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 68/594 357/18343
#> GO:0006457 GO:0006457 protein folding 37/594 182/18343
#> GO:0051604 GO:0051604 protein maturation 37/594 277/18343
#> GO:0001666 GO:0001666 response to hypoxia 31/594 315/18343
#> GO:0036293 GO:0036293 response to decreased oxygen levels 31/594 324/18343
#> GO:0070482 GO:0070482 response to oxygen levels 31/594 325/18343
#> pvalue p.adjust qvalue
#> GO:0009408 4.061892e-33 4.687423e-30 4.604903e-30
#> GO:0006457 1.898872e-19 1.095649e-16 1.076360e-16
#> GO:0051604 2.478851e-13 9.535313e-11 9.367447e-11
#> GO:0001666 4.135255e-08 4.772084e-06 4.688073e-06
#> GO:0036293 7.874138e-08 8.086783e-06 7.944418e-06
#> GO:0070482 8.444264e-08 8.086783e-06 7.944418e-06
#> geneID
#> GO:0009408 Hop3/ATFKBP65/HSP18.5/HSP17.6B/ATHSP23.6-MITO/ATHSFA2/ATHS83/ATHSP101/ATMBF1C/DjC53/ATHSP17.4/AT-HSP17.6A/HSP70-8/ATBAG6/HSP17.6A/HSP17.8/HKL/NA/ATFKBP62/CLPB-M/ATERDJ3A/NA/ATHSP70/HSP17.6II/HSP17.6C/CPN10/ATFD1/AtHsp90.5/HSP60/HSC70-5/AtHsp90-6/HSP17.4B/HSP23.5/AT-P5C1/HSP15.7/SES1/Fes1A/AtHsp90.2/HSA32/BIP1/NA/BIP/AR192/Cpn60beta2/DREB2/NA/HSP26.5/AtGolS1/ATHSP22.0/NA/PUB48/HSP21/NA/HSP18.2/HSP70-5/AT-HSFA3/PPI2/HTT1/DREB2/AtLFG4/AtPARK13/AtERF53/CP5/NA/ERF54/BIP3/NA/NA
#> 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:0001666 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/HUP26/NA/NA/AtTZF5/STMP5/ATL92/NA/NIMIN-2/NA/TN9/CYP81F2/NA/HUP32/NA
#> GO:0036293 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/HUP26/NA/NA/AtTZF5/STMP5/ATL92/NA/NIMIN-2/NA/TN9/CYP81F2/NA/HUP32/NA
#> GO:0070482 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/HUP26/NA/NA/AtTZF5/STMP5/ATL92/NA/NIMIN-2/NA/TN9/CYP81F2/NA/HUP32/NA
#> Count
#> GO:0009408 68
#> GO:0006457 37
#> GO:0051604 37
#> GO:0001666 31
#> GO:0036293 31
#> GO:0070482 31