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.
- mydf: data frame with geneIDs in column 1, and interest-category classifications in column 2.
- geneID2GO: a list of named vectors of GO IDs–one vector of GO-terms for each geneID.
- pval: p-value threshold for significance. Defaults to 0.05.
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”
-
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 compartment; 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 < 3 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 .....
#> ( 128 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 336 GO terms and 437 relations. )
#>
#> Annotating nodes ...............
#> ( 193 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 59 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 8: 3 nodes to be scored (0 eliminated genes)
#>
#> Level 7: 3 nodes to be scored (0 eliminated genes)
#>
#> Level 6: 10 nodes to be scored (10 eliminated genes)
#>
#> Level 5: 11 nodes to be scored (10 eliminated genes)
#>
#> Level 4: 11 nodes to be scored (42 eliminated genes)
#>
#> Level 3: 15 nodes to be scored (76 eliminated genes)
#>
#> Level 2: 5 nodes to be scored (97 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (183 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_5_all --- no of nodes: 16
#>
#> ==============================================================================
#> GO enrichment results for interest category: A.HS.Sensitive
#> Ontology: MF GO.ID Term Annotated Significant
#> 1 GO:0003924 GTPase activity 3 2
#> 2 GO:0016791 phosphatase activity 7 3
#> 3 GO:0003735 structural constituent of ribosome 7 3
#> 4 GO:0140096 catalytic activity, acting on a protein 17 4
#> 5 GO:0016887 ATP hydrolysis activity 6 2
#> 6 GO:0016787 hydrolase activity 29 10
#> 7 GO:0003729 mRNA binding 13 3
#> 8 GO:0022857 transmembrane transporter activity 8 2
#> 9 GO:0016301 kinase activity 8 2
#> 10 GO:0004540 RNA nuclease activity 3 1
#> Expected topGO go.category interest.category
#> 1 0.48 0.068 MF A.HS.Sensitive
#> 2 1.12 0.084 MF A.HS.Sensitive
#> 3 1.12 0.084 MF A.HS.Sensitive
#> 4 2.73 0.244 MF A.HS.Sensitive
#> 5 0.96 0.247 MF A.HS.Sensitive
#> 6 4.66 0.248 MF A.HS.Sensitive
#> 7 2.09 0.348 MF A.HS.Sensitive
#> 8 1.28 0.377 MF A.HS.Sensitive
#> 9 1.28 0.408 MF A.HS.Sensitive
#> 10 0.48 0.410 MF A.HS.Sensitive
#>
#> ==============================================================================
#>
#> interest-category 1 of 4
#> ontology 1 of 3
#>
#> Building most specific GOs .....
#> ( 114 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 535 GO terms and 1001 relations. )
#>
#> Annotating nodes ...............
#> ( 176 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 105 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 9: 1 nodes to be scored (0 eliminated genes)
#>
#> Level 8: 4 nodes to be scored (0 eliminated genes)
#>
#> Level 7: 7 nodes to be scored (4 eliminated genes)
#>
#> Level 6: 15 nodes to be scored (22 eliminated genes)
#>
#> Level 5: 27 nodes to be scored (50 eliminated genes)
#>
#> Level 4: 26 nodes to be scored (93 eliminated genes)
#>
#> Level 3: 18 nodes to be scored (130 eliminated genes)
#>
#> Level 2: 6 nodes to be scored (162 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (165 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.A.HS.Sensitive.BP_weight01_5_all --- no of nodes: 23
#>
#> ==============================================================================
#> GO enrichment results for interest category: A.HS.Sensitive
#> Ontology: BP GO.ID Term Annotated Significant
#> 1 GO:0016311 dephosphorylation 3 2
#> 2 GO:0009410 response to xenobiotic stimulus 22 6
#> 3 GO:1901135 carbohydrate derivative metabolic proces... 5 2
#> 4 GO:0015031 protein transport 5 2
#> 5 GO:0044237 cellular metabolic process 66 10
#> 6 GO:0006996 organelle organization 8 2
#> 7 GO:0006468 protein phosphorylation 9 2
#> 8 GO:0007049 cell cycle 3 1
#> 9 GO:0048519 negative regulation of biological proces... 3 1
#> 10 GO:0030522 intracellular receptor signaling pathway 3 1
#> Expected topGO go.category interest.category
#> 1 0.41 0.049 BP A.HS.Sensitive
#> 2 3.00 0.056 BP A.HS.Sensitive
#> 3 0.68 0.134 BP A.HS.Sensitive
#> 4 0.68 0.134 BP A.HS.Sensitive
#> 5 9.00 0.251 BP A.HS.Sensitive
#> 6 1.09 0.299 BP A.HS.Sensitive
#> 7 1.23 0.354 BP A.HS.Sensitive
#> 8 0.41 0.358 BP A.HS.Sensitive
#> 9 0.41 0.358 BP A.HS.Sensitive
#> 10 0.41 0.358 BP A.HS.Sensitive
#>
#> ==============================================================================
#>
#> interest-category 1 of 4
#> ontology 2 of 3
#>
#> Building most specific GOs .....
#> ( 100 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 245 GO terms and 416 relations. )
#>
#> Annotating nodes ...............
#> ( 434 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 80 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 11: 2 nodes to be scored (0 eliminated genes)
#>
#> Level 10: 4 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 5 nodes to be scored (23 eliminated genes)
#>
#> Level 8: 8 nodes to be scored (70 eliminated genes)
#>
#> Level 7: 9 nodes to be scored (93 eliminated genes)
#>
#> Level 6: 13 nodes to be scored (115 eliminated genes)
#>
#> Level 5: 10 nodes to be scored (171 eliminated genes)
#>
#> Level 4: 11 nodes to be scored (342 eliminated genes)
#>
#> Level 3: 15 nodes to be scored (358 eliminated genes)
#>
#> Level 2: 2 nodes to be scored (404 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (432 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.A.HS.Sensitive.CC_weight01_5_all --- no of nodes: 23
#>
#> ==============================================================================
#> GO enrichment results for interest category: A.HS.Sensitive
#> Ontology: CC GO.ID Term Annotated Significant Expected
#> 1 GO:0005739 mitochondrion 46 13 7.63
#> 2 GO:0031966 mitochondrial membrane 3 2 0.50
#> 3 GO:0140513 nuclear protein-containing complex 12 4 1.99
#> 4 GO:0034399 nuclear periphery 8 3 1.33
#> 5 GO:0005737 cytoplasm 176 39 29.20
#> 6 GO:0005840 ribosome 8 3 1.33
#> 7 GO:0005783 endoplasmic reticulum 19 5 3.15
#> 8 GO:0020011 apicoplast 42 9 6.97
#> 9 GO:0005794 Golgi apparatus 6 2 1.00
#> 10 GO:0031981 nuclear lumen 15 5 2.49
#> topGO go.category interest.category
#> 1 0.068 CC A.HS.Sensitive
#> 2 0.073 CC A.HS.Sensitive
#> 3 0.121 CC A.HS.Sensitive
#> 4 0.132 CC A.HS.Sensitive
#> 5 0.163 CC A.HS.Sensitive
#> 6 0.164 CC A.HS.Sensitive
#> 7 0.192 CC A.HS.Sensitive
#> 8 0.245 CC A.HS.Sensitive
#> 9 0.261 CC A.HS.Sensitive
#> 10 0.297 CC A.HS.Sensitive
#>
#> ==============================================================================
#>
#> interest-category 1 of 4
#> ontology 3 of 3
#>
#> Building most specific GOs .....
#> ( 128 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 336 GO terms and 437 relations. )
#>
#> Annotating nodes ...............
#> ( 193 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 16 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: 4 nodes to be scored (7 eliminated genes)
#>
#> Level 3: 5 nodes to be scored (42 eliminated genes)
#>
#> Level 2: 3 nodes to be scored (64 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (143 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.and.CG.phenotype.MF_weight01_5_all --- no of nodes: 16
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.and.CG.phenotype
#> Ontology: MF GO.ID Term Annotated Significant
#> 1 GO:0019899 enzyme binding 3 1
#> 2 GO:0022804 active transmembrane transporter activit... 3 1
#> 3 GO:0016791 phosphatase activity 7 1
#> 4 GO:0003723 RNA binding 35 1
#> 5 GO:0005515 protein binding 79 2
#> 6 GO:0003674 molecular_function 193 4
#> 7 GO:0003676 nucleic acid binding 47 1
#> 8 GO:0005488 binding 128 3
#> 9 GO:0005215 transporter activity 11 1
#> 10 GO:0042578 phosphoric ester hydrolase activity 7 1
#> Expected topGO go.category interest.category
#> 1 0.06 0.061 MF HS.and.CG.phenotype
#> 2 0.06 0.061 MF HS.and.CG.phenotype
#> 3 0.15 0.138 MF HS.and.CG.phenotype
#> 4 0.73 0.554 MF HS.and.CG.phenotype
#> 5 1.64 0.786 MF HS.and.CG.phenotype
#> 6 4.00 1.000 MF HS.and.CG.phenotype
#> 7 0.97 1.000 MF HS.and.CG.phenotype
#> 8 2.65 1.000 MF HS.and.CG.phenotype
#> 9 0.23 1.000 MF HS.and.CG.phenotype
#> 10 0.15 1.000 MF HS.and.CG.phenotype
#>
#> ==============================================================================
#>
#> interest-category 2 of 4
#> ontology 1 of 3
#>
#> Building most specific GOs .....
#> ( 114 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 535 GO terms and 1001 relations. )
#>
#> Annotating nodes ...............
#> ( 176 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 56 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 9: 2 nodes to be scored (0 eliminated genes)
#>
#> Level 8: 4 nodes to be scored (0 eliminated genes)
#>
#> Level 7: 4 nodes to be scored (9 eliminated genes)
#>
#> Level 6: 6 nodes to be scored (18 eliminated genes)
#>
#> Level 5: 12 nodes to be scored (33 eliminated genes)
#>
#> Level 4: 13 nodes to be scored (50 eliminated genes)
#>
#> Level 3: 9 nodes to be scored (88 eliminated genes)
#>
#> Level 2: 5 nodes to be scored (105 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (113 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.and.CG.phenotype.BP_weight01_5_all --- no of nodes: 45
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.and.CG.phenotype
#> Ontology: BP GO.ID Term Annotated Significant
#> 1 GO:0045454 cell redox homeostasis 3 1
#> 2 GO:0034470 ncRNA processing 3 1
#> 3 GO:0006457 protein folding 4 1
#> 4 GO:0006888 endoplasmic reticulum to Golgi vesicle-m... 4 1
#> 5 GO:0065003 protein-containing complex assembly 5 1
#> 6 GO:0042254 ribosome biogenesis 6 1
#> 7 GO:0006351 DNA-templated transcription 6 1
#> 8 GO:0006259 DNA metabolic process 8 1
#> 9 GO:0065007 biological regulation 21 1
#> 10 GO:1901564 organonitrogen compound metabolic proces... 44 1
#> Expected topGO go.category interest.category
#> 1 0.10 0.099 BP HS.and.CG.phenotype
#> 2 0.10 0.099 BP HS.and.CG.phenotype
#> 3 0.14 0.131 BP HS.and.CG.phenotype
#> 4 0.14 0.131 BP HS.and.CG.phenotype
#> 5 0.17 0.161 BP HS.and.CG.phenotype
#> 6 0.20 0.190 BP HS.and.CG.phenotype
#> 7 0.20 0.190 BP HS.and.CG.phenotype
#> 8 0.27 0.247 BP HS.and.CG.phenotype
#> 9 0.72 0.539 BP HS.and.CG.phenotype
#> 10 1.50 1.000 BP HS.and.CG.phenotype
#>
#> ==============================================================================
#>
#> interest-category 2 of 4
#> ontology 2 of 3
#>
#> Building most specific GOs .....
#> ( 100 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 245 GO terms and 416 relations. )
#>
#> Annotating nodes ...............
#> ( 434 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 68 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 11: 2 nodes to be scored (0 eliminated genes)
#>
#> Level 10: 4 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 5 nodes to be scored (23 eliminated genes)
#>
#> Level 8: 7 nodes to be scored (70 eliminated genes)
#>
#> Level 7: 7 nodes to be scored (90 eliminated genes)
#>
#> Level 6: 12 nodes to be scored (101 eliminated genes)
#>
#> Level 5: 8 nodes to be scored (165 eliminated genes)
#>
#> Level 4: 10 nodes to be scored (335 eliminated genes)
#>
#> Level 3: 10 nodes to be scored (352 eliminated genes)
#>
#> Level 2: 2 nodes to be scored (389 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (416 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.and.CG.phenotype.CC_weight01_5_all --- no of nodes: 34
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.and.CG.phenotype
#> Ontology: CC GO.ID Term Annotated Significant
#> 1 GO:0005730 nucleolus 5 2
#> 2 GO:0032993 protein-DNA complex 6 2
#> 3 GO:0030684 preribosome 3 1
#> 4 GO:0030660 Golgi-associated vesicle membrane 3 1
#> 5 GO:1903561 extracellular vesicle 17 2
#> 6 GO:0000785 chromatin 4 1
#> 7 GO:0030120 vesicle coat 4 1
#> 8 GO:0005794 Golgi apparatus 6 1
#> 9 GO:0005634 nucleus 176 9
#> 10 GO:0020005 symbiont-containing vacuole membrane 9 1
#> Expected topGO go.category interest.category
#> 1 0.18 0.012 CC HS.and.CG.phenotype
#> 2 0.22 0.069 CC HS.and.CG.phenotype
#> 3 0.11 0.107 CC HS.and.CG.phenotype
#> 4 0.11 0.107 CC HS.and.CG.phenotype
#> 5 0.63 0.126 CC HS.and.CG.phenotype
#> 6 0.15 0.140 CC HS.and.CG.phenotype
#> 7 0.15 0.140 CC HS.and.CG.phenotype
#> 8 0.22 0.203 CC HS.and.CG.phenotype
#> 9 6.49 0.235 CC HS.and.CG.phenotype
#> 10 0.33 0.289 CC HS.and.CG.phenotype
#>
#> ==============================================================================
#>
#> interest-category 2 of 4
#> ontology 3 of 3
#>
#> Building most specific GOs .....
#> ( 128 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 336 GO terms and 437 relations. )
#>
#> Annotating nodes ...............
#> ( 193 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 49 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: 6 nodes to be scored (6 eliminated genes)
#>
#> Level 5: 9 nodes to be scored (8 eliminated genes)
#>
#> Level 4: 14 nodes to be scored (36 eliminated genes)
#>
#> Level 3: 13 nodes to be scored (71 eliminated genes)
#>
#> Level 2: 4 nodes to be scored (119 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (169 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.Neutral.MF_weight01_5_all --- no of nodes: 19
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.Neutral
#> Ontology: MF GO.ID Term Annotated Significant
#> 1 GO:0043565 sequence-specific DNA binding 3 2
#> 2 GO:0008757 S-adenosylmethionine-dependent methyltra... 3 2
#> 3 GO:0016853 isomerase activity 3 2
#> 4 GO:0008094 ATP-dependent activity, acting on DNA 3 2
#> 5 GO:0016779 nucleotidyltransferase activity 4 2
#> 6 GO:0050839 cell adhesion molecule binding 17 5
#> 7 GO:0003677 DNA binding 8 4
#> 8 GO:0046872 metal ion binding 5 2
#> 9 GO:0003729 mRNA binding 13 3
#> 10 GO:0016409 palmitoyltransferase activity 3 1
#> Expected topGO go.category interest.category
#> 1 0.51 0.076 MF HS.Neutral
#> 2 0.51 0.076 MF HS.Neutral
#> 3 0.51 0.076 MF HS.Neutral
#> 4 0.51 0.076 MF HS.Neutral
#> 5 0.68 0.136 MF HS.Neutral
#> 6 2.91 0.142 MF HS.Neutral
#> 7 1.37 0.188 MF HS.Neutral
#> 8 0.85 0.203 MF HS.Neutral
#> 9 2.22 0.389 MF HS.Neutral
#> 10 0.51 0.432 MF HS.Neutral
#>
#> ==============================================================================
#>
#> interest-category 3 of 4
#> ontology 1 of 3
#>
#> Building most specific GOs .....
#> ( 114 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 535 GO terms and 1001 relations. )
#>
#> Annotating nodes ...............
#> ( 176 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 146 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 10: 3 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 7 nodes to be scored (0 eliminated genes)
#>
#> Level 8: 12 nodes to be scored (33 eliminated genes)
#>
#> Level 7: 17 nodes to be scored (40 eliminated genes)
#>
#> Level 6: 22 nodes to be scored (54 eliminated genes)
#>
#> Level 5: 32 nodes to be scored (82 eliminated genes)
#>
#> Level 4: 24 nodes to be scored (112 eliminated genes)
#>
#> Level 3: 21 nodes to be scored (135 eliminated genes)
#>
#> Level 2: 7 nodes to be scored (162 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (170 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.Neutral.BP_weight01_5_all --- no of nodes: 77
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.Neutral
#> Ontology: BP GO.ID Term Annotated Significant
#> 1 GO:0006355 regulation of DNA-templated transcriptio... 5 4
#> 2 GO:0020033 antigenic variation 27 8
#> 3 GO:0006913 nucleocytoplasmic transport 3 2
#> 4 GO:0051276 chromosome organization 3 2
#> 5 GO:0020013 modulation by symbiont of host erythrocy... 20 5
#> 6 GO:0060255 regulation of macromolecule metabolic pr... 8 6
#> 7 GO:0020035 adhesion of symbiont to microvasculature 22 5
#> 8 GO:0010468 regulation of gene expression 7 5
#> 9 GO:0051171 regulation of nitrogen compound metaboli... 7 5
#> 10 GO:0051701 biological process involved in interacti... 53 10
#> Expected topGO go.category interest.category
#> 1 0.65 0.001 BP HS.Neutral
#> 2 3.53 0.011 BP HS.Neutral
#> 3 0.39 0.045 BP HS.Neutral
#> 4 0.39 0.045 BP HS.Neutral
#> 5 2.61 0.097 BP HS.Neutral
#> 6 1.05 0.107 BP HS.Neutral
#> 7 2.88 0.137 BP HS.Neutral
#> 8 0.91 0.210 BP HS.Neutral
#> 9 0.91 0.210 BP HS.Neutral
#> 10 6.93 0.212 BP HS.Neutral
#>
#> ==============================================================================
#>
#> interest-category 3 of 4
#> ontology 2 of 3
#>
#> Building most specific GOs .....
#> ( 100 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 245 GO terms and 416 relations. )
#>
#> Annotating nodes ...............
#> ( 434 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 69 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 11: 2 nodes to be scored (0 eliminated genes)
#>
#> Level 10: 4 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 3 nodes to be scored (23 eliminated genes)
#>
#> Level 8: 4 nodes to be scored (82 eliminated genes)
#>
#> Level 7: 7 nodes to be scored (86 eliminated genes)
#>
#> Level 6: 10 nodes to be scored (100 eliminated genes)
#>
#> Level 5: 8 nodes to be scored (164 eliminated genes)
#>
#> Level 4: 12 nodes to be scored (341 eliminated genes)
#>
#> Level 3: 16 nodes to be scored (364 eliminated genes)
#>
#> Level 2: 2 nodes to be scored (413 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (433 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.HS.Neutral.CC_weight01_5_all --- no of nodes: 19
#>
#> ==============================================================================
#> GO enrichment results for interest category: HS.Neutral
#> Ontology: CC GO.ID Term Annotated Significant
#> 1 GO:0020030 infected host cell surface knob 18 5
#> 2 GO:0020002 host cell plasma membrane 28 6
#> 3 GO:0030430 host cell cytoplasm 80 15
#> 4 GO:0020036 Maurer's cleft 43 8
#> 5 GO:0005634 nucleus 176 27
#> 6 GO:0020008 rhoptry 8 2
#> 7 GO:0034399 nuclear periphery 8 2
#> 8 GO:0140535 intracellular protein-containing complex 8 2
#> 9 GO:0043657 host cell 105 19
#> 10 GO:0020005 symbiont-containing vacuole membrane 9 2
#> Expected topGO go.category interest.category
#> 1 2.49 0.087 CC HS.Neutral
#> 2 3.87 0.175 CC HS.Neutral
#> 3 11.06 0.228 CC HS.Neutral
#> 4 5.94 0.228 CC HS.Neutral
#> 5 24.33 0.258 CC HS.Neutral
#> 6 1.11 0.305 CC HS.Neutral
#> 7 1.11 0.305 CC HS.Neutral
#> 8 1.11 0.305 CC HS.Neutral
#> 9 14.52 0.334 CC HS.Neutral
#> 10 1.24 0.360 CC HS.Neutral
#>
#> ==============================================================================
#>
#> interest-category 3 of 4
#> ontology 3 of 3
#>
#> Building most specific GOs .....
#> ( 128 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 336 GO terms and 437 relations. )
#>
#> Annotating nodes ...............
#> ( 193 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 84 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 8: 3 nodes to be scored (0 eliminated genes)
#>
#> Level 7: 4 nodes to be scored (0 eliminated genes)
#>
#> Level 6: 12 nodes to be scored (10 eliminated genes)
#>
#> Level 5: 17 nodes to be scored (14 eliminated genes)
#>
#> Level 4: 21 nodes to be scored (50 eliminated genes)
#>
#> Level 3: 19 nodes to be scored (93 eliminated genes)
#>
#> Level 2: 7 nodes to be scored (136 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (187 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.not.classified.MF_weight01_5_all --- no of nodes: 11
#>
#> ==============================================================================
#> GO enrichment results for interest category: not.classified
#> Ontology: MF GO.ID Term Annotated Significant
#> 1 GO:0042393 histone binding 6 6
#> 2 GO:0016874 ligase activity 4 4
#> 3 GO:0008289 lipid binding 4 4
#> 4 GO:0140101 catalytic activity, acting on a tRNA 4 4
#> 5 GO:0140030 modification-dependent protein binding 4 4
#> 6 GO:0003743 translation initiation factor activity 4 4
#> 7 GO:0005515 protein binding 79 55
#> 8 GO:0008233 peptidase activity 6 5
#> 9 GO:0016765 transferase activity, transferring alkyl... 3 3
#> 10 GO:0140097 catalytic activity, acting on DNA 6 4
#> Expected topGO go.category interest.category
#> 1 3.89 0.071 MF not.classified
#> 2 2.59 0.173 MF not.classified
#> 3 2.59 0.173 MF not.classified
#> 4 2.59 0.173 MF not.classified
#> 5 2.59 0.173 MF not.classified
#> 6 2.59 0.173 MF not.classified
#> 7 51.17 0.262 MF not.classified
#> 8 3.89 0.269 MF not.classified
#> 9 1.94 0.269 MF not.classified
#> 10 3.89 0.276 MF not.classified
#>
#> ==============================================================================
#>
#> interest-category 4 of 4
#> ontology 1 of 3
#>
#> Building most specific GOs .....
#> ( 114 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 535 GO terms and 1001 relations. )
#>
#> Annotating nodes ...............
#> ( 176 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 200 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 10: 4 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 11 nodes to be scored (0 eliminated genes)
#>
#> Level 8: 17 nodes to be scored (36 eliminated genes)
#>
#> Level 7: 23 nodes to be scored (54 eliminated genes)
#>
#> Level 6: 31 nodes to be scored (74 eliminated genes)
#>
#> Level 5: 41 nodes to be scored (105 eliminated genes)
#>
#> Level 4: 34 nodes to be scored (133 eliminated genes)
#>
#> Level 3: 29 nodes to be scored (143 eliminated genes)
#>
#> Level 2: 9 nodes to be scored (169 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (176 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.not.classified.BP_weight01_5_all --- no of nodes: 34
#>
#> ==============================================================================
#> GO enrichment results for interest category: not.classified
#> Ontology: BP GO.ID Term Annotated Significant
#> 1 GO:0048870 cell motility 5 5
#> 2 GO:0006413 translational initiation 4 4
#> 3 GO:0020035 adhesion of symbiont to microvasculature 22 17
#> 4 GO:0044409 entry into host 11 9
#> 5 GO:0035891 exit from host cell 7 6
#> 6 GO:0032502 developmental process 3 3
#> 7 GO:0002377 immunoglobulin production 3 3
#> 8 GO:0065008 regulation of biological quality 3 3
#> 9 GO:0030003 intracellular monoatomic cation homeosta... 3 3
#> 10 GO:0050776 regulation of immune response 3 3
#> Expected topGO go.category interest.category
#> 1 3.49 0.16 BP not.classified
#> 2 2.80 0.24 BP not.classified
#> 3 15.38 0.29 BP not.classified
#> 4 7.69 0.30 BP not.classified
#> 5 4.89 0.32 BP not.classified
#> 6 2.10 0.34 BP not.classified
#> 7 2.10 0.34 BP not.classified
#> 8 2.10 0.34 BP not.classified
#> 9 2.10 0.34 BP not.classified
#> 10 2.10 0.34 BP not.classified
#>
#> ==============================================================================
#>
#> interest-category 4 of 4
#> ontology 2 of 3
#>
#> Building most specific GOs .....
#> ( 100 GO terms found. )
#>
#> Build GO DAG topology ..........
#> ( 245 GO terms and 416 relations. )
#>
#> Annotating nodes ...............
#> ( 434 genes annotated to the GO terms. )
#>
#> -- Weight01 Algorithm --
#>
#> the algorithm is scoring 105 nontrivial nodes
#> parameters:
#> test statistic: fisher
#>
#> Level 11: 2 nodes to be scored (0 eliminated genes)
#>
#> Level 10: 6 nodes to be scored (0 eliminated genes)
#>
#> Level 9: 7 nodes to be scored (23 eliminated genes)
#>
#> Level 8: 13 nodes to be scored (90 eliminated genes)
#>
#> Level 7: 12 nodes to be scored (97 eliminated genes)
#>
#> Level 6: 16 nodes to be scored (122 eliminated genes)
#>
#> Level 5: 13 nodes to be scored (182 eliminated genes)
#>
#> Level 4: 15 nodes to be scored (346 eliminated genes)
#>
#> Level 3: 18 nodes to be scored (364 eliminated genes)
#>
#> Level 2: 2 nodes to be scored (413 eliminated genes)
#>
#> Level 1: 1 nodes to be scored (433 eliminated genes)
#> /Users/Jenna/Library/CloudStorage/Box-Box/Genomics/omicshub/projects/pfGO/Routput/GO/hierarchy.plots/tGO.not.classified.CC_weight01_5_all --- no of nodes: 25
#>
#> ==============================================================================
#> GO enrichment results for interest category: not.classified
#> Ontology: CC GO.ID Term Annotated Significant
#> 1 GO:0020003 symbiont-containing vacuole 18 14
#> 2 GO:0009986 cell surface 24 20
#> 3 GO:0020009 microneme 6 6
#> 4 GO:0071944 cell periphery 19 14
#> 5 GO:0020002 host cell plasma membrane 28 22
#> 6 GO:0032991 protein-containing complex 55 35
#> 7 GO:0044228 host cell surface 4 4
#> 8 GO:0031982 vesicle 41 29
#> 9 GO:0020026 merozoite dense granule 3 3
#> 10 GO:0005852 eukaryotic translation initiation factor... 3 3
#> Expected topGO go.category interest.category
#> 1 11.86 0.023 CC not.classified
#> 2 15.82 0.046 CC not.classified
#> 3 3.95 0.080 CC not.classified
#> 4 12.52 0.081 CC not.classified
#> 5 18.45 0.102 CC not.classified
#> 6 36.24 0.130 CC not.classified
#> 7 2.64 0.187 CC not.classified
#> 8 27.02 0.282 CC not.classified
#> 9 1.98 0.285 CC not.classified
#> 10 1.98 0.285 CC not.classified
#>
#> ==============================================================================
#>
#> interest-category 4 of 4
#> ontology 3 of 3
#> Joining with `by = join_by(GO.ID, go.category, interest.category)`
#>
#> ==============================================================================
#> Significant terms from final GO enrichment results table (saved to 'Routput/GO/all.combined.GO.results.tsv':
#> GO.ID Term Annotated Significant
#> 1 GO:0016311 dephosphorylation 3 2
#> 2 GO:0009410 response to xenobiotic stimulus 22 6
#> 3 GO:0005739 mitochondrion 46 13
#> 4 GO:0031966 mitochondrial membrane 3 2
#> 5 GO:0003924 GTPase activity 3 2
#> 6 GO:0016791 phosphatase activity 7 3
#> 7 GO:0003735 structural constituent of ribosome 7 3
#> 8 GO:0006355 regulation of DNA-templated transcriptio... 5 4
#> 9 GO:0020033 antigenic variation 27 8
#> 10 GO:0006913 nucleocytoplasmic transport 3 2
#> 11 GO:0051276 chromosome organization 3 2
#> 12 GO:0020013 modulation by symbiont of host erythrocy... 20 5
#> 13 GO:0020030 infected host cell surface knob 18 5
#> 14 GO:0043565 sequence-specific DNA binding 3 2
#> 15 GO:0008757 S-adenosylmethionine-dependent methyltra... 3 2
#> 16 GO:0016853 isomerase activity 3 2
#> 17 GO:0008094 ATP-dependent activity, acting on DNA 3 2
#> 18 GO:0045454 cell redox homeostasis 3 1
#> 19 GO:0034470 ncRNA processing 3 1
#> 20 GO:0005730 nucleolus 5 2
#> 21 GO:0032993 protein-DNA complex 6 2
#> 22 GO:0019899 enzyme binding 3 1
#> 23 GO:0022804 active transmembrane transporter activit... 3 1
#> 24 GO:0020003 symbiont-containing vacuole 18 14
#> 25 GO:0009986 cell surface 24 20
#> 26 GO:0020009 microneme 6 6
#> 27 GO:0071944 cell periphery 19 14
#> 28 GO:0042393 histone binding 6 6
#> Expected topGO go.category interest.category
#> 1 0.41 0.049 BP A.HS.Sensitive
#> 2 3.00 0.056 BP A.HS.Sensitive
#> 3 7.63 0.068 CC A.HS.Sensitive
#> 4 0.50 0.073 CC A.HS.Sensitive
#> 5 0.48 0.068 MF A.HS.Sensitive
#> 6 1.12 0.084 MF A.HS.Sensitive
#> 7 1.12 0.084 MF A.HS.Sensitive
#> 8 0.65 0.001 BP HS.Neutral
#> 9 3.53 0.011 BP HS.Neutral
#> 10 0.39 0.045 BP HS.Neutral
#> 11 0.39 0.045 BP HS.Neutral
#> 12 2.61 0.097 BP HS.Neutral
#> 13 2.49 0.087 CC HS.Neutral
#> 14 0.51 0.076 MF HS.Neutral
#> 15 0.51 0.076 MF HS.Neutral
#> 16 0.51 0.076 MF HS.Neutral
#> 17 0.51 0.076 MF HS.Neutral
#> 18 0.10 0.099 BP HS.and.CG.phenotype
#> 19 0.10 0.099 BP HS.and.CG.phenotype
#> 20 0.18 0.012 CC HS.and.CG.phenotype
#> 21 0.22 0.069 CC HS.and.CG.phenotype
#> 22 0.06 0.061 MF HS.and.CG.phenotype
#> 23 0.06 0.061 MF HS.and.CG.phenotype
#> 24 11.86 0.023 CC not.classified
#> 25 15.82 0.046 CC not.classified
#> 26 3.95 0.080 CC not.classified
#> 27 12.52 0.081 CC not.classified
#> 28 3.89 0.071 MF not.classified
#>
#> ==============================================================================
#>
#>
#>
#> 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")