Genes_by_pathway_kegg

A few numbers from library(KEGGREST) pathways.list <- keggList("pathway", "hsa") # Pull all genes for each pathway pathway.codes <- sub("path:", "", names(pathways.list)) Genes_by_pathway.kegg <- sapply(pathway.codes,function(pwid){ pw <- keggGet(pwid) if (is.null(pw[[1]]$GENE)) return(NA) pw2 <- pw[[1]]$GENE[c(FALSE,TRUE)] # may need to modify this to c(FALSE, TRUE) for other organisms pw2 <- unlist(lapply(strsplit(pw2, split = ";", fixed = T), function(x)x[1])) return(pw2) })

Usage

data(Genes_by_pathway_kegg)

Format

a list.

Examples

data(Genes_by_pathway_kegg)
str(Genes_by_pathway_kegg)
#> List of 345
#>  $ hsa00010: chr [1:67] "HK3" "HK1" "HK2" "HKDC1" ...
#>  $ hsa00020: chr [1:30] "CS" "ACLY" "ACO2" "ACO1" ...
#>  $ hsa00030: chr [1:30] "GPI" "G6PD" "PGLS" "H6PD" ...
#>  $ hsa00040: chr [1:34] "GUSB" "KL" "UGT2A1" "UGT2A3" ...
#>  $ hsa00051: chr [1:33] "MPI" "PMM2" "PMM1" "GMPPB" ...
#>  $ hsa00052: chr [1:31] "GALM" "GALK1" "GALT" "GALE" ...
#>  $ hsa00053: chr [1:30] "UGDH" "UGT2A1" "UGT2A3" "UGT2B17" ...
#>  $ hsa00061: chr [1:18] "ACACA" "ACACB" "ACSF3" "MCAT" ...
#>  $ hsa00062: chr [1:27] "ACAA2" "HADHB" "HADH" "HADHA" ...
#>  $ hsa00071: chr [1:43] "ACAT2" "ACAT1" "ACAA1" "ACAA2" ...
#>  $ hsa00072: chr [1:10] "HMGCS1" "HMGCS2" "HMGCL" "HMGCLL1" ...
#>  $ hsa00100: chr [1:20] "FDFT1" "SQLE" "LSS" "CYP51A1" ...
#>  $ hsa00120: chr [1:17] "CYP46A1" "CYP39A1" "HSD3B7" "CH25H" ...
#>  $ hsa00130: chr [1:11] "TAT" "COQ2" "COQ6" "COQ3" ...
#>  $ hsa00140: chr [1:61] "CYP11A1" "CYP17A1" "STS" "SULT2B1" ...
#>  $ hsa00190: chr [1:134] "ND1" "ND2" "ND3" "ND4" ...
#>  $ hsa00220: chr [1:22] "OTC" "ASS1" "ASL" "ARG2" ...
#>  $ hsa00230: chr [1:130] "NUDT9" "ADPRM" "NUDT5" "PGM1" ...
#>  $ hsa00232: chr [1:6] "CYP1A2" "NAT2" "NAT1" "CYP2A6" ...
#>  $ hsa00240: chr [1:56] "CAD" "DHODH" "UMPS" "CMPK1" ...
#>  $ hsa00250: chr [1:37] "GOT1" "GOT1L1" "GOT2" "IL4I1" ...
#>  $ hsa00260: chr [1:40] "SHMT2" "SHMT1" "AGXT" "GRHPR" ...
#>  $ hsa00270: chr [1:50] "CTH" "KYAT3" "KYAT1" "CBS" ...
#>  $ hsa00280: chr [1:48] "BCAT2" "BCAT1" "IL4I1" "BCKDHA" ...
#>  $ hsa00290: chr [1:4] "SDS" "SDSL" "BCAT2" "BCAT1"
#>  $ hsa00310: chr [1:63] "AASS" "ALDH7A1" "AADAT" "DHTKD1" ...
#>  $ hsa00330: chr [1:51] "GATM" "GAMT" "CKM" "CKMT1A" ...
#>  $ hsa00340: chr [1:22] "HAL" "UROC1" "AMDHD1" "FTCD" ...
#>  $ hsa00350: chr [1:36] "GOT1" "GOT1L1" "GOT2" "TAT" ...
#>  $ hsa00360: chr [1:17] "PAH" "DDC" "AOC3" "AOC2" ...
#>  $ hsa00380: chr [1:42] "TDO2" "IDO1" "IDO2" "AFMID" ...
#>  $ hsa00400: chr [1:6] "GOT1" "GOT1L1" "GOT2" "TAT" ...
#>  $ hsa00410: chr [1:31] "GADL1" "CSAD" "GAD1" "GAD2" ...
#>  $ hsa00430: chr [1:11] "CDO1" "GAD1" "GAD2" "GADL1" ...
#>  $ hsa00440: chr [1:6] "PCYT2" "SELENOI" "CEPT1" "PCYT1B" ...
#>  $ hsa00450: chr [1:17] "KYAT3" "KYAT1" "MTR" "CTH" ...
#>  $ hsa00471: chr [1:5] "GLS2" "GLS" "GLUD2" "GLUD1" ...
#>  $ hsa00472: chr "DAO"
#>  $ hsa00480: chr [1:58] "GGT7" "GGT6" "GGT1" "GGT5" ...
#>  $ hsa00500: chr [1:36] "MGAM" "MGAM2" "GAA" "GANC" ...
#>  $ hsa00510: chr [1:50] "SRD5A3" "DOLK" "DPAGT1" "ALG5" ...
#>  $ hsa00511: chr [1:18] "NEU1" "NEU3" "NEU4" "NEU2" ...
#>  $ hsa00512: chr [1:36] "GALNTL6" "GALNT5" "GALNT17" "GALNT11" ...
#>  $ hsa00513: chr [1:39] "ALG13" "ALG14" "ALG1" "ALG2" ...
#>  $ hsa00514: chr [1:47] "OGT" "EOGT" "POFUT1" "POFUT2" ...
#>  $ hsa00515: chr [1:23] "POMT1" "POMT2" "POMGNT1" "B4GALT1" ...
#>  $ hsa00520: chr [1:48] "CHIA" "CHIT1" "HEXA" "HEXB" ...
#>  $ hsa00524: chr [1:5] "HK3" "HK1" "HK2" "HKDC1" ...
#>  $ hsa00531: chr [1:19] "HYAL2" "HYAL1" "SPAM1" "HYAL4" ...
#>  $ hsa00532: chr [1:20] "XYLT1" "XYLT2" "B4GALT7" "B3GALT6" ...
#>  $ hsa00533: chr [1:14] "FUT8" "B4GALT1" "B4GALT2" "B4GALT3" ...
#>  $ hsa00534: chr [1:24] "XYLT1" "XYLT2" "B4GALT7" "B3GALT6" ...
#>  $ hsa00561: chr [1:61] "GLYCTK" "ALDH2" "ALDH3A2" "ALDH1B1" ...
#>  $ hsa00562: chr [1:73] "PIK3C3" "MTM1" "MTMR1" "MTMR2" ...
#>  $ hsa00563: chr [1:26] "PIGA" "PIGC" "PIGH" "PIGP" ...
#>  $ hsa00564: chr [1:98] "GPD1L" "GPD1" "GPD2" "GPAM" ...
#>  $ hsa00565: chr [1:49] "AGPS" "PLPP1" "PLPP3" "PLPP2" ...
#>  $ hsa00590: chr [1:61] "PLA2G10" "PLA2G2D" "PLA2G2E" "PLA2G3" ...
#>  $ hsa00591: chr [1:29] "PLA2G10" "PLA2G2D" "PLA2G2E" "PLA2G3" ...
#>  $ hsa00592: chr [1:25] "PLA2G10" "PLA2G2D" "PLA2G2E" "PLA2G3" ...
#>  $ hsa00600: chr [1:49] "SPTLC1" "SPTLC2" "SPTLC3" "KDSR" ...
#>  $ hsa00601: chr [1:27] "B3GNT5" "B3GALT1" "B3GALT2" "B3GALT5" ...
#>  $ hsa00603: chr [1:15] "A3GALT2" "B3GALNT1" "GBGT1" "A4GALT" ...
#>  $ hsa00604: chr [1:15] "B4GALNT1" "B3GALT4" "ST3GAL2" "ST3GAL1" ...
#>  $ hsa00620: chr [1:47] "ACSS1" "ACSS2" "PDHA2" "PDHA1" ...
#>  $ hsa00630: chr [1:30] "ACSS1" "ACSS2" "MDH1" "MDH2" ...
#>  $ hsa00640: chr [1:34] "ACSS1" "ACSS2" "ACSS3" "BCKDHA" ...
#>  $ hsa00650: chr [1:28] "ACAT2" "ACAT1" "HADH" "HADHA" ...
#>  $ hsa00670: chr [1:20] "DHFR" "DHFR2" "MTHFD1L" "MTHFD1" ...
#>  $ hsa00730: chr [1:16] "NFS1" "NTPCR" "ALPL" "ALPI" ...
#>  $ hsa00740: chr [1:8] "RFK" "ACP5" "ACP1" "ACP2" ...
#>  $ hsa00750: chr [1:6] "PNPO" "PDXK" "PDXP" "PHOSPHO2" ...
#>  $ hsa00760: chr [1:35] "ASPDH" "QPRT" "NAPRT" "PNP" ...
#>  $ hsa00770: chr [1:21] "PANK1" "PANK3" "PANK2" "PPCS" ...
#>  $ hsa00780: chr [1:3] "OXSM" "HLCS" "BTD"
#>  $ hsa00785: chr [1:4] "LIPT2" "LIAS" "LIPT1" "ACSM1"
#>  $ hsa00790: chr [1:26] "GCH1" "ALPL" "ALPI" "ALPP" ...
#>  $ hsa00830: chr [1:68] "BCO1" "ADH1A" "ADH1B" "ADH1C" ...
#>  $ hsa00860: chr [1:43] "ALAS1" "ALAS2" "EARS2" "EPRS1" ...
#>  $ hsa00900: chr [1:22] "ACAT2" "ACAT1" "HMGCS1" "HMGCS2" ...
#>  $ hsa00910: chr [1:17] "GLUD2" "GLUD1" "GLUL" "CPS1" ...
#>  $ hsa00920: chr [1:10] "PAPSS2" "PAPSS1" "BPNT1" "BPNT2" ...
#>  $ hsa00970: chr [1:66] "TRNA" "TRNR" "TRNN" "TRND" ...
#>  $ hsa00980: chr [1:78] "CYP1A1" "CYP2C9" "CYP3A4" "CYP1B1" ...
#>  $ hsa00982: chr [1:72] "CYP2D6" "cytochrome P450 2D6-like [KO:K17712] [EC:1.14.14.1]" "CYP2D7" "CYP2D6" ...
#>  $ hsa00983: chr [1:80] "HPRT1" "IMPDH1" "IMPDH2" "GMPS" ...
#>  $ hsa01040: chr [1:27] "ELOVL1" "ELOVL2" "ELOVL3" "ELOVL4" ...
#>  $ hsa01100: logi NA
#>  $ hsa01200: logi NA
#>  $ hsa01210: logi NA
#>  $ hsa01212: logi NA
#>  $ hsa01230: logi NA
#>  $ hsa01240: logi NA
#>  $ hsa01521: logi NA
#>  $ hsa01522: logi NA
#>  $ hsa01523: logi NA
#>  $ hsa01524: logi NA
#>  $ hsa02010: chr [1:45] "DEFB1" "ABCA1" "ABCA2" "ABCA3" ...
#>  $ hsa03008: chr [1:110] "CSNK2B" "CSNK2A1" "CSNK2A2" "CSNK2A3" ...
#>   [list output truncated]