{"id":464,"date":"2022-04-20T16:30:13","date_gmt":"2022-04-20T08:30:13","guid":{"rendered":"https:\/\/linguopeng.top\/?p=464"},"modified":"2022-04-20T16:49:06","modified_gmt":"2022-04-20T08:49:06","slug":"keggrest","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=464","title":{"rendered":"KEGGREST"},"content":{"rendered":"\n
#\u4f1a\u4e86\u5b83\u5c31\u53ef\u4ee5\u77e5\u9053\u54ea\u4e2a\u57fa\u56e0\u5c5e\u4e8e\u54ea\u4e2a\u901a\u8def\uff0c\u4ee5\u53ca\u4e0d\u540c\u901a\u8def\u4e2d\u5305\u542b\u7684\u57fa\u56e0\n#\u53c2\u8003https:\/\/www.jieandze1314.com\/post\/cnposts\/185\/\n# if (!require(\"BiocManager\", quietly = TRUE))\n#   install.packages(\"BiocManager\")\n# BiocManager::install(\"KEGGREST\")\nlibrary(KEGGREST)\nlibrary(tidyverse)\n# 1.1\u5148\u770b\u770b\u80fd\u83b7\u53d6\u5230\u6570\u636e\u5e93\u7684\u4ec0\u4e48\u5185\u5bb9\nlistDatabases()\n# > listDatabases()\n# [1] \"pathway\"  \"brite\"    \"module\"   \"ko\"       \"genome\"   \"vg\"       \"ag\"       \"compound\" \"glycan\"  \n# [10] \"reaction\" \"rclass\"   \"enzyme\"   \"disease\"  \"drug\"     \"dgroup\"   \"environ\"  \"genes\"    \"ligand\"  \n# [19] \"kegg\"\n#\u83b7\u53d6\u5168\u90e8\u7269\u79cd \u8017\u65f6\u53ef\u6839\u636e\u63d0\u5171\u7684\u94fe\u63a5\u8bbf\u95ee\n#keggList(\"organism\")\n# http:\/\/rest.kegg.jp\/list\/organism\n#\u5982\u679c\u76f4\u63a5\u7528keggList(\"pathway\") \u5f97\u5230\u7684\u662fmap\u7684\u901a\u8def\nhead(keggList(\"pathway\"))\n# > head(keggList(\"pathway\"))\n# path:map00010                              path:map00020 \n# \"Glycolysis \/ Gluconeogenesis\"                \"Citrate cycle (TCA cycle)\" \n# path:map00030                              path:map00040 \n# \"Pentose phosphate pathway\" \"Pentose and glucuronate interconversions\" \n# path:map00051                              path:map00052 \n# \"Fructose and mannose metabolism\"                     \"Galactose metabolism\" \n## \u603b\u5171\u6709\u591a\u5c11\u6761map\u901a\u8def\nlength(keggList(\"pathway\"))\n# [1] 551\n#\u5982\u679c\u60f3\u83b7\u5f97\u67d0\u7269\u79cd\u7684\u5168\u90e8\u901a\u8def\uff08\u6bd4\u5982\u4eba\uff09\nres <- keggList(\"pathway\", \"hsa\") \nlength(res)\n# [1] 347\n# 347\u6761\u4eba\u7684\u901a\u8def\n# \u5982\u679c\u60f3\u6839\u636e\u4e00\u4e9b\u5173\u952e\u8bcd\u6311\u9009\u901a\u8def\u3010\u6bd4\u8f83\u91cd\u8981\u3011\n# \u6bd4\u5982\u6211\u73b0\u5728\u60f3\u770b\u4eba\u7c7b\u7684\u901a\u8def\u4e2d\u548c\u7ec6\u80de\u51cb\u4ea1\u3001\u5206\u5316\u6709\u5173\u7684\noptions(stringsAsFactors = F)\npat=keggList(\"pathway\", \"hsa\") \npat=as.data.frame(res)\npat$id=stringr::str_split(rownames(pat),\":\",simplify = T)[,2]\n# \u770b\u5230\u6211\u4eec\u8fd9\u91cc\u8bbe\u7f6e\u4e86\u4e0d\u533a\u5206\u5927\u5c0f\u5199\uff08\u8fd9\u91cc\u5199apoptosis\uff0c\u4f46\u8bc6\u522b\u51fa\u6765\u7684\u662fApoptosis\uff09\uff1b\u5e76\u4e14\u4e0d\u7528\u5199\u5168\u5355\u8bcd\uff08\u8fd9\u91cc\u5199\u7684\u662fdifferent\uff0c\u4f46\u4f1a\u8bc6\u522b\u51fadifferentiation\uff09\np=pat[grepl('different|apoptosis',pat[,1],ignore.case=T),] \np\n# > p\n# res       id\n# path:hsa04210                        Apoptosis - Homo sapiens (human) hsa04210\n# path:hsa04215     Apoptosis - multiple species - Homo sapiens (human) hsa04215\n# path:hsa04380       Osteoclast differentiation - Homo sapiens (human) hsa04380\n# path:hsa04658 Th1 and Th2 cell differentiation - Homo sapiens (human) hsa04658\n# path:hsa04659        Th17 cell differentiation - Homo sapiens (human) hsa04659\n# 2.3 \u5229\u7528keggGet()\u63d0\u53d6\u6307\u5b9a\u4fe1\u606f\n# \u6765\u67e5\u770b\u4e00\u4e2a\u4eba\u7c7b\u7684\u57fa\u56e0\u548c\u4e00\u4e2a\u5927\u80a0\u6746\u83cc\u7684\u57fa\u56e0\nquery <- keggGet(c(\"hsa:10458\", \"ece:Z5100\"))\nlength(query)\nnames(query[[1]])\n# > names(query[[1]])\n# [1] \"ENTRY\"     \"SYMBOL\"    \"NAME\"      \"ORTHOLOGY\" \"ORGANISM\"  \"PATHWAY\"   \"NETWORK\"   \"BRITE\"    \n# [9] \"POSITION\"  \"MOTIF\"     \"DBLINKS\"   \"STRUCTURE\" \"AASEQ\"     \"NTSEQ\"  \n# \u770b\u770b\u8fd9\u4e2a\u57fa\u56e0\u6d89\u53ca\u7684\u901a\u8def\nquery[[1]]$PATHWAY\n# > query[[1]]$PATHWAY\n# hsa04520                                hsa04810 \n# \"Adherens junction\"      \"Regulation of actin cytoskeleton\" \n# hsa05130                                hsa05135 \n# \"Pathogenic Escherichia coli infection\"                    \"Yersinia infection\" \n#\u548c\u7f51\u9875\u4e00\u81f4\uff1ahttps:\/\/www.kegg.jp\/dbget-bin\/www_bget?hsa:10458\n# \u83b7\u5f97\u86cb\u767d\u5e8f\u5217\nkeggGet(c(\"hsa:10458\", \"ece:Z5100\"), \"aaseq\") \n# > keggGet(c(\"hsa:10458\", \"ece:Z5100\"), \"aaseq\") \n# AAStringSet object of length 2:\n#   width seq                                                                        names               \n# [1]   552 MSLSRSEEMHRLTENVYKTIMEQFNPSLRNFIAMGK...VQLKPTVTNDRCDLSAQGPEGREHGDGSARTLAGR hsa:10458 K05627 ...\n# [2]   248 MLNGISNAASTLGRQLVGIASRVSSAGGTGFSVAPQ...PARQAPPPPTGPSGLPPLAQALKDHLAAYEQSKKG ece:Z5100 K12786 ...\n# \u83b7\u5f97DNA\u5e8f\u5217\nkeggGet(c(\"hsa:10458\", \"ece:Z5100\"), \"ntseq\")\n# > keggGet(c(\"hsa:10458\", \"ece:Z5100\"), \"ntseq\")\n# DNAStringSet object of length 2:\n#   width seq                                                                        names               \n# [1]  1659 ATGTCTCTGTCTCGCTCAGAGGAGATGCACCGGCTC...GGGATGGGAGCGCCCGCACCCTGGCTGGAAGATGA hsa:10458 K05627 ...\n# [2]   747 ATGCTTAATGGAATTAGTAACGCTGCTTCTACACTA...ATTTAGCTGCCTATGAGCAATCGAAGAAAGGGTAA ece:Z5100 K12786 ...\n# \u5982\u679c\u60f3\u63d0\u53d6\u5e8f\u5217\u53ef\u4ee5\u76f4\u63a5as.character()\uff0c\u4f8b\u5982\nas.character(keggGet(c(\"hsa:10458\", \"ece:Z5100\"), \"ntseq\")[1])\nas.character(keggGet(c(\"hsa:10458\", \"ece:Z5100\"), \"ntseq\")[2])\n# > as.character(keggGet(c(\"hsa:10458\", \"ece:Z5100\"), \"ntseq\")[1])\n# hsa:10458 K05627 BAI1-associated protein 2 | (RefSeq) BAIAP2, BAP2, FLAF3, IRSP53, WAML; BAR\/IMD domain containing adaptor protein 2 (N) \n# \"ATGTCTCTGTCTCGCTCAGAGGAGATGCACCGGCTCACGGAAAATGTCTATAAGACCATCATGGAGCAGTTCAACCCTAGCCTCCGGAACTTCATCGCCATGGGGAAGAATTACGAGAAGGCACTGGCAGGTGTGACGTATGCAGCCAAAGGCTACTTTGACGCCCTGGTGAAGATGGGGGAGCTGGCCAGCGAGAGCCAGGGCTCCAAAGAACTCGGAGACGTTCTCTTCCAGATGGCTGAAGTCCACAGGCAGATCCAGAATCAGCTGGAAGAAATGCTGAAGTCTTTTCACAACGAGCTGCTTACGCAGCTGGAGCAGAAGGTGGAGCTGGACTCCAGGTATCTGAGTGCTGCGCTGAAGAAATACCAGACTGAGCAAAGGAGCAAAGGCGACGCCCTGGACAAGTGTCAGGCTGAGCTGAAGAAGCTTCGGAAGAAGAGCCAGGGCAGCAAGAATCCTCAGAAGTACTCGGACAAGGAGCTGCAGTACATCGACGCCATCAGCAACAAGCAGGGCGAGCTGGAGAATTACGTGTCCGACGGCTACAAGACCGCACTGACAGAGGAGCGCAGGCGCTTCTGCTTCCTGGTGGAGAAGCAGTGCGCCGTGGCCAAGAACTCCGCGGCCTACCACTCCAAGGGCAAGGAGCTGCTGGCGCAGAAGCTGCCGCTGTGGCAACAGGCCTGTGCCGACCCCAGCAAGATCCCGGAGCGCGCGGTGCAGCTCATGCAGCAGGTGGCCAGCAACGGCGCCACCCTCCCCAGCGCCCTGTCGGCCTCCAAGTCCAACCTGGTCATTTCCGACCCCATTCCGGGGGCCAAGCCCCTGCCGGTGCCCCCCGAGCTGGCACCGTTCGTGGGGCGGATGTCTGCCCAGGAGAGCACACCCATCATGAACGGCGTCACAGGCCCGGATGGCGAGGACTACAGCCCGTGGGCTGACCGCAAGGCTGCCCAGCCCAAATCCCTGTCTCCTCCGCAGTCTCAGAGCAAGCTCAGCGACTCCTACTCCAACACACTCCCCGTGCGCAAGAGCGTGACCCCAAAAAACAGCTATGCCACCACCGAGAACAAGACTCTGCCTCGCTCGAGCTCCATGGCAGCCGGCCTGGAGCGCAATGGCCGTATGCGGGTGAAGGCCATCTTCTCCCACGCTGCTGGGGACAACAGCACCCTCCTGAGCTTCAAGGAGGGTGACCTCATTACCCTGCTGGTGCCTGAGGCCCGCGATGGCTGGCACTACGGAGAGAGTGAGAAGACCAAGATGCGGGGCTGGTTTCCCTTCTCCTACACCCGGGTCTTGGACAGCGATGGCAGTGACAGGCTGCACATGAGCCTGCAGCAAGGGAAGAGCAGCAGCACGGGCAACCTCCTGGACAAGGACGACCTGGCCATCCCACCCCCCGATTACGGCGCCGCCTCCCGGGCCTTCCCCGCCCAGACGGCCAGCGGCTTCAAGCAGAGGCCCTACAGTGTGGCCGTGCCCGCCTTCTCCCAGGGCCTGGATGACTATGGAGCGCGGTCCATGAGCAGGAATCCCTTTGCCCACGTCCAGCTGAAGCCGACAGTGACCAACGACAGGTGTGATCTGTCCGCCCAAGGGCCAGAAGGCCGGGAGCACGGGGATGGGAGCGCCCGCACCCTGGCTGGAAGATGA\"\n# > as.character(keggGet(c(\"hsa:10458\", \"ece:Z5100\"), \"ntseq\")[2])\n# ece:Z5100 K12786 LEE-encoded effector EspF | (GenBank) espF; espF (N) \n# \"ATGCTTAATGGAATTAGTAACGCTGCTTCTACACTAGGGCGGCAGCTTGTAGGTATCGCAAGTCGAGTGAGCTCTGCGGGGGGAACTGGATTTTCTGTAGCCCCTCAGGCCGTGCGTCTTACTCCGGTGAAAGTTCATTCCCCTTTTTCTCCAGGCTCGTCGAATGTTAATGCGAGAACGATTTTTAATGTGAGCAGCCAGGTGACTTCATTTACTCCCTCTCGTCCGGCACCGCCGCCACCGACAAGTGGACAGGCATCCGGGGCATCCCGACCTTTACCGCCCATTGCACAGGCATTAAAAGAGCACTTGGCTGCCTATGAAAAATCGAAAGGTCCTGAGGCTTTAGGTTTTAAGCCCGCCCGTCAGGCACCGCCGCCACCGACAAGTGGACAGGCATCCGGGGCATCCCGACCTTTACCGCCCATTGCACAGGCATTAAAAGAGCACTTGGCTGCCTATGAAAAATCGAAAGGTCCTGAGGCTTTAGGTTTTAAGCCCGCCCGTCAGGCACCGCCGCCACCGACAAGTGGACAGGCATCCGGGGCATCCCGACCTTTACCGCCCATTGCACAGGCATTAAAAGAGCACTTGGCTGCCTATGAAAAATCGAAAGGTCCTGAGGCTTTAGGTTTTAAGCCCGCCCGTCAGGCACCACCGCCACCGACAGGGCCTAGTGGACTACCGCCCCTTGCACAGGCATTAAAAGATCATTTAGCTGCCTATGAGCAATCGAAGAAAGGGTAA\" \n#\u5982\u679c\u60f3\u770b\u5355\u4e2a\u901a\u8def\u7684\u56fe\u7247\n# png <- keggGet(\"hsa05130\", \"image\") \n# t <- tempfile()\n# # library(png)\n# # writePNG(png, t)\n# # if (interactive()) browseURL(t)\n#  \u6839\u636e\u901a\u8def\u627e\u57fa\u56e0\u3010\u5e38\u7528\u3011\n# \u5148\u770b\u5355\u4e2a\u901a\u8def\u7684\u64cd\u4f5c\n# \u9996\u5148\u5f97\u5230\u5168\u90e8\u7684\u57fa\u56e0\u7ed3\u679c\uff08\u5176\u4e2d\u4f1a\u5305\u542bEntrez ID\u548cSymbol\u4ee5\u53ca\u8be6\u7ec6\u7684\u57fa\u56e0\u4fe1\u606f\uff09\nall=keggGet('hsa04210')[[1]]$GENE\n# [271] \"5595\"                                                                                                     \n# [272] \"MAPK3; mitogen-activated protein kinase 3 [KO:K04371] [EC:2.7.11.24]\" \nentrez=all[seq(1,length(all),2)]\nsymbol=stringr::str_split(all[seq(2,length(all),2)],\";\",simplify = T)[,1]\nid=data.frame(entrezID=entrez,symbolID=symbol)\n# \u6839\u636e\u4e00\u4e9b\u5173\u952e\u8bcd\u6311\u9009\u4e86\u901a\u8def\uff0c\u5e76\u4fdd\u6301\u4e3ap\np=pat[grepl('different|apoptosis',pat[,1],ignore.case=T),] \np\n# > p\n# res       id\n# path:hsa04210                        Apoptosis - Homo sapiens (human) hsa04210\n# path:hsa04215     Apoptosis - multiple species - Homo sapiens (human) hsa04215\n# path:hsa04380       Osteoclast differentiation - Homo sapiens (human) hsa04380\n# path:hsa04658 Th1 and Th2 cell differentiation - Homo sapiens (human) hsa04658\n# path:hsa04659        Th17 cell differentiation - Homo sapiens (human) hsa04659\n# \u4e4b\u524dp\u662f\u5b57\u7b26\u4e32\uff0c\u73b0\u5728\u53d8\u6210\u5217\u8868\uff0c\u7528\u4e8e\u5b58\u50a8\u4e00\u4f1a\u5f97\u5230\u7684\u5404\u4e2a\u7ed3\u679c\npp=lapply(p$id, function(x){\n  # \u5176\u5b9e\u8fd8\u662f\u50cf\u5355\u4e2a\u5904\u7406\u4e00\u6837\n  all=keggGet(x)[[1]]$GENE\n  entrez=all[seq(1,length(all),2)]\n  symbol=stringr::str_split(all[seq(2,length(all),2)],\";\",simplify = T)[,1]\n  id=data.frame(entrezID=entrez,symbolID=symbol)\n})\nnames(pp)=as.character(p$id)\n# \u641c\u7d22\u57fa\u56e0\u4fe1\u606f\u4e2d\u7684\u4e24\u4e2a\u8bcd\nhead(keggFind(\"genes\", c(\"shiga\", \"toxin\")),3)\n#\u641c\u7d22\u5316\u5b66\u516c\u5f0f\nhead(keggFind(\"compound\", \"C7H10O5\", \"formula\"))\n# \u5229\u7528keggConv()\u8f6c\u6362KEGG ID\nkeggConv(\"ncbi-proteinid\", c(\"hsa:10458\", \"ece:Z5100\"))\nhead(keggLink(\"pathway\", \"hsa\"))\n# \u6216\u8005\u6307\u5b9a\u4e00\u4e2a\u6216\u591a\u4e2a\u57fa\u56e0\uff08\u57fa\u56e0\u652f\u6301\u8de8\u7269\u79cd\uff09\nkeggLink(\"pathway\", c(\"hsa:10458\", \"ece:Z5100\"))\n####################\u603b\u7ed3#########\n# \u627e\u5168\u90e8\u901a\u8def\n# keggList(\"pathway\")\n# \n# \u6839\u636e\u57fa\u56e0\u627e\u901a\u8def\n# keggLink(\"pathway\", c(\"hsa:10458\", \"ece:Z5100\"))\n# \n# \u6839\u636e\u5173\u952e\u8bcd\u627e\u901a\u8def\n# options(stringsAsFactors = F)\n# pat=keggList(\"pathway\", \"hsa\") \n# pat=as.data.frame(res)\n# pat$id=stringr::str_split(rownames(pat),\":\",simplify = T)[,2]\n# # \u770b\u5230\u6211\u4eec\u8fd9\u91cc\u8bbe\u7f6e\u4e86\u4e0d\u533a\u5206\u5927\u5c0f\u5199\uff08\u8fd9\u91cc\u5199apoptosis\uff0c\u4f46\u8bc6\u522b\u51fa\u6765\u7684\u662fApoptosis\uff09\uff1b\u5e76\u4e14\u4e0d\u7528\u5199\u5168\u5355\u8bcd\uff08\u8fd9\u91cc\u5199\u7684\u662fdifferent\uff0c\u4f46\u4f1a\u8bc6\u522b\u51fadifferentiation\uff09\n# p=pat[grepl('different|apoptosis',pat[,1],ignore.case=T),] \n# \u6839\u636e\u901a\u8def\u627e\u57fa\u56e0\n# # \u8fd9\u4e2ap\u53ef\u4ee5\u81ea\u5df1\u5b9a\u4e49\uff0c\u4e5f\u53ef\u4ee5\u6839\u636e\u4e0a\u9762\u5173\u952e\u8bcd\u627e\u901a\u8def\n# p=pat[grepl('different|apoptosis',pat[,1],ignore.case=T),] \n# # \u4e4b\u524dp\u662f\u5b57\u7b26\u4e32\uff0c\u73b0\u5728\u53d8\u6210\u5217\u8868\uff0c\u7528\u4e8e\u5b58\u50a8\u4e00\u4f1a\u5f97\u5230\u7684\u5404\u4e2a\u7ed3\u679c\n# p=as.list(p)\n# pp=lapply(p, function(x){\n#   # \u5176\u5b9e\u8fd8\u662f\u50cf\u5355\u4e2a\u5904\u7406\u4e00\u6837\n#   all=keggGet(x)[[1]]$GENE\n#   entrez=all[seq(1,length(all),2)]\n#   symbol=stringr::str_split(all[seq(2,length(all),2)],\";\",simplify = T)[,1]\n#   id=data.frame(entrezID=entrez,symbolID=symbol)\n# })\n# names(pp)=as.character(p)<\/code><\/pre>\n\n\n\n
\"\"<\/div><\/figure>\n\n\n\n
1 \u524d\u8a00\n\u5728\u6b63\u5f0f\u5b66\u4e60\u8fd9\u4e2a\u5305\u4e4b\u524d\uff0c\u8fd8\u662f\u5148\u8865\u5145\u4e00\u70b9KEGG\u6570\u636e\u5e93\u7684\u77e5\u8bc6\u5427\n\nKEGG\u6570\u636e\u5e93\u662f\u4e00\u4e2a\u7efc\u5408\u6570\u636e\u5e93\uff0c\u5176\u4e2d\u6211\u4eec\u6700\u5e38\u7528\u7684\u5c31\u662f\u901a\u8def\uff08PATHWAY\uff09\u4e86\uff0c\u4e3b\u8981\u4ecb\u7ecd\u4e86\u7ec6\u80de\u751f\u5316\u8fc7\u7a0b\uff08\u8fd8\u6709\u56fe\u6ce8\uff09\uff0c\u5982\u7ec6\u80de\u4ee3\u8c22\u3001\u7ec6\u80de\u5468\u671f\u3001\u819c\u8f6c\u8fd0\u3001\u4fe1\u53f7\u4f20\u9012\u3002\u4f46PATHWAY\u53ea\u80fd\u7b97\u4e0a\u662f\u4e00\u4e2a\u5c0f\u5206\u652f\uff0c\u5168\u90e8\u7684\u6570\u636e\u5e93\u53ef\u4ee5\u770b\u4e0b\u9762\uff1a\n\n1.1 \u9996\u5148\uff0cKEGG\u4e3b\u8981\u67094\u5927\u5206\u7c7b\n\u7cfb\u7edf\u4fe1\u606f Systems information\n\n\u57fa\u56e0\u7ec4\u4fe1\u606f Genomic information\n\n\u5316\u5b66\u4fe1\u606f Chemical information\n\n\u5065\u5eb7\u4fe1\u606fHealth information\n\n\u540e\u6765\u5065\u5eb7\u4fe1\u606f+\u836f\u7269\u6807\u7b7e Drug labels = KEGG MEDICUS\n\n\u7136\u540e\u6bcf\u4e2a\u5206\u7c7b\u4e0b\u9762\u53c8\u6709\u81ea\u5df1\u7684\u5b50\u6570\u636e\u5e93\uff0c\u6bd4\u5982\u5e38\u7528\u7684pathway\u6570\u636e\u5e93\u5c31\u662f\u5728\u7cfb\u7edf\u4fe1\u606f\u4e4b\u4e0b\u7684\n1.2 \u6bcf\u4e2a\u5206\u7c7b\u90fd\u6709\u5404\u81ea\u7684\u989c\u8272\r\n1.3 \u6bcf\u4e2a\u5206\u652f\u6709\u5404\u81ea\u7684\u4f5c\u7528\n\u6765\u81ea\u5b98\u7f51\u7684\u63cf\u8ff0\uff1ahttps:\/\/www.kegg.jp\/kegg\/kegg1a.html\nKEGG\u6570\u636e\u5e93\u662f\u751f\u7269\u7cfb\u7edf\u7684\u6570\u636e\u91cd\u73b0\uff0c\u7531\u57fa\u56e0\u3001\u86cb\u767d\u8d28\uff08\u57fa\u56e0\u7ec4\u4fe1\u606f\uff09\u548c\u5316\u5b66\u7269\u8d28\uff08\u5316\u5b66\u4fe1\u606f\uff09\u7684\u5206\u5b50\u6a21\u5757\u7ec4\u5efa\u800c\u6210\u3002\u8fd9\u4e9b\u5206\u5b50\u6a21\u5757\u4e4b\u95f4\u6784\u6210\u4e86\u76f8\u4e92\u4f5c\u7528\u7684\u5173\u7cfb\u7f51\u7edc\uff08\u7cfb\u7edf\u4fe1\u606f\uff09\u3002\u53e6\u5916\u8fd8\u5305\u542b\u4e86\u5bf9\u751f\u547d\u6d3b\u52a8\u6709\u5f71\u54cd\u7684\u75be\u75c5\u548c\u836f\u7269\u8d44\u6e90\uff08\u5065\u5eb7\u4fe1\u606f\u548c\u836f\u7269\u4fe1\u606f\uff09\u3002\n1.4 \u6bd4\u8f83\u5e38\u7528\u7684\u5b50\u6570\u636e\u5e93\r\n1.4.1 KEGG PATHWAY\u4ee3\u8c22\u901a\u8def\u6570\u636e\u5e93\r\n\u6765\u81ea\uff1ahttps:\/\/www.kegg.jp\/kegg\/kegg3a.html\r\n\r\n\u5305\u542b\u4e86\u8bb8\u591a\u624b\u5de5\u7ed8\u5236\u6216\u8ba1\u7b97\u673a\u6a21\u62df\u7684\u4ee3\u8c22\u901a\u8def\uff0c\u5305\u542b\u4e86\u7ec6\u80de\u8fc7\u7a0b\u3001\u9057\u4f20\u4fe1\u606f\u3001\u65b0\u9648\u4ee3\u8c22\u3001\u75be\u75c5\u3001\u836f\u7269\u5f00\u53d1\u7b49\u7684\u5206\u5b50\u4e92\u4f5c\u548c\u53cd\u5e94\u7f51\u7edc\u56fe\u3002\r\n\r\n\u6bcf\u4e2apathway map\u90fd\u662f\u901a\u8fc72-4\u4e2a\u5b57\u6bcd\u7684\u524d\u7f00 + 5\u4f4d\u6570\u5b57\u7ec4\u6210\r\n\r\n\u5176\u4e2d\u524d\u7f00\u67095\u79cd\u7c7b\u578b\uff1a\r\n\r\nmap - Reference pathway\uff1a\u624b\u5de5\u7ed8\u5236\uff1b\u6839\u636e\u5df2\u6709\u7684\u77e5\u8bc6\u7ed8\u5236\u7684\u5168\u9762\u7684\u4f9b\u53c2\u8003\u7684\u4ee3\u8c22\u56fe\uff0c\u4e5f\u662f\u4e3a\u540e\u9762\u51e0\u79cd\u7684\u57fa\u7840\u3002\u56fe\u4e2d\u7684\u5c0f\u6846\u90fd\u662f\u767d\u8272\uff08\u540e\u671f\u53ef\u4ee5\u586b\u5145\uff09\uff1b\u6bcf\u4e2a\u8282\u70b9\u8868\u793a\u67d0\u4e2a\u57fa\u56e0\u3001\u8be5\u57fa\u56e0\u7f16\u7801\u7684\u9176\u6216\u8005\u9176\u53c2\u4e0e\u7684\u53cd\u5e94\uff0c\u53ef\u4ee5\u70b9\u51fb\u5176\u4e2d\u7684\u94fe\u63a5\u67e5\u770b\u8be6\u7ec6\u4fe1\u606f\r\norg - Organism-specific pathway map\uff1a\u8ba1\u7b97\u673a\u6a21\u62df\uff1b\u7269\u79cd\u7279\u6709\u7684\u4ee3\u8c22\u901a\u8def\uff1b\u7eff\u8272\u5c0f\u6846\u8868\u793a\u7269\u79cd\u7279\u6709\u7684\u57fa\u56e0\u6216\u9176\uff0c\u70b9\u51fb\u7eff\u8272\u6846\u7684\u57fa\u56e0\u4f1a\u770b\u5230\u66f4\u8be6\u7ec6\u7684\u4fe1\u606f\r\nko - Reference pathway (KO)\uff1a\u8ba1\u7b97\u673a\u6a21\u62df\uff0c\u8282\u70b9\u53ea\u4ee3\u8868\u57fa\u56e0\uff1b\u70b9\u51fb\u84dd\u8272\u6846\u4f1a\u770b\u5230\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u4fe1\u606f\r\nec - Reference pathway (EC)\uff1a\u8ba1\u7b97\u673a\u6a21\u62df\uff0c\u8282\u70b9\u53ea\u4ee3\u8868\u76f8\u5173\u7684\u9176\r\nrn - Reference pathway (Reaction)\uff1a\u8ba1\u7b97\u673a\u6a21\u62df\uff0c\u8282\u70b9\u53ea\u4ee3\u8868\u53c2\u4e0e\u7684\u67d0\u4e2a\u53cd\u5e94\u3001\u53cd\u5e94\u7269\u53ca\u53cd\u5e94\u7c7b\u578b\n\n1.4.2 KEGG ORTHOLOGY \u76f4\u7cfb\u540c\u6e90\u6570\u636e\u5e93\r\n\u8fd9\u4e2a\u6570\u636e\u5e93\u662f\u57fa\u4e8e\uff1a\u540c\u6e90\u57fa\u56e0\u529f\u80fd\u76f8\u4f3c\u3002\u4f1a\u628a\u6bcf\u4e2a\u529f\u80fd\u5df2\u77e5\u7684\u57fa\u56e0\u548c\u5176\u4ed6\u540c\u6e90\u7684\u57fa\u56e0\u5f52\u4e3a\u4e00\u7c7b\uff0c\u5373\u4e00\u4e2aKO\u53f7\uff0c\u5b83\u4e0d\u5206\u7269\u79cd\uff0c\u6bd4\u5982ko00010\uff08https:\/\/www.kegg.jp\/kegg-bin\/show_pathway?ko00010\uff09\u5c31\u662f\u7cd6\u9175\u89e3\n\u56fe\u4e2d\u53c8\u8fd9\u4e48\u51e0\u4e2a\u5f62\u72b6\uff1a\r\n\r\n\u5706\u89d2\u77e9\u5f62\uff1a\u5176\u4ed6\u7684KO\u901a\u8def\r\n\r\n**\u65b9\u6846\uff1a**\u5982\u679c\u628a\u9f20\u6807\u60ac\u505c\u5728\u65b9\u6846\u4e0a\uff0c\u5c31\u4f1a\u5f39\u51faK+\u6570\u5b57\u3002\u6bd4\u5982\u8fd9\u91cc\u7684K02777\u3001K02779\u7b49\uff0c\u8868\u793a\u6240\u6709\u7269\u79cd\u7684\u4e00\u4e2a\u540c\u6e90\u57fa\u56e0\n\u81f3\u4e8e\u8fd9\u4e2a\u540c\u6e90\u57fa\u56e0\u5728\u5404\u4e2a\u7269\u79cd\u4e2d\u5206\u522b\u662f\u4ec0\u4e48\uff0c\u53ef\u4ee5\u770b\u8be6\u60c5\uff0c\u4f8b\u5982K02777\uff08h**\u5c0f\u5706\u5708\uff1a**\u5982\u679c\u628a\u9f20\u6807\u60ac\u505c\u5728\u65b9\u6846\u4e0a\uff0c\u4f1a\u5f39\u51fa\u5316\u5408\u7269\u4fe1\u606f\uff08C\u7b26\u53f7\uff09ttps:\/\/www.kegg.jp\/dbget-bin\/www_bget?ko:K02777\uff09\n<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-464","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/464","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=464"}],"version-history":[{"count":4,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/464\/revisions"}],"predecessor-version":[{"id":470,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/464\/revisions\/470"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=464"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=464"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=464"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}