``` r
interacting_miRNAs_high0.6 <- unique(high0.6_cor_bind_FA$miRNA) %>% na.omit
results_high0.6_cor_targets <- NULL  # initialize empty df

for(miRNA in interacting_miRNAs_high0.6) {
  
  # Run topGO enrichment function
  miRNA_results <- miRNA_topGO_FE(miRNA, high0.6_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_high0.6_cor_targets <- rbind(results_high0.6_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 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 15 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 6:	2 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 5:	3 nodes to be scored	(35 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(40 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(145 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(149 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(186 eliminated genes)
```

```
##        GO.ID                                           Term Annotated
## 1 GO:0005290 L-histidine transmembrane transporter activity         9
##   Significant Expected Fisher               type
## 1           1        0 0.0032 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 32 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:	5 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 5:	7 nodes to be scored	(153 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(227 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(465 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(716 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1029 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:0004771                         sterol esterase activity         5
## 5 GO:0004966                        galanin receptor activity        12
## 6 GO:0004222                    metalloendopeptidase activity        15
## 7 GO:0005201      extracellular matrix structural constituent        17
##   Significant Expected Fisher               type
## 1           1     0.01 0.0057 Biological.Process
## 2           1     0.01 0.0071 Biological.Process
## 3           2     0.15 0.0093 Molecular.Function
## 4           1     0.01 0.0143 Molecular.Function
## 5           1     0.03 0.0341 Molecular.Function
## 6           1     0.04 0.0425 Molecular.Function
## 7           1     0.05 0.0480 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 47 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	(15 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(15 eliminated genes)
```

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

```
## 
## 	 Level 5:	9 nodes to be scored	(64 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(78 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(136 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(363 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(528 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 17 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	(178 eliminated genes)
```

```
## 
## 	 Level 3:	4 nodes to be scored	(317 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(460 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(934 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0002218 activation of innate immune response        15           1
## 2 GO:0009034               tryptophanase activity         2           1
## 3 GO:0003964 RNA-directed DNA polymerase activity       122           2
##   Expected Fisher               type
## 1     0.03 0.0320 Biological.Process
## 2     0.00 0.0029 Molecular.Function
## 3     0.18 0.0108 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 60 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:	2 nodes to be scored	(52 eliminated genes)
```

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

```
## 
## 	 Level 6:	8 nodes to be scored	(57 eliminated genes)
```

```
## 
## 	 Level 5:	12 nodes to be scored	(111 eliminated genes)
```

```
## 
## 	 Level 4:	9 nodes to be scored	(148 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(337 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(574 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(743 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 31 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:	5 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(455 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(610 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(765 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1479 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0002040               sprouting angiogenesis        12           1
## 2 GO:0002218 activation of innate immune response        15           1
## 3 GO:0003964 RNA-directed DNA polymerase activity       122           3
## 4 GO:0009034               tryptophanase activity         2           1
##   Expected Fisher               type
## 1     0.03 0.0340 Biological.Process
## 2     0.04 0.0420 Biological.Process
## 3     0.26 0.0015 Molecular.Function
## 4     0.00 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 56 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:	2 nodes to be scored	(52 eliminated genes)
```

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

```
## 
## 	 Level 6:	8 nodes to be scored	(57 eliminated genes)
```

```
## 
## 	 Level 5:	11 nodes to be scored	(111 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(148 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(311 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(534 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(697 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 17 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	(178 eliminated genes)
```

```
## 
## 	 Level 3:	4 nodes to be scored	(317 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(460 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(934 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0002040               sprouting angiogenesis        12           1
## 2 GO:0002218 activation of innate immune response        15           1
## 3 GO:0003964 RNA-directed DNA polymerase activity       122           3
## 4 GO:0009034               tryptophanase activity         2           1
##   Expected  Fisher               type
## 1     0.03 0.02500 Biological.Process
## 2     0.03 0.03200 Biological.Process
## 3     0.22 0.00078 Molecular.Function
## 4     0.00 0.00360 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 9 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 6:	1 nodes to be scored	(15 eliminated genes)
```

```
## 
## 	 Level 5:	1 nodes to be scored	(25 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(25 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(38 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(218 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 18 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:	2 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(275 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(277 eliminated genes)
```

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

```
## 
## 	 Level 2:	1 nodes to be scored	(802 eliminated genes)
```

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

```
##        GO.ID                           Term Annotated Significant Expected
## 1 GO:0001701 in utero embryonic development        15           1     0.01
##   Fisher               type
## 1  0.011 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 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 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 10 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 6:	1 nodes to be scored	(65 eliminated genes)
```

```
## 
## 	 Level 5:	1 nodes to be scored	(65 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(65 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(192 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(221 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 16 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 6:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 4:	4 nodes to be scored	(40 eliminated genes)
```

```
## 
## 	 Level 3:	4 nodes to be scored	(61 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(212 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(795 eliminated genes)
```

```
##        GO.ID                      Term Annotated Significant Expected Fisher
## 1 GO:0001822        kidney development        65           1     0.05  0.046
## 2 GO:0005096 GTPase activator activity        12           1     0.01  0.013
## 3 GO:0004180 carboxypeptidase activity        28           1     0.03  0.030
## 4 GO:0001653 peptide receptor activity        40           1     0.04  0.043
##                 type
## 1 Biological.Process
## 2 Molecular.Function
## 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 74 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:	4 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(143 eliminated genes)
```

```
## 
## 	 Level 7:	5 nodes to be scored	(145 eliminated genes)
```

```
## 
## 	 Level 6:	11 nodes to be scored	(172 eliminated genes)
```

```
## 
## 	 Level 5:	16 nodes to be scored	(268 eliminated genes)
```

```
## 
## 	 Level 4:	12 nodes to be scored	(323 eliminated genes)
```

```
## 
## 	 Level 3:	7 nodes to be scored	(455 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(768 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(906 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 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	(100 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(383 eliminated genes)
```

```
## 
## 	 Level 6:	11 nodes to be scored	(398 eliminated genes)
```

```
## 
## 	 Level 5:	12 nodes to be scored	(429 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(504 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(797 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(1255 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1890 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0001825                                   blastocyst formation         1
## 2 GO:0004035                          alkaline phosphatase activity         1
## 3 GO:0004325                                ferrochelatase activity         1
## 4 GO:0004777 succinate-semialdehyde dehydrogenase (NAD+) activit...         1
## 5 GO:0008137               NADH dehydrogenase (ubiquinone) activity         1
## 6 GO:0004176                       ATP-dependent peptidase activity         2
## 7 GO:0003943             N-acetylgalactosamine-4-sulfatase activity         8
## 8 GO:0003697                            single-stranded DNA binding         8
##   Significant Expected Fisher               type
## 1           1     0.00 0.0014 Biological.Process
## 2           1     0.00 0.0043 Molecular.Function
## 3           1     0.00 0.0043 Molecular.Function
## 4           1     0.00 0.0043 Molecular.Function
## 5           1     0.00 0.0043 Molecular.Function
## 6           1     0.01 0.0086 Molecular.Function
## 7           1     0.03 0.0341 Molecular.Function
## 8           1     0.03 0.0341 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 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	(28 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(37 eliminated genes)
```

```
## 
## 	 Level 5:	10 nodes to be scored	(58 eliminated genes)
```

```
## 
## 	 Level 4:	9 nodes to be scored	(151 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(497 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(654 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(704 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 59 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:	5 nodes to be scored	(375 eliminated genes)
```

```
## 
## 	 Level 6:	8 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 5:	9 nodes to be scored	(560 eliminated genes)
```

```
## 
## 	 Level 4:	12 nodes to be scored	(580 eliminated genes)
```

```
## 
## 	 Level 3:	14 nodes to be scored	(790 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(1413 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2341 eliminated genes)
```

```
##        GO.ID                                         Term Annotated Significant
## 1 GO:0032259                                  methylation         5           1
## 2 GO:0000038 very long-chain fatty acid metabolic process         9           1
## 3 GO:0000278                           mitotic cell cycle       160           2
## 4 GO:0004568                           chitinase activity         1           1
## 5 GO:0005178                             integrin binding         4           1
##   Expected Fisher               type
## 1     0.02  0.018 Biological.Process
## 2     0.03  0.032 Biological.Process
## 3     0.57  0.047 Biological.Process
## 4     0.01  0.005 Molecular.Function
## 5     0.02  0.020 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 17 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:	2 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(275 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(277 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 Significant Expected Fisher
## 1 GO:0003341 cilium movement        20           1     0.01  0.014
##                 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 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	(35 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(44 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(71 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(246 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(352 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:0000165 MAPK cascade        35           1     0.02  0.025
##                 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 78 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:	7 nodes to be scored	(16 eliminated genes)
```

```
## 
## 	 Level 8:	7 nodes to be scored	(16 eliminated genes)
```

```
## 
## 	 Level 7:	10 nodes to be scored	(17 eliminated genes)
```

```
## 
## 	 Level 6:	9 nodes to be scored	(87 eliminated genes)
```

```
## 
## 	 Level 5:	12 nodes to be scored	(174 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(187 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(262 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(356 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(683 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 6:	2 nodes to be scored	(0 eliminated genes)
```

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

```
## 
## 	 Level 4:	5 nodes to be scored	(58 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(713 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(956 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1564 eliminated genes)
```

```
##        GO.ID                                             Term Annotated
## 1 GO:0001945                         lymph vessel development         5
## 2 GO:0001658 branching involved in ureteric bud morphogenesis         4
## 3 GO:0001889                                liver development         8
## 4 GO:0004771                         sterol esterase activity         5
##   Significant Expected  Fisher               type
## 1           2     0.02 0.00015 Biological.Process
## 2           1     0.02 0.01692 Biological.Process
## 3           1     0.03 0.03360 Biological.Process
## 4           1     0.01 0.01100 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 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 61 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## 
## 	 Level 8:	4 nodes to be scored	(0 eliminated genes)
```

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

```
## 
## 	 Level 6:	10 nodes to be scored	(87 eliminated genes)
```

```
## 
## 	 Level 5:	12 nodes to be scored	(246 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(439 eliminated genes)
```

```
## 
## 	 Level 3:	8 nodes to be scored	(731 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(933 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1074 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 71 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	(100 eliminated genes)
```

```
## 
## 	 Level 7:	10 nodes to be scored	(407 eliminated genes)
```

```
## 
## 	 Level 6:	11 nodes to be scored	(491 eliminated genes)
```

```
## 
## 	 Level 5:	13 nodes to be scored	(740 eliminated genes)
```

```
## 
## 	 Level 4:	13 nodes to be scored	(778 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(1160 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(1619 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2195 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000165                                           MAPK cascade        35
## 2 GO:0002674     negative regulation of acute inflammatory response         4
## 3 GO:0001409 guanine nucleotide transmembrane transporter activi...        30
## 4 GO:0004623                              phospholipase A2 activity         4
## 5 GO:0005524                                            ATP binding       263
## 6 GO:0001640 adenylate cyclase inhibiting G protein-coupled glut...         9
## 7 GO:0003924                                        GTPase activity        66
##   Significant Expected Fisher               type
## 1           2     0.15 0.0084 Biological.Process
## 2           1     0.02 0.0169 Biological.Process
## 3           2     0.16 0.0110 Molecular.Function
## 4           1     0.02 0.0210 Molecular.Function
## 5           4     1.42 0.0460 Molecular.Function
## 6           1     0.05 0.0480 Molecular.Function
## 7           2     0.36 0.0480 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 76 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:	3 nodes to be scored	(10 eliminated genes)
```

```
## 
## 	 Level 8:	5 nodes to be scored	(14 eliminated genes)
```

```
## 
## 	 Level 7:	6 nodes to be scored	(44 eliminated genes)
```

```
## 
## 	 Level 6:	10 nodes to be scored	(135 eliminated genes)
```

```
## 
## 	 Level 5:	18 nodes to be scored	(335 eliminated genes)
```

```
## 
## 	 Level 4:	16 nodes to be scored	(376 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(487 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(539 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 30 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:	5 nodes to be scored	(152 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(166 eliminated genes)
```

```
## 
## 	 Level 3:	7 nodes to be scored	(511 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(1033 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1672 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000038           very long-chain fatty acid metabolic process         9
## 2 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsens...        10
## 3 GO:0001409 guanine nucleotide transmembrane transporter activi...        30
## 4 GO:0005085             guanyl-nucleotide exchange factor activity        12
##   Significant Expected Fisher               type
## 1           1     0.03 0.0320 Biological.Process
## 2           1     0.04 0.0350 Biological.Process
## 3           2     0.06 0.0016 Molecular.Function
## 4           1     0.03 0.0257 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 161 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	(2 eliminated genes)
```

```
## 
## 	 Level 11:	5 nodes to be scored	(143 eliminated genes)
```

```
## 
## 	 Level 10:	8 nodes to be scored	(143 eliminated genes)
```

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

```
## 
## 	 Level 8:	10 nodes to be scored	(156 eliminated genes)
```

```
## 
## 	 Level 7:	16 nodes to be scored	(176 eliminated genes)
```

```
## 
## 	 Level 6:	27 nodes to be scored	(306 eliminated genes)
```

```
## 
## 	 Level 5:	34 nodes to be scored	(353 eliminated genes)
```

```
## 
## 	 Level 4:	22 nodes to be scored	(432 eliminated genes)
```

```
## 
## 	 Level 3:	15 nodes to be scored	(756 eliminated genes)
```

```
## 
## 	 Level 2:	8 nodes to be scored	(1007 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1102 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 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	(9 eliminated genes)
```

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

```
## 
## 	 Level 7:	7 nodes to be scored	(322 eliminated genes)
```

```
## 
## 	 Level 6:	8 nodes to be scored	(332 eliminated genes)
```

```
## 
## 	 Level 5:	10 nodes to be scored	(501 eliminated genes)
```

```
## 
## 	 Level 4:	10 nodes to be scored	(531 eliminated genes)
```

```
## 
## 	 Level 3:	12 nodes to be scored	(1073 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(1355 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2089 eliminated genes)
```

```
##        GO.ID                                             Term Annotated
## 1 GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening         2
## 2 GO:0006886                  intracellular protein transport         5
## 3 GO:0001782                               B cell homeostasis         7
## 4 GO:0001764                                 neuron migration         8
## 5 GO:0001222                transcription corepressor binding         3
## 6 GO:0005242      inward rectifier potassium channel activity         9
## 7 GO:0003777                       microtubule motor activity        16
##   Significant Expected Fisher               type
## 1           1     0.01 0.0099 Biological.Process
## 2           1     0.02 0.0246 Biological.Process
## 3           1     0.03 0.0343 Biological.Process
## 4           1     0.04 0.0391 Biological.Process
## 5           1     0.01 0.0086 Molecular.Function
## 6           1     0.03 0.0257 Molecular.Function
## 7           1     0.05 0.0452 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 7 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:	3 nodes to be scored	(293 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(293 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(814 eliminated genes)
```

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 39 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	(1 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(16 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(16 eliminated genes)
```

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

```
## 
## 	 Level 5:	7 nodes to be scored	(30 eliminated genes)
```

```
## 
## 	 Level 4:	5 nodes to be scored	(34 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(50 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(84 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(452 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 6 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## 
## 	 Level 5:	1 nodes to be scored	(0 eliminated genes)
```

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

```
## 
## 	 Level 3:	1 nodes to be scored	(4 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(6 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(115 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0002230 positive regulation of defense response to virus by...         1
## 2 GO:0002218                   activation of innate immune response        15
## 3 GO:0004753                    saccharopine dehydrogenase activity         1
##   Significant Expected  Fisher               type
## 1           1     0.00 0.00140 Biological.Process
## 2           1     0.02 0.02120 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 10 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 6:	1 nodes to be scored	(65 eliminated genes)
```

```
## 
## 	 Level 5:	1 nodes to be scored	(65 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(65 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(192 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(221 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 15 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:	2 nodes to be scored	(3 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(125 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(201 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(213 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(336 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(774 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0001822                   kidney development        65           1
## 2 GO:0004382             GDP phosphatase activity         3           1
## 3 GO:0003964 RNA-directed DNA polymerase activity       122           2
##   Expected Fisher               type
## 1     0.05 0.0460 Biological.Process
## 2     0.00 0.0032 Molecular.Function
## 3     0.13 0.0056 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 20 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:	3 nodes to be scored	(18 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(38 eliminated genes)
```

```
## 
## 	 Level 4:	4 nodes to be scored	(196 eliminated genes)
```

```
## 
## 	 Level 3:	2 nodes to be scored	(301 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(452 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(626 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 6 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:	2 nodes to be scored	(264 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(497 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(809 eliminated genes)
```

```
##        GO.ID                                       Term Annotated Significant
## 1 GO:0001818 negative regulation of cytokine production        18           1
##   Expected Fisher               type
## 1     0.01  0.013 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 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 26 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:	3 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 4:	5 nodes to be scored	(399 eliminated genes)
```

```
## 
## 	 Level 3:	7 nodes to be scored	(427 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(1059 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1422 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0003964 RNA-directed DNA polymerase activity       122           2
##   Expected Fisher               type
## 1     0.18  0.011 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 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 6 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## 
## 	 Level 5:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(66 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(181 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(181 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(465 eliminated genes)
```

```
##        GO.ID                Term Annotated Significant Expected  Fisher
## 1 GO:0008218     bioluminescence        10           3     0.02 2.6e-07
## 2 GO:0005509 calcium ion binding        66           1     0.02 2.4e-02
##                 type
## 1 Biological.Process
## 2 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 57 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## 
## 	 Level 7:	6 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 6:	8 nodes to be scored	(113 eliminated genes)
```

```
## 
## 	 Level 5:	8 nodes to be scored	(178 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(454 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(719 eliminated genes)
```

```
## 
## 	 Level 2:	9 nodes to be scored	(922 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1091 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 71 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:	8 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	9 nodes to be scored	(276 eliminated genes)
```

```
## 
## 	 Level 5:	15 nodes to be scored	(517 eliminated genes)
```

```
## 
## 	 Level 4:	15 nodes to be scored	(623 eliminated genes)
```

```
## 
## 	 Level 3:	14 nodes to be scored	(1124 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(1469 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2106 eliminated genes)
```

```
##        GO.ID                                     Term Annotated Significant
## 1 GO:0001822                       kidney development        65           4
## 2 GO:0000165                             MAPK cascade        35           3
## 3 GO:0000723                     telomere maintenance         4           1
## 4 GO:0005178                         integrin binding         4           1
## 5 GO:0004674 protein serine/threonine kinase activity        55           2
##   Expected Fisher               type
## 1     0.51 0.0011 Biological.Process
## 2     0.27 0.0020 Biological.Process
## 3     0.03 0.0309 Biological.Process
## 4     0.02 0.0230 Molecular.Function
## 5     0.32 0.0390 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 5 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 4:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 3:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(497 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(809 eliminated genes)
```

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 186 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 11:	5 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 10:	8 nodes to be scored	(210 eliminated genes)
```

```
## 
## 	 Level 9:	12 nodes to be scored	(212 eliminated genes)
```

```
## 
## 	 Level 8:	14 nodes to be scored	(293 eliminated genes)
```

```
## 
## 	 Level 7:	17 nodes to be scored	(330 eliminated genes)
```

```
## 
## 	 Level 6:	29 nodes to be scored	(428 eliminated genes)
```

```
## 
## 	 Level 5:	36 nodes to be scored	(545 eliminated genes)
```

```
## 
## 	 Level 4:	29 nodes to be scored	(794 eliminated genes)
```

```
## 
## 	 Level 3:	21 nodes to be scored	(996 eliminated genes)
```

```
## 
## 	 Level 2:	9 nodes to be scored	(1150 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1348 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 122 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## 
## 	 Level 9:	6 nodes to be scored	(0 eliminated genes)
```

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

```
## 
## 	 Level 7:	14 nodes to be scored	(129 eliminated genes)
```

```
## 
## 	 Level 6:	21 nodes to be scored	(165 eliminated genes)
```

```
## 
## 	 Level 5:	28 nodes to be scored	(425 eliminated genes)
```

```
## 
## 	 Level 4:	21 nodes to be scored	(663 eliminated genes)
```

```
## 
## 	 Level 3:	17 nodes to be scored	(1596 eliminated genes)
```

```
## 
## 	 Level 2:	7 nodes to be scored	(1739 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2083 eliminated genes)
```

```
##         GO.ID                                               Term Annotated
## 1  GO:0001843                                neural tube closure         7
## 2  GO:0001841                              neural tube formation         8
## 3  GO:0001662                           behavioral fear response         1
## 4  GO:0002181                            cytoplasmic translation        21
## 5  GO:0000054              ribosomal subunit export from nucleus         3
## 6  GO:0003746             translation elongation factor activity         7
## 7  GO:0004561             alpha-N-acetylglucosaminidase activity         1
## 8  GO:0004568                                 chitinase activity         1
## 9  GO:0003724                              RNA helicase activity         1
## 10 GO:0008641 ubiquitin-like modifier activating enzyme activity         1
## 11 GO:0004441   inositol-1,4-bisphosphate 1-phosphatase activity         1
## 12 GO:0004305                       ethanolamine kinase activity         1
## 13 GO:0004438        phosphatidylinositol-3-phosphatase activity         2
## 14 GO:0003727                        single-stranded RNA binding         2
## 15 GO:0032450                 maltose alpha-glucosidase activity         2
## 16 GO:0004185              serine-type carboxypeptidase activity         2
## 17 GO:0005198                       structural molecule activity        54
##    Significant Expected Fisher               type
## 1            2     0.10 0.0042 Biological.Process
## 2            3     0.12 0.0135 Biological.Process
## 3            1     0.01 0.0149 Biological.Process
## 4            2     0.31 0.0374 Biological.Process
## 5            1     0.04 0.0440 Biological.Process
## 6            2     0.09 0.0035 Molecular.Function
## 7            1     0.01 0.0133 Molecular.Function
## 8            1     0.01 0.0133 Molecular.Function
## 9            1     0.01 0.0133 Molecular.Function
## 10           1     0.01 0.0133 Molecular.Function
## 11           1     0.01 0.0133 Molecular.Function
## 12           1     0.01 0.0133 Molecular.Function
## 13           1     0.03 0.0265 Molecular.Function
## 14           1     0.03 0.0265 Molecular.Function
## 15           1     0.03 0.0265 Molecular.Function
## 16           1     0.03 0.0265 Molecular.Function
## 17           4     0.72 0.0366 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 17 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:	2 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(275 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(277 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)
```

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 7 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## 
## 	 Level 5:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(28 eliminated genes)
```

```
## 
## 	 Level 3:	2 nodes to be scored	(35 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(146 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(527 eliminated genes)
```

```
##        GO.ID                      Term Annotated Significant Expected Fisher
## 1 GO:0004180 carboxypeptidase activity        28           1     0.01   0.01
##                 type
## 1 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 36 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:	4 nodes to be scored	(21 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(22 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(307 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(443 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 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:0015969 guanosine tetraphosphate metabolic process         9           1
## 2 GO:0019700      organic phosphonate catabolic process        12           1
##   Expected Fisher               type
## 1     0.01  0.013 Biological.Process
## 2     0.02  0.017 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 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 13 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:	2 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 5:	3 nodes to be scored	(35 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(40 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(145 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(149 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(186 eliminated genes)
```

```
##        GO.ID                                          Term Annotated
## 1 GO:0005302 L-tyrosine transmembrane transporter activity         9
##   Significant Expected Fisher               type
## 1           1        0 0.0032 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 10 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	(3 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(6 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(32 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(37 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 14 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 6:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	3 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(67 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(204 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(278 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(982 eliminated genes)
```

```
##        GO.ID                            Term Annotated Significant Expected
## 1 GO:0002933             lipid hydroxylation         3           1     0.00
## 2 GO:0002161 aminoacyl-tRNA editing activity         1           1     0.00
## 3 GO:0005509             calcium ion binding        66           1     0.05
##    Fisher               type
## 1 0.00210 Biological.Process
## 2 0.00072 Molecular.Function
## 3 0.04699 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 37 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	(10 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(10 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(64 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(64 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(198 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(413 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(609 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 21 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:	4 nodes to be scored	(18 eliminated genes)
```

```
## 
## 	 Level 4:	4 nodes to be scored	(70 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(554 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(840 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1612 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0001581 detection of chemical stimulus involved in sensory ...        10
## 2 GO:0002221         pattern recognition receptor signaling pathway        11
## 3 GO:0001965                        G-protein alpha-subunit binding        16
## 4 GO:0005507                                     copper ion binding        18
## 5 GO:0004197                   cysteine-type endopeptidase activity        18
##   Significant Expected Fisher               type
## 1           1     0.02  0.021 Biological.Process
## 2           1     0.02  0.023 Biological.Process
## 3           1     0.04  0.040 Molecular.Function
## 4           1     0.05  0.045 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 70 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:	4 nodes to be scored	(142 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(172 eliminated genes)
```

```
## 
## 	 Level 7:	5 nodes to be scored	(180 eliminated genes)
```

```
## 
## 	 Level 6:	11 nodes to be scored	(194 eliminated genes)
```

```
## 
## 	 Level 5:	16 nodes to be scored	(283 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(378 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(440 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(540 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 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:0000209 protein polyubiquitination        30           1     0.04  0.042
##                 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 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 11 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 6:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(68 eliminated genes)
```

```
## 
## 	 Level 3:	2 nodes to be scored	(185 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(186 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(523 eliminated genes)
```

```
##        GO.ID                           Term Annotated Significant Expected
## 1 GO:0004089 carbonate dehydratase activity         2           1     0.00
## 2 GO:0005509            calcium ion binding        66           1     0.05
##   Fisher               type
## 1 0.0014 Molecular.Function
## 2 0.0470 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 128 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 13:	3 nodes to be scored	(0 eliminated genes)
```

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

```
## 
## 	 Level 11:	7 nodes to be scored	(17 eliminated genes)
```

```
## 
## 	 Level 10:	7 nodes to be scored	(69 eliminated genes)
```

```
## 
## 	 Level 9:	10 nodes to be scored	(86 eliminated genes)
```

```
## 
## 	 Level 8:	8 nodes to be scored	(140 eliminated genes)
```

```
## 
## 	 Level 7:	8 nodes to be scored	(158 eliminated genes)
```

```
## 
## 	 Level 6:	18 nodes to be scored	(165 eliminated genes)
```

```
## 
## 	 Level 5:	26 nodes to be scored	(338 eliminated genes)
```

```
## 
## 	 Level 4:	19 nodes to be scored	(460 eliminated genes)
```

```
## 
## 	 Level 3:	11 nodes to be scored	(735 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(876 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1000 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 70 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:	7 nodes to be scored	(2 eliminated genes)
```

```
## 
## 	 Level 6:	14 nodes to be scored	(198 eliminated genes)
```

```
## 
## 	 Level 5:	13 nodes to be scored	(332 eliminated genes)
```

```
## 
## 	 Level 4:	14 nodes to be scored	(433 eliminated genes)
```

```
## 
## 	 Level 3:	12 nodes to be scored	(923 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(1330 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1991 eliminated genes)
```

```
##         GO.ID                                                   Term Annotated
## 1  GO:0000454             snoRNA guided rRNA pseudouridine synthesis         1
## 2  GO:0000971 tRNA exon ligation utilizing 2',3' cyclic phosphate...         1
## 3  GO:0009058                                   biosynthetic process       207
## 4  GO:0060271                                        cilium assembly         3
## 5  GO:0000463 maturation of LSU-rRNA from tricistronic rRNA trans...         3
## 6  GO:0001558                              regulation of cell growth         3
## 7  GO:0001508                                       action potential         4
## 8  GO:0003735                     structural constituent of ribosome        13
## 9  GO:0003944 N-acetylglucosamine-1-phosphodiester alpha-N-acetyl...         1
## 10 GO:0000009                 alpha-1,6-mannosyltransferase activity         1
## 11 GO:0005536                                        glucose binding         1
## 12 GO:0004568                                     chitinase activity         1
## 13 GO:0005315 inorganic phosphate transmembrane transporter activ...         1
## 14 GO:0000224 peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine a...         2
## 15 GO:0032450                     maltose alpha-glucosidase activity         2
## 16 GO:0003727                            single-stranded RNA binding         2
## 17 GO:0005539                              glycosaminoglycan binding         5
##    Significant Expected Fisher               type
## 1            1     0.01 0.0099 Biological.Process
## 2            1     0.01 0.0099 Biological.Process
## 3            2     2.05 0.0108 Biological.Process
## 4            1     0.03 0.0295 Biological.Process
## 5            1     0.03 0.0295 Biological.Process
## 6            1     0.03 0.0295 Biological.Process
## 7            1     0.04 0.0391 Biological.Process
## 8            2     0.12 0.0057 Molecular.Function
## 9            1     0.01 0.0090 Molecular.Function
## 10           1     0.01 0.0090 Molecular.Function
## 11           1     0.01 0.0090 Molecular.Function
## 12           1     0.01 0.0090 Molecular.Function
## 13           1     0.01 0.0090 Molecular.Function
## 14           1     0.02 0.0179 Molecular.Function
## 15           1     0.02 0.0179 Molecular.Function
## 16           1     0.02 0.0179 Molecular.Function
## 17           1     0.05 0.0443 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 16 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:	1 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 6:	1 nodes to be scored	(17 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(22 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(26 eliminated genes)
```

```
## 
## 	 Level 3:	4 nodes to be scored	(41 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(52 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 74 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 8:	3 nodes to be scored	(107 eliminated genes)
```

```
## 
## 	 Level 7:	7 nodes to be scored	(189 eliminated genes)
```

```
## 
## 	 Level 6:	11 nodes to be scored	(204 eliminated genes)
```

```
## 
## 	 Level 5:	12 nodes to be scored	(394 eliminated genes)
```

```
## 
## 	 Level 4:	16 nodes to be scored	(474 eliminated genes)
```

```
## 
## 	 Level 3:	13 nodes to be scored	(738 eliminated genes)
```

```
## 
## 	 Level 2:	5 nodes to be scored	(1435 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2157 eliminated genes)
```

```
##        GO.ID                                         Term Annotated Significant
## 1 GO:0008218                              bioluminescence        10           3
## 2 GO:0000038 very long-chain fatty acid metabolic process         9           1
## 3 GO:0004089               carbonate dehydratase activity         2           1
## 4 GO:0003746       translation elongation factor activity         7           1
## 5 GO:0005245       voltage-gated calcium channel activity         7           1
## 6 GO:0005542                           folic acid binding        10           1
##   Expected   Fisher               type
## 1     0.03 0.000001 Biological.Process
## 2     0.03 0.025000 Biological.Process
## 3     0.01 0.008600 Molecular.Function
## 4     0.03 0.029900 Molecular.Function
## 5     0.03 0.029900 Molecular.Function
## 6     0.04 0.042500 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 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 20 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:	1 nodes to be scored	(2 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(2 eliminated genes)
```

```
## 
## 	 Level 5:	4 nodes to be scored	(2 eliminated genes)
```

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

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

```
## 
## 	 Level 2:	2 nodes to be scored	(199 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(277 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 17 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:	3 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 7:	1 nodes to be scored	(112 eliminated genes)
```

```
## 
## 	 Level 6:	2 nodes to be scored	(133 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(133 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(136 eliminated genes)
```

```
## 
## 	 Level 3:	2 nodes to be scored	(264 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(497 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(809 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0001755                            neural crest cell migration         2
## 2 GO:0001002 RNA polymerase III type 1 promoter sequence-specifi...         1
##   Significant Expected  Fisher               type
## 1           1        0 0.00140 Biological.Process
## 2           1        0 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 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 49 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	(7 eliminated genes)
```

```
## 
## 	 Level 7:	4 nodes to be scored	(69 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(74 eliminated genes)
```

```
## 
## 	 Level 5:	7 nodes to be scored	(224 eliminated genes)
```

```
## 
## 	 Level 4:	11 nodes to be scored	(296 eliminated genes)
```

```
## 
## 	 Level 3:	12 nodes to be scored	(411 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(856 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(2047 eliminated genes)
```

```
##        GO.ID                                          Term Annotated
## 1 GO:0001516            prostaglandin biosynthetic process         2
## 2 GO:0000028              ribosomal small subunit assembly         3
## 3 GO:0001523                    retinoid metabolic process         9
## 4 GO:0004252            serine-type endopeptidase activity        53
## 5 GO:0005245        voltage-gated calcium channel activity         7
## 6 GO:0005542                            folic acid binding        10
## 7 GO:0047869 dimethylpropiothetin dethiomethylase activity        19
##   Significant Expected Fisher               type
## 1           1     0.00 0.0042 Biological.Process
## 2           1     0.01 0.0064 Biological.Process
## 3           1     0.02 0.0190 Biological.Process
## 4           2     0.11 0.0051 Molecular.Function
## 5           1     0.02 0.0150 Molecular.Function
## 6           1     0.02 0.0214 Molecular.Function
## 7           1     0.04 0.0404 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 2 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

```
## 
## 	 Level 2:	1 nodes to be scored	(0 eliminated genes)
```

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

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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:	1 nodes to be scored	(0 eliminated genes)
```

```
## 
## 	 Level 9:	2 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 8:	1 nodes to be scored	(7 eliminated genes)
```

```
## 
## 	 Level 7:	3 nodes to be scored	(21 eliminated genes)
```

```
## 
## 	 Level 6:	6 nodes to be scored	(24 eliminated genes)
```

```
## 
## 	 Level 5:	11 nodes to be scored	(47 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(76 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(468 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(576 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 46 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:	3 nodes to be scored	(383 eliminated genes)
```

```
## 
## 	 Level 6:	7 nodes to be scored	(397 eliminated genes)
```

```
## 
## 	 Level 5:	9 nodes to be scored	(408 eliminated genes)
```

```
## 
## 	 Level 4:	9 nodes to be scored	(534 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(866 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(1184 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1706 eliminated genes)
```

```
##        GO.ID                                           Term Annotated
## 1 GO:0002933                            lipid hydroxylation         3
## 2 GO:0001731 formation of translation preinitiation complex         1
## 3 GO:0004089                 carbonate dehydratase activity         2
## 4 GO:0047869  dimethylpropiothetin dethiomethylase activity        19
##   Significant Expected  Fisher               type
## 1           2     0.01 9.0e-06 Biological.Process
## 2           1     0.00 2.1e-03 Biological.Process
## 3           1     0.01 5.0e-03 Molecular.Function
## 4           1     0.05 4.7e-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 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 0 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## [1] GO.ID       Term        Annotated   Significant Expected    Fisher     
## <0 rows> (or 0-length row.names)
##  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 33 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:	4 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(31 eliminated genes)
```

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

```
## 
## 	 Level 4:	4 nodes to be scored	(49 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(256 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(270 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(811 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:	2 nodes to be scored	(263 eliminated genes)
```

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

```
## 
## 	 Level 5:	6 nodes to be scored	(275 eliminated genes)
```

```
## 
## 	 Level 4:	8 nodes to be scored	(353 eliminated genes)
```

```
## 
## 	 Level 3:	10 nodes to be scored	(426 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(973 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1620 eliminated genes)
```

```
##        GO.ID                                      Term Annotated Significant
## 1 GO:0001782                        B cell homeostasis         7           1
## 2 GO:0001889                         liver development         8           1
## 3 GO:0001523                retinoid metabolic process         9           1
## 4 GO:0001701            in utero embryonic development        15           1
## 5 GO:0005542                        folic acid binding        10           1
## 6 GO:0004609 phosphatidylserine decarboxylase activity        13           1
##   Expected Fisher               type
## 1     0.02  0.020 Biological.Process
## 2     0.02  0.023 Biological.Process
## 3     0.03  0.025 Biological.Process
## 4     0.04  0.042 Biological.Process
## 5     0.03  0.025 Molecular.Function
## 6     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 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 22 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:	2 nodes to be scored	(267 eliminated genes)
```

```
## 
## 	 Level 5:	3 nodes to be scored	(275 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(277 eliminated genes)
```

```
## 
## 	 Level 3:	7 nodes to be scored	(328 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(340 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1559 eliminated genes)
```

```
##        GO.ID                                   Term Annotated Significant
## 1 GO:0004842 ubiquitin-protein transferase activity        35           1
##   Expected Fisher               type
## 1     0.03  0.025 Molecular.Function
```

``` r
head(results_high0.6_cor_targets)
```

```
##        GO.ID                                             Term Annotated
## 1 GO:0005290   L-histidine transmembrane transporter activity         9
## 2 GO:0001658 branching involved in ureteric bud morphogenesis         4
## 3 GO:0001945                         lymph vessel development         5
## 4 GO:0004252               serine-type endopeptidase activity        53
## 5 GO:0004771                         sterol esterase activity         5
## 6 GO:0004966                        galanin receptor activity        12
##   Significant Expected Fisher               type         miRNA
## 1           1     0.00 0.0032 Molecular.Function Cluster_10452
## 2           1     0.01 0.0057 Biological.Process Cluster_11565
## 3           1     0.01 0.0071 Biological.Process Cluster_11565
## 4           2     0.15 0.0093 Molecular.Function Cluster_11565
## 5           1     0.01 0.0143 Molecular.Function Cluster_11565
## 6           1     0.03 0.0341 Molecular.Function Cluster_11565
```