This function returns the enriched biological processes in a set of genes, as compared to a background set of genes. The GO terms are retreived by the clusterProfiler package and the bioconductor organism databases (for example org.At.tair.db). The frequencies comparisons between GO terms in the genes of interest and the background are performed using Fischer tests, with 0.05 adjusted pvalues threshold. Those significantly enriched GO terms are then simplified with a semantic similarity threshold that can be chosen. It returns a dataframe containing, for each significant GO, their gene count, gene symbols, adjusted pvalue, description, etc.
enrich_go( genes, background, org = org.At.tair.db::org.At.tair.db, sim_cutoff = 0.85, GO_type = "BP", fdr = 0.05, pval = 0.05 )
| genes | gene set of interest. MUST be entrez IDs, that can be obtained from DIANE's
functions |
|---|---|
| background | gene set considered as the "universe" against which perfom
the tests. MUST be entrez IDS that can be obtained from DIANE's
functions |
| org | organism, in the format of bioconductor organisms databases (e.g org.xx.xx.db). Possible values are, for DIANE's recognized organisms : org.Mm.eg.db, org.Hs.eg.db, org.Dm.eg.db, org.Ce.eg.db, org.EcK12.eg.db, org.At.tair.db |
| sim_cutoff | similarity cutoff to use for pooling similar GO terms |
| GO_type | character between BP (Biological Process), CC(Cellular Component) or MF (Molecular Function), depending on the GO subtype to use in the analysis |
| fdr | adjusted pvalues threshold, default id 0.05 |
| pval | pvalues threshold, default id 0.05 |
data.frame with gene significant gene ontologies, and their characteristics as columns
data("abiotic_stresses") genes <- abiotic_stresses$heat_DEGs genes <- get_locus(genes) background <- get_locus(rownames(abiotic_stresses$normalized_counts)) genes <- convert_from_agi(genes) background <- convert_from_agi(background) go <- enrich_go(genes, background) head(go)#> ID Description GeneRatio #> GO:0009408 GO:0009408 response to heat 50/499 #> GO:0006457 GO:0006457 protein folding 38/499 #> GO:0006979 GO:0006979 response to oxidative stress 31/499 #> GO:0009651 GO:0009651 response to salt stress 31/499 #> GO:0071456 GO:0071456 cellular response to hypoxia 25/499 #> GO:0036294 GO:0036294 cellular response to decreased oxygen levels 25/499 #> BgRatio pvalue p.adjust qvalue #> GO:0009408 230/15734 7.272616e-28 8.923500e-25 8.811348e-25 #> GO:0006457 174/15734 1.761225e-21 1.080512e-18 1.066932e-18 #> GO:0006979 417/15734 1.041411e-05 5.555703e-04 5.485878e-04 #> GO:0009651 443/15734 3.378788e-05 1.727405e-03 1.705695e-03 #> GO:0071456 224/15734 4.885258e-08 4.995176e-06 4.932397e-06 #> GO:0036294 227/15734 6.356699e-08 5.571193e-06 5.501173e-06 #> geneID #> GO:0009408 Hop3/ATFKBP65/HSP18.5/HSP17.6B/ATHSFA2/ATHS83/ATHSP101/ATMBF1C/DjC53/ATHSP17.4/AT-HSP17.6A/HSP70T-2/ATBAG6/HSP17.6A/HSP17.8/HKL/ATFKBP62/CLPB-M/ATERDJ3A/ATHSP70/HSP17.6II/HSP17.6C/CPN10/AtHsp90.5/HSP60/HSC70-5/HSP17.4B/AT-P5C1/HSP15.7/SES1/Fes1A/AtHsp90.2/HSA32/BIP1/BIP/AR192/DREB2/AtGolS1/ATHSP22.0/PUB48/HSP21/HSP18.2/Hsp70b/AT-HSFA3/HTT1/DREB2/AtPARK13/AtERF53/ERF54/BIP3 #> GO:0006457 ATFKBP65/HSP18.5/HSP17.6B/NA/ATHS83/ATHSP17.4/AT-HSP17.6A/HSP70T-2/ATBAG6/HSP17.6A/HSP17.8/ATFKBP62/DNAJ/CLPB-M/NA/ATHSP70/HSP17.6II/HSP17.6C/CPN10/AtHsp90.5/HSP60/HSC70-5/AtHsp90-6/HSP17.4B/HSP15.7/SES1/AtHsp90.2/ATCNX1/BIP1/BIP/AR192/Cpn60beta2/CYP40/ATHSP22.0/NA/HSP18.2/Hsp70b/BIP3 #> GO:0006979 HSP18.5/HSP17.6B/ATHSFA2/ATHSP17.4/AT-HSP17.6A/HSP17.6A/HSP17.8/HSP17.6II/HSP17.6C/HSP17.4B/HSP15.7/NA/DREB2/AtGolS1/ATHSP22.0/NA/APX1B/ATWRKY54/AtGolS3/HSP18.2/NA/NA/ANAC092/PRX40/ATFER3/BIP3/PRX9/ATWRKY30/ATFER1/NA/NA #> GO:0009651 HSP18.5/HSP17.6B/ATGRP7/ATHSP17.4/AT-HSP17.6A/HSP17.6A/HSP17.8/HSP17.6II/HSP17.6C/AtHsp90.5/HSP17.4B/AT-P5C1/HSP15.7/Fes1A/AtHsp90.2/ABX45/AtGolS1/ATHSP22.0/HSP18.2/CFM9/ANAC092/AtLtpI-11/5PTASE11/AtERF53/AtLEA3/FAR5/AtRLP30/NA/ERD7/WSD1/ATTSPO #> GO:0071456 ATHSFA2/ATHSP101/ATMBF1C/ATHSP17.4/AT-HSP17.6A/HSP17.6A/HSP17.8/HKL/HSP17.6II/AT-HSFB2B/HSP17.4B/HSP15.7/ETR2/DREB2/NA/MPSR1/ATHSP22.0/NA/STMP5/NA/NA/CYP81F2/NA/NA/NA #> GO:0036294 ATHSFA2/ATHSP101/ATMBF1C/ATHSP17.4/AT-HSP17.6A/HSP17.6A/HSP17.8/HKL/HSP17.6II/AT-HSFB2B/HSP17.4B/HSP15.7/ETR2/DREB2/NA/MPSR1/ATHSP22.0/NA/STMP5/NA/NA/CYP81F2/NA/NA/NA #> Count #> GO:0009408 50 #> GO:0006457 38 #> GO:0006979 31 #> GO:0009651 31 #> GO:0071456 25 #> GO:0036294 25