Downloads a Gene Matrix Transposed (GMT) file from a specified URL, reads it into R as a list, and removes the temporary file afterward.
getGMT(url, name = NULL, cache_dir = NULL, redownload = FALSE)A named list where each element is a character vector of gene names for a given gene set.
url <- paste0(
"https://maayanlab.cloud/Enrichr/geneSetLibrary",
"?mode=text&libraryName=KEGG_2019_Human"
)
gmt_list <- getGMT(url)
#> Auto-detected name: KEGG_2019_Human
#> Downloading KEGG_2019_Human from Enrichr...
# list available gene sets
names(gmt_list)
#> [1] "ABC transporters"
#> [2] "AGE-RAGE signaling pathway in diabetic complications"
#> [3] "AMPK signaling pathway"
#> [4] "Acute myeloid leukemia"
#> [5] "Adherens junction"
#> [6] "Adipocytokine signaling pathway"
#> [7] "Adrenergic signaling in cardiomyocytes"
#> [8] "African trypanosomiasis"
#> [9] "Alanine, aspartate and glutamate metabolism"
#> [10] "Alcoholism"
#> [11] "Aldosterone synthesis and secretion"
#> [12] "Aldosterone-regulated sodium reabsorption"
#> [13] "Allograft rejection"
#> [14] "Alzheimer disease"
#> [15] "Amino sugar and nucleotide sugar metabolism"
#> [16] "Aminoacyl-tRNA biosynthesis"
#> [17] "Amoebiasis"
#> [18] "Amphetamine addiction"
#> [19] "Amyotrophic lateral sclerosis (ALS)"
#> [20] "Antigen processing and presentation"
#> [21] "Apelin signaling pathway"
#> [22] "Apoptosis"
#> [23] "Arachidonic acid metabolism"
#> [24] "Arginine and proline metabolism"
#> [25] "Arginine biosynthesis"
#> [26] "Arrhythmogenic right ventricular cardiomyopathy (ARVC)"
#> [27] "Ascorbate and aldarate metabolism"
#> [28] "Asthma"
#> [29] "Autoimmune thyroid disease"
#> [30] "Autophagy"
#> [31] "Axon guidance"
#> [32] "B cell receptor signaling pathway"
#> [33] "Bacterial invasion of epithelial cells"
#> [34] "Basal cell carcinoma"
#> [35] "Basal transcription factors"
#> [36] "Base excision repair"
#> [37] "Bile secretion"
#> [38] "Biosynthesis of unsaturated fatty acids"
#> [39] "Bladder cancer"
#> [40] "Breast cancer"
#> [41] "Butanoate metabolism"
#> [42] "C-type lectin receptor signaling pathway"
#> [43] "Caffeine metabolism"
#> [44] "Calcium signaling pathway"
#> [45] "Carbohydrate digestion and absorption"
#> [46] "Cardiac muscle contraction"
#> [47] "Cell adhesion molecules (CAMs)"
#> [48] "Cell cycle"
#> [49] "Cellular senescence"
#> [50] "Central carbon metabolism in cancer"
#> [51] "Chagas disease (American trypanosomiasis)"
#> [52] "Chemical carcinogenesis"
#> [53] "Chemokine signaling pathway"
#> [54] "Cholesterol metabolism"
#> [55] "Choline metabolism in cancer"
#> [56] "Cholinergic synapse"
#> [57] "Chronic myeloid leukemia"
#> [58] "Circadian entrainment"
#> [59] "Circadian rhythm"
#> [60] "Citrate cycle (TCA cycle)"
#> [61] "Cocaine addiction"
#> [62] "Collecting duct acid secretion"
#> [63] "Colorectal cancer"
#> [64] "Complement and coagulation cascades"
#> [65] "Cortisol synthesis and secretion"
#> [66] "Cushing syndrome"
#> [67] "Cysteine and methionine metabolism"
#> [68] "Cytokine-cytokine receptor interaction"
#> [69] "Cytosolic DNA-sensing pathway"
#> [70] "D-Glutamine and D-glutamate metabolism"
#> [71] "DNA replication"
#> [72] "Dilated cardiomyopathy (DCM)"
#> [73] "Dopaminergic synapse"
#> [74] "Drug metabolism"
#> [75] "ECM-receptor interaction"
#> [76] "Endocrine and other factor-regulated calcium reabsorption"
#> [77] "Endocytosis"
#> [78] "Endometrial cancer"
#> [79] "Epithelial cell signaling in Helicobacter pylori infection"
#> [80] "Epstein-Barr virus infection"
#> [81] "ErbB signaling pathway"
#> [82] "Estrogen signaling pathway"
#> [83] "Ether lipid metabolism"
#> [84] "Fanconi anemia pathway"
#> [85] "Fat digestion and absorption"
#> [86] "Fatty acid biosynthesis"
#> [87] "Fatty acid degradation"
#> [88] "Fatty acid elongation"
#> [89] "Fc epsilon RI signaling pathway"
#> [90] "Fc gamma R-mediated phagocytosis"
#> [91] "Ferroptosis"
#> [92] "Fluid shear stress and atherosclerosis"
#> [93] "Focal adhesion"
#> [94] "Folate biosynthesis"
#> [95] "FoxO signaling pathway"
#> [96] "Fructose and mannose metabolism"
#> [97] "GABAergic synapse"
#> [98] "Galactose metabolism"
#> [99] "Gap junction"
#> [100] "Gastric acid secretion"
#> [101] "Gastric cancer"
#> [102] "Glioma"
#> [103] "Glucagon signaling pathway"
#> [104] "Glutamatergic synapse"
#> [105] "Glutathione metabolism"
#> [106] "Glycerolipid metabolism"
#> [107] "Glycerophospholipid metabolism"
#> [108] "Glycine, serine and threonine metabolism"
#> [109] "Glycolysis / Gluconeogenesis"
#> [110] "Glycosaminoglycan biosynthesis"
#> [111] "Glycosaminoglycan degradation"
#> [112] "Glycosphingolipid biosynthesis"
#> [113] "Glycosylphosphatidylinositol (GPI)-anchor biosynthesis"
#> [114] "Glyoxylate and dicarboxylate metabolism"
#> [115] "GnRH signaling pathway"
#> [116] "Graft-versus-host disease"
#> [117] "HIF-1 signaling pathway"
#> [118] "Hedgehog signaling pathway"
#> [119] "Hematopoietic cell lineage"
#> [120] "Hepatitis B"
#> [121] "Hepatitis C"
#> [122] "Hepatocellular carcinoma"
#> [123] "Herpes simplex virus 1 infection"
#> [124] "Hippo signaling pathway"
#> [125] "Histidine metabolism"
#> [126] "Homologous recombination"
#> [127] "Human T-cell leukemia virus 1 infection"
#> [128] "Human cytomegalovirus infection"
#> [129] "Human immunodeficiency virus 1 infection"
#> [130] "Human papillomavirus infection"
#> [131] "Huntington disease"
#> [132] "Hypertrophic cardiomyopathy (HCM)"
#> [133] "IL-17 signaling pathway"
#> [134] "Inflammatory bowel disease (IBD)"
#> [135] "Inflammatory mediator regulation of TRP channels"
#> [136] "Influenza A"
#> [137] "Inositol phosphate metabolism"
#> [138] "Insulin resistance"
#> [139] "Insulin secretion"
#> [140] "Insulin signaling pathway"
#> [141] "Intestinal immune network for IgA production"
#> [142] "JAK-STAT signaling pathway"
#> [143] "Kaposi sarcoma-associated herpesvirus infection"
#> [144] "Legionellosis"
#> [145] "Leishmaniasis"
#> [146] "Leukocyte transendothelial migration"
#> [147] "Linoleic acid metabolism"
#> [148] "Long-term depression"
#> [149] "Long-term potentiation"
#> [150] "Longevity regulating pathway"
#> [151] "Lysine degradation"
#> [152] "Lysosome"
#> [153] "MAPK signaling pathway"
#> [154] "Malaria"
#> [155] "Mannose type O-glycan biosynthesis"
#> [156] "Maturity onset diabetes of the young"
#> [157] "Measles"
#> [158] "Melanogenesis"
#> [159] "Melanoma"
#> [160] "Metabolism of xenobiotics by cytochrome P450"
#> [161] "MicroRNAs in cancer"
#> [162] "Mineral absorption"
#> [163] "Mismatch repair"
#> [164] "Mitophagy"
#> [165] "Morphine addiction"
#> [166] "Mucin type O-glycan biosynthesis"
#> [167] "N-Glycan biosynthesis"
#> [168] "NF-kappa B signaling pathway"
#> [169] "NOD-like receptor signaling pathway"
#> [170] "Natural killer cell mediated cytotoxicity"
#> [171] "Necroptosis"
#> [172] "Neomycin, kanamycin and gentamicin biosynthesis"
#> [173] "Neuroactive ligand-receptor interaction"
#> [174] "Neurotrophin signaling pathway"
#> [175] "Nicotinate and nicotinamide metabolism"
#> [176] "Nicotine addiction"
#> [177] "Nitrogen metabolism"
#> [178] "Non-alcoholic fatty liver disease (NAFLD)"
#> [179] "Non-homologous end-joining"
#> [180] "Non-small cell lung cancer"
#> [181] "Notch signaling pathway"
#> [182] "Nucleotide excision repair"
#> [183] "Olfactory transduction"
#> [184] "One carbon pool by folate"
#> [185] "Oocyte meiosis"
#> [186] "Osteoclast differentiation"
#> [187] "Other glycan degradation"
#> [188] "Other types of O-glycan biosynthesis"
#> [189] "Ovarian steroidogenesis"
#> [190] "Oxidative phosphorylation"
#> [191] "Oxytocin signaling pathway"
#> [192] "PI3K-Akt signaling pathway"
#> [193] "PPAR signaling pathway"
#> [194] "Pancreatic cancer"
#> [195] "Pancreatic secretion"
#> [196] "Pantothenate and CoA biosynthesis"
#> [197] "Parathyroid hormone synthesis, secretion and action"
#> [198] "Parkinson disease"
#> [199] "Pathogenic Escherichia coli infection"
#> [200] "Pathways in cancer"
#> [201] "Pentose and glucuronate interconversions"
#> [202] "Pentose phosphate pathway"
#> [203] "Peroxisome"
#> [204] "Pertussis"
#> [205] "Phagosome"
#> [206] "Phenylalanine metabolism"
#> [207] "Phenylalanine, tyrosine and tryptophan biosynthesis"
#> [208] "Phosphatidylinositol signaling system"
#> [209] "Phospholipase D signaling pathway"
#> [210] "Phosphonate and phosphinate metabolism"
#> [211] "Phototransduction"
#> [212] "Platelet activation"
#> [213] "Porphyrin and chlorophyll metabolism"
#> [214] "Primary bile acid biosynthesis"
#> [215] "Primary immunodeficiency"
#> [216] "Prion diseases"
#> [217] "Progesterone-mediated oocyte maturation"
#> [218] "Prolactin signaling pathway"
#> [219] "Propanoate metabolism"
#> [220] "Prostate cancer"
#> [221] "Proteasome"
#> [222] "Protein digestion and absorption"
#> [223] "Protein export"
#> [224] "Protein processing in endoplasmic reticulum"
#> [225] "Proteoglycans in cancer"
#> [226] "Proximal tubule bicarbonate reclamation"
#> [227] "Purine metabolism"
#> [228] "Pyrimidine metabolism"
#> [229] "Pyruvate metabolism"
#> [230] "RIG-I-like receptor signaling pathway"
#> [231] "RNA degradation"
#> [232] "RNA polymerase"
#> [233] "RNA transport"
#> [234] "Rap1 signaling pathway"
#> [235] "Ras signaling pathway"
#> [236] "Regulation of actin cytoskeleton"
#> [237] "Regulation of lipolysis in adipocytes"
#> [238] "Relaxin signaling pathway"
#> [239] "Renal cell carcinoma"
#> [240] "Renin secretion"
#> [241] "Renin-angiotensin system"
#> [242] "Retinol metabolism"
#> [243] "Retrograde endocannabinoid signaling"
#> [244] "Rheumatoid arthritis"
#> [245] "Riboflavin metabolism"
#> [246] "Ribosome"
#> [247] "Ribosome biogenesis in eukaryotes"
#> [248] "SNARE interactions in vesicular transport"
#> [249] "Salivary secretion"
#> [250] "Salmonella infection"
#> [251] "Selenocompound metabolism"
#> [252] "Serotonergic synapse"
#> [253] "Shigellosis"
#> [254] "Signaling pathways regulating pluripotency of stem cells"
#> [255] "Small cell lung cancer"
#> [256] "Sphingolipid metabolism"
#> [257] "Sphingolipid signaling pathway"
#> [258] "Spliceosome"
#> [259] "Staphylococcus aureus infection"
#> [260] "Starch and sucrose metabolism"
#> [261] "Steroid biosynthesis"
#> [262] "Steroid hormone biosynthesis"
#> [263] "Sulfur metabolism"
#> [264] "Sulfur relay system"
#> [265] "Synaptic vesicle cycle"
#> [266] "Synthesis and degradation of ketone bodies"
#> [267] "Systemic lupus erythematosus"
#> [268] "T cell receptor signaling pathway"
#> [269] "TGF-beta signaling pathway"
#> [270] "TNF signaling pathway"
#> [271] "Taste transduction"
#> [272] "Taurine and hypotaurine metabolism"
#> [273] "Terpenoid backbone biosynthesis"
#> [274] "Th1 and Th2 cell differentiation"
#> [275] "Th17 cell differentiation"
#> [276] "Thermogenesis"
#> [277] "Thiamine metabolism"
#> [278] "Thyroid cancer"
#> [279] "Thyroid hormone signaling pathway"
#> [280] "Thyroid hormone synthesis"
#> [281] "Tight junction"
#> [282] "Toll-like receptor signaling pathway"
#> [283] "Toxoplasmosis"
#> [284] "Transcriptional misregulation in cancer"
#> [285] "Tryptophan metabolism"
#> [286] "Tuberculosis"
#> [287] "Type I diabetes mellitus"
#> [288] "Type II diabetes mellitus"
#> [289] "Tyrosine metabolism"
#> [290] "Ubiquinone and other terpenoid-quinone biosynthesis"
#> [291] "Ubiquitin mediated proteolysis"
#> [292] "VEGF signaling pathway"
#> [293] "Valine, leucine and isoleucine degradation"
#> [294] "Vascular smooth muscle contraction"
#> [295] "Vasopressin-regulated water reabsorption"
#> [296] "Vibrio cholerae infection"
#> [297] "Viral carcinogenesis"
#> [298] "Viral myocarditis"
#> [299] "Vitamin B6 metabolism"
#> [300] "Vitamin digestion and absorption"
#> [301] "Wnt signaling pathway"
#> [302] "alpha-Linolenic acid metabolism"
#> [303] "beta-Alanine metabolism"
#> [304] "cAMP signaling pathway"
#> [305] "cGMP-PKG signaling pathway"
#> [306] "mRNA surveillance pathway"
#> [307] "mTOR signaling pathway"
#> [308] "p53 signaling pathway"
# inspect the first few genes in the first gene set
head(gmt_list[[1]])
#> [1] "ABCA1" "ABCA10" "ABCA12" "ABCA13" "ABCA2" "ABCA3"