List all the available biological pathways in KEGG, Reactome and WikiPathways
Source:R/utils.R
listPathways.RdThis function can be used to retrieve a list of valid biological pathways present in KEGG, Reactome and WikiPathways.
Arguments
- organism
The name of the organism under consideration. The different databases have different supported organisms. To see the list of supported organisms for a given database, use the
supportedOrganisms()function- database
The name of the database to use. It must be one of:
KEGG,Reactome, andWikiPathways
Note
This function uses the graphite package to retrieve biological pathways
from KEGG, Reactome and WikiPathways.
References
Sales, G., Calura, E., Cavalieri, D. et al. graphite - a Bioconductor package to convert pathway topology to gene network. BMC Bioinformatics 13, 20 (2012), https://doi.org/10.1186/1471-2105-13-20.
Author
Jacopo Ronchi, jacopo.ronchi@unimib.it
Examples
# list the mouse pathways present in WikiPathways
listPathways("Mus musculus", "WikiPathways")
#> [1] "Statin pathway"
#> [2] "Cholesterol biosynthesis"
#> [3] "Selenium metabolism / selenoproteins"
#> [4] "TGF-beta signaling pathway"
#> [5] "Hedgehog signaling pathway"
#> [6] "Glucuronidation"
#> [7] "EBV LMP1 signaling"
#> [8] "Estrogen signaling"
#> [9] "Transcriptional activation by Nfe2l2 in response to phytochemicals"
#> [10] "Methylation"
#> [11] "EPO receptor signaling"
#> [12] "Amino acid conjugation of benzoic acid"
#> [13] "Type II interferon signaling (IFNG)"
#> [14] "Apoptosis"
#> [15] "Nod-like receptor (NLR) signaling pathway"
#> [16] "Retinol metabolism"
#> [17] "ErbB signaling pathway"
#> [18] "Aflatoxin B1 metabolism"
#> [19] "Mitochondrial gene expression"
#> [20] "Estrogen metabolism"
#> [21] "Polyol pathway"
#> [22] "SIDS susceptibility pathways"
#> [23] "Endochondral ossification"
#> [24] "Selenium micronutrient network"
#> [25] "Folic acid network"
#> [26] "Oxidation by cytochrome P450"
#> [27] "Oxidative damage response"
#> [28] "Dopaminergic neurogenesis"
#> [29] "Regulation of cardiac hypertrophy by miR-208"
#> [30] "MicroRNAs in cardiomyocyte hypertrophy"
#> [31] "Glycolysis and gluconeogenesis"
#> [32] "Iron homeostasis"
#> [33] "Cytoplasmic ribosomal proteins"
#> [34] "Glutathione metabolism"
#> [35] "Apoptosis modulation by HSP70"
#> [36] "Acetylcholine synthesis"
#> [37] "Mechanisms associated with pluripotency"
#> [38] "One-carbon metabolism and related pathways"
#> [39] "Kennedy pathway"
#> [40] "Heme biosynthesis"
#> [41] "GPCRs, class A rhodopsin-like"
#> [42] "Splicing factor NOVA regulated synaptic proteins"
#> [43] "Complement activation, classical pathway"
#> [44] "Ptf1a related regulatory pathway"
#> [45] "Hypertrophy model"
#> [46] "Heart development"
#> [47] "Neural crest differentiation"
#> [48] "Alzheimer's disease"
#> [49] "Serotonin receptor 2 and STAT3 signaling"
#> [50] "SREBF and miR33 in cholesterol and lipid homeostasis"
#> [51] "Serotonin and anxiety-related events"
#> [52] "Serotonin and anxiety"
#> [53] "BDNF pathway"
#> [54] "Purine metabolism"
#> [55] "Chemokine signaling pathway"
#> [56] "PPAR signaling pathway"
#> [57] "Fatty acid oxidation"
#> [58] "G protein signaling pathways"
#> [59] "miRNAs and TFs in iPS Cell Generation"
#> [60] "Osteoblast signaling"
#> [61] "Spinal cord injury"
#> [62] "Mapk cascade"
#> [63] "Primary focal segmental glomerulosclerosis (FSGS)"
#> [64] "Focal adhesion: PI3K-Akt-mTOR signaling pathway"
#> [65] "Gene regulatory network modelling somitogenesis"
#> [66] "White fat cell differentiation"
#> [67] "Notch signaling pathway"
#> [68] "Electron transport chain"
#> [69] "G13 signaling pathway"
#> [70] "Translation factors"
#> [71] "Glycogen metabolism"
#> [72] "Eicosanoid synthesis"
#> [73] "Fatty acid omega-oxidation"
#> [74] "ESC pluripotency pathways"
#> [75] "p38 Mapk signaling pathway"
#> [76] "ApoE and miR-146 in inflammation and atherosclerosis"
#> [77] "Tyrobp causal network in microglia"
#> [78] "Microglia pathogen phagocytosis pathway"
#> [79] "Lung fibrosis"
#> [80] "Parkinson's disease"
#> [81] "EDA signaling in hair follicle development"
#> [82] "Novel Jun-Dmp1 pathway"
#> [83] "BMP signaling pathway in eyelid development"
#> [84] "Hfe effect on hepcidin production"
#> [85] "Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling"
#> [86] "IL-1 signaling pathway"
#> [87] "Prostaglandin synthesis and regulation"
#> [88] "Myometrial relaxation and contraction pathways"
#> [89] "Wnt signaling in kidney disease"
#> [90] "Robo4 and VEGF signaling pathways crosstalk"
#> [91] "ACE inhibitor pathway"
#> [92] "miR-127 in mesendoderm differentiation"
#> [93] "Wnt signaling pathway"
#> [94] "Oxidative stress response"
#> [95] "G1 to S cell cycle control"
#> [96] "Distal convoluted tubule 1 (DCT1) cell"
#> [97] "Ethanol metabolism resulting in production of ROS by CYP2E1"
#> [98] "Nuclear receptors in lipid metabolism and toxicity"
#> [99] "Eicosanoid lipid synthesis map"
#> [100] "TCA cycle"
#> [101] "Sphingolipid metabolism overview"
#> [102] "Glycerolipids and glycerophospholipids"
#> [103] "Cholesterol metabolism with Bloch and Kandutsch-Russell pathways"
#> [104] "Eicosanoid metabolism via cyclooxygenases (COX)"
#> [105] "Eicosanoid metabolism via lipoxygenases (LOX)"
#> [106] "Eicosanoid metabolism via cytochrome P450 monooxygenases"
#> [107] "One-carbon metabolism"
#> [108] "Omega-3 / omega-6 fatty acid synthesis"
#> [109] "Omega-9 fatty acid synthesis"
#> [110] "Oxidative stress and redox pathway"
#> [111] "Circulating monocytes and cardiac macrophages in diastolic dysfunction"
#> [112] "Elongation of (very) long chain fatty acids"
#> [113] "Osteoclast signaling"
#> [114] "Inflammatory response pathway"
#> [115] "Blood clotting cascade"
#> [116] "Lipids measured in liver metastasis from breast cancer"
#> [117] "Sphingolipid metabolism (integrated pathway)"
#> [118] "Regulation of Pgc1a expression by a Gsk3b-Tfeb signaling axis in skeletal muscle"
#> [119] "GDNF/RET signaling axis"
#> [120] "Peroxiredoxin 2 induced ovarian failure"
#> [121] "Mapk signaling pathway"
#> [122] "Deregulation of renin-angiotensin system by SARS-CoV infection"
#> [123] "Hypoxia-dependent self-renewal of myoblasts"
#> [124] "Hypoxia-dependent proliferation of myoblasts"
#> [125] "Hypoxia-dependent differentiation of myoblasts"
#> [126] "Burn wound healing"
#> [127] "Fibrin complement receptor 3 signaling pathway"
#> [128] "Proteasome degradation"
#> [129] "Biogenic amine synthesis"
#> [130] "Regulation of actin cytoskeleton"
#> [131] "Lac-Phe pathway"
#> [132] "Comprehensive IL-17A signaling"
#> [133] "Dravet syndrome: Scn1a-A1783V point mutation model"
#> [134] "Globo series sphingolipid metabolism"
#> [135] "Synthesis and degradation of ketone bodies"
#> [136] "Exercise-induced circadian regulation"
#> [137] "Steroid biosynthesis"
#> [138] "Calcium regulation in cardiac cells"
#> [139] "Signal transduction of S1P receptor"
#> [140] "FAS pathway and stress induction of HSP regulation"
#> [141] "Leptin-insulin signaling overlap"
#> [142] "Integrin-mediated cell adhesion"
#> [143] "miR-1 in cardiac development"
#> [144] "Pentose phosphate pathway"
#> [145] "Insulin signaling"
#> [146] "Amino acid metabolism"
#> [147] "Leptin and adiponectin"
#> [148] "Wnt signaling pathway and pluripotency"
#> [149] "Glutathione and one-carbon metabolism"
#> [150] "Focal adhesion"
#> [151] "Toll-like receptor signaling"
#> [152] "Oxidative phosphorylation"
#> [153] "Arachidonate epoxygenase / epoxide hydrolase"
#> [154] "Metapathway biotransformation"
#> [155] "Fatty acid beta-oxidation"
#> [156] "Fatty acid biosynthesis"
#> [157] "Tryptophan metabolism"
#> [158] "Nucleotide GPCRs"
#> [159] "GPCRs, small ligand"
#> [160] "Monoamine GPCRs"