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
)gene set of interest. MUST be entrez IDs, that can be obtained from DIANE's
functions convert_from_X(gene_IDs) depending on your organism.
If your gene IDs are splicing aware, remove this information before with
get_locus(gene_IDs).
gene set considered as the "universe" against which perfom
the tests. MUST be entrez IDS that can be obtained from DIANE's
functions convert_from_X(gene_IDs) depending on your organism.
If your gene IDs are splicing aware, remove this information before with
get_locus(gene_IDs).
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
similarity cutoff to use for pooling similar GO terms
character between BP (Biological Process), CC(Cellular Component) or MF (Molecular Function), depending on the GO subtype to use in the analysis
adjusted pvalues threshold, default id 0.05
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 BgRatio
#> GO:0009408 GO:0009408 response to heat 53/452 273/14432
#> GO:0006457 GO:0006457 protein folding 37/452 184/14432
#> GO:0051604 GO:0051604 protein maturation 37/452 301/14432
#> GO:0009651 GO:0009651 response to salt stress 34/452 460/14432
#> GO:0006979 GO:0006979 response to oxidative stress 30/452 411/14432
#> GO:0009617 GO:0009617 response to bacterium 29/452 500/14432
#> RichFactor FoldEnrichment zScore pvalue p.adjust
#> GO:0009408 0.19413919 6.198710 15.592812 2.651355e-27 3.072920e-24
#> GO:0006457 0.20108696 6.420546 13.305735 7.164868e-20 4.152041e-17
#> GO:0051604 0.12292359 3.924852 9.220715 9.754511e-13 3.768493e-10
#> GO:0009651 0.07391304 2.359985 5.330249 3.220788e-06 1.777568e-04
#> GO:0006979 0.07299270 2.330599 4.920876 1.569792e-05 7.277556e-04
#> GO:0009617 0.05800000 1.851894 3.486002 1.088333e-03 3.709937e-02
#> qvalue
#> GO:0009408 2.994636e-24
#> GO:0006457 4.046265e-17
#> GO:0051604 3.672488e-10
#> GO:0009651 1.732283e-04
#> GO:0006979 7.092155e-04
#> GO:0009617 3.615423e-02
#> geneID
#> GO:0009408 Hop3/ATFKBP65/HSP18.5/HSP17.6B/ATHSFA2/ATHS83/ATHSP101/ATMBF1C/DjC53/ATHSP17.4/AT-HSP17.6A/HSP70-8/ATBAG6/HSP17.6A/HSP17.8/HKL/ATFKBP62/CLPB-M/ATERDJ3A/ATHSP70/HSP17.6II/HSP17.6C/CPN10/AtHsp90.5/HSP60/HSC70-5/AtHsp90-6/HSP17.4B/AT-P5C1/HSP15.7/SES1/Fes1A/AtHsp90.2/HSA32/BIP1/BIP/AR192/PAP3/DREB2/HSP26.5/AtGolS1/ATHSP22.0/PUB48/HSP21/HSP18.2/HSP70-5/AT-HSFA3/HTT1/DREB2/AtPARK13/AtERF53/ERF54/BIP3
#> GO:0006457 ATFKBP65/HSP18.5/HSP17.6B/NA/ATHS83/ATHSP17.4/AT-HSP17.6A/HSP70-8/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/HSP18.2/HSP70-5/BIP3
#> GO:0051604 ATFKBP65/HSP18.5/HSP17.6B/NA/ATHS83/ATHSP17.4/AT-HSP17.6A/HSP70-8/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/HSP18.2/HSP70-5/BIP3
#> 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/ATKEA1/AtGolS1/ATHSP22.0/ATEGY3/HSP18.2/CFM9/ANAC092/AtLtpI-11/5PTASE11/AtERF53/AtLEA3/FAR5/STMP4/AtRLP30/NA/ERD7/WSD1/ATTSPO
#> GO:0006979 HSP18.5/HSP17.6B/ATHSFA2/ATHSP17.4/AT-HSP17.6A/HSP17.6A/HSP17.8/HSP17.6II/HSP17.6C/HSP17.4B/HSP15.7/DREB2/AtGolS1/ATHSP22.0/HUP26/APX1B/ATWRKY54/AtGolS3/HSP18.2/NA/NA/ANAC092/PRX40/ATFER3/BIP3/PER9/ATWRKY30/ATFER1/NA/NA
#> GO:0009617 ATHS83/ATHSP70/AtHsp90.2/LecRK-I.4/ATWRKY54/LecRK-V.8/SAI-LLP1/CRK21/PCC1/SIB1/ESP/STMP5/LecRK-V.9/ATWRKY38/AtRLP30/AIG1/AtBG3/CYP81F2/AtGH3.12/ATFER1/AtS40-2/AtPP2-B13/VLG/CML46/CRK13/CRK31/LecRK-I.10/LecRK-V.6/CYP82G1
#> Count
#> GO:0009408 53
#> GO:0006457 37
#> GO:0051604 37
#> GO:0009651 34
#> GO:0006979 30
#> GO:0009617 29