The goal of pfGO is to package handy functions and datasets specifically enabling Plasmodium falciparum functional enrichment analyses. pfGO acts as a wrapper around the topGO package for much of its enrichment functionality, while also providing several functions for incorporating latest gene-ontology and functional annotations.
pfGO enables chaining together many parallel enrichment-analyses at once, generating thorough logs and outputs supporting reproducible analyses.
You can install pfGO from GitHub with:
# install.packages("devtools")
devtools::install_github("oberstal/pfGO")
# or if authenticating via ssh:
devtools::install_git("https://github.com/oberstal/pfGO")See individual functions/data objects for further documentation. E.g.:
?run.topGO.meta
?Pfal_geneID2GO
# for all available functions/data:
?pfGO
# then scroll to the bottom and click the "index" link.This is a basic example demonstrating how to run an enrichment analysis on piggyBac pooled phenotypic screening results to identify processes enabling parasite survival of host fever (using data as published previously):
library(pfGO)# load included pf GO database and example-data to be tested for functional enrichment
data(Pfal_geneID2GO)
data(exampleMydf)
# run the topGO pipeline on all experimental categories of interest from exampleMydf
run.topGO.meta(mydf = exampleMydf, geneID2GO = Pfal_geneID2GO, pval = 0.05)View example console output here
Tests for functional enrichment in gene-categories of interest. Enrichments are performed by each ontology (molecular function, biological process, cellular component), for each interest category, sequentially.
mydf: data frame with geneIDs in column 1, and interest-category classifications in column 2. Additional columns are ignored.geneID2GO: a list of named vectors of GO IDs–one vector of GO-terms for each geneID.pval: p-value threshold for significance (Fisher test). Defaults to 0.05.minTermSize: minimum number of genes that must be mapped to a GO term for it to be included in the enrichment analysis. Defaults to 5.algorithm: algorithm to run for the enrichment analysis. Accepted values are c(“classic”, “elim”, “weight”, “weight01”, “lea”, “parentchild”). Defaults to “weight01”.- See the topGO package documentation and associated publications for details on algorithms.
run.topGO.meta creates several output-files, including:
-
enrichment results
-
significant genes per significant term
- available in
./Routput/GO/all.combined.sig.genes.per.sig.terms.tsv
- available in
-
plots of the GO-term hierarchy relevant to the analysis
-
thorough log-files for each gene-category of interest tested against the background of all other genes in the analysis
-
system logs recording all package versions, etc.
Primary results from run.topGO.meta will be in
./Routput/GO/all.combined.GO.results.tsv. Note that run.topGO.meta
will automatically create the ./Routput directory (and other required
output directories nested in ./Routput) in your working directory for
you if it does not exist.
The run.topGO.meta function:
- defines which genes are “interesting” and which should be defined as background for each category specified in mydf,
- makes the GOdata object for topGO,
- tests each category of interest for enriched GO-terms against all the other genes included in mydf (the “gene universe”),
- and then outputs results to several tables (.tsv files that can be opened in Excel).
Enrichments are performed by each ontology (molecular function,
biological process, cellular component; MF, BP, and CC, respectively)
sequentially on all groups of interest. Results are combined in the
final output-table (./Routput/GO/all.combined.GO.results.tsv).
TopGO automatically accounts for genes that cannot be mapped to GO terms
(or are mapped to terms with < minTermSize genes in the analysis)
with “feasible genes” indicated in the topGO.log files in the
./Routput/GO/ folder.
Concepts for common use-cases:
RNAseq:
In an RNAseq analysis, common interest-categories might be “upregulated”, “downregulated”, and “neutral” genes. The gene universe would consist of all genes expressed above your threshold cutoffs (not necessarily all genes in the genome).
piggyBac screens:
In pooled piggyBac-mutant screening, common categories might be “sensitive”, “tolerant”, and “neutral”. The gene universe would consist of all genes represented in your screened library of mutants (again, not all genes in the genome).
See the included data object exampleMydf as an example.
Using your own custom GO database:
A correctly formatted geneID2GO object is included for P. falciparum enrichment analyses (Pfal_geneID2GO). You may also provide your own, so long as it is a named character-vector of GO-terms (each vector named by geneID, with GO terms as each element).
You can use the included formatGOdb.curated() function to format a custom GO database from curated GeneDB annotations for several non-model organisms (or the formatGOdb() function to include all GO annotations, if you aren’t picky about including automated electronic annotations). If you’re studying a model organism, several annotations are already available through the AnnotationDbi bioconductor package that loads with topGO.
Example console output generated running the quick-start example data (piggyBac pooled phenotypic screening results to identify processes enabling parasite survival of host fever (similar to as published previously):
# load included pf GO database and example-data to be tested for functional enrichment
data(Pfal_geneID2GO_curated)
data(exampleMydf)
# run the topGO pipeline on all experimental categories of interest from exampleMydf
run.topGO.meta(mydf = exampleMydf, geneID2GO = Pfal_geneID2GO_curated, pval = 0.1)
#>
#> Building most specific GOs .....
#> ( 283 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 554 GO terms and 715 relations. )
#>
#> Annotating nodes ...............
#> ( 334 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 80 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 9: 1 nodes to be scored (0 eliminated genes)
#>
#> Level 8: 5 nodes to be scored (0 eliminated genes)
#>
#> Level 7: 9 nodes to be scored (11 eliminated genes)
#>
#> Level 6: 12 nodes to be scored (33 eliminated genes)
#>
#> Level 5: 14 nodes to be scored (66 eliminated genes)
#>
#> Level 4: 15 nodes to be scored (94 eliminated genes)
#>
#> Level 3: 17 nodes to be scored (127 eliminated genes)
#>
#> Level 2: 6 nodes to be scored (218 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (314 eliminated genes)
#> Loading required package: Rgraphviz
#> Loading required package: grid
#>
#> Attaching package: 'grid'
#> The following object is masked from 'package:topGO':
#>
#> depth
#>
#> Attaching package: 'Rgraphviz'
#> The following objects are masked from 'package:IRanges':
#>
#> from, to
#> The following objects are masked from 'package:S4Vectors':
#>
#> from, to
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.A.HS.Sensitive.MF_weight01_10_all --- no of nodes: 28
#>
#> ==============================================================================
#> GO enrichment results for interest category: A.HS.Sensitive
#> Ontology: MF GO.ID Term Annotated Significant
#> 1 GO:0120543 macromolecular conformation isomerase ac... 14 3
#> 2 GO:0016740 transferase activity 71 12
#> 3 GO:0003723 RNA binding 58 12
#> 4 GO:0003924 GTPase activity 5 2
#> 5 GO:0005319 lipid transporter activity 5 2
#> 6 GO:0016301 kinase activity 26 6
#> 7 GO:0016791 phosphatase activity 11 3
#> 8 GO:0004518 nuclease activity 6 2
#> 9 GO:0004674 protein serine/threonine kinase activity 17 4
#> 10 GO:0005198 structural molecule activity 16 4
#> Expected topGO go.category interest.category algorithm statistic
#> 1 2.14 0.064 MF A.HS.Sensitive weight01 fisher
#> 2 10.84 0.076 MF A.HS.Sensitive weight01 fisher
#> 3 8.86 0.158 MF A.HS.Sensitive weight01 fisher
#> 4 0.76 0.169 MF A.HS.Sensitive weight01 fisher
#> 5 0.76 0.169 MF A.HS.Sensitive weight01 fisher
#> 6 3.97 0.222 MF A.HS.Sensitive weight01 fisher
#> 7 1.68 0.227 MF A.HS.Sensitive weight01 fisher
#> 8 0.92 0.229 MF A.HS.Sensitive weight01 fisher
#> 9 2.60 0.251 MF A.HS.Sensitive weight01 fisher
#> 10 2.44 0.278 MF A.HS.Sensitive weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 1 of 4
#> ontology 1 of 3
#>
#> Building most specific GOs .....
#> ( 358 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 1125 GO terms and 2077 relations. )
#>
#> Annotating nodes ...............
#> ( 354 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 187 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: 3 nodes to be scored (11 eliminated genes)
#>
#> Level 10: 7 nodes to be scored (11 eliminated genes)
#>
#> Level 9: 12 nodes to be scored (24 eliminated genes)
#>
#> Level 8: 18 nodes to be scored (51 eliminated genes)
#>
#> Level 7: 22 nodes to be scored (87 eliminated genes)
#>
#> Level 6: 33 nodes to be scored (127 eliminated genes)
#>
#> Level 5: 40 nodes to be scored (200 eliminated genes)
#>
#> Level 4: 27 nodes to be scored (256 eliminated genes)
#>
#> Level 3: 17 nodes to be scored (327 eliminated genes)
#>
#> Level 2: 5 nodes to be scored (343 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (348 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.A.HS.Sensitive.BP_weight01_10_all --- no of nodes: 57
#>
#> ==============================================================================
#> GO enrichment results for interest category: A.HS.Sensitive
#> Ontology: BP GO.ID Term Annotated Significant
#> 1 GO:0010468 regulation of gene expression 27 6
#> 2 GO:0044283 small molecule biosynthetic process 5 3
#> 3 GO:0061024 membrane organization 9 4
#> 4 GO:0035556 intracellular signal transduction 22 7
#> 5 GO:0009410 response to xenobiotic stimulus 28 8
#> 6 GO:0008610 lipid biosynthetic process 12 3
#> 7 GO:0006364 rRNA processing 14 6
#> 8 GO:0006401 RNA catabolic process 7 3
#> 9 GO:0000460 maturation of 5.8S rRNA 7 3
#> 10 GO:0006163 purine nucleotide metabolic process 8 3
#> Expected topGO go.category interest.category algorithm statistic
#> 1 4.27 0.0073 BP A.HS.Sensitive weight01 fisher
#> 2 0.79 0.0298 BP A.HS.Sensitive weight01 fisher
#> 3 1.42 0.0384 BP A.HS.Sensitive weight01 fisher
#> 4 3.48 0.0421 BP A.HS.Sensitive weight01 fisher
#> 5 4.43 0.0556 BP A.HS.Sensitive weight01 fisher
#> 6 1.90 0.0673 BP A.HS.Sensitive weight01 fisher
#> 7 2.21 0.0752 BP A.HS.Sensitive weight01 fisher
#> 8 1.11 0.0822 BP A.HS.Sensitive weight01 fisher
#> 9 1.11 0.0822 BP A.HS.Sensitive weight01 fisher
#> 10 1.27 0.1171 BP A.HS.Sensitive weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 1 of 4
#> ontology 2 of 3
#>
#> Building most specific GOs .....
#> ( 195 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 367 GO terms and 616 relations. )
#>
#> Annotating nodes ...............
#> ( 526 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 99 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 11: 1 nodes to be scored (0 eliminated genes)
#>
#> Level 10: 3 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 6 nodes to be scored (16 eliminated genes)
#>
#> Level 8: 13 nodes to be scored (65 eliminated genes)
#>
#> Level 7: 12 nodes to be scored (96 eliminated genes)
#>
#> Level 6: 16 nodes to be scored (173 eliminated genes)
#>
#> Level 5: 15 nodes to be scored (239 eliminated genes)
#>
#> Level 4: 14 nodes to be scored (425 eliminated genes)
#>
#> Level 3: 16 nodes to be scored (459 eliminated genes)
#>
#> Level 2: 2 nodes to be scored (496 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (525 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.A.HS.Sensitive.CC_weight01_10_all --- no of nodes: 35
#>
#> ==============================================================================
#> GO enrichment results for interest category: A.HS.Sensitive
#> Ontology: CC GO.ID Term Annotated Significant Expected topGO
#> 1 GO:0005743 mitochondrial inner membrane 5 3 0.80 0.031
#> 2 GO:1902494 catalytic complex 42 8 6.71 0.032
#> 3 GO:0005739 mitochondrion 51 14 8.14 0.120
#> 4 GO:0005768 endosome 8 3 1.28 0.121
#> 5 GO:0034399 nuclear periphery 8 3 1.28 0.121
#> 6 GO:0031966 mitochondrial membrane 6 4 0.96 0.155
#> 7 GO:0019866 organelle inner membrane 6 4 0.96 0.155
#> 8 GO:0030139 endocytic vesicle 17 3 2.71 0.161
#> 9 GO:0005929 cilium 5 2 0.80 0.182
#> 10 GO:0020011 apicoplast 42 9 6.71 0.211
#> go.category interest.category algorithm statistic
#> 1 CC A.HS.Sensitive weight01 fisher
#> 2 CC A.HS.Sensitive weight01 fisher
#> 3 CC A.HS.Sensitive weight01 fisher
#> 4 CC A.HS.Sensitive weight01 fisher
#> 5 CC A.HS.Sensitive weight01 fisher
#> 6 CC A.HS.Sensitive weight01 fisher
#> 7 CC A.HS.Sensitive weight01 fisher
#> 8 CC A.HS.Sensitive weight01 fisher
#> 9 CC A.HS.Sensitive weight01 fisher
#> 10 CC A.HS.Sensitive weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 1 of 4
#> ontology 3 of 3
#>
#> Building most specific GOs .....
#> ( 283 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 554 GO terms and 715 relations. )
#>
#> Annotating nodes ...............
#> ( 334 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 52 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 9: 1 nodes to be scored (0 eliminated genes)
#>
#> Level 8: 1 nodes to be scored (0 eliminated genes)
#>
#> Level 7: 4 nodes to be scored (11 eliminated genes)
#>
#> Level 6: 7 nodes to be scored (12 eliminated genes)
#>
#> Level 5: 11 nodes to be scored (35 eliminated genes)
#>
#> Level 4: 9 nodes to be scored (57 eliminated genes)
#>
#> Level 3: 13 nodes to be scored (77 eliminated genes)
#>
#> Level 2: 5 nodes to be scored (169 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (299 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.and.CG.phenotype.MF_weight01_10_all --- no of nodes: 21
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.and.CG.phenotype
#> Ontology: MF GO.ID Term Annotated Significant
#> 1 GO:0003677 DNA binding 26 6
#> 2 GO:0008094 ATP-dependent activity, acting on DNA 8 3
#> 3 GO:0003690 double-stranded DNA binding 9 3
#> 4 GO:1990837 sequence-specific double-stranded DNA bi... 7 2
#> 5 GO:0016773 phosphotransferase activity, alcohol gro... 25 2
#> 6 GO:0003688 DNA replication origin binding 5 1
#> 7 GO:0003697 single-stranded DNA binding 5 1
#> 8 GO:0016301 kinase activity 26 2
#> 9 GO:0003684 damaged DNA binding 6 1
#> 10 GO:0030674 protein-macromolecule adaptor activity 6 1
#> Expected topGO go.category interest.category algorithm statistic
#> 1 0.93 0.0012 MF HS.and.CG.phenotype weight01 fisher
#> 2 0.29 0.0018 MF HS.and.CG.phenotype weight01 fisher
#> 3 0.32 0.0603 MF HS.and.CG.phenotype weight01 fisher
#> 4 0.25 0.0658 MF HS.and.CG.phenotype weight01 fisher
#> 5 0.90 0.1643 MF HS.and.CG.phenotype weight01 fisher
#> 6 0.18 0.1681 MF HS.and.CG.phenotype weight01 fisher
#> 7 0.18 0.1681 MF HS.and.CG.phenotype weight01 fisher
#> 8 0.93 0.1940 MF HS.and.CG.phenotype weight01 fisher
#> 9 0.22 0.1985 MF HS.and.CG.phenotype weight01 fisher
#> 10 0.22 0.1985 MF HS.and.CG.phenotype weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 2 of 4
#> ontology 1 of 3
#>
#> Building most specific GOs .....
#> ( 358 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 1125 GO terms and 2077 relations. )
#>
#> Annotating nodes ...............
#> ( 354 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 84 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 10: 3 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 3 nodes to be scored (0 eliminated genes)
#>
#> Level 8: 6 nodes to be scored (24 eliminated genes)
#>
#> Level 7: 11 nodes to be scored (53 eliminated genes)
#>
#> Level 6: 16 nodes to be scored (81 eliminated genes)
#>
#> Level 5: 17 nodes to be scored (132 eliminated genes)
#>
#> Level 4: 13 nodes to be scored (208 eliminated genes)
#>
#> Level 3: 9 nodes to be scored (257 eliminated genes)
#>
#> Level 2: 5 nodes to be scored (287 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (295 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.and.CG.phenotype.BP_weight01_10_all --- no of nodes: 48
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.and.CG.phenotype
#> Ontology: BP GO.ID Term Annotated Significant
#> 1 GO:0065004 protein-DNA complex assembly 6 2
#> 2 GO:0006457 protein folding 11 2
#> 3 GO:0043933 protein-containing complex organization 30 4
#> 4 GO:0006281 DNA repair 18 2
#> 5 GO:0006270 DNA replication initiation 5 1
#> 6 GO:0006366 transcription by RNA polymerase II 5 1
#> 7 GO:0006891 intra-Golgi vesicle-mediated transport 5 1
#> 8 GO:0065007 biological regulation 74 2
#> 9 GO:0006338 chromatin remodeling 6 1
#> 10 GO:0019725 cellular homeostasis 6 1
#> Expected topGO go.category interest.category algorithm statistic
#> 1 0.20 0.015 BP HS.and.CG.phenotype weight01 fisher
#> 2 0.37 0.049 BP HS.and.CG.phenotype weight01 fisher
#> 3 1.02 0.055 BP HS.and.CG.phenotype weight01 fisher
#> 4 0.61 0.119 BP HS.and.CG.phenotype weight01 fisher
#> 5 0.17 0.159 BP HS.and.CG.phenotype weight01 fisher
#> 6 0.17 0.159 BP HS.and.CG.phenotype weight01 fisher
#> 7 0.17 0.159 BP HS.and.CG.phenotype weight01 fisher
#> 8 2.51 0.180 BP HS.and.CG.phenotype weight01 fisher
#> 9 0.20 0.188 BP HS.and.CG.phenotype weight01 fisher
#> 10 0.20 0.188 BP HS.and.CG.phenotype weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 2 of 4
#> ontology 2 of 3
#>
#> Building most specific GOs .....
#> ( 195 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 367 GO terms and 616 relations. )
#>
#> Annotating nodes ...............
#> ( 526 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 80 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 11: 1 nodes to be scored (0 eliminated genes)
#>
#> Level 10: 3 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 5 nodes to be scored (16 eliminated genes)
#>
#> Level 8: 8 nodes to be scored (64 eliminated genes)
#>
#> Level 7: 8 nodes to be scored (91 eliminated genes)
#>
#> Level 6: 14 nodes to be scored (130 eliminated genes)
#>
#> Level 5: 14 nodes to be scored (215 eliminated genes)
#>
#> Level 4: 11 nodes to be scored (413 eliminated genes)
#>
#> Level 3: 13 nodes to be scored (458 eliminated genes)
#>
#> Level 2: 2 nodes to be scored (481 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (514 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.and.CG.phenotype.CC_weight01_10_all --- no of nodes: 46
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.and.CG.phenotype
#> Ontology: CC GO.ID Term Annotated Significant
#> 1 GO:0032993 protein-DNA complex 5 3
#> 2 GO:0140513 nuclear protein-containing complex 41 4
#> 3 GO:0043231 intracellular membrane-bounded organelle 360 18
#> 4 GO:0005730 nucleolus 16 2
#> 5 GO:0031982 vesicle 54 5
#> 6 GO:1903561 extracellular vesicle 17 2
#> 7 GO:0005634 nucleus 238 13
#> 8 GO:0005743 mitochondrial inner membrane 5 1
#> 9 GO:0030120 vesicle coat 5 1
#> 10 GO:0032040 small-subunit processome 5 1
#> Expected topGO go.category interest.category algorithm statistic
#> 1 0.20 0.00052 CC HS.and.CG.phenotype weight01 fisher
#> 2 1.64 0.07194 CC HS.and.CG.phenotype weight01 fisher
#> 3 14.37 0.11288 CC HS.and.CG.phenotype weight01 fisher
#> 4 0.64 0.13010 CC HS.and.CG.phenotype weight01 fisher
#> 5 2.16 0.13579 CC HS.and.CG.phenotype weight01 fisher
#> 6 0.68 0.14398 CC HS.and.CG.phenotype weight01 fisher
#> 7 9.50 0.15948 CC HS.and.CG.phenotype weight01 fisher
#> 8 0.20 0.18495 CC HS.and.CG.phenotype weight01 fisher
#> 9 0.20 0.18495 CC HS.and.CG.phenotype weight01 fisher
#> 10 0.20 0.18495 CC HS.and.CG.phenotype weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 2 of 4
#> ontology 3 of 3
#>
#> Building most specific GOs .....
#> ( 283 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 554 GO terms and 715 relations. )
#>
#> Annotating nodes ...............
#> ( 334 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 85 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 8: 4 nodes to be scored (0 eliminated genes)
#>
#> Level 7: 7 nodes to be scored (0 eliminated genes)
#>
#> Level 6: 11 nodes to be scored (24 eliminated genes)
#>
#> Level 5: 16 nodes to be scored (61 eliminated genes)
#>
#> Level 4: 20 nodes to be scored (91 eliminated genes)
#>
#> Level 3: 20 nodes to be scored (140 eliminated genes)
#>
#> Level 2: 6 nodes to be scored (240 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (318 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.Neutral.MF_weight01_10_all --- no of nodes: 35
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.Neutral
#> Ontology: MF GO.ID Term Annotated Significant
#> 1 GO:0050839 cell adhesion molecule binding 17 5
#> 2 GO:0120545 nucleic acid conformation isomerase acti... 11 2
#> 3 GO:0004722 protein serine/threonine phosphatase act... 5 2
#> 4 GO:0003729 mRNA binding 16 4
#> 5 GO:0140993 histone modifying activity 6 2
#> 6 GO:0008270 zinc ion binding 7 2
#> 7 GO:0008757 S-adenosylmethionine-dependent methyltra... 7 2
#> 8 GO:0097367 carbohydrate derivative binding 18 2
#> 9 GO:0016772 transferase activity, transferring phosp... 33 3
#> 10 GO:0008094 ATP-dependent activity, acting on DNA 8 2
#> Expected topGO go.category interest.category algorithm statistic
#> 1 2.39 0.074 MF HS.Neutral weight01 fisher
#> 2 1.55 0.142 MF HS.Neutral weight01 fisher
#> 3 0.70 0.147 MF HS.Neutral weight01 fisher
#> 4 2.25 0.174 MF HS.Neutral weight01 fisher
#> 5 0.84 0.201 MF HS.Neutral weight01 fisher
#> 6 0.99 0.257 MF HS.Neutral weight01 fisher
#> 7 0.99 0.257 MF HS.Neutral weight01 fisher
#> 8 2.53 0.269 MF HS.Neutral weight01 fisher
#> 9 4.64 0.281 MF HS.Neutral weight01 fisher
#> 10 1.13 0.313 MF HS.Neutral weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 3 of 4
#> ontology 1 of 3
#>
#> Building most specific GOs .....
#> ( 358 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 1125 GO terms and 2077 relations. )
#>
#> Annotating nodes ...............
#> ( 354 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 198 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 (11 eliminated genes)
#>
#> Level 10: 9 nodes to be scored (11 eliminated genes)
#>
#> Level 9: 10 nodes to be scored (17 eliminated genes)
#>
#> Level 8: 16 nodes to be scored (77 eliminated genes)
#>
#> Level 7: 32 nodes to be scored (95 eliminated genes)
#>
#> Level 6: 38 nodes to be scored (140 eliminated genes)
#>
#> Level 5: 37 nodes to be scored (235 eliminated genes)
#>
#> Level 4: 26 nodes to be scored (277 eliminated genes)
#>
#> Level 3: 18 nodes to be scored (318 eliminated genes)
#>
#> Level 2: 7 nodes to be scored (343 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (348 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.Neutral.BP_weight01_10_all --- no of nodes: 71
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.Neutral
#> Ontology: BP GO.ID Term Annotated Significant
#> 1 GO:0072594 establishment of protein localization to... 6 4
#> 2 GO:0020033 antigenic variation 27 8
#> 3 GO:0006355 regulation of DNA-templated transcriptio... 12 5
#> 4 GO:0006605 protein targeting 8 4
#> 5 GO:0015931 nucleobase-containing compound transport 5 3
#> 6 GO:0033365 protein localization to organelle 5 3
#> 7 GO:0010558 negative regulation of macromolecule bio... 9 3
#> 8 GO:0098609 cell-cell adhesion 19 5
#> 9 GO:0020013 symbiont-mediated perturbation of host e... 20 5
#> 10 GO:0006886 intracellular protein transport 9 3
#> Expected topGO go.category interest.category algorithm statistic
#> 1 0.66 0.0016 BP HS.Neutral weight01 fisher
#> 2 2.97 0.0049 BP HS.Neutral weight01 fisher
#> 3 1.32 0.0056 BP HS.Neutral weight01 fisher
#> 4 0.88 0.0064 BP HS.Neutral weight01 fisher
#> 5 0.55 0.0106 BP HS.Neutral weight01 fisher
#> 6 0.55 0.0106 BP HS.Neutral weight01 fisher
#> 7 0.99 0.0325 BP HS.Neutral weight01 fisher
#> 8 2.09 0.0456 BP HS.Neutral weight01 fisher
#> 9 2.20 0.0559 BP HS.Neutral weight01 fisher
#> 10 0.99 0.0651 BP HS.Neutral weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 3 of 4
#> ontology 2 of 3
#>
#> Building most specific GOs .....
#> ( 195 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 367 GO terms and 616 relations. )
#>
#> Annotating nodes ...............
#> ( 526 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 98 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 11: 1 nodes to be scored (0 eliminated genes)
#>
#> Level 10: 3 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 4 nodes to be scored (16 eliminated genes)
#>
#> Level 8: 11 nodes to be scored (75 eliminated genes)
#>
#> Level 7: 10 nodes to be scored (87 eliminated genes)
#>
#> Level 6: 17 nodes to be scored (146 eliminated genes)
#>
#> Level 5: 16 nodes to be scored (233 eliminated genes)
#>
#> Level 4: 16 nodes to be scored (425 eliminated genes)
#>
#> Level 3: 17 nodes to be scored (465 eliminated genes)
#>
#> Level 2: 2 nodes to be scored (499 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (525 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.Neutral.CC_weight01_10_all --- no of nodes: 35
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.Neutral
#> Ontology: CC GO.ID Term Annotated Significant Expected
#> 1 GO:0020030 infected host cell surface knob 18 5 2.36
#> 2 GO:0005768 endosome 8 3 1.05
#> 3 GO:0000785 chromatin 9 3 1.18
#> 4 GO:0043657 host cell 26 6 3.41
#> 5 GO:0035770 ribonucleoprotein granule 5 2 0.66
#> 6 GO:0020002 host cell plasma membrane 28 6 3.67
#> 7 GO:0020036 Maurer's cleft 44 8 5.77
#> 8 GO:0016020 membrane 102 14 13.38
#> 9 GO:0030659 cytoplasmic vesicle membrane 8 2 1.05
#> 10 GO:0030430 host cell cytoplasm 74 14 9.71
#> topGO go.category interest.category algorithm statistic
#> 1 0.073 CC HS.Neutral weight01 fisher
#> 2 0.074 CC HS.Neutral weight01 fisher
#> 3 0.085 CC HS.Neutral weight01 fisher
#> 4 0.111 CC HS.Neutral weight01 fisher
#> 5 0.130 CC HS.Neutral weight01 fisher
#> 6 0.147 CC HS.Neutral weight01 fisher
#> 7 0.205 CC HS.Neutral weight01 fisher
#> 8 0.244 CC HS.Neutral weight01 fisher
#> 9 0.245 CC HS.Neutral weight01 fisher
#> 10 0.260 CC HS.Neutral weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 3 of 4
#> ontology 3 of 3
#>
#> Building most specific GOs .....
#> ( 283 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 554 GO terms and 715 relations. )
#>
#> Annotating nodes ...............
#> ( 334 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 112 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 9: 1 nodes to be scored (0 eliminated genes)
#>
#> Level 8: 5 nodes to be scored (0 eliminated genes)
#>
#> Level 7: 11 nodes to be scored (11 eliminated genes)
#>
#> Level 6: 14 nodes to be scored (33 eliminated genes)
#>
#> Level 5: 24 nodes to be scored (73 eliminated genes)
#>
#> Level 4: 24 nodes to be scored (104 eliminated genes)
#>
#> Level 3: 24 nodes to be scored (158 eliminated genes)
#>
#> Level 2: 8 nodes to be scored (258 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (328 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.not.classified.MF_weight01_10_all --- no of nodes: 44
#>
#> ==============================================================================
#> GO enrichment results for interest category: not.classified
#> Ontology: MF GO.ID Term Annotated Significant
#> 1 GO:0004197 cysteine-type endopeptidase activity 6 6
#> 2 GO:0004843 cysteine-type deubiquitinase activity 5 5
#> 3 GO:0022890 inorganic cation transmembrane transport... 5 5
#> 4 GO:0008324 monoatomic cation transmembrane transpor... 5 5
#> 5 GO:0044877 protein-containing complex binding 13 11
#> 6 GO:0008047 enzyme activator activity 8 7
#> 7 GO:0140097 catalytic activity, acting on DNA 12 7
#> 8 GO:0005524 ATP binding 11 9
#> 9 GO:0003735 structural constituent of ribosome 14 11
#> 10 GO:0016747 acyltransferase activity, transferring g... 7 6
#> Expected topGO go.category interest.category algorithm statistic
#> 1 4.02 0.089 MF not.classified weight01 fisher
#> 2 3.35 0.134 MF not.classified weight01 fisher
#> 3 3.35 0.134 MF not.classified weight01 fisher
#> 4 3.35 0.134 MF not.classified weight01 fisher
#> 5 8.72 0.140 MF not.classified weight01 fisher
#> 6 5.37 0.198 MF not.classified weight01 fisher
#> 7 8.05 0.209 MF not.classified weight01 fisher
#> 8 7.38 0.238 MF not.classified weight01 fisher
#> 9 9.39 0.266 MF not.classified weight01 fisher
#> 10 4.69 0.268 MF not.classified weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 4 of 4
#> ontology 1 of 3
#>
#> Building most specific GOs .....
#> ( 358 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 1125 GO terms and 2077 relations. )
#>
#> Annotating nodes ...............
#> ( 354 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 251 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: 3 nodes to be scored (11 eliminated genes)
#>
#> Level 10: 12 nodes to be scored (11 eliminated genes)
#>
#> Level 9: 17 nodes to be scored (24 eliminated genes)
#>
#> Level 8: 25 nodes to be scored (98 eliminated genes)
#>
#> Level 7: 39 nodes to be scored (125 eliminated genes)
#>
#> Level 6: 47 nodes to be scored (174 eliminated genes)
#>
#> Level 5: 45 nodes to be scored (261 eliminated genes)
#>
#> Level 4: 31 nodes to be scored (293 eliminated genes)
#>
#> Level 3: 22 nodes to be scored (329 eliminated genes)
#>
#> Level 2: 7 nodes to be scored (345 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (353 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.not.classified.BP_weight01_10_all --- no of nodes: 46
#>
#> ==============================================================================
#> GO enrichment results for interest category: not.classified
#> Ontology: BP GO.ID Term Annotated Significant
#> 1 GO:0051604 protein maturation 22 16
#> 2 GO:0006511 ubiquitin-dependent protein catabolic pr... 10 9
#> 3 GO:0006412 translation 26 21
#> 4 GO:0016579 protein deubiquitination 5 5
#> 5 GO:0051640 organelle localization 5 5
#> 6 GO:0048583 regulation of response to stimulus 5 5
#> 7 GO:0007165 signal transduction 27 17
#> 8 GO:0051603 proteolysis involved in protein cataboli... 17 15
#> 9 GO:0070925 organelle assembly 12 10
#> 10 GO:0044409 symbiont entry into host 16 13
#> Expected topGO go.category interest.category algorithm statistic
#> 1 15.35 0.12 BP not.classified weight01 fisher
#> 2 6.98 0.14 BP not.classified weight01 fisher
#> 3 18.14 0.15 BP not.classified weight01 fisher
#> 4 3.49 0.16 BP not.classified weight01 fisher
#> 5 3.49 0.16 BP not.classified weight01 fisher
#> 6 3.49 0.16 BP not.classified weight01 fisher
#> 7 18.84 0.18 BP not.classified weight01 fisher
#> 8 11.86 0.23 BP not.classified weight01 fisher
#> 9 8.37 0.23 BP not.classified weight01 fisher
#> 10 11.16 0.23 BP not.classified weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 4 of 4
#> ontology 2 of 3
#>
#> Building most specific GOs .....
#> ( 195 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 367 GO terms and 616 relations. )
#>
#> Annotating nodes ...............
#> ( 526 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 120 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 11: 1 nodes to be scored (0 eliminated genes)
#>
#> Level 10: 5 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 7 nodes to be scored (16 eliminated genes)
#>
#> Level 8: 16 nodes to be scored (86 eliminated genes)
#>
#> Level 7: 14 nodes to be scored (102 eliminated genes)
#>
#> Level 6: 20 nodes to be scored (183 eliminated genes)
#>
#> Level 5: 19 nodes to be scored (251 eliminated genes)
#>
#> Level 4: 17 nodes to be scored (428 eliminated genes)
#>
#> Level 3: 18 nodes to be scored (465 eliminated genes)
#>
#> Level 2: 2 nodes to be scored (500 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (525 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.not.classified.CC_weight01_10_all --- no of nodes: 32
#>
#> ==============================================================================
#> GO enrichment results for interest category: not.classified
#> Ontology: CC GO.ID Term Annotated Significant
#> 1 GO:0032991 protein-containing complex 125 88
#> 2 GO:0020003 symbiont-containing vacuole 18 14
#> 3 GO:0009986 cell surface 24 20
#> 4 GO:0020009 microneme 6 6
#> 5 GO:1990234 transferase complex 22 18
#> 6 GO:0020002 host cell plasma membrane 28 22
#> 7 GO:0031410 cytoplasmic vesicle 37 24
#> 8 GO:0071944 cell periphery 26 19
#> 9 GO:0044164 host cell cytosol 7 6
#> 10 GO:0043232 intracellular membraneless organelle 65 46
#> Expected topGO go.category interest.category algorithm statistic
#> 1 83.65 0.016 CC not.classified weight01 fisher
#> 2 12.05 0.027 CC not.classified weight01 fisher
#> 3 16.06 0.058 CC not.classified weight01 fisher
#> 4 4.02 0.089 CC not.classified weight01 fisher
#> 5 14.72 0.103 CC not.classified weight01 fisher
#> 6 18.74 0.125 CC not.classified weight01 fisher
#> 7 24.76 0.205 CC not.classified weight01 fisher
#> 8 17.40 0.265 CC not.classified weight01 fisher
#> 9 4.68 0.266 CC not.classified weight01 fisher
#> 10 43.50 0.294 CC not.classified weight01 fisher
#>
#> ==============================================================================
#>
#> interest-category 4 of 4
#> ontology 3 of 3
#> Joining with `by = join_by(GO.ID, go.category, interest.category, algorithm,
#> statistic)`
#>
#> ==============================================================================
#> Significant terms from final GO enrichment results table (saved to 'Routput/GO/all.combined.GO.results.tsv':
#> GO.ID Term Annotated Significant
#> 1 GO:0010468 regulation of gene expression 27 6
#> 2 GO:0044283 small molecule biosynthetic process 5 3
#> 3 GO:0061024 membrane organization 9 4
#> 4 GO:0035556 intracellular signal transduction 22 7
#> 5 GO:0009410 response to xenobiotic stimulus 28 8
#> 6 GO:0008610 lipid biosynthetic process 12 3
#> 7 GO:0006364 rRNA processing 14 6
#> 8 GO:0006401 RNA catabolic process 7 3
#> 9 GO:0000460 maturation of 5.8S rRNA 7 3
#> 10 GO:0005743 mitochondrial inner membrane 5 3
#> 11 GO:1902494 catalytic complex 42 8
#> 12 GO:0120543 macromolecular conformation isomerase ac... 14 3
#> 13 GO:0016740 transferase activity 71 12
#> 14 GO:0072594 establishment of protein localization to... 6 4
#> 15 GO:0020033 antigenic variation 27 8
#> 16 GO:0006355 regulation of DNA-templated transcriptio... 12 5
#> 17 GO:0006605 protein targeting 8 4
#> 18 GO:0015931 nucleobase-containing compound transport 5 3
#> 19 GO:0033365 protein localization to organelle 5 3
#> 20 GO:0010558 negative regulation of macromolecule bio... 9 3
#> 21 GO:0098609 cell-cell adhesion 19 5
#> 22 GO:0020013 symbiont-mediated perturbation of host e... 20 5
#> 23 GO:0006886 intracellular protein transport 9 3
#> 24 GO:0020030 infected host cell surface knob 18 5
#> 25 GO:0005768 endosome 8 3
#> 26 GO:0000785 chromatin 9 3
#> 27 GO:0050839 cell adhesion molecule binding 17 5
#> 28 GO:0065004 protein-DNA complex assembly 6 2
#> 29 GO:0006457 protein folding 11 2
#> 30 GO:0043933 protein-containing complex organization 30 4
#> 31 GO:0032993 protein-DNA complex 5 3
#> 32 GO:0140513 nuclear protein-containing complex 41 4
#> 33 GO:0003677 DNA binding 26 6
#> 34 GO:0008094 ATP-dependent activity, acting on DNA 8 3
#> 35 GO:0003690 double-stranded DNA binding 9 3
#> 36 GO:1990837 sequence-specific double-stranded DNA bi... 7 2
#> 37 GO:0032991 protein-containing complex 125 88
#> 38 GO:0020003 symbiont-containing vacuole 18 14
#> 39 GO:0009986 cell surface 24 20
#> 40 GO:0020009 microneme 6 6
#> 41 GO:0004197 cysteine-type endopeptidase activity 6 6
#> Expected topGO go.category interest.category algorithm statistic
#> 1 4.27 0.00730 BP A.HS.Sensitive weight01 fisher
#> 2 0.79 0.02980 BP A.HS.Sensitive weight01 fisher
#> 3 1.42 0.03840 BP A.HS.Sensitive weight01 fisher
#> 4 3.48 0.04210 BP A.HS.Sensitive weight01 fisher
#> 5 4.43 0.05560 BP A.HS.Sensitive weight01 fisher
#> 6 1.90 0.06730 BP A.HS.Sensitive weight01 fisher
#> 7 2.21 0.07520 BP A.HS.Sensitive weight01 fisher
#> 8 1.11 0.08220 BP A.HS.Sensitive weight01 fisher
#> 9 1.11 0.08220 BP A.HS.Sensitive weight01 fisher
#> 10 0.80 0.03100 CC A.HS.Sensitive weight01 fisher
#> 11 6.71 0.03200 CC A.HS.Sensitive weight01 fisher
#> 12 2.14 0.06400 MF A.HS.Sensitive weight01 fisher
#> 13 10.84 0.07600 MF A.HS.Sensitive weight01 fisher
#> 14 0.66 0.00160 BP HS.Neutral weight01 fisher
#> 15 2.97 0.00490 BP HS.Neutral weight01 fisher
#> 16 1.32 0.00560 BP HS.Neutral weight01 fisher
#> 17 0.88 0.00640 BP HS.Neutral weight01 fisher
#> 18 0.55 0.01060 BP HS.Neutral weight01 fisher
#> 19 0.55 0.01060 BP HS.Neutral weight01 fisher
#> 20 0.99 0.03250 BP HS.Neutral weight01 fisher
#> 21 2.09 0.04560 BP HS.Neutral weight01 fisher
#> 22 2.20 0.05590 BP HS.Neutral weight01 fisher
#> 23 0.99 0.06510 BP HS.Neutral weight01 fisher
#> 24 2.36 0.07300 CC HS.Neutral weight01 fisher
#> 25 1.05 0.07400 CC HS.Neutral weight01 fisher
#> 26 1.18 0.08500 CC HS.Neutral weight01 fisher
#> 27 2.39 0.07400 MF HS.Neutral weight01 fisher
#> 28 0.20 0.01500 BP HS.and.CG.phenotype weight01 fisher
#> 29 0.37 0.04900 BP HS.and.CG.phenotype weight01 fisher
#> 30 1.02 0.05500 BP HS.and.CG.phenotype weight01 fisher
#> 31 0.20 0.00052 CC HS.and.CG.phenotype weight01 fisher
#> 32 1.64 0.07194 CC HS.and.CG.phenotype weight01 fisher
#> 33 0.93 0.00120 MF HS.and.CG.phenotype weight01 fisher
#> 34 0.29 0.00180 MF HS.and.CG.phenotype weight01 fisher
#> 35 0.32 0.06030 MF HS.and.CG.phenotype weight01 fisher
#> 36 0.25 0.06580 MF HS.and.CG.phenotype weight01 fisher
#> 37 83.65 0.01600 CC not.classified weight01 fisher
#> 38 12.05 0.02700 CC not.classified weight01 fisher
#> 39 16.06 0.05800 CC not.classified weight01 fisher
#> 40 4.02 0.08900 CC not.classified weight01 fisher
#> 41 4.02 0.08900 MF not.classified weight01 fisher
#>
#> ==============================================================================
#>
#>
#>
#> All interesting-gene categories have been tested for GO-term enrichment.
#>
#> See ALL TOP 30 enriched terms by interesting-gene category in 'Routput/GO/all.combined.GO.results.tsv'.
#>
#> See log files for topGO-analyses by each interesting-gene category, including all genes in the analysis by GO term in 'Routput/GO/topGO.log.*.txt'.
#>
#> See all significant genes mapped to all significant GO terms in 'Routput/GO/all.combined.sig.genes.per.sig.terms.tsv'.
#>
#> ==============================================================================# if you've run the pipeline, your significant genes in significant terms per category of interest can be loaded:
sig.genes <- read.delim("Routput/GO/all.combined.sig.genes.per.sig.terms.tsv")