pathway_enrichment performs hypergeometric test of enrichment of a set of genes in user-provided genesets of enricher databases
Examples
data(mini_mac)
top_genes <- mini_mac@tools$diff_exprs[["Staurosporine_10"]]$gene
data(genesets)
compute_single_enrichr(genes = top_genes, genesets = genesets, species="human")
#> Term Overlap
#> Adipogenesis Adipogenesis 5/200
#> Interferon Gamma Response Interferon Gamma Response 5/200
#> mTORC1 Signaling mTORC1 Signaling 5/200
#> Angiogenesis Angiogenesis 1/36
#> Apical Surface Apical Surface 1/44
#> Reactive Oxygen Species Pathway Reactive Oxygen Species Pathway 1/49
#> Androgen Response Androgen Response 2/100
#> Pperoxisome Pperoxisome 2/104
#> Bile Acid Metabolism Bile Acid Metabolism 2/112
#> Cholesterol Homeostasis Cholesterol Homeostasis 1/74
#> Mitotic Spindle Mitotic Spindle 3/199
#> Apical Junction Apical Junction 3/200
#> Estrogen Response Early Estrogen Response Early 3/200
#> Estrogen Response Late Estrogen Response Late 3/200
#> Inflammatory Response Inflammatory Response 3/200
#> p53 Pathway p53 Pathway 3/200
#> Xenobiotic Metabolism Xenobiotic Metabolism 3/200
#> Protein Secretion Protein Secretion 1/96
#> Interferon Alpha Response Interferon Alpha Response 1/97
#> Unfolded Protein Response Unfolded Protein Response 1/113
#> IL-2/STAT5 Signaling IL-2/STAT5 Signaling 2/199
#> Complement Complement 2/200
#> E2F Targets E2F Targets 2/200
#> Epithelial Mesenchymal Transition Epithelial Mesenchymal Transition 2/200
#> G2-M Checkpoint G2-M Checkpoint 2/200
#> Hypoxia Hypoxia 2/200
#> KRAS Signaling Up KRAS Signaling Up 2/200
#> TNF-alpha Signaling via NF-kB TNF-alpha Signaling via NF-kB 2/200
#> Spermatogenesis Spermatogenesis 1/135
#> UV Response Dn UV Response Dn 1/144
#> DNA Repair DNA Repair 1/150
#> Fatty Acid Metabolism Fatty Acid Metabolism 1/158
#> UV Response Up UV Response Up 1/158
#> Apoptosis Apoptosis 1/161
#> Glycolysis Glycolysis 1/200
#> heme Metabolism heme Metabolism 1/200
#> P.value Adjusted.P.value
#> Adipogenesis 0.563 0.994
#> Interferon Gamma Response 0.563 0.994
#> mTORC1 Signaling 0.563 0.994
#> Angiogenesis 0.598 0.994
#> Apical Surface 0.672 0.994
#> Reactive Oxygen Species Pathway 0.711 0.994
#> Androgen Response 0.717 0.994
#> Pperoxisome 0.737 0.994
#> Bile Acid Metabolism 0.774 0.994
#> Cholesterol Homeostasis 0.847 0.994
#> Mitotic Spindle 0.878 0.994
#> Apical Junction 0.880 0.994
#> Estrogen Response Early 0.880 0.994
#> Estrogen Response Late 0.880 0.994
#> Inflammatory Response 0.880 0.994
#> p53 Pathway 0.880 0.994
#> Xenobiotic Metabolism 0.880 0.994
#> Protein Secretion 0.913 0.994
#> Interferon Alpha Response 0.915 0.994
#> Unfolded Protein Response 0.943 0.994
#> IL-2/STAT5 Signaling 0.961 0.994
#> Complement 0.962 0.994
#> E2F Targets 0.962 0.994
#> Epithelial Mesenchymal Transition 0.962 0.994
#> G2-M Checkpoint 0.962 0.994
#> Hypoxia 0.962 0.994
#> KRAS Signaling Up 0.962 0.994
#> TNF-alpha Signaling via NF-kB 0.962 0.994
#> Spermatogenesis 0.968 0.994
#> UV Response Dn 0.974 0.994
#> DNA Repair 0.978 0.994
#> Fatty Acid Metabolism 0.982 0.994
#> UV Response Up 0.982 0.994
#> Apoptosis 0.983 0.994
#> Glycolysis 0.994 0.994
#> heme Metabolism 0.994 0.994
#> Genes Combined.Score
#> Adipogenesis ELMOD3;GPAM;ATP1B3;DHCR7;CAT 0.0000
#> Interferon Gamma Response VAMP8;NMI;PTGS2;NAMPT;CIITA 0.0000
#> mTORC1 Signaling XBP1;CTSC;NAMPT;DHCR7;SLC37A4 0.0000
#> Angiogenesis S100A4 0.0548
#> Apical Surface CD160 -0.0384
#> Reactive Oxygen Species Pathway CAT -0.0702
#> Androgen Response ACTN1;CENPN -0.1064
#> Pperoxisome PEX11A;CAT -0.1148
#> Bile Acid Metabolism PEX11A;CAT -0.1243
#> Cholesterol Homeostasis DHCR7 -0.1051
#> Mitotic Spindle SMC4;CDC42EP1;DOCK4 -0.1170
#> Apical Junction ACTN1;CLDN18;NLGN2 -0.1160
#> Estrogen Response Early PEX11A;XBP1;DHCR7 -0.1160
#> Estrogen Response Late XBP1;PLXNB1;DHCR7 -0.1160
#> Inflammatory Response NMI;NAMPT;ROS1 -0.1160
#> p53 Pathway VAMP8;S100A4;EPHX1 -0.1160
#> Xenobiotic Metabolism AHCY;EPHX1;CAT -0.1160
#> Protein Secretion CTSC -0.0838
#> Interferon Alpha Response NMI -0.0826
#> Unfolded Protein Response XBP1 -0.0642
#> IL-2/STAT5 Signaling XBP1;AHCY -0.0536
#> Complement CTSC;DOCK4 -0.0528
#> E2F Targets SMC4;CTCF -0.0528
#> Epithelial Mesenchymal Transition MGP;PDGFRB -0.0528
#> G2-M Checkpoint SMC4;CTCF -0.0528
#> Hypoxia S100A4;SLC37A4 -0.0528
#> KRAS Signaling Up PTGS2;ANXA10 -0.0528
#> TNF-alpha Signaling via NF-kB PTGS2;NAMPT -0.0528
#> Spermatogenesis DMC1 -0.0431
#> UV Response Dn PDGFRB -0.0362
#> DNA Repair EIF1B -0.0321
#> Fatty Acid Metabolism EPHX1 -0.0273
#> UV Response Up EPHX1 -0.0273
#> Apoptosis PDGFRB -0.0257
#> Glycolysis SLC37A4 -0.0112
#> heme Metabolism CAT -0.0112