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GO enrichment for Microbiome modified
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Lazzat Aibekova authored and Lazzat Aibekova committed Jun 24, 2019
1 parent 4376604 commit 8f1a66e
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Showing 51 changed files with 129 additions and 93 deletions.
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2 changes: 1 addition & 1 deletion GO_enrichment_Microbiome.R
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Expand Up @@ -30,7 +30,7 @@ samples <- tibble(id = dir(file.path("mondet/kallisto"))) %>% mutate(path = past
contrast = read.csv("contrasts_mite_life_stages.csv", header = F)
gene2GO = readMappings2("GOterm/vdesgoassoc.csv")
t2g = read.csv("IDrna_gene_map.csv", header=T)
for (id in 1:length(contrast$V1))
for (id in 4:length(contrast$V1))
{
print(paste(id, "id"))
first_contrast = toString(contrast$V1[id])
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4 changes: 2 additions & 2 deletions GO_enrichment_loop.R
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Expand Up @@ -38,7 +38,7 @@ gene2GO = readMappings2("GOterm/vdesgoassoc.csv")

#LOOP trhough contrasts
for (id in 1:length(contrast$V1))
{
{ 
print(paste(id, "id"))
first_contrast = toString(contrast$V1[id])
second_contrast = toString(contrast$V2[id])
Expand Down Expand Up @@ -100,7 +100,7 @@ for (id in 1:length(contrast$V1))


#Build sampleOGdata
sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "BP", allGenes = geneList, geneSel = topDiffGenes, nodeSize = 3, annot = annFUN.gene2GO, gene2GO = gene2GO)
sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "BP", allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10, annot = annFUN.gene2GO, gene2GO = gene2GO)

#Fisher's exact test - based on gene counts
resultFisher <- runTest(sampleGOdata, algorithm = "classic", statistic = "fisher")
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_arresting_prelaying_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0009987","cellular process",19,19,19,1,"1","0.060","0.060"
"GO:0006725","cellular aromatic compound metabolic pro...",9,9,9,2,"1","0.093","0.093"
"GO:0046483","heterocycle metabolic process",9,9,9,3,"1","0.093","0.093"
"GO:1901360","organic cyclic compound metabolic proces...",9,9,9,4,"1","0.093","0.093"
"GO:0006807","nitrogen compound metabolic process",13,13,13,5,"1","0.121","0.121"
"GO:0006810","transport",57,11,12.52,170,"0.772","0.020","0.020"
"GO:0051234","establishment of localization",57,11,12.52,171,"0.772","0.020","0.020"
"GO:0018193","peptidyl-amino acid modification",7,4,1.54,2,"0.043","0.031","0.031"
"GO:0006457","protein folding",4,3,0.88,1,"0.034","0.033","0.033"
"GO:0051179","localization",60,12,13.18,163,"0.728","0.046","0.046"
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_arresting_prelaying_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0006807","nitrogen compound metabolic process",6,6,6,1,"1","0.36","0.36"
"GO:0006793","phosphorus metabolic process",3,3,3,2,"1","0.40","0.40"
"GO:0006796","phosphate-containing compound metabolic ...",3,3,3,3,"1","0.40","0.40"
"GO:0042592","homeostatic process",3,3,3,4,"1","0.40","0.40"
"GO:0065008","regulation of biological quality",3,3,3,5,"1","0.40","0.40"
"GO:0031400","negative regulation of protein modificat...",8,1,1.66,258,"0.850","0.0074","0.0074"
"GO:0042325","regulation of phosphorylation",8,1,1.66,259,"0.850","0.0074","0.0074"
"GO:0005975","carbohydrate metabolic process",8,5,1.66,1,"0.011","0.0097","0.0097"
"GO:0006950","response to stress",21,2,4.35,296,"0.958","0.0124","0.0124"
"GO:0050790","regulation of catalytic activity",12,1,2.49,290,"0.943","0.0128","0.0128"
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_emerging_phoretic_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0009987","cellular process",3,3,3,1,"1","0.086","0.086"
"GO:0050789","regulation of biological process",3,3,3,2,"1","0.278","0.278"
"GO:0065007","biological regulation",3,3,3,3,"1","0.278","0.278"
"GO:0008152","metabolic process",7,7,7,4,"1","0.591","0.591"
"GO:0006810","transport",3,3,3,5,"1","0.761","0.761"
"GO:0034470","ncRNA processing",3,3,0.65,1,"0.0095","0.014","0.014"
"GO:0034660","ncRNA metabolic process",3,3,0.65,2,"0.0095","0.014","0.014"
"GO:0034641","cellular nitrogen compound metabolic pro...",51,16,11.01,6,"0.0393","0.018","0.018"
"GO:0006725","cellular aromatic compound metabolic pro...",42,15,9.06,3,"0.0125","0.042","0.042"
"GO:0008152","metabolic process",116,29,25.03,13,"0.1039","0.055","0.055"
Binary file modified GO_enrichment_microbiome_output/contrast_emerging_phoretic_downregulated.png
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_emerging_phoretic_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0008152","metabolic process",4,4,4,1,"1","0.22","0.22"
"GO:0006807","nitrogen compound metabolic process",3,3,3,2,"1","0.72","0.72"
"GO:0043170","macromolecule metabolic process",3,3,3,3,"1","0.72","0.72"
"GO:0044238","primary metabolic process",3,3,3,4,"1","0.72","0.72"
"GO:0071704","organic substance metabolic process",3,3,3,5,"1","0.72","0.72"
"GO:0006974","cellular response to DNA damage stimulus",4,1,0.59,113,"0.475","0.0076","0.0076"
"GO:0006457","protein folding",4,3,0.59,2,"0.011","0.0086","0.0086"
"GO:0006082","organic acid metabolic process",5,3,0.74,4,"0.024","0.0176","0.0176"
"GO:0019752","carboxylic acid metabolic process",5,3,0.74,5,"0.024","0.0176","0.0176"
"GO:0043436","oxoacid metabolic process",5,3,0.74,6,"0.024","0.0176","0.0176"
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_emerging_young_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0016043","cellular component organization",7,7,7,1,"1","0.13","0.13"
"GO:0071840","cellular component organization or bioge...",7,7,7,2,"1","0.13","0.13"
"GO:0006725","cellular aromatic compound metabolic pro...",6,6,6,3,"1","0.14","0.14"
"GO:0034641","cellular nitrogen compound metabolic pro...",6,6,6,4,"1","0.14","0.14"
"GO:0046483","heterocycle metabolic process",6,6,6,5,"1","0.14","0.14"
"GO:0065008","regulation of biological quality",18,9,4.71,6,"0.020","0.003","0.003"
"GO:0007018","microtubule-based movement",3,3,0.78,5,"0.017","0.012","0.012"
"GO:0019439","aromatic compound catabolic process",4,3,1.05,14,"0.056","0.012","0.012"
"GO:0044270","cellular nitrogen compound catabolic pro...",4,3,1.05,15,"0.056","0.012","0.012"
"GO:0046700","heterocycle catabolic process",4,3,1.05,16,"0.056","0.012","0.012"
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_emerging_young_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0006810","transport",13,13,13,1,"1","0.21","0.21"
"GO:0051179","localization",13,13,13,2,"1","0.21","0.21"
"GO:0051234","establishment of localization",13,13,13,3,"1","0.21","0.21"
"GO:0055085","transmembrane transport",9,9,9,4,"1","0.26","0.26"
"GO:0009653","anatomical structure morphogenesis",3,3,3,5,"1","0.52","0.52"
"GO:0032269","negative regulation of cellular protein ...",8,4,2.48,20,"0.2099","0.0068","0.0068"
"GO:0006325","chromatin organization",4,4,1.24,1,"0.0087","0.0074","0.0074"
"GO:0016311","dephosphorylation",7,4,2.17,7,"0.1364","0.0130","0.0130"
"GO:0031400","negative regulation of protein modificat...",7,3,2.17,80,"0.3761","0.0130","0.0130"
"GO:0010563","negative regulation of phosphorus metabo...",6,3,1.86,46,"0.2734","0.0246","0.0246"
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_laying_nonlaying_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0065007","biological regulation",11,11,11,1,"1","0.020","0.020"
"GO:0050789","regulation of biological process",10,10,10,2,"1","0.038","0.038"
"GO:0019222","regulation of metabolic process",5,5,5,3,"1","0.099","0.099"
"GO:0048519","negative regulation of biological proces...",5,5,5,4,"1","0.099","0.099"
"GO:0060255","regulation of macromolecule metabolic pr...",5,5,5,5,"1","0.099","0.099"
"GO:0006091","generation of precursor metabolites and ...",3,3,0.96,1,"0.032","0.0082","0.0082"
"GO:0005975","carbohydrate metabolic process",12,7,3.84,2,"0.049","0.0157","0.0157"
"GO:0006259","DNA metabolic process",6,3,1.92,73,"0.292","0.0243","0.0243"
"GO:0019693","ribose phosphate metabolic process",4,3,1.28,5,"0.098","0.0309","0.0309"
"GO:0006753","nucleoside phosphate metabolic process",6,3,1.92,74,"0.292","0.0379","0.0379"
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_laying_nonlaying_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0044271","cellular nitrogen compound biosynthetic ...",6,6,6,1,"1","0.063","0.063"
"GO:0009058","biosynthetic process",8,8,8,2,"1","0.076","0.076"
"GO:1901576","organic substance biosynthetic process",8,8,8,3,"1","0.076","0.076"
"GO:0009987","cellular process",29,29,29,4,"1","0.084","0.084"
"GO:0050789","regulation of biological process",13,13,13,5,"1","0.111","0.111"
"GO:0098655","cation transmembrane transport",5,4,1.58,2,"0.036","0.032","0.032"
"GO:0098660","inorganic ion transmembrane transport",5,4,1.58,3,"0.036","0.032","0.032"
"GO:0098662","inorganic cation transmembrane transport",5,4,1.58,4,"0.036","0.032","0.032"
"GO:0022613","ribonucleoprotein complex biogenesis",3,3,0.95,1,"0.031","0.035","0.035"
"GO:0055114","oxidation-reduction process",9,5,2.85,20,"0.116","0.055","0.055"
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_laying_postlaying_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0055114","oxidation-reduction process",3,3,3,1,"1","0.12","0.12"
"GO:0005975","carbohydrate metabolic process",4,4,4,2,"1","0.12","0.12"
"GO:0006396","RNA processing",3,3,3,3,"1","0.35","0.35"
"GO:0008152","metabolic process",23,23,23,4,"1","0.39","0.39"
"GO:0009056","catabolic process",3,3,3,5,"1","0.40","0.40"
"GO:0005975","carbohydrate metabolic process",12,6,3.22,4,"0.068","0.019","0.019"
"GO:0000278","mitotic cell cycle",7,4,1.88,5,"0.085","0.019","0.019"
"GO:0009057","macromolecule catabolic process",4,2,1.07,45,"0.292","0.026","0.026"
"GO:0044238","primary metabolic process",112,30,30.01,156,"0.564","0.026","0.026"
"GO:0010256","endomembrane system organization",3,3,0.8,1,"0.018","0.034","0.034"
Binary file modified GO_enrichment_microbiome_output/contrast_laying_postlaying_downregulated.png
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_laying_postlaying_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0080090","regulation of primary metabolic process",3,3,3,1,"1","0.027","0.027"
"GO:0006811","ion transport",5,5,5,2,"1","0.046","0.046"
"GO:0055085","transmembrane transport",7,7,7,3,"1","0.089","0.089"
"GO:0019222","regulation of metabolic process",4,4,4,4,"1","0.111","0.111"
"GO:0006812","cation transport",3,3,3,5,"1","0.176","0.176"
"GO:0000902","cell morphogenesis",5,3,1.38,4,"0.13","0.064","0.064"
"GO:0032989","cellular component morphogenesis",5,3,1.38,5,"0.13","0.064","0.064"
"GO:0055114","oxidation-reduction process",14,5,3.86,54,"0.34","0.074","0.074"
"GO:0009607","response to biotic stimulus",3,2,0.83,7,"0.19","0.081","0.081"
"GO:0009058","biosynthetic process",51,12,14.08,259,"0.82","0.097","0.097"
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6 changes: 6 additions & 0 deletions GO_enrichment_microbiome_output/contrast_phoretic_arresting_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0006974","cellular response to DNA damage stimulus",5,3,1.04,2,"0.062","0.0081","0.0081"
"GO:0006281","DNA repair",4,2,0.83,10,"0.192","0.0216","0.0216"
"GO:0099173","postsynapse organization",4,1,0.83,118,"0.610","0.0318","0.0318"
"GO:0006259","DNA metabolic process",7,3,1.46,6,"0.159","0.0371","0.0371"
"GO:0007155","cell adhesion",6,2,1.25,28,"0.365","0.0557","0.0557"
Binary file added GO_enrichment_microbiome_output/contrast_phoretic_arresting_downregulated.png
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6 changes: 6 additions & 0 deletions GO_enrichment_microbiome_output/contrast_phoretic_arresting_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0032989","cellular component morphogenesis",5,0,0.56,125,"1","0.011","0.011"
"GO:0009792","embryo development ending in birth or eg...",5,0,0.56,126,"1","0.017","0.017"
"GO:0048468","cell development",9,0,1,127,"1","0.026","0.026"
"GO:0000902","cell morphogenesis",4,0,0.44,128,"1","0.028","0.028"
"GO:0000904","cell morphogenesis involved in different...",4,0,0.44,129,"1","0.028","0.028"
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6 changes: 6 additions & 0 deletions GO_enrichment_microbiome_output/contrast_phoretic_phoreticCaged_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0006366","transcription by RNA polymerase II",4,0,0.19,118,"1","0.019","0.019"
"GO:0032259","methylation",3,0,0.14,119,"1","0.027","0.027"
"GO:0005975","carbohydrate metabolic process",6,0,0.28,120,"1","0.038","0.038"
"GO:0006357","regulation of transcription by RNA polym...",3,0,0.14,121,"1","0.052","0.052"
"GO:0045184","establishment of protein localization",10,0,0.47,122,"1","0.060","0.060"
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6 changes: 6 additions & 0 deletions GO_enrichment_microbiome_output/contrast_phoretic_phoreticCaged_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0000904","cell morphogenesis involved in different...",4,0,0.26,168,"1","0.013","0.013"
"GO:0006955","immune response",4,0,0.26,169,"1","0.013","0.013"
"GO:0007409","axonogenesis",4,0,0.26,170,"1","0.013","0.013"
"GO:0048667","cell morphogenesis involved in neuron di...",4,0,0.26,171,"1","0.013","0.013"
"GO:0050776","regulation of immune response",4,0,0.26,172,"1","0.013","0.013"
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_postlaying_emerging_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0051234","establishment of localization",3,3,3,1,"1","0.23","0.23"
"GO:0051179","localization",4,4,4,2,"1","0.43","0.43"
"GO:0034641","cellular nitrogen compound metabolic pro...",5,5,5,3,"1","0.47","0.47"
"GO:0043170","macromolecule metabolic process",7,7,7,4,"1","0.69","0.69"
"GO:0044260","cellular macromolecule metabolic process",7,7,7,5,"1","0.69","0.69"
"GO:0040007","growth",7,0,1.52,240,"1.000","0.065","0.065"
"GO:0007165","signal transduction",27,8,5.86,14,"0.202","0.081","0.081"
"GO:0005975","carbohydrate metabolic process",7,4,1.52,1,"0.041","0.087","0.087"
"GO:0007186","G protein-coupled receptor signaling pat...",6,3,1.3,5,"0.118","0.097","0.097"
"GO:0071705","nitrogen compound transport",15,6,3.26,3,"0.078","0.120","0.120"
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_postlaying_emerging_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0044281","small molecule metabolic process",3,3,3,1,"1","0.17","0.17"
"GO:0009987","cellular process",7,7,7,2,"1","0.20","0.20"
"GO:0006793","phosphorus metabolic process",3,3,3,3,"1","0.64","0.64"
"GO:0006796","phosphate-containing compound metabolic ...",3,3,3,4,"1","0.64","0.64"
"GO:0044237","cellular metabolic process",6,6,6,5,"1","0.64","0.64"
"GO:0044283","small molecule biosynthetic process",6,4,1.04,1,"0.0092","0.0049","0.0049"
"GO:1903047","mitotic cell cycle process",6,2,1.04,61,"0.2805","0.0087","0.0087"
"GO:0017144","drug metabolic process",5,3,0.87,4,"0.0381","0.0122","0.0122"
"GO:1901361","organic cyclic compound catabolic proces...",7,3,1.22,26,"0.1033","0.0222","0.0222"
"GO:0009166","nucleotide catabolic process",4,2,0.7,29,"0.1409","0.0300","0.0300"
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6 changes: 6 additions & 0 deletions GO_enrichment_microbiome_output/contrast_postlaying_nonlaying_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0051716","cellular response to stimulus",42,5,2.85,13,"0.131","0.0036","0.0036"
"GO:0008033","tRNA processing",3,2,0.2,1,"0.012","0.0056","0.0056"
"GO:0007154","cell communication",29,4,1.97,11,"0.116","0.0099","0.0099"
"GO:0048523","negative regulation of cellular process",17,2,1.16,53,"0.324","0.0143","0.0143"
"GO:0048519","negative regulation of biological proces...",21,2,1.43,67,"0.429","0.0168","0.0168"
Binary file added GO_enrichment_microbiome_output/contrast_postlaying_nonlaying_downregulated.png
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6 changes: 6 additions & 0 deletions GO_enrichment_microbiome_output/contrast_postlaying_nonlaying_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0044283","small molecule biosynthetic process",7,0,0.44,172,"1","0.0088","0.0088"
"GO:0009166","nucleotide catabolic process",4,0,0.25,173,"1","0.0155","0.0155"
"GO:0034404","nucleobase-containing small molecule bio...",4,0,0.25,174,"1","0.0155","0.0155"
"GO:0046434","organophosphate catabolic process",4,0,0.25,175,"1","0.0155","0.0155"
"GO:1901292","nucleoside phosphate catabolic process",4,0,0.25,176,"1","0.0155","0.0155"
Binary file added GO_enrichment_microbiome_output/contrast_postlaying_nonlaying_upregulated.png
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_prelaying_laying_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0006464","cellular protein modification process",3,3,3,1,"1","1","1"
"GO:0006793","phosphorus metabolic process",3,3,3,2,"1","1","1"
"GO:0006796","phosphate-containing compound metabolic ...",3,3,3,3,"1","1","1"
"GO:0006807","nitrogen compound metabolic process",3,3,3,4,"1","1","1"
"GO:0008150","biological_process",3,3,3,5,"1","1","1"
"GO:0044238","primary metabolic process",119,24,16.69,1,"0.0034","0.00058","0.00058"
"GO:0006796","phosphate-containing compound metabolic ...",39,8,5.47,33,"0.1512","0.00565","0.00565"
"GO:1901564","organonitrogen compound metabolic proces...",59,13,8.28,9,"0.0355","0.00604","0.00604"
"GO:1901135","carbohydrate derivative metabolic proces...",13,2,1.82,202,"0.5691","0.01133","0.01133"
"GO:0019538","protein metabolic process",48,11,6.73,12,"0.0428","0.01166","0.01166"
Binary file modified GO_enrichment_microbiome_output/contrast_prelaying_laying_downregulated.png
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_prelaying_laying_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0009987","cellular process",9,9,9,1,"1","0.17","0.17"
"GO:0008152","metabolic process",8,8,8,2,"1","0.29","0.29"
"GO:0044237","cellular metabolic process",8,8,8,3,"1","0.29","0.29"
"GO:0065007","biological regulation",4,4,4,4,"1","0.30","0.30"
"GO:0044281","small molecule metabolic process",3,3,3,5,"1","0.32","0.32"
"GO:0046907","intracellular transport",17,5,2.91,36,"0.14","0.0074","0.0074"
"GO:0009725","response to hormone",4,2,0.69,21,"0.14","0.0121","0.0121"
"GO:0014070","response to organic cyclic compound",4,2,0.69,22,"0.14","0.0121","0.0121"
"GO:0032870","cellular response to hormone stimulus",4,2,0.69,23,"0.14","0.0121","0.0121"
"GO:0048545","response to steroid hormone",4,2,0.69,24,"0.14","0.0121","0.0121"
Binary file modified GO_enrichment_microbiome_output/contrast_prelaying_laying_upregulated.png
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_young_males_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0009059","macromolecule biosynthetic process",36,36,36,1,"1","0.039","0.039"
"GO:0034645","cellular macromolecule biosynthetic proc...",35,35,35,2,"1","0.046","0.046"
"GO:0006351","transcription, DNA-templated",26,26,26,3,"1","0.076","0.076"
"GO:0032774","RNA biosynthetic process",26,26,26,4,"1","0.076","0.076"
"GO:0097659","nucleic acid-templated transcription",26,26,26,5,"1","0.076","0.076"
"GO:0030163","protein catabolic process",6,6,3.64,20,"0.0477","0.0071","0.0071"
"GO:0070925","organelle assembly",4,4,2.42,83,"0.1328","0.0116","0.0116"
"GO:0051641","cellular localization",28,23,16.96,1,"0.0096","0.0118","0.0118"
"GO:0006511","ubiquitin-dependent protein catabolic pr...",5,5,3.03,38,"0.0797","0.0164","0.0164"
"GO:0019941","modification-dependent protein catabolic...",5,5,3.03,39,"0.0797","0.0164","0.0164"
Binary file modified GO_enrichment_microbiome_output/contrast_young_males_downregulated.png
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_young_males_upregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0055085","transmembrane transport",9,9,9,1,"1","0.035","0.035"
"GO:0006810","transport",15,15,15,2,"1","0.045","0.045"
"GO:0042592","homeostatic process",4,4,4,3,"1","0.070","0.070"
"GO:0051179","localization",16,16,16,4,"1","0.103","0.103"
"GO:0051234","establishment of localization",16,16,16,5,"1","0.103","0.103"
"GO:0018193","peptidyl-amino acid modification",3,3,1.07,3,"0.044","0.014","0.014"
"GO:0006325","chromatin organization",4,4,1.42,1,"0.015","0.032","0.032"
"GO:0044267","cellular protein metabolic process",36,17,12.82,6,"0.080","0.044","0.044"
"GO:0043085","positive regulation of catalytic activit...",3,3,1.07,4,"0.044","0.061","0.061"
"GO:0051338","regulation of transferase activity",3,3,1.07,5,"0.044","0.061","0.061"
Binary file modified GO_enrichment_microbiome_output/contrast_young_males_upregulated.png
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10 changes: 5 additions & 5 deletions GO_enrichment_microbiome_output/contrast_young_phoretic_downregulated.csv
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"GO.ID","Term","Annotated","Significant","Expected","Rank in classicFisher","classicFisher","classicKS","elimKS"
"GO:0016043","cellular component organization",5,5,5,1,"1","0.012","0.012"
"GO:0071840","cellular component organization or bioge...",5,5,5,2,"1","0.012","0.012"
"GO:0006996","organelle organization",4,4,4,3,"1","0.030","0.030"
"GO:0000902","cell morphogenesis",3,3,3,4,"1","0.077","0.077"
"GO:0007010","cytoskeleton organization",3,3,3,5,"1","0.077","0.077"
"GO:0007018","microtubule-based movement",3,3,1.05,2,"0.042","0.0075","0.0075"
"GO:0006464","cellular protein modification process",24,9,8.44,138,"0.482","0.0108","0.0108"
"GO:0036211","protein modification process",24,9,8.44,139,"0.482","0.0108","0.0108"
"GO:0016310","phosphorylation",16,8,5.63,13,"0.152","0.0235","0.0235"
"GO:0044283","small molecule biosynthetic process",6,5,2.11,1,"0.021","0.0302","0.0302"
Binary file modified GO_enrichment_microbiome_output/contrast_young_phoretic_downregulated.png
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