21 GO:0005096                              GTPase activator activity        12
##    Significant Expected  Fisher               type
## 1            2     0.17 0.01100 Biological.Process
## 2            2     0.24 0.02200 Biological.Process
## 3            2     0.28 0.02900 Biological.Process
## 4            1     0.03 0.03500 Biological.Process
## 5            1     0.03 0.03500 Biological.Process
## 6            1     0.03 0.03500 Biological.Process
## 7            1     0.03 0.03500 Biological.Process
## 8            1     0.03 0.03500 Biological.Process
## 9            2     0.31 0.03600 Biological.Process
## 10          17     7.58 0.00099 Molecular.Function
## 11           4     0.52 0.00791 Molecular.Function
## 12           2     0.17 0.01141 Molecular.Function
## 13           1     0.03 0.02882 Molecular.Function
## 14           1     0.03 0.02882 Molecular.Function
## 15           1     0.03 0.02882 Molecular.Function
## 16           1     0.03 0.02882 Molecular.Function
## 17           1     0.03 0.02882 Molecular.Function
## 18           1     0.03 0.02882 Molecular.Function
## 19           1     0.03 0.02882 Molecular.Function
## 20           1     0.03 0.02882 Molecular.Function
## 21           2     0.35 0.04490 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 56 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 14:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 11:	3 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 10:	3 nodes to be scored	(5 eliminated genes)
```

```
## 
## 	 Level 9:	6 nodes to be scored	(5 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(42 eliminated genes)
```

```
## 
## 	 Level 7:	5 nodes to be scored	(55 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(120 eliminated genes)
```

```
## 
## 	 Level 5:	7 nodes to be scored	(293 eliminated genes)
```

```
## 
## 	 Level 4:	9 nodes to be scored	(369 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(621 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(693 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(859 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 12 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 7:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	1 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(275 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(293 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(305 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1010 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000472 endonucleolytic cleavage to generate mature 5'-end ...         1
## 2 GO:0001889                                      liver development         8
## 3 GO:0010181                                            FMN binding         1
##   Significant Expected  Fisher               type
## 1           1     0.00 0.00210 Biological.Process
## 2           1     0.02 0.01690 Biological.Process
## 3           1     0.00 0.00036 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 87 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	2 nodes to be scored	(10 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(14 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(15 eliminated genes)
```

```
## 
## 	 Level 6:	12 nodes to be scored	(144 eliminated genes)
```

```
## 
## 	 Level 5:	20 nodes to be scored	(373 eliminated genes)
```

```
## 
## 	 Level 4:	19 nodes to be scored	(420 eliminated genes)
```

```
## 
## 	 Level 3:	13 nodes to be scored	(737 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(884 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1041 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 64 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(399 eliminated genes)
```

```
## 
## 	 Level 6:	9 nodes to be scored	(425 eliminated genes)
```

```
## 
## 	 Level 5:	13 nodes to be scored	(686 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(733 eliminated genes)
```

```
## 
## 	 Level 3:	13 nodes to be scored	(1282 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(1445 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2068 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0001960 negative regulation of cytokine-mediated signaling ...         1
## 2 GO:0000302                    response to reactive oxygen species         6
## 3 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsens...        10
## 4 GO:0004492               methylmalonyl-CoA decarboxylase activity         1
## 5 GO:0005536                                        glucose binding         1
## 6 GO:0003964                   RNA-directed DNA polymerase activity       122
##   Significant Expected Fisher               type
## 1           1     0.00 0.0035 Biological.Process
## 2           1     0.02 0.0211 Biological.Process
## 3           1     0.04 0.0350 Biological.Process
## 4           1     0.01 0.0061 Molecular.Function
## 5           1     0.01 0.0061 Molecular.Function
## 6           3     0.75 0.0359 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 149 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	7 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 10:	9 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 9:	8 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 8:	10 nodes to be scored	(37 eliminated genes)
```

```
## 
## 	 Level 7:	16 nodes to be scored	(42 eliminated genes)
```

```
## 
## 	 Level 6:	22 nodes to be scored	(106 eliminated genes)
```

```
## 
## 	 Level 5:	31 nodes to be scored	(319 eliminated genes)
```

```
## 
## 	 Level 4:	21 nodes to be scored	(431 eliminated genes)
```

```
## 
## 	 Level 3:	13 nodes to be scored	(577 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(640 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(762 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 44 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	7 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	11 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(505 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(1009 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(1147 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1906 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0002230 positive regulation of defense response to virus by...         1
## 2 GO:0007175 negative regulation of epidermal growth factor-acti...         1
## 3 GO:0002933                                    lipid hydroxylation         3
## 4 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsens...        10
## 5 GO:0004753                    saccharopine dehydrogenase activity         1
## 6 GO:0000016                                       lactase activity         4
## 7 GO:0008376               acetylgalactosaminyltransferase activity        14
##   Significant Expected Fisher               type
## 1           1     0.00 0.0035 Biological.Process
## 2           1     0.00 0.0035 Biological.Process
## 3           1     0.01 0.0106 Biological.Process
## 4           1     0.04 0.0350 Biological.Process
## 5           1     0.00 0.0032 Molecular.Function
## 6           1     0.01 0.0129 Molecular.Function
## 7           1     0.05 0.0445 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 134 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	6 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	8 nodes to be scored	(203 eliminated genes)
```

```
## 
## 	 Level 9:	12 nodes to be scored	(215 eliminated genes)
```

```
## 
## 	 Level 8:	10 nodes to be scored	(216 eliminated genes)
```

```
## 
## 	 Level 7:	10 nodes to be scored	(219 eliminated genes)
```

```
## 
## 	 Level 6:	19 nodes to be scored	(374 eliminated genes)
```

```
## 
## 	 Level 5:	23 nodes to be scored	(433 eliminated genes)
```

```
## 
## 	 Level 4:	18 nodes to be scored	(473 eliminated genes)
```

```
## 
## 	 Level 3:	14 nodes to be scored	(699 eliminated genes)
```

```
## 
## 	 Level 2:	9 nodes to be scored	(871 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1031 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 63 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	6 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	8 nodes to be scored	(270 eliminated genes)
```

```
## 
## 	 Level 5:	12 nodes to be scored	(434 eliminated genes)
```

```
## 
## 	 Level 4:	14 nodes to be scored	(524 eliminated genes)
```

```
## 
## 	 Level 3:	14 nodes to be scored	(1210 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(1566 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2315 eliminated genes)
```

```
##        GO.ID                                               Term Annotated
## 1 GO:0001822                                 kidney development        65
## 2 GO:0000165                                       MAPK cascade        35
## 3 GO:0000335 negative regulation of transposition, DNA-mediated         1
## 4 GO:0004104                            cholinesterase activity         1
## 5 GO:0004382                           GDP phosphatase activity         3
## 6 GO:0000340                  RNA 7-methylguanosine cap binding         4
## 7 GO:0005178                                   integrin binding         4
## 8 GO:0005524                                        ATP binding       263
##   Significant Expected    Fisher               type
## 1           7     0.83 0.0000068 Biological.Process
## 2           4     0.45 0.0007600 Biological.Process
## 3           1     0.01 0.0127600 Biological.Process
## 4           1     0.01 0.0100000 Molecular.Function
## 5           1     0.03 0.0300000 Molecular.Function
## 6           1     0.04 0.0400000 Molecular.Function
## 7           1     0.04 0.0400000 Molecular.Function
## 8           6     2.65 0.0430000 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 94 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	4 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	5 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	7 nodes to be scored	(151 eliminated genes)
```

```
## 
## 	 Level 8:	5 nodes to be scored	(151 eliminated genes)
```

```
## 
## 	 Level 7:	8 nodes to be scored	(152 eliminated genes)
```

```
## 
## 	 Level 6:	15 nodes to be scored	(184 eliminated genes)
```

```
## 
## 	 Level 5:	18 nodes to be scored	(288 eliminated genes)
```

```
## 
## 	 Level 4:	16 nodes to be scored	(320 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(395 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(582 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(660 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 39 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	7 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 4:	9 nodes to be scored	(399 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(921 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(1351 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1909 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0015969             guanosine tetraphosphate metabolic process         9
## 2 GO:0000122 negative regulation of transcription by RNA polymer...       140
## 3 GO:0003964                   RNA-directed DNA polymerase activity       122
## 4 GO:0005178                                       integrin binding         4
##   Significant Expected  Fisher               type
## 1           2     0.05 0.00099 Biological.Process
## 2           3     0.79 0.03687 Biological.Process
## 3           3     0.53 0.01400 Molecular.Function
## 4           1     0.02 0.01700 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 114 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	5 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 8:	6 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 7:	9 nodes to be scored	(169 eliminated genes)
```

```
## 
## 	 Level 6:	20 nodes to be scored	(293 eliminated genes)
```

```
## 
## 	 Level 5:	25 nodes to be scored	(380 eliminated genes)
```

```
## 
## 	 Level 4:	19 nodes to be scored	(517 eliminated genes)
```

```
## 
## 	 Level 3:	12 nodes to be scored	(720 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(897 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1078 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 80 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	4 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 8:	5 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 7:	9 nodes to be scored	(375 eliminated genes)
```

```
## 
## 	 Level 6:	14 nodes to be scored	(402 eliminated genes)
```

```
## 
## 	 Level 5:	15 nodes to be scored	(564 eliminated genes)
```

```
## 
## 	 Level 4:	12 nodes to be scored	(758 eliminated genes)
```

```
## 
## 	 Level 3:	13 nodes to be scored	(1127 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(1506 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2015 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0006511          ubiquitin-dependent protein catabolic process         7
## 2 GO:0001002 RNA polymerase III type 1 promoter sequence-specifi...         1
## 3 GO:0000703 oxidized pyrimidine nucleobase lesion DNA N-glycosy...         1
## 4 GO:0003980 UDP-glucose:glycoprotein glucosyltransferase activi...         1
## 5 GO:0000340                      RNA 7-methylguanosine cap binding         4
## 6 GO:0016836                                   hydro-lyase activity         4
## 7 GO:0005524                                            ATP binding       263
##   Significant Expected Fisher               type
## 1           1     0.03 0.0290 Biological.Process
## 2           1     0.01 0.0076 Molecular.Function
## 3           1     0.01 0.0076 Molecular.Function
## 4           1     0.01 0.0076 Molecular.Function
## 5           1     0.03 0.0299 Molecular.Function
## 6           1     0.03 0.0299 Molecular.Function
## 7           5     1.99 0.0422 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 5 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 5:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(20 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(20 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(63 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 38 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(375 eliminated genes)
```

```
## 
## 	 Level 6:	5 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 5:	7 nodes to be scored	(408 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(414 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(595 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(903 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1745 eliminated genes)
```

```
##        GO.ID                                          Term Annotated
## 1 GO:0003341                               cilium movement        20
## 2 GO:0000048                  peptidyltransferase activity         1
## 3 GO:0005337 nucleoside transmembrane transporter activity         1
##   Significant Expected Fisher               type
## 1           1     0.01 0.0140 Biological.Process
## 2           1     0.00 0.0018 Molecular.Function
## 3           1     0.00 0.0018 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 5 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 4:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(10 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(443 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 54 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 7:	6 nodes to be scored	(332 eliminated genes)
```

```
## 
## 	 Level 6:	8 nodes to be scored	(341 eliminated genes)
```

```
## 
## 	 Level 5:	8 nodes to be scored	(499 eliminated genes)
```

```
## 
## 	 Level 4:	10 nodes to be scored	(578 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(945 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(1111 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1890 eliminated genes)
```

```
##        GO.ID                                   Term Annotated Significant
## 1 GO:0008218                        bioluminescence        10           6
## 2 GO:0004089         carbonate dehydratase activity         2           1
## 3 GO:0005245 voltage-gated calcium channel activity         7           1
##   Expected  Fisher               type
## 1     0.04 1.9e-14 Biological.Process
## 2     0.01 5.0e-03 Molecular.Function
## 3     0.02 1.8e-02 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 265 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	5 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	8 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	11 nodes to be scored	(217 eliminated genes)
```

```
## 
## 	 Level 9:	19 nodes to be scored	(234 eliminated genes)
```

```
## 
## 	 Level 8:	23 nodes to be scored	(273 eliminated genes)
```

```
## 
## 	 Level 7:	28 nodes to be scored	(288 eliminated genes)
```

```
## 
## 	 Level 6:	41 nodes to be scored	(480 eliminated genes)
```

```
## 
## 	 Level 5:	50 nodes to be scored	(751 eliminated genes)
```

```
## 
## 	 Level 4:	38 nodes to be scored	(863 eliminated genes)
```

```
## 
## 	 Level 3:	30 nodes to be scored	(1067 eliminated genes)
```

```
## 
## 	 Level 2:	10 nodes to be scored	(1206 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1381 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 137 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	8 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	8 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 7:	15 nodes to be scored	(465 eliminated genes)
```

```
## 
## 	 Level 6:	23 nodes to be scored	(501 eliminated genes)
```

```
## 
## 	 Level 5:	27 nodes to be scored	(769 eliminated genes)
```

```
## 
## 	 Level 4:	25 nodes to be scored	(968 eliminated genes)
```

```
## 
## 	 Level 3:	20 nodes to be scored	(1603 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(1850 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2395 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0001822                                     kidney development        65
## 2 GO:0000165                                           MAPK cascade        35
## 3 GO:0000335     negative regulation of transposition, DNA-mediated         1
## 4 GO:0001409 guanine nucleotide transmembrane transporter activi...        30
## 5 GO:0005524                                            ATP binding       263
## 6 GO:0005381            iron ion transmembrane transporter activity         1
## 7 GO:0004140                          dephospho-CoA kinase activity         1
## 8 GO:0005324             long-chain fatty acid transporter activity         1
## 9 GO:0003777                             microtubule motor activity        16
##   Significant Expected   Fisher               type
## 1          12     2.30 0.000001 Biological.Process
## 2           4     1.24 0.032000 Biological.Process
## 3           1     0.04 0.035000 Biological.Process
## 4           4     0.65 0.003600 Molecular.Function
## 5          12     5.68 0.009000 Molecular.Function
## 6           1     0.02 0.021600 Molecular.Function
## 7           1     0.02 0.021600 Molecular.Function
## 8           1     0.02 0.021600 Molecular.Function
## 9           2     0.35 0.045400 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 23 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(30 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(38 eliminated genes)
```

```
## 
## 	 Level 6:	2 nodes to be scored	(40 eliminated genes)
```

```
## 
## 	 Level 5:	3 nodes to be scored	(44 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(111 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(154 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(468 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(532 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 35 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	5 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	5 nodes to be scored	(268 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(301 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(337 eliminated genes)
```

```
## 
## 	 Level 3:	7 nodes to be scored	(548 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(1068 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1777 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000052                           citrulline metabolic process         1
## 2 GO:0000209                             protein polyubiquitination        30
## 3 GO:0003980 UDP-glucose:glycoprotein glucosyltransferase activi...         1
## 4 GO:0004559                             alpha-mannosidase activity         7
## 5 GO:0005507                                     copper ion binding        18
##   Significant Expected Fisher               type
## 1           1     0.00 0.0014 Biological.Process
## 2           1     0.04 0.0421 Biological.Process
## 3           1     0.00 0.0025 Molecular.Function
## 4           1     0.02 0.0175 Molecular.Function
## 5           1     0.05 0.0446 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## Warning in getSigGroups(object, test.stat): No enrichment can pe performed -
## there are no feasible GO terms!
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 30 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(2 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(2 eliminated genes)
```

```
## 
## 	 Level 6:	2 nodes to be scored	(60 eliminated genes)
```

```
## 
## 	 Level 5:	5 nodes to be scored	(90 eliminated genes)
```

```
## 
## 	 Level 4:	5 nodes to be scored	(102 eliminated genes)
```

```
## 
## 	 Level 3:	4 nodes to be scored	(557 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(938 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1000 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0005391 P-type sodium:potassium-exchanging transporter acti...         2
##   Significant Expected Fisher               type
## 1           1        0 0.0036 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 372 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 14:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 13:	4 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	7 nodes to be scored	(11 eliminated genes)
```

```
## 
## 	 Level 11:	12 nodes to be scored	(156 eliminated genes)
```

```
## 
## 	 Level 10:	18 nodes to be scored	(215 eliminated genes)
```

```
## 
## 	 Level 9:	31 nodes to be scored	(235 eliminated genes)
```

```
## 
## 	 Level 8:	33 nodes to be scored	(334 eliminated genes)
```

```
## 
## 	 Level 7:	48 nodes to be scored	(422 eliminated genes)
```

```
## 
## 	 Level 6:	61 nodes to be scored	(527 eliminated genes)
```

```
## 
## 	 Level 5:	68 nodes to be scored	(836 eliminated genes)
```

```
## 
## 	 Level 4:	44 nodes to be scored	(929 eliminated genes)
```

```
## 
## 	 Level 3:	34 nodes to be scored	(1153 eliminated genes)
```

```
## 
## 	 Level 2:	10 nodes to be scored	(1279 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1372 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 261 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	5 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	17 nodes to be scored	(3 eliminated genes)
```

```
## 
## 	 Level 8:	17 nodes to be scored	(153 eliminated genes)
```

```
## 
## 	 Level 7:	34 nodes to be scored	(489 eliminated genes)
```

```
## 
## 	 Level 6:	54 nodes to be scored	(583 eliminated genes)
```

```
## 
## 	 Level 5:	51 nodes to be scored	(909 eliminated genes)
```

```
## 
## 	 Level 4:	43 nodes to be scored	(1332 eliminated genes)
```

```
## 
## 	 Level 3:	28 nodes to be scored	(2045 eliminated genes)
```

```
## 
## 	 Level 2:	10 nodes to be scored	(2278 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2570 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0002064                            epithelial cell development         4
## 2  GO:0000122 negative regulation of transcription by RNA polymer...       140
## 3  GO:0001732 formation of cytoplasmic translation initiation com...         6
## 4  GO:0005388                    P-type calcium transporter activity         4
## 5  GO:0005198                           structural molecule activity        54
## 6  GO:0003756                   protein disulfide isomerase activity         5
## 7  GO:0001786                             phosphatidylserine binding         4
## 8  GO:0005539                              glycosaminoglycan binding         5
## 9  GO:0002020                                       protease binding         5
## 10 GO:0003682                                      chromatin binding        13
## 11 GO:0004843                  cysteine-type deubiquitinase activity         6
##    Significant Expected  Fisher               type
## 1            3     0.24 0.00078 Biological.Process
## 2           14     8.33 0.03213 Biological.Process
## 3            2     0.36 0.04492 Biological.Process
## 4            4     0.23 0.00001 Molecular.Function
## 5           10     3.09 0.00025 Molecular.Function
## 6            3     0.29 0.00169 Molecular.Function
## 7            2     0.23 0.01812 Molecular.Function
## 8            2     0.29 0.02907 Molecular.Function
## 9            2     0.29 0.02907 Molecular.Function
## 10           3     0.74 0.03449 Molecular.Function
## 11           2     0.34 0.04199 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 52 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 7:	6 nodes to be scored	(5 eliminated genes)
```

```
## 
## 	 Level 6:	10 nodes to be scored	(73 eliminated genes)
```

```
## 
## 	 Level 5:	10 nodes to be scored	(99 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(173 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(273 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(337 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(848 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 51 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	6 nodes to be scored	(269 eliminated genes)
```

```
## 
## 	 Level 6:	7 nodes to be scored	(273 eliminated genes)
```

```
## 
## 	 Level 5:	8 nodes to be scored	(430 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(517 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(729 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(1292 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2073 eliminated genes)
```

```
##        GO.ID                                  Term Annotated Significant
## 1 GO:0001947                         heart looping         4           1
## 2 GO:0000902                    cell morphogenesis         7           1
## 3 GO:0019700 organic phosphonate catabolic process        12           1
## 4 GO:0001666                   response to hypoxia        14           1
## 5 GO:0000049                          tRNA binding        30           2
## 6 GO:0004565           beta-galactosidase activity         3           1
## 7 GO:0005525                           GTP binding         6           1
##   Expected Fisher               type
## 1     0.01  0.014 Biological.Process
## 2     0.02  0.025 Biological.Process
## 3     0.04  0.042 Biological.Process
## 4     0.05  0.049 Biological.Process
## 5     0.16  0.011 Molecular.Function
## 6     0.02  0.016 Molecular.Function
## 7     0.03  0.032 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 45 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	4 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 5:	7 nodes to be scored	(113 eliminated genes)
```

```
## 
## 	 Level 4:	10 nodes to be scored	(121 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(486 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(661 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(779 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 30 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(305 eliminated genes)
```

```
## 
## 	 Level 4:	5 nodes to be scored	(337 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(360 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(485 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1723 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0015969             guanosine tetraphosphate metabolic process         9
## 2 GO:0004180                              carboxypeptidase activity        28
## 3 GO:0001409 guanine nucleotide transmembrane transporter activi...        30
##   Significant Expected  Fisher               type
## 1           2     0.03 0.00022 Biological.Process
## 2           1     0.03 0.03000 Molecular.Function
## 3           1     0.03 0.03200 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 55 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	4 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(74 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(121 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(131 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(569 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(743 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(907 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 30 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(399 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(462 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(1094 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1588 eliminated genes)
```

```
##        GO.ID                                       Term Annotated Significant
## 1 GO:0001822                         kidney development        65           3
## 2 GO:0000165                               MAPK cascade        35           2
## 3 GO:0015969 guanosine tetraphosphate metabolic process         9           1
##   Expected Fisher               type
## 1     0.32 0.0029 Biological.Process
## 2     0.17 0.0116 Biological.Process
## 3     0.04 0.0439 Biological.Process
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 29 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 12:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	1 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 9:	1 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(8 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(8 eliminated genes)
```

```
## 
## 	 Level 6:	5 nodes to be scored	(8 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(36 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(99 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(228 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(239 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(246 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 34 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 5:	9 nodes to be scored	(35 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(136 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(838 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(1062 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1705 eliminated genes)
```

```
##        GO.ID                                          Term Annotated
## 1 GO:0001843                           neural tube closure         7
## 2 GO:0003684                           damaged DNA binding         4
## 3 GO:0003943    N-acetylgalactosamine-4-sulfatase activity         8
## 4 GO:0005302 L-tyrosine transmembrane transporter activity         9
## 5 GO:0004197          cysteine-type endopeptidase activity        18
##   Significant Expected Fisher               type
## 1           1     0.00  0.005 Biological.Process
## 2           1     0.01  0.010 Molecular.Function
## 3           1     0.02  0.020 Molecular.Function
## 4           1     0.02  0.022 Molecular.Function
## 5           1     0.05  0.045 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 59 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	4 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(3 eliminated genes)
```

```
## 
## 	 Level 7:	8 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 6:	8 nodes to be scored	(25 eliminated genes)
```

```
## 
## 	 Level 5:	9 nodes to be scored	(61 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(82 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(171 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(318 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(729 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 42 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 7:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	7 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	9 nodes to be scored	(30 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(185 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(626 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(1241 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1867 eliminated genes)
```

```
##        GO.ID                                  Term Annotated Significant
## 1 GO:0000054 ribosomal subunit export from nucleus         3           1
## 2 GO:0000028      ribosomal small subunit assembly         3           1
## 3 GO:0001561            fatty acid alpha-oxidation         3           1
## 4 GO:0002933                   lipid hydroxylation         3           1
## 5 GO:0002161       aminoacyl-tRNA editing activity         1           1
## 6 GO:0003697           single-stranded DNA binding         8           1
## 7 GO:0005542                    folic acid binding        10           1
## 8 GO:0004222         metalloendopeptidase activity        15           1
##   Expected Fisher               type
## 1     0.01 0.0085 Biological.Process
## 2     0.01 0.0085 Biological.Process
## 3     0.01 0.0085 Biological.Process
## 4     0.01 0.0085 Biological.Process
## 5     0.00 0.0029 Molecular.Function
## 6     0.02 0.0229 Molecular.Function
## 7     0.03 0.0285 Molecular.Function
## 8     0.04 0.0425 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 144 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	6 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 8:	7 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 7:	17 nodes to be scored	(181 eliminated genes)
```

```
## 
## 	 Level 6:	26 nodes to be scored	(213 eliminated genes)
```

```
## 
## 	 Level 5:	28 nodes to be scored	(524 eliminated genes)
```

```
## 
## 	 Level 4:	23 nodes to be scored	(599 eliminated genes)
```

```
## 
## 	 Level 3:	19 nodes to be scored	(797 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(872 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1039 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 94 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	5 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(100 eliminated genes)
```

```
## 
## 	 Level 7:	9 nodes to be scored	(409 eliminated genes)
```

```
## 
## 	 Level 6:	18 nodes to be scored	(427 eliminated genes)
```

```
## 
## 	 Level 5:	20 nodes to be scored	(663 eliminated genes)
```

```
## 
## 	 Level 4:	16 nodes to be scored	(907 eliminated genes)
```

```
## 
## 	 Level 3:	13 nodes to be scored	(1667 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(1873 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2338 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000050                                             urea cycle         2
## 2 GO:0003676                                   nucleic acid binding       497
## 3 GO:0005085             guanyl-nucleotide exchange factor activity        12
## 4 GO:0004143                         diacylglycerol kinase activity         1
## 5 GO:0004568                                     chitinase activity         1
## 6 GO:0004571 mannosyl-oligosaccharide 1,2-alpha-mannosidase acti...         2
##   Significant Expected Fisher               type
## 1           1     0.02 0.0170 Biological.Process
## 2          12     6.98 0.0076 Molecular.Function
## 3           2     0.17 0.0116 Molecular.Function
## 4           1     0.01 0.0140 Molecular.Function
## 5           1     0.01 0.0140 Molecular.Function
## 6           1     0.03 0.0279 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 87 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	4 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	5 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(172 eliminated genes)
```

```
## 
## 	 Level 7:	6 nodes to be scored	(199 eliminated genes)
```

```
## 
## 	 Level 6:	15 nodes to be scored	(214 eliminated genes)
```

```
## 
## 	 Level 5:	20 nodes to be scored	(304 eliminated genes)
```

```
## 
## 	 Level 4:	13 nodes to be scored	(414 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(457 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(554 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(691 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## Warning in getSigGroups(object, test.stat): No enrichment can pe performed -
## there are no feasible GO terms!
```

```
##        GO.ID                Term Annotated Significant Expected Fisher
## 1 GO:0001666 response to hypoxia        14           1     0.04  0.039
##                 type
## 1 Biological.Process
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 13 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 7:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	1 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(13 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(23 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(94 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(532 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 69 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 7:	8 nodes to be scored	(332 eliminated genes)
```

```
## 
## 	 Level 6:	12 nodes to be scored	(346 eliminated genes)
```

```
## 
## 	 Level 5:	12 nodes to be scored	(534 eliminated genes)
```

```
## 
## 	 Level 4:	13 nodes to be scored	(707 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(1115 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(1175 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2055 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0008218                                        bioluminescence        10
## 2 GO:0019700                  organic phosphonate catabolic process        12
## 3 GO:0001409 guanine nucleotide transmembrane transporter activi...        30
## 4 GO:0004089                         carbonate dehydratase activity         2
## 5 GO:0004758                 serine C-palmitoyltransferase activity         5
## 6 GO:0005245                 voltage-gated calcium channel activity         7
##   Significant Expected Fisher               type
## 1           1     0.01 0.0140 Biological.Process
## 2           1     0.02 0.0170 Biological.Process
## 3           3     0.14 0.0003 Molecular.Function
## 4           1     0.01 0.0093 Molecular.Function
## 5           1     0.02 0.0232 Molecular.Function
## 6           1     0.03 0.0324 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 380 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 14:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 13:	6 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	8 nodes to be scored	(11 eliminated genes)
```

```
## 
## 	 Level 11:	12 nodes to be scored	(158 eliminated genes)
```

```
## 
## 	 Level 10:	17 nodes to be scored	(211 eliminated genes)
```

```
## 
## 	 Level 9:	28 nodes to be scored	(233 eliminated genes)
```

```
## 
## 	 Level 8:	31 nodes to be scored	(321 eliminated genes)
```

```
## 
## 	 Level 7:	44 nodes to be scored	(385 eliminated genes)
```

```
## 
## 	 Level 6:	62 nodes to be scored	(444 eliminated genes)
```

```
## 
## 	 Level 5:	75 nodes to be scored	(624 eliminated genes)
```

```
## 
## 	 Level 4:	48 nodes to be scored	(857 eliminated genes)
```

```
## 
## 	 Level 3:	36 nodes to be scored	(1190 eliminated genes)
```

```
## 
## 	 Level 2:	11 nodes to be scored	(1312 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1404 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 223 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	8 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	15 nodes to be scored	(42 eliminated genes)
```

```
## 
## 	 Level 7:	33 nodes to be scored	(356 eliminated genes)
```

```
## 
## 	 Level 6:	48 nodes to be scored	(575 eliminated genes)
```

```
## 
## 	 Level 5:	43 nodes to be scored	(868 eliminated genes)
```

```
## 
## 	 Level 4:	37 nodes to be scored	(1249 eliminated genes)
```

```
## 
## 	 Level 3:	26 nodes to be scored	(2019 eliminated genes)
```

```
## 
## 	 Level 2:	11 nodes to be scored	(2271 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2620 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0001508                                       action potential         4
## 2  GO:0001732 formation of cytoplasmic translation initiation com...         6
## 3  GO:0009058                                   biosynthetic process       207
## 4  GO:0001771                        immunological synapse formation         1
## 5  GO:0006777         Mo-molybdopterin cofactor biosynthetic process         1
## 6  GO:0000183                         rDNA heterochromatin formation         1
## 7  GO:0000971 tRNA exon ligation utilizing 2',3' cyclic phosphate...         1
## 8  GO:0001706                                     endoderm formation         1
## 9  GO:0001967                                      suckling behavior         1
## 10 GO:0000454             snoRNA guided rRNA pseudouridine synthesis         1
## 11 GO:0002943                          tRNA dihydrouridine synthesis         1
## 12 GO:0007601                                      visual perception         1
## 13 GO:0000904         cell morphogenesis involved in differentiation         1
## 14 GO:0000105                         histidine biosynthetic process         1
## 15 GO:0001937 negative regulation of endothelial cell proliferati...         1
## 16 GO:0002100               tRNA wobble adenosine to inosine editing         1
## 17 GO:0003735                     structural constituent of ribosome        13
## 18 GO:0001786                             phosphatidylserine binding         4
## 19 GO:0003964                   RNA-directed DNA polymerase activity       122
## 20 GO:0000009                 alpha-1,6-mannosyltransferase activity         1
## 21 GO:0005315 inorganic phosphate transmembrane transporter activ...         1
## 22 GO:0004108                         citrate (Si)-synthase activity         1
## 23 GO:0004856                                  xylulokinase activity         1
## 24 GO:0004638      phosphoribosylaminoimidazole carboxylase activity         1
## 25 GO:0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activi...         1
## 26 GO:0004736                          pyruvate carboxylase activity         1
## 27 GO:0004568                                     chitinase activity         1
## 28 GO:0003944 N-acetylglucosamine-1-phosphodiester alpha-N-acetyl...         1
## 29 GO:0008768                       UDP-sugar diphosphatase activity         1
## 30 GO:0004096                                      catalase activity         1
## 31 GO:0004114     3',5'-cyclic-nucleotide phosphodiesterase activity         1
## 32 GO:0000033                 alpha-1,3-mannosyltransferase activity         1
## 33 GO:0005536                                        glucose binding         1
##    Significant Expected Fisher               type
## 1            2     0.18 0.0110 Biological.Process
## 2            2     0.27 0.0260 Biological.Process
## 3           11     9.24 0.0440 Biological.Process
## 4            1     0.04 0.0450 Biological.Process
## 5            1     0.04 0.0450 Biological.Process
## 6            1     0.04 0.0450 Biological.Process
## 7            1     0.04 0.0450 Biological.Process
## 8            1     0.04 0.0450 Biological.Process
## 9            1     0.04 0.0450 Biological.Process
## 10           1     0.04 0.0450 Biological.Process
## 11           1     0.04 0.0450 Biological.Process
## 12           1     0.04 0.0450 Biological.Process
## 13           1     0.04 0.0450 Biological.Process
## 14           1     0.04 0.0450 Biological.Process
## 15           1     0.04 0.0450 Biological.Process
## 16           1     0.04 0.0450 Biological.Process
## 17           4     0.55 0.0016 Molecular.Function
## 18           2     0.17 0.0100 Molecular.Function
## 19          11     5.14 0.0124 Molecular.Function
## 20           1     0.04 0.0421 Molecular.Function
## 21           1     0.04 0.0421 Molecular.Function
## 22           1     0.04 0.0421 Molecular.Function
## 23           1     0.04 0.0421 Molecular.Function
## 24           1     0.04 0.0421 Molecular.Function
## 25           1     0.04 0.0421 Molecular.Function
## 26           1     0.04 0.0421 Molecular.Function
## 27           1     0.04 0.0421 Molecular.Function
## 28           1     0.04 0.0421 Molecular.Function
## 29           1     0.04 0.0421 Molecular.Function
## 30           1     0.04 0.0421 Molecular.Function
## 31           1     0.04 0.0421 Molecular.Function
## 32           1     0.04 0.0421 Molecular.Function
## 33           1     0.04 0.0421 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 5 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 5:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(6 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(95 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(107 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## Warning in getSigGroups(object, test.stat): No enrichment can pe performed -
## there are no feasible GO terms!
```

```
##        GO.ID                       Term Annotated Significant Expected Fisher
## 1 GO:0006836 neurotransmitter transport         6           1        0 0.0043
##                 type
## 1 Biological.Process
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 131 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	4 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	5 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	8 nodes to be scored	(143 eliminated genes)
```

```
## 
## 	 Level 8:	8 nodes to be scored	(186 eliminated genes)
```

```
## 
## 	 Level 7:	13 nodes to be scored	(216 eliminated genes)
```

```
## 
## 	 Level 6:	23 nodes to be scored	(259 eliminated genes)
```

```
## 
## 	 Level 5:	31 nodes to be scored	(369 eliminated genes)
```

```
## 
## 	 Level 4:	19 nodes to be scored	(480 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(813 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(986 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1073 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 121 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	5 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	6 nodes to be scored	(107 eliminated genes)
```

```
## 
## 	 Level 7:	14 nodes to be scored	(452 eliminated genes)
```

```
## 
## 	 Level 6:	21 nodes to be scored	(475 eliminated genes)
```

```
## 
## 	 Level 5:	24 nodes to be scored	(738 eliminated genes)
```

```
## 
## 	 Level 4:	22 nodes to be scored	(892 eliminated genes)
```

```
## 
## 	 Level 3:	18 nodes to be scored	(1424 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(1747 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2440 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0008218                                        bioluminescence        10
## 2  GO:0001731         formation of translation preinitiation complex         1
## 3  GO:0002790                                      peptide secretion         2
## 4  GO:0000028                       ribosomal small subunit assembly         3
## 5  GO:0002933                                    lipid hydroxylation         3
## 6  GO:0004368 glycerol-3-phosphate dehydrogenase (quinone) activi...         1
## 7  GO:0004142      diacylglycerol cholinephosphotransferase activity         1
## 8  GO:0004325                                ferrochelatase activity         1
## 9  GO:0004176                       ATP-dependent peptidase activity         2
## 10 GO:0000774             adenyl-nucleotide exchange factor activity         2
## 11 GO:0004089                         carbonate dehydratase activity         2
## 12 GO:0003985                acetyl-CoA C-acetyltransferase activity         2
## 13 GO:0004252                     serine-type endopeptidase activity        53
## 14 GO:0005319                             lipid transporter activity         3
##    Significant Expected   Fisher               type
## 1            3     0.08 0.000041 Biological.Process
## 2            1     0.01 0.007800 Biological.Process
## 3            1     0.02 0.015500 Biological.Process
## 4            1     0.02 0.023200 Biological.Process
## 5            1     0.02 0.023200 Biological.Process
## 6            1     0.01 0.012000 Molecular.Function
## 7            1     0.01 0.012000 Molecular.Function
## 8            1     0.01 0.012000 Molecular.Function
## 9            1     0.02 0.024000 Molecular.Function
## 10           1     0.02 0.024000 Molecular.Function
## 11           1     0.02 0.024000 Molecular.Function
## 12           1     0.02 0.024000 Molecular.Function
## 13           3     0.63 0.024000 Molecular.Function
## 14           1     0.04 0.035000 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 18 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 7:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(105 eliminated genes)
```

```
## 
## 	 Level 4:	4 nodes to be scored	(123 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(240 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(285 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(302 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 18 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 7:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	3 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 4:	4 nodes to be scored	(188 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(443 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(935 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1404 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000972 transcription-dependent tethering of RNA polymerase...         1
## 2 GO:0003341                                        cilium movement        20
##   Significant Expected Fisher               type
## 1           1     0.00 0.0021 Biological.Process
## 2           1     0.04 0.0420 Biological.Process
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 121 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	3 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	4 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	5 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 8:	5 nodes to be scored	(157 eliminated genes)
```

```
## 
## 	 Level 7:	9 nodes to be scored	(160 eliminated genes)
```

```
## 
## 	 Level 6:	20 nodes to be scored	(218 eliminated genes)
```

```
## 
## 	 Level 5:	27 nodes to be scored	(318 eliminated genes)
```

```
## 
## 	 Level 4:	21 nodes to be scored	(378 eliminated genes)
```

```
## 
## 	 Level 3:	14 nodes to be scored	(494 eliminated genes)
```

```
## 
## 	 Level 2:	9 nodes to be scored	(880 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1099 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 46 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	4 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(115 eliminated genes)
```

```
## 
## 	 Level 6:	8 nodes to be scored	(136 eliminated genes)
```

```
## 
## 	 Level 5:	8 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(200 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(383 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(671 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1626 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0001755                            neural crest cell migration         2
## 2 GO:0002218                   activation of innate immune response        15
## 3 GO:0001002 RNA polymerase III type 1 promoter sequence-specifi...         1
## 4 GO:0004660                   protein farnesyltransferase activity         2
## 5 GO:0004719 protein-L-isoaspartate (D-aspartate) O-methyltransf...         3
## 6 GO:0004867           serine-type endopeptidase inhibitor activity         4
##   Significant Expected Fisher               type
## 1           1     0.01 0.0057 Biological.Process
## 2           1     0.04 0.0419 Biological.Process
## 3           1     0.00 0.0022 Molecular.Function
## 4           1     0.00 0.0043 Molecular.Function
## 5           1     0.01 0.0065 Molecular.Function
## 6           1     0.01 0.0086 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 51 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 12:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	2 nodes to be scored	(2 eliminated genes)
```

```
## 
## 	 Level 9:	4 nodes to be scored	(2 eliminated genes)
```

```
## 
## 	 Level 8:	5 nodes to be scored	(2 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(14 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(36 eliminated genes)
```

```
## 
## 	 Level 5:	8 nodes to be scored	(64 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(88 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(166 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(362 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(614 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 56 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 7:	5 nodes to be scored	(70 eliminated genes)
```

```
## 
## 	 Level 6:	7 nodes to be scored	(146 eliminated genes)
```

```
## 
## 	 Level 5:	8 nodes to be scored	(290 eliminated genes)
```

```
## 
## 	 Level 4:	12 nodes to be scored	(375 eliminated genes)
```

```
## 
## 	 Level 3:	12 nodes to be scored	(490 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(935 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2047 eliminated genes)
```

```
##        GO.ID                                        Term Annotated Significant
## 1 GO:0001516          prostaglandin biosynthetic process         2           1
## 2 GO:0000028            ribosomal small subunit assembly         3           1
## 3 GO:0001523                  retinoid metabolic process         9           1
## 4 GO:0005381 iron ion transmembrane transporter activity         1           1
## 5 GO:0004252          serine-type endopeptidase activity        53           2
## 6 GO:0005245      voltage-gated calcium channel activity         7           1
## 7 GO:0005542                          folic acid binding        10           1
##   Expected Fisher               type
## 1     0.00 0.0042 Biological.Process
## 2     0.01 0.0064 Biological.Process
## 3     0.02 0.0190 Biological.Process
## 4     0.00 0.0029 Molecular.Function
## 5     0.15 0.0093 Molecular.Function
## 6     0.02 0.0200 Molecular.Function
## 7     0.03 0.0285 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 27 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	1 nodes to be scored	(15 eliminated genes)
```

```
## 
## 	 Level 10:	1 nodes to be scored	(63 eliminated genes)
```

```
## 
## 	 Level 9:	2 nodes to be scored	(63 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(64 eliminated genes)
```

```
## 
## 	 Level 7:	1 nodes to be scored	(66 eliminated genes)
```

```
## 
## 	 Level 6:	1 nodes to be scored	(97 eliminated genes)
```

```
## 
## 	 Level 5:	3 nodes to be scored	(242 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(268 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(346 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(467 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(595 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 23 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(275 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(443 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(685 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(802 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1010 eliminated genes)
```

```
##        GO.ID                                       Term Annotated Significant
## 1 GO:0000380 alternative mRNA splicing, via spliceosome        15           1
## 2 GO:0003341                            cilium movement        20           1
##   Expected Fisher               type
## 1     0.02  0.021 Biological.Process
## 2     0.03  0.028 Biological.Process
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 96 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 14:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 13:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(11 eliminated genes)
```

```
## 
## 	 Level 11:	4 nodes to be scored	(15 eliminated genes)
```

```
## 
## 	 Level 10:	6 nodes to be scored	(65 eliminated genes)
```

```
## 
## 	 Level 9:	6 nodes to be scored	(66 eliminated genes)
```

```
## 
## 	 Level 8:	7 nodes to be scored	(74 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(80 eliminated genes)
```

```
## 
## 	 Level 6:	10 nodes to be scored	(268 eliminated genes)
```

```
## 
## 	 Level 5:	16 nodes to be scored	(378 eliminated genes)
```

```
## 
## 	 Level 4:	16 nodes to be scored	(492 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(787 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(947 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1069 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 34 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	5 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(286 eliminated genes)
```

```
## 
## 	 Level 4:	5 nodes to be scored	(306 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(357 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(470 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1649 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000076                   DNA replication checkpoint signaling         1
## 2 GO:0001516                     prostaglandin biosynthetic process         2
## 3 GO:0000381 regulation of alternative mRNA splicing, via splice...        11
## 4 GO:0004777 succinate-semialdehyde dehydrogenase (NAD+) activit...         1
## 5 GO:0004601                                    peroxidase activity         7
## 6 GO:0004181                       metallocarboxypeptidase activity        10
##   Significant Expected Fisher               type
## 1           1     0.00 0.0035 Biological.Process
## 2           1     0.01 0.0071 Biological.Process
## 3           1     0.04 0.0384 Biological.Process
## 4           1     0.00 0.0018 Molecular.Function
## 5           1     0.01 0.0126 Molecular.Function
## 6           1     0.02 0.0179 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 133 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 11:	4 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	4 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 9:	6 nodes to be scored	(143 eliminated genes)
```

```
## 
## 	 Level 8:	5 nodes to be scored	(149 eliminated genes)
```

```
## 
## 	 Level 7:	13 nodes to be scored	(167 eliminated genes)
```

```
## 
## 	 Level 6:	23 nodes to be scored	(187 eliminated genes)
```

```
## 
## 	 Level 5:	29 nodes to be scored	(299 eliminated genes)
```

```
## 
## 	 Level 4:	22 nodes to be scored	(395 eliminated genes)
```

```
## 
## 	 Level 3:	16 nodes to be scored	(644 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(758 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(891 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 73 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(100 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(383 eliminated genes)
```

```
## 
## 	 Level 6:	13 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 5:	16 nodes to be scored	(409 eliminated genes)
```

```
## 
## 	 Level 4:	16 nodes to be scored	(606 eliminated genes)
```

```
## 
## 	 Level 3:	14 nodes to be scored	(1054 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(1464 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2009 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0002933                                    lipid hydroxylation         3
## 2  GO:0001731         formation of translation preinitiation complex         1
## 3  GO:0000028                       ribosomal small subunit assembly         3
## 4  GO:0009734                      auxin-activated signaling pathway         4
## 5  GO:0004342             glucosamine-6-phosphate deaminase activity         2
## 6  GO:0004066 asparagine synthase (glutamine-hydrolyzing) activit...         1
## 7  GO:0004142      diacylglycerol cholinephosphotransferase activity         1
## 8  GO:0004089                         carbonate dehydratase activity         2
## 9  GO:0004252                     serine-type endopeptidase activity        53
## 10 GO:0004601                                    peroxidase activity         7
##    Significant Expected   Fisher               type
## 1            2     0.02 0.000110 Biological.Process
## 2            1     0.01 0.006380 Biological.Process
## 3            1     0.02 0.019030 Biological.Process
## 4            1     0.03 0.025300 Biological.Process
## 5            2     0.01 0.000031 Molecular.Function
## 6            1     0.01 0.005800 Molecular.Function
## 7            1     0.01 0.005800 Molecular.Function
## 8            1     0.01 0.011500 Molecular.Function
## 9            2     0.31 0.036200 Molecular.Function
## 10           1     0.04 0.039700 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 31 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(37 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(40 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(42 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(151 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(182 eliminated genes)
```

```
## 
## 	 Level 3:	4 nodes to be scored	(360 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(508 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(954 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 9 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 7:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	1 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 3:	2 nodes to be scored	(134 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(257 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(412 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0006836           neurotransmitter transport         6           1
## 2 GO:0008218                      bioluminescence        10           1
## 3 GO:0003964 RNA-directed DNA polymerase activity       122           1
##   Expected Fisher               type
## 1     0.02  0.017 Biological.Process
## 2     0.03  0.028 Biological.Process
## 3     0.04  0.044 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## Warning in getSigGroups(object, test.stat): No enrichment can pe performed -
## there are no feasible GO terms!
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 24 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	3 nodes to be scored	(275 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(278 eliminated genes)
```

```
## 
## 	 Level 3:	7 nodes to be scored	(294 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(306 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1398 eliminated genes)
```

```
##        GO.ID                                   Term Annotated Significant
## 1 GO:0004013        adenosylhomocysteinase activity         1           1
## 2 GO:0005200 structural constituent of cytoskeleton         4           1
##   Expected Fisher               type
## 1        0 0.0011 Molecular.Function
## 2        0 0.0043 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 140 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 14:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 13:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 12:	1 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 11:	2 nodes to be scored	(3 eliminated genes)
```

```
## 
## 	 Level 10:	5 nodes to be scored	(3 eliminated genes)
```

```
## 
## 	 Level 9:	7 nodes to be scored	(3 eliminated genes)
```

```
## 
## 	 Level 8:	10 nodes to be scored	(14 eliminated genes)
```

```
## 
## 	 Level 7:	16 nodes to be scored	(34 eliminated genes)
```

```
## 
## 	 Level 6:	27 nodes to be scored	(280 eliminated genes)
```

```
## 
## 	 Level 5:	30 nodes to be scored	(346 eliminated genes)
```

```
## 
## 	 Level 4:	20 nodes to be scored	(417 eliminated genes)
```

```
## 
## 	 Level 3:	12 nodes to be scored	(723 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(875 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(989 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 49 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 9:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	8 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	11 nodes to be scored	(293 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(431 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(925 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(1283 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1620 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000290 deadenylation-dependent decapping of nuclear-transc...         1
## 2 GO:0001782                                     B cell homeostasis         7
## 3 GO:0001889                                      liver development         8
## 4 GO:0001523                             retinoid metabolic process         9
## 5 GO:0002291 T cell activation via T cell receptor contact with ...        10
## 6 GO:0004609              phosphatidylserine decarboxylase activity        13
##   Significant Expected Fisher               type
## 1           1     0.00 0.0043 Biological.Process
## 2           1     0.03 0.0295 Biological.Process
## 3           1     0.03 0.0336 Biological.Process
## 4           1     0.04 0.0377 Biological.Process
## 5           1     0.04 0.0418 Biological.Process
## 6           2     0.08 0.0030 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

```
## 
## Building most specific GOs .....
```

```
## 	( 272 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 1229 GO terms and 2373 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 1411 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 38 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 11:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 10:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	3 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 8:	4 nodes to be scored	(43 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(58 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(127 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(289 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(338 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(612 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(679 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(778 eliminated genes)
```

```
## 
## Building most specific GOs .....
```

```
## 	( 460 GO terms found. )
```

```
## 
## Build GO DAG topology ..........
```

```
## 	( 909 GO terms and 1190 relations. )
```

```
## 
## Annotating nodes ...............
```

```
## 	( 2776 genes annotated to the GO terms. )
```

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 45 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 10:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 7:	5 nodes to be scored	(332 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(341 eliminated genes)
```

```
## 
## 	 Level 5:	7 nodes to be scored	(377 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(395 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(608 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(633 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1973 eliminated genes)
```

```
##        GO.ID                                   Term Annotated Significant
## 1 GO:0006400                      tRNA modification         4           1
## 2 GO:0005245 voltage-gated calcium channel activity         7           1
## 3 GO:0004177                aminopeptidase activity         7           1
##   Expected Fisher               type
## 1     0.01 0.0057 Biological.Process
## 2     0.01 0.0130 Molecular.Function
## 3     0.01 0.0130 Molecular.Function
```

``` r
head(results_high0.5_cor_targets)
```

```
##        GO.ID                                               Term Annotated
## 1 GO:0006598                        polyamine catabolic process         3
## 2 GO:0001745                         compound eye morphogenesis         3
## 3 GO:0000014 single-stranded DNA endodeoxyribonuclease activity         3
## 4 GO:0005290     L-histidine transmembrane transporter activity         9
## 5 GO:0001658   branching involved in ureteric bud morphogenesis         4
## 6 GO:0001945                           lymph vessel development         5
##   Significant Expected Fisher               type         miRNA
## 1           1     0.00 0.0042 Biological.Process Cluster_10452
## 2           1     0.00 0.0042 Biological.Process Cluster_10452
## 3           1     0.01 0.0065 Molecular.Function Cluster_10452
## 4           1     0.02 0.0193 Molecular.Function Cluster_10452
## 5           1     0.01 0.0057 Biological.Process Cluster_11565
## 6           1     0.01 0.0071 Biological.Process Cluster_11565
```