``` r
interacting_miRNAs_high0.7 <- unique(high0.7_cor_bind_FA$miRNA) %>% na.omit
results_high0.7_cor_targets <- NULL  # initialize empty df

for(miRNA in interacting_miRNAs_high0.7) {
  
  # Run topGO enrichment function
  miRNA_results <- miRNA_topGO_FE(miRNA, high0.7_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_high0.7_cor_targets <- rbind(results_high0.7_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 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	(5 eliminated genes)
```

```
## 
## 	 Level 5:	1 nodes to be scored	(47 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(58 eliminated genes)
```

```
## 
## 	 Level 3:	1 nodes to be scored	(192 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 21 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:	3 nodes to be scored	(12 eliminated genes)
```

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

```
## 
## 	 Level 4:	5 nodes to be scored	(90 eliminated genes)
```

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

```
## 
## 	 Level 2:	2 nodes to be scored	(467 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(755 eliminated genes)
```

```
##        GO.ID                      Term Annotated Significant Expected Fisher
## 1 GO:0001945  lymph vessel development         5           1     0.00 0.0035
## 2 GO:0004771  sterol esterase activity         5           1     0.01 0.0072
## 3 GO:0004966 galanin receptor activity        12           1     0.02 0.0172
##                 type
## 1 Biological.Process
## 2 Molecular.Function
## 3 Molecular.Function
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

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

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

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

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

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

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

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 18 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 5:	2 nodes to be scored	(35 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(44 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(97 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(307 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(429 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:0001649           osteoblast differentiation        26           1
## 2 GO:0000165                         MAPK cascade        35           1
## 3 GO:0009034               tryptophanase activity         2           1
## 4 GO:0003964 RNA-directed DNA polymerase activity       122           2
##   Expected Fisher               type
## 1     0.04 0.0370 Biological.Process
## 2     0.05 0.0490 Biological.Process
## 3     0.00 0.0029 Molecular.Function
## 4     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 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 14 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:	2 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(178 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(315 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(438 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(877 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0000165                         MAPK cascade        35           1
## 2 GO:0003964 RNA-directed DNA polymerase activity       122           2
##   Expected Fisher               type
## 1     0.02 0.0250 Biological.Process
## 2     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 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 14 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:	2 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(178 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(315 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(438 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(877 eliminated genes)
```

```
##        GO.ID                                 Term Annotated Significant
## 1 GO:0000165                         MAPK cascade        35           1
## 2 GO:0003964 RNA-directed DNA polymerase activity       122           2
##   Expected Fisher               type
## 1     0.02 0.0250 Biological.Process
## 2     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 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 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 36 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:	3 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 6:	4 nodes to be scored	(268 eliminated genes)
```

```
## 
## 	 Level 5:	6 nodes to be scored	(276 eliminated genes)
```

```
## 
## 	 Level 4:	6 nodes to be scored	(279 eliminated genes)
```

```
## 
## 	 Level 3:	9 nodes to be scored	(306 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(475 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1833 eliminated genes)
```

```
##        GO.ID                                     Term Annotated Significant
## 1 GO:0008137 NADH dehydrogenase (ubiquinone) activity         1           1
## 2 GO:0004176         ATP-dependent peptidase activity         2           1
##   Expected Fisher               type
## 1        0 0.0011 Molecular.Function
## 2        0 0.0022 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 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 17 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	(5 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(71 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(82 eliminated genes)
```

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

```
## 
## 	 Level 2:	4 nodes to be scored	(247 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(290 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 11 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

```
## 
## 	 Level 4:	2 nodes to be scored	(0 eliminated genes)
```

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

```
## 
## 	 Level 2:	3 nodes to be scored	(721 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1042 eliminated genes)
```

```
##        GO.ID                                            Term Annotated
## 1 GO:0001945                        lymph vessel development         5
## 2 GO:0002175 protein localization to paranode region of axon        24
##   Significant Expected Fisher               type
## 1           1     0.01 0.0071 Biological.Process
## 2           1     0.03 0.0337 Biological.Process
##  Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
##  - attr(*, "names")= chr [1:30094] "FUN_002326" "FUN_002315" "FUN_002316" "FUN_002303" ...
```

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

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

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

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

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

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

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 29 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 6:	4 nodes to be scored	(18 eliminated genes)
```

```
## 
## 	 Level 5:	5 nodes to be scored	(73 eliminated genes)
```

```
## 
## 	 Level 4:	5 nodes to be scored	(240 eliminated genes)
```

```
## 
## 	 Level 3:	4 nodes to be scored	(371 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(517 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(628 eliminated genes)
```

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

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

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

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

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

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

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

```
## 
## 	 Level 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:	4 nodes to be scored	(383 eliminated genes)
```

```
## 
## 	 Level 6:	5 nodes to be scored	(463 eliminated genes)
```

```
## 
## 	 Level 5:	5 nodes to be scored	(474 eliminated genes)
```

```
## 
## 	 Level 4:	4 nodes to be scored	(492 eliminated genes)
```

```
## 
## 	 Level 3:	6 nodes to be scored	(636 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(881 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(1394 eliminated genes)
```

```
##        GO.ID                                       Term Annotated Significant
## 1 GO:0000165                               MAPK cascade        35           2
## 2 GO:0001818 negative regulation of cytokine production        18           1
## 3 GO:0003924                            GTPase activity        66           2
##   Expected Fisher               type
## 1     0.07 0.0018 Biological.Process
## 2     0.04 0.0378 Biological.Process
## 3     0.10 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 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 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 21 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	(65 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(100 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(109 eliminated genes)
```

```
## 
## 	 Level 3:	4 nodes to be scored	(263 eliminated genes)
```

```
## 
## 	 Level 2:	6 nodes to be scored	(467 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(598 eliminated genes)
```

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

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

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

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

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

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

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 9 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 4:	2 nodes to be scored	(53 eliminated genes)
```

```
## 
## 	 Level 3:	2 nodes to be scored	(105 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
## 1 GO:0001822                 kidney development        65           2     0.14
## 2 GO:0004252 serine-type endopeptidase activity        53           1     0.02
##   Fisher               type
## 1 0.0061 Biological.Process
## 2 0.0190 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 12:	1 nodes to be scored	(0 eliminated genes)
```

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

```
## 
## 	 Level 10:	2 nodes to be scored	(63 eliminated genes)
```

```
## 
## 	 Level 9:	3 nodes to be scored	(63 eliminated genes)
```

```
## 
## 	 Level 8:	3 nodes to be scored	(101 eliminated genes)
```

```
## 
## 	 Level 7:	2 nodes to be scored	(106 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(139 eliminated genes)
```

```
## 
## 	 Level 5:	5 nodes to be scored	(289 eliminated genes)
```

```
## 
## 	 Level 4:	7 nodes to be scored	(338 eliminated genes)
```

```
## 
## 	 Level 3:	5 nodes to be scored	(527 eliminated genes)
```

```
## 
## 	 Level 2:	4 nodes to be scored	(679 eliminated genes)
```

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

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

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

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

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

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

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

```
## 
## 			 -- Weight01 Algorithm -- 
## 
## 		 the algorithm is scoring 21 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	(1 eliminated genes)
```

```
## 
## 	 Level 6:	3 nodes to be scored	(1 eliminated genes)
```

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

```
## 
## 	 Level 4:	3 nodes to be scored	(33 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(196 eliminated genes)
```

```
## 
## 	 Level 2:	3 nodes to be scored	(363 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(807 eliminated genes)
```

```
##        GO.ID                                             Term Annotated
## 1 GO:0004305                     ethanolamine kinase activity         1
## 2 GO:0004441 inositol-1,4-bisphosphate 1-phosphatase activity         1
## 3 GO:0005085       guanyl-nucleotide exchange factor activity        12
##   Significant Expected Fisher               type
## 1           1     0.00 0.0018 Molecular.Function
## 2           1     0.00 0.0018 Molecular.Function
## 3           1     0.02 0.0214 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 12 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 5:	1 nodes to be scored	(12 eliminated genes)
```

```
## 
## 	 Level 4:	2 nodes to be scored	(13 eliminated genes)
```

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

```
## 
## 	 Level 2:	2 nodes to be scored	(84 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 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:	2 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 4:	3 nodes to be scored	(122 eliminated genes)
```

```
## 
## 	 Level 3:	3 nodes to be scored	(169 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(292 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(578 eliminated genes)
```

```
##        GO.ID                                   Term Annotated Significant
## 1 GO:0019700  organic phosphonate catabolic process        12           1
## 2 GO:0004842 ubiquitin-protein transferase activity        35           1
##   Expected Fisher               type
## 1     0.01 0.0085 Biological.Process
## 2     0.03 0.0250 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 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	(18 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(52 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:0005507 copper ion binding        18           1     0.01 0.0065
##                 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 27 nontrivial nodes
## 		 parameters: 
## 			 test statistic: fisher
```

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

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

```
## 
## 	 Level 11:	2 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 10:	2 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 9:	3 nodes to be scored	(1 eliminated genes)
```

```
## 
## 	 Level 8:	2 nodes to be scored	(6 eliminated genes)
```

```
## 
## 	 Level 7:	1 nodes to be scored	(82 eliminated genes)
```

```
## 
## 	 Level 6:	1 nodes to be scored	(83 eliminated genes)
```

```
## 
## 	 Level 5:	2 nodes to be scored	(242 eliminated genes)
```

```
## 
## 	 Level 4:	5 nodes to be scored	(268 eliminated genes)
```

```
## 
## 	 Level 3:	4 nodes to be scored	(326 eliminated genes)
```

```
## 
## 	 Level 2:	2 nodes to be scored	(447 eliminated genes)
```

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

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

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

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

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

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

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

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

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

```
##        GO.ID                                                   Term Annotated
## 1 GO:0000971 tRNA exon ligation utilizing 2',3' cyclic phosphate...         1
##   Significant Expected  Fisher               type
## 1           1        0 0.00071 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 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 20 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:	3 nodes to be scored	(152 eliminated genes)
```

```
## 
## 	 Level 4:	5 nodes to be scored	(156 eliminated genes)
```

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

```
## 
## 	 Level 2:	2 nodes to be scored	(296 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(655 eliminated genes)
```

```
##        GO.ID                                                   Term Annotated
## 1 GO:0008218                                        bioluminescence        10
## 2 GO:0004089                         carbonate dehydratase activity         2
## 3 GO:0001409 guanine nucleotide transmembrane transporter activi...        30
##   Significant Expected   Fisher               type
## 1           2     0.01 0.000045 Biological.Process
## 2           1     0.00 0.002200 Molecular.Function
## 3           1     0.03 0.032100 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 12 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	(9 eliminated genes)
```

```
## 
## 	 Level 5:	1 nodes to be scored	(9 eliminated genes)
```

```
## 
## 	 Level 4:	1 nodes to be scored	(9 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 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:0001523                    retinoid metabolic process         9
## 2 GO:0005245        voltage-gated calcium channel activity         7
## 3 GO:0005542                            folic acid binding        10
## 4 GO:0047869 dimethylpropiothetin dethiomethylase activity        19
##   Significant Expected Fisher               type
## 1           1     0.01 0.0064 Biological.Process
## 2           1     0.01 0.0130 Molecular.Function
## 3           1     0.02 0.0180 Molecular.Function
## 4           1     0.03 0.0340 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 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:0005509 calcium ion binding        66           1     0.02  0.024
##                 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 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 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	(103 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
## 1 GO:0001701 in utero embryonic development        15           1     0.01
## 2 GO:0004175         endopeptidase activity       103           1     0.04
##   Fisher               type
## 1  0.011 Biological.Process
## 2  0.037 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 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	(35 eliminated genes)
```

```
## 
## 	 Level 2:	1 nodes to be scored	(35 eliminated genes)
```

```
## 
## 	 Level 1:	1 nodes to be scored	(549 eliminated genes)
```

```
##        GO.ID                                   Term Annotated Significant
## 1 GO:0004842 ubiquitin-protein transferase activity        35           1
##   Expected Fisher               type
## 1     0.01  0.013 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)
```

``` r
head(results_high0.7_cor_targets)
```

```
##        GO.ID                       Term Annotated Significant Expected Fisher
## 1 GO:0001945   lymph vessel development         5           1     0.00 0.0035
## 2 GO:0004771   sterol esterase activity         5           1     0.01 0.0072
## 3 GO:0004966  galanin receptor activity        12           1     0.02 0.0172
## 4 GO:0001649 osteoblast differentiation        26           1     0.04 0.0370
## 5 GO:0000165               MAPK cascade        35           1     0.05 0.0490
## 6 GO:0009034     tryptophanase activity         2           1     0.00 0.0029
##                 type         miRNA
## 1 Biological.Process Cluster_11565
## 2 Molecular.Function Cluster_11565
## 3 Molecular.Function Cluster_11565
## 4 Biological.Process Cluster_12081
## 5 Biological.Process Cluster_12081
## 6 Molecular.Function Cluster_12081
```