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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"ClusterProfiler KEGG\u5bcc\u96c6\u5206\u6790\uff1a\u5c0f\u767d\u5fc5\u5907\uff0c\u8f7b\u677e\u638c\u63e1\u7684\u57fa\u56e0\u8868\u8fbe\u89e3\u8bfb\u79d8\u7c4d\uff01\",\"time\":\"2023-06-21 19:00:26\",\"timeStamp\":\"1687345226\"};\n<\/script><br \/>\n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488611&idx=2&sn=ba9d239bbdeb57cfeaa210331be57f6b&chksm=cf7c84a6f80b0db09f41656ed2011bf953b9750ec8a28aa221308c8973b61a6e0c9798b7486d#rd\" target=\"_blank\" rel=\"noopener\">ClusterProfiler KEGG\u5bcc\u96c6\u5206\u6790\uff1a\u5c0f\u767d\u5fc5\u5907\uff0c\u8f7b\u677e\u638c\u63e1\u7684\u57fa\u56e0\u8868\u8fbe\u89e3\u8bfb\u79d8\u7c4d\uff01<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span class=\"rich_media_meta rich_media_meta_text\">\u5c0f\u5e08\u59b9 <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-06-21 19:00:26<\/em><\/div>\n<p><content><\/p>\n<div class=\"reprint\">\n<p>\u8f6c\u81ea\u516c\u4f17\u53f7\uff1aR\u8bed\u8a00\u5b66\u5f92<br \/><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg5MDk3Mzg4OA==&mid=2247483994&idx=1&sn=8b8631ab41d56321d8b27579b452f506\" target=\"_blank\" title=\"\u9605\u8bfb\u539f\u6587\" rel=\"noopener\">http:\/\/mp.weixin.qq.com\/s?__biz=Mzg5MDk3Mzg4OA==&mid=2247483994&idx=1&sn=8b8631ab41d56321d8b27579b452f506<\/a><\/p>\n<\/div>\n<section style=\"font-size: 16px;margin-bottom: 24px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 20px;margin-bottom: 25px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(249, 172, 172);box-shadow: rgb(249, 172, 172) 0px 0px 5px 3px;\">\n<section style=\"text-align: center;transform: translate3d(2px, 0px, 0px);margin-top: -14px;margin-bottom: -14px;\" powered-by=\"xiumi.us\">\n<p>{ \u70b9\u51fb\u84dd\u5b57\uff0c\u5173\u6ce8\u6211\u4eec }<\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">KEGG\uff08Kyoto Encyclopedia of Genes and Genomes\uff09\u662f\u4e00\u4e2a\u5e7f\u6cdb\u4f7f\u7528\u7684\u57fa\u56e0\u901a\u8def\u6570\u636e\u5e93\uff0c\u63d0\u4f9b\u4e86\u5173\u4e8e\u751f\u7269\u7cfb\u7edf\u529f\u80fd\u548c\u8c03\u63a7\u7684\u4e30\u5bcc\u4fe1\u606f\u3002\u4eca\u5929\u5c0f\u5e08\u59b9 \u5c06\u4ecb\u7ecd\u5982\u4f55\u4f7f\u7528R\u8bed\u8a00\u4e2d\u7684clusterProfiler\u5305\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\uff0c\u4ee5\u63ed\u793a\u7ed9\u5b9a\u57fa\u56e0\u96c6\u5408\u4e2d\u5bcc\u96c6\u7684KEGG\u901a\u8def\u3002\u4f7f\u7528clusterProfiler\u8fdb\u884cKEGG\uff08Kyoto Encyclopedia of Genes and Genomes\uff09\u5206\u6790\u7684\u6b65\u9aa4\u4e0eGO\u5206\u6790\u7c7b\u4f3c\uff0c\u4e0b\u9762\u63a5\u7740\u8ddf\u5c0f\u5e08\u59b9\u4e00\u8d77\u6765\u5b66\u4e60\u5427\uff01<\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>1<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u5b89\u88c5\u52a0\u8f7d\u5305<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u5728\u5f00\u59cb\u4e4b\u524d\uff0c\u786e\u4fdd\u5df2\u5728R\u73af\u5883\u4e2d\u5b89\u88c5\u4e86clusterProfiler\u5305\u3002\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u4ee3\u7801\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span> (!require(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>, quietly = <span class=\"code-snippet__literal\">TRUE<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\"> install.packages(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"clusterProfiler\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">library(clusterProfiler)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>2<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u51c6\u5907\u8f93\u5165\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 2em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u4e3a\u4e86\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\uff0c\u6211\u4eec\u9700\u8981\u51c6\u5907\u4e00\u4e2a\u57fa\u56e0\u5217\u8868\uff0c\u8be5\u5217\u8868\u5305\u542b\u6211\u4eec\u611f\u5174\u8da3\u7684\u57fa\u56e0\u3002\u57fa\u56e0\u5217\u8868\u53ef\u4ee5\u662f\u57fa\u56e0\u7b26\u53f7\u3001Ensembl ID\u6216\u5176\u4ed6\u5e38\u89c1\u7684\u57fa\u56e0\u8bc6\u522b\u7b26\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u51c6\u5907\u4e86\u4e00\u4e2a\u540d\u4e3a”gene.txt”\u7684\u6587\u672c\u6587\u4ef6\uff0c\u5176\u4e2d\u5305\u542bEnsembl\u7b26\u53f7\u5217\u8868\uff0c\u6bcf\u884c\u4e00\u4e2a\u57fa\u56e0\u3002<\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9980430528375733\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_iaoQl9icEJdicuG0SNOrsJAhV7sXVw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicCLvh0ZA9P36PkjOicib2NHnHaUBZmciaoQl9icEJdicuG0SNOrsJAhV7sXVw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"511\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe1 \u57fa\u56e0\u5217\u8868\u6587\u4ef6\u5185\u5bb9\u793a\u4f8b<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\">\u4ee3\u7801\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">genes <- read.delim(<span class=\"code-snippet__string\">'gene.txt'<\/span>, header = <span class=\"code-snippet__literal\">TRUE<\/span>, stringsAsFactors = <span class=\"code-snippet__literal\">FALSE<\/span>)[[<span class=\"code-snippet__number\">1<\/span>]]<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>3<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u8fdb\u884c\u57fa\u56e0ID\u8f6c\u6362<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 2em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u5728\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\u4e4b\u524d\uff0c\u6211\u4eec\u9700\u8981\u5bf9\u57fa\u56e0\u5217\u8868\u8fdb\u884c\u57fa\u56e0\u6ce8\u91ca\uff0c\u5c06\u57fa\u56e0\u8bc6\u522b\u7b26\u6620\u5c04\u5230ENTREZID\u4fe1\u606f\u3002\u5728clusterProfiler\u4e2d\uff0c\u53ef\u4ee5\u4f7f\u7528bitr\u51fd\u6570\u8fdb\u884c\u57fa\u56e0\u6ce8\u91ca\u3002<\/p>\n<p powered-by=\"xiumi.us\">\u4ee3\u7801\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5c06ENSEMBL ID\u6620\u5c04\u5230ENTREZID\uff08\u4ee5\u4eba\u7c7b\u4e3a\u4f8b\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gene2kegg <- bitr(genes, fromType = <span class=\"code-snippet__string\">\"ENSEMBL\"<\/span>, toType = <span class=\"code-snippet__string\">\"ENTREZID\"<\/span>, OrgDb = org.Hs.eg.db)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>4<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528enrichKEGG\u51fd\u6570\u5bf9\u6ce8\u91ca\u540e\u7684\u57fa\u56e0\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\u3002\u8be5\u51fd\u6570\u6839\u636e\u57fa\u56e0\u5728\u7279\u5b9aKEGG\u901a\u8def\u4e2d\u7684\u5bcc\u96c6\u7a0b\u5ea6\u8ba1\u7b97\u5bcc\u96c6\u5206\u6570\u548c\u8c03\u6574\u7684p\u503c\u3002\u60a8\u53ef\u4ee5\u9009\u62e9\u4e0d\u540c\u7684\u7edf\u8ba1\u65b9\u6cd5\u548c\u53c2\u6570\u8bbe\u7f6e\u3002\u76f8\u6bd4\u4e0a\u8ff0GO\u5bcc\u96c6\uff0cclusterProfiler\u7684KEGG\u5bcc\u96c6\u5206\u6790\u53ef\u4ee5\u76f4\u63a5\u94fe\u63a5\u5230KEGG\u7684\u5728\u7ebf\u6570\u636e\u5e93\u83b7\u53d6\u5df2\u6709\u7269\u79cd\u7684\u6ce8\u91ca\u3002<\/p>\n<p powered-by=\"xiumi.us\">\u4ee3\u7801\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">getOption(<span class=\"code-snippet__string\">\"clusterProfiler.download.method\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">R.utils::setOption(<span class=\"code-snippet__string\">\"clusterProfiler.download.method\"<\/span>,<span class=\"code-snippet__string\">\"auto\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#KEGG \u5bcc\u96c6\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6bcf\u6b21\u6253\u5f00 R \u8ba1\u7b97\u65f6\uff0c\u5b83\u4f1a\u81ea\u52a8\u8fde\u63a5 KEGG \u5b98\u7f51\u83b7\u5f97\u6700\u8fd1\u7684\u7269\u79cd\u6ce8\u91ca\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">kegg <- enrichKEGG(<\/span><\/code><code><span class=\"code-snippet_outer\"> gene = gene2kegg$ENTREZID, <span class=\"code-snippet__comment\">#\u57fa\u56e0\u5217\u8868\u6587\u4ef6\u4e2d\u7684\u57fa\u56e0\u540d\u79f0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> keyType = <span class=\"code-snippet__string\">'kegg'<\/span>, <span class=\"code-snippet__comment\">#KEGG \u5bcc\u96c6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> organism = <span class=\"code-snippet__string\">\"hsa\"<\/span>, <span class=\"code-snippet__comment\">#\u4f8b\u5982\uff0chsa \u4ee3\u8868\u4eba\u7c7b\uff0c\u5176\u5b83\u7269\u79cd\u66f4\u6539\u8fd9\u884c\u5373\u53ef<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> pAdjustMethod = <span class=\"code-snippet__string\">\"BH\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> pvalueCutoff = <span class=\"code-snippet__number\">0.1<\/span>, <span class=\"code-snippet__comment\">#\u6307\u5b9a p \u503c\u9608\u503c\uff08\u53ef\u6307\u5b9a 1 \u4ee5\u8f93\u51fa\u5168\u90e8\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> qvalueCutoff = <span class=\"code-snippet__number\">0.2<\/span>) <span class=\"code-snippet__comment\">#\u6307\u5b9a q \u503c\u9608\u503c\uff08\u53ef\u6307\u5b9a 1 \u4ee5\u8f93\u51fa\u5168\u90e8\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u7ed3\u679c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">write.table(kegg, <span class=\"code-snippet__string\">'kegg.txt'<\/span>, sep = <span class=\"code-snippet__string\">'t'<\/span>, <span class=\"code-snippet__built_in\">quote<\/span> = <span class=\"code-snippet__literal\">FALSE<\/span>, row.names = <span class=\"code-snippet__literal\">FALSE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\">\u5728\u4e0a\u8ff0\u4ee3\u7801\u4e2d\uff0c\u6211\u4eec\u6307\u5b9a\u4e86\u6ce8\u91ca\u540e\u7684\u57fa\u56e0\uff08gene = gene2kegg$ENTREZID\uff09\uff0c\u9009\u62e9\u4e86\u4eba\u7c7b\uff08organism = “hsa”\uff09\u4f5c\u4e3a\u7814\u7a76\u5bf9\u8c61\uff0c\u5e76\u8bbe\u7f6e\u4e86p\u503c\u548cq\u503c\u7684\u9608\u503c\uff08pvalueCutoff = 0.05, qvalueCutoff = 0.2\uff09\u3002\u53ef\u4ee5\u901a\u8fc7KEGG\u5b98\u7f51\uff08KEGG Organisms: Complete Genomes\uff09\u67e5\u770bKEGG\u6570\u636e\u5e93\u4e2d\u63d0\u4f9b\u7684\u7269\u79cd\u6ce8\u91ca\u5217\u8868\u3002<\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>5<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u7ed3\u679c\u89e3\u91ca\u548c\u53ef\u89c6\u5316<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u7ecf\u8fc7KEGG\u5bcc\u96c6\u5206\u6790\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u5bf9\u7ed3\u679c\u8fdb\u884c\u89e3\u91ca\u548c\u53ef\u89c6\u5316\uff0c\u4ee5\u66f4\u597d\u5730\u7406\u89e3\u57fa\u56e0\u96c6\u5408\u4e2d\u5bcc\u96c6\u7684KEGG\u901a\u8def\u3002\u53ef\u4ee5\u4f7f\u7528summary\u51fd\u6570\u548cbarplot\u3001dotplot\u51fd\u6570\u5bf9\u7ed3\u679c\u8fdb\u884c\u6458\u8981\u548c\u53ef\u89c6\u5316\u3002<\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\"><strong>summary\u51fd\u6570\uff1asummary(kegg)<\/strong><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.20277777777777778\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_l3WUaKGDAZibsLLqR9RpJTYT7ZUm2w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicC1M5LbXv3kxNd5ZOl0lzicond9Pl3WUaKGDAZibsLLqR9RpJTYT7ZUm2w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe2 \u67e5\u770b\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u6458\u8981<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"text-indent: 2em;\">\u901a\u8fc7summary\u51fd\u6570\uff0c\u6211\u4eec\u53ef\u4ee5\u67e5\u770bKEGG\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\u6458\u8981\u4fe1\u606f\uff0c\u5305\u62ec\u5bcc\u96c6\u7684KEGG\u901a\u8def\u3001\u8c03\u6574\u7684p\u503c\u3001\u57fa\u56e0\u6570\u7b49\u3002\u8fd9\u4e9b\u4fe1\u606f\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u7406\u89e3\u57fa\u56e0\u96c6\u5408\u5728\u4e0d\u540c\u901a\u8def\u4e2d\u7684\u5bcc\u96c6\u60c5\u51b5\u3002<\/span><\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\"><strong>barplot\u51fd\u6570\uff1abarplot(kegg)<\/strong><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9825581395348837\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_gibBFmZnGj87ZDrs2R7OCib0TEMP7A.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicCicHw6icvCpwr3nuDzzZicHdVbhIkzgibBFmZnGj87ZDrs2R7OCib0TEMP7A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"860\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe3 \u5bcc\u96c6\u67f1\u5f62\u56fe<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\"><strong><span style=\"text-indent: 2em;\">dotplot\u51fd\u6570\uff1adotplot(kegg)<\/span><\/strong><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9905992949471211\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_m8zfbcllMicUQsEq05LzpibZYicDSQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicCmGj76hzhG6gpDZ3oSaVGsQ6qsaem8zfbcllMicUQsEq05LzpibZYicDSQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"851\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe4 \u5bcc\u96c6\u6c14\u6ce1\u56fe<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"text-indent: 2em;\">\u4f7f\u7528barplot\u51fd\u6570\u548cdotplot\u51fd\u6570\uff0c\u6211\u4eec\u53ef\u4ee5\u751f\u6210\u5bcc\u96c6\u7ed3\u679c\u7684\u53ef\u89c6\u5316\u56fe\u8868\uff0c\u4ee5\u66f4\u76f4\u89c2\u5730\u5c55\u793a\u57fa\u56e0\u96c6\u5408\u7684KEGG\u5bcc\u96c6\u60c5\u51b5\u3002\u8be5\u51fd\u6570\u53ef\u4ee5\u751f\u6210\u67f1\u72b6\u56fe\u6216\u6c14\u6ce1\u56fe\uff0c\u5176\u4e2d\u6bcf\u4e2a\u67f1\u5b50\u6216\u6c14\u6ce1\u4ee3\u8868\u4e00\u4e2a\u5bcc\u96c6\u7684KEGG\u901a\u8def\uff0c\u5176\u9ad8\u5ea6\u6216\u5927\u5c0f\u8868\u793a\u5bcc\u96c6\u7a0b\u5ea6\u7684\u6307\u6807\uff08\u5982p\u503c\u3001\u57fa\u56e0\u6570\u7b49\uff09\u3002<\/span><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">pathview\u5305\u53ef\u4ee5\u53ef\u89c6\u5316KEGG \u901a\u8def\uff0c\u6211\u4eec\u53ef\u4ee5\u7528\u5b83\u67e5\u770b\u7279\u5b9a\u901a\u8def\u56fe\u3002<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\">\u4ee3\u7801\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"pathview\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">library(pathview)<\/span><\/code><code><span class=\"code-snippet_outer\">hsa04750 <- pathview(gene.data = geneList,<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"> pathway.id = <span class=\"code-snippet__string\">\"hsa04750\"<\/span>, <span class=\"code-snippet__comment\">#\u4e0a\u8ff0\u7ed3\u679c\u4e2d\u7684hsa04750\u901a\u8def<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"> species = <span class=\"code-snippet__string\">\"hsa\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"> limit = <span class=\"code-snippet__built_in\">list<\/span>(gene=<span class=\"code-snippet__built_in\">max<\/span>(<span class=\"code-snippet__built_in\">abs<\/span>(geneList)), cpd=<span class=\"code-snippet__number\">1<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6296296296296297\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_6AmGjkhvaU84Ryj2dd0iaiahrjehGg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicCCIPW7O8n02MdzWqpAub8Fr7QNy6AmGjkhvaU84Ryj2dd0iaiahrjehGg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe5 \u7279\u5b9a\u901a\u8def\uff08hsa04750\uff09\u56fe<\/p>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\"><span style=\"text-indent: 2em;\">\u9664\u4e86\u4e0a\u8ff0\u57fa\u672c\u7684KEGG\u5bcc\u96c6\u5206\u6790\u5916\uff0cclusterProfiler\u8fd8\u63d0\u4f9b\u4e86\u5176\u4ed6\u529f\u80fd\u548c\u5de5\u5177\uff0c\u4ee5\u8fdb\u4e00\u6b65\u6df1\u5165\u5206\u6790\u548c\u89e3\u91ca\u57fa\u56e0\u96c6\u5408\u7684\u751f\u7269\u5b66\u610f\u4e49\u3002\u4f8b\u5982\uff1a<\/span><\/p>\n<ul style=\"list-style-type: \uf06c;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" powered-by=\"xiumi.us\">\n<li>\n<p>\u901a\u8fc7\u8bbe\u7f6e\u4e0d\u540c\u7684p\u503c\u548cq\u503c\u9608\u503c\uff0c\u53ef\u4ee5\u8c03\u6574\u5bcc\u96c6\u7ed3\u679c\u7684\u4e25\u683c\u7a0b\u5ea6\u3002<\/p>\n<\/li>\n<li>\n<p>\u53ef\u4ee5\u4f7f\u7528compareCluster\u51fd\u6570\u8fdb\u884c\u57fa\u56e0\u96c6\u5408\u4e4b\u95f4\u7684KEGG\u901a\u8def\u6bd4\u8f83\u5206\u6790\uff0c\u627e\u51fa\u4e0d\u540c\u96c6\u5408\u4e4b\u95f4\u7684\u5dee\u5f02\u548c\u76f8\u4f3c\u6027\u3002<\/p>\n<\/li>\n<li>\n<p>\u53ef\u4ee5\u4f7f\u7528geneSets\u51fd\u6570\u751f\u6210\u57fa\u56e0\u96c6\u5408\u7684\u5bcc\u96c6\u7ed3\u679c\u8868\u683c\uff0c\u4ee5\u4fbf\u8fdb\u4e00\u6b65\u8fdb\u884c\u7edf\u8ba1\u5206\u6790\u6216\u5bfc\u51fa\u7ed3\u679c\u3002<\/p>\n<\/li>\n<li>\n<p>\u53ef\u4ee5\u4f7f\u7528geneSetPlot\u51fd\u6570\u751f\u6210\u5355\u4e2aKEGG\u901a\u8def\u7684\u5bcc\u96c6\u7ed3\u679c\u56fe\u8868\uff0c\u4ee5\u8be6\u7ec6\u5c55\u793a\u8be5\u901a\u8def\u4e2d\u7684\u57fa\u56e0\u548c\u5176\u6ce8\u91ca\u4fe1\u606f\u3002<\/p>\n<\/li>\n<\/ul>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><span style=\"text-indent: 2em;\">\u901a\u8fc7\u4f7f\u7528clusterProfiler\u5305\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\uff0c\u6211\u4eec\u53ef\u4ee5\u8f7b\u677e\u5730\u63a2\u7d22\u7ed9\u5b9a\u57fa\u56e0\u96c6\u5408\u5728KEGG\u901a\u8def\u4e2d\u7684\u5bcc\u96c6\u60c5\u51b5\uff0c\u8fdb\u4e00\u6b65\u7406\u89e3\u57fa\u56e0\u7684\u751f\u7269\u5b66\u529f\u80fd\u548c\u8c03\u63a7\u673a\u5236\u3002\u4ee5\u4e0a\u6559\u7a0b\u5c0f\u5e08\u59b9\u63d0\u4f9b\u4e86\u57fa\u672c\u7684\u6b65\u9aa4\u548c\u793a\u4f8b\u4ee3\u7801\uff0c\u4f9b\u65b0\u624b\u5feb\u901f\u5165\u95e8\u5e76\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\u3002\u968f\u7740\u8fdb\u4e00\u6b65\u5b66\u4e60\u548c\u5b9e\u8df5\uff0c\u60a8\u53ef\u4ee5\u5229\u7528clusterProfiler\u7684\u66f4\u591a\u529f\u80fd\u548c\u5de5\u5177\uff0c\u6df1\u5165\u6316\u6398\u57fa\u56e0\u96c6\u5408\u7684\u751f\u7269\u5b66\u610f\u4e49\u3002\u66f4\u591a\u5b66\u4e60\u8d44\u6e90\u8bf7\u5927\u5bb6\u79fb\u6b65\u5c0f\u5e08\u59b9\u4e13\u5c5e\u4e91\u751f\u4fe1\u5e73\u53f0\uff08\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)\uff09\u641c\u7d22\u66f4\u591a\u8d44\u6e90\u54e6\uff01<\/span><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><br \/><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_FR3wic4MfRmIDKtUUHZdHrGxiaj1ow.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/oCSOtP61aEWjRWAeR9wicY9JyrK13cNBaaEibns0HMqkENpTUga2VEOTxwbRFR3wic4MfRmIDKtUUHZdHrGxiaj1ow\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"900\" style=\"letter-spacing: 0.578px;text-align: center;\" data-recalc-dims=\"1\"><br \/><\/p>\n<\/section>\n<\/section>\n<p style=\"display: none;margin-bottom: 24px;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>ClusterProfiler KEGG\u5bcc\u96c6\u5206\u6790\uff1a\u5c0f\u767d\u5fc5\u5907\uff0c\u8f7b\u677e\u638c\u63e1\u7684\u57fa\u56e0\u8868\u8fbe\u89e3\u8bfb\u79d8\u7c4d\uff01 \u5c0f\u5e08\u59b9 & […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59096"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=59096"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59096\/revisions"}],"predecessor-version":[{"id":59103,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59096\/revisions\/59103"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=59096"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=59096"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=59096"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":59096,"date":"2024-06-17T07:36:59","date_gmt":"2024-06-16T23:36:59","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59096"},"modified":"2024-06-17T07:36:59","modified_gmt":"2024-06-16T23:36:59","slug":"clusterprofiler-kegg%e5%af%8c%e9%9b%86%e5%88%86%e6%9e%90%ef%bc%9a%e5%b0%8f%e7%99%bd%e5%bf%85%e5%a4%87%ef%bc%8c%e8%bd%bb%e6%9d%be%e6%8e%8c%e6%8f%a1%e7%9a%84%e5%9f%ba%e5%9b%a0%e8%a1%a8%e8%be%be-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59096","title":{"rendered":"ClusterProfiler KEGG\u5bcc\u96c6\u5206\u6790\uff1a\u5c0f\u767d\u5fc5\u5907\uff0c\u8f7b\u677e\u638c\u63e1\u7684\u57fa\u56e0\u8868\u8fbe\u89e3\u8bfb\u79d8\u7c4d\uff01"},"content":{"rendered":"

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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"ClusterProfiler KEGG\u5bcc\u96c6\u5206\u6790\uff1a\u5c0f\u767d\u5fc5\u5907\uff0c\u8f7b\u677e\u638c\u63e1\u7684\u57fa\u56e0\u8868\u8fbe\u89e3\u8bfb\u79d8\u7c4d\uff01\",\"time\":\"2023-06-21 19:00:26\",\"timeStamp\":\"1687345226\"};\n<\/script><br \/>\n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488611&idx=2&sn=ba9d239bbdeb57cfeaa210331be57f6b&chksm=cf7c84a6f80b0db09f41656ed2011bf953b9750ec8a28aa221308c8973b61a6e0c9798b7486d#rd\" target=\"_blank\" rel=\"noopener\">ClusterProfiler KEGG\u5bcc\u96c6\u5206\u6790\uff1a\u5c0f\u767d\u5fc5\u5907\uff0c\u8f7b\u677e\u638c\u63e1\u7684\u57fa\u56e0\u8868\u8fbe\u89e3\u8bfb\u79d8\u7c4d\uff01<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span class=\"rich_media_meta rich_media_meta_text\">\u5c0f\u5e08\u59b9 <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-06-21 19:00:26<\/em><\/div>\n<p><content><\/p>\n<div class=\"reprint\">\n<p>\u8f6c\u81ea\u516c\u4f17\u53f7\uff1aR\u8bed\u8a00\u5b66\u5f92<br \/><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg5MDk3Mzg4OA==&mid=2247483994&idx=1&sn=8b8631ab41d56321d8b27579b452f506\" target=\"_blank\" title=\"\u9605\u8bfb\u539f\u6587\" rel=\"noopener\">http:\/\/mp.weixin.qq.com\/s?__biz=Mzg5MDk3Mzg4OA==&mid=2247483994&idx=1&sn=8b8631ab41d56321d8b27579b452f506<\/a><\/p>\n<\/div>\n<section style=\"font-size: 16px;margin-bottom: 24px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 20px;margin-bottom: 25px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;background-color: rgb(249, 172, 172);box-shadow: rgb(249, 172, 172) 0px 0px 5px 3px;\">\n<section style=\"text-align: center;transform: translate3d(2px, 0px, 0px);margin-top: -14px;margin-bottom: -14px;\" powered-by=\"xiumi.us\">\n<p>{ \u70b9\u51fb\u84dd\u5b57\uff0c\u5173\u6ce8\u6211\u4eec }<\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">KEGG\uff08Kyoto Encyclopedia of Genes and Genomes\uff09\u662f\u4e00\u4e2a\u5e7f\u6cdb\u4f7f\u7528\u7684\u57fa\u56e0\u901a\u8def\u6570\u636e\u5e93\uff0c\u63d0\u4f9b\u4e86\u5173\u4e8e\u751f\u7269\u7cfb\u7edf\u529f\u80fd\u548c\u8c03\u63a7\u7684\u4e30\u5bcc\u4fe1\u606f\u3002\u4eca\u5929\u5c0f\u5e08\u59b9 \u5c06\u4ecb\u7ecd\u5982\u4f55\u4f7f\u7528R\u8bed\u8a00\u4e2d\u7684clusterProfiler\u5305\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\uff0c\u4ee5\u63ed\u793a\u7ed9\u5b9a\u57fa\u56e0\u96c6\u5408\u4e2d\u5bcc\u96c6\u7684KEGG\u901a\u8def\u3002\u4f7f\u7528clusterProfiler\u8fdb\u884cKEGG\uff08Kyoto Encyclopedia of Genes and Genomes\uff09\u5206\u6790\u7684\u6b65\u9aa4\u4e0eGO\u5206\u6790\u7c7b\u4f3c\uff0c\u4e0b\u9762\u63a5\u7740\u8ddf\u5c0f\u5e08\u59b9\u4e00\u8d77\u6765\u5b66\u4e60\u5427\uff01<\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>1<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u5b89\u88c5\u52a0\u8f7d\u5305<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\">\u5728\u5f00\u59cb\u4e4b\u524d\uff0c\u786e\u4fdd\u5df2\u5728R\u73af\u5883\u4e2d\u5b89\u88c5\u4e86clusterProfiler\u5305\u3002\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u4ee3\u7801\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span> (!require(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>, quietly = <span class=\"code-snippet__literal\">TRUE<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\"> install.packages(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"clusterProfiler\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">library(clusterProfiler)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>2<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u51c6\u5907\u8f93\u5165\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 2em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u4e3a\u4e86\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\uff0c\u6211\u4eec\u9700\u8981\u51c6\u5907\u4e00\u4e2a\u57fa\u56e0\u5217\u8868\uff0c\u8be5\u5217\u8868\u5305\u542b\u6211\u4eec\u611f\u5174\u8da3\u7684\u57fa\u56e0\u3002\u57fa\u56e0\u5217\u8868\u53ef\u4ee5\u662f\u57fa\u56e0\u7b26\u53f7\u3001Ensembl ID\u6216\u5176\u4ed6\u5e38\u89c1\u7684\u57fa\u56e0\u8bc6\u522b\u7b26\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u51c6\u5907\u4e86\u4e00\u4e2a\u540d\u4e3a”gene.txt”\u7684\u6587\u672c\u6587\u4ef6\uff0c\u5176\u4e2d\u5305\u542bEnsembl\u7b26\u53f7\u5217\u8868\uff0c\u6bcf\u884c\u4e00\u4e2a\u57fa\u56e0\u3002<\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9980430528375733\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_iaoQl9icEJdicuG0SNOrsJAhV7sXVw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicCLvh0ZA9P36PkjOicib2NHnHaUBZmciaoQl9icEJdicuG0SNOrsJAhV7sXVw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"511\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe1 \u57fa\u56e0\u5217\u8868\u6587\u4ef6\u5185\u5bb9\u793a\u4f8b<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\">\u4ee3\u7801\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">genes <- read.delim(<span class=\"code-snippet__string\">'gene.txt'<\/span>, header = <span class=\"code-snippet__literal\">TRUE<\/span>, stringsAsFactors = <span class=\"code-snippet__literal\">FALSE<\/span>)[[<span class=\"code-snippet__number\">1<\/span>]]<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>3<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u8fdb\u884c\u57fa\u56e0ID\u8f6c\u6362<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 2em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u5728\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\u4e4b\u524d\uff0c\u6211\u4eec\u9700\u8981\u5bf9\u57fa\u56e0\u5217\u8868\u8fdb\u884c\u57fa\u56e0\u6ce8\u91ca\uff0c\u5c06\u57fa\u56e0\u8bc6\u522b\u7b26\u6620\u5c04\u5230ENTREZID\u4fe1\u606f\u3002\u5728clusterProfiler\u4e2d\uff0c\u53ef\u4ee5\u4f7f\u7528bitr\u51fd\u6570\u8fdb\u884c\u57fa\u56e0\u6ce8\u91ca\u3002<\/p>\n<p powered-by=\"xiumi.us\">\u4ee3\u7801\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5c06ENSEMBL ID\u6620\u5c04\u5230ENTREZID\uff08\u4ee5\u4eba\u7c7b\u4e3a\u4f8b\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gene2kegg <- bitr(genes, fromType = <span class=\"code-snippet__string\">\"ENSEMBL\"<\/span>, toType = <span class=\"code-snippet__string\">\"ENTREZID\"<\/span>, OrgDb = org.Hs.eg.db)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>4<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528enrichKEGG\u51fd\u6570\u5bf9\u6ce8\u91ca\u540e\u7684\u57fa\u56e0\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\u3002\u8be5\u51fd\u6570\u6839\u636e\u57fa\u56e0\u5728\u7279\u5b9aKEGG\u901a\u8def\u4e2d\u7684\u5bcc\u96c6\u7a0b\u5ea6\u8ba1\u7b97\u5bcc\u96c6\u5206\u6570\u548c\u8c03\u6574\u7684p\u503c\u3002\u60a8\u53ef\u4ee5\u9009\u62e9\u4e0d\u540c\u7684\u7edf\u8ba1\u65b9\u6cd5\u548c\u53c2\u6570\u8bbe\u7f6e\u3002\u76f8\u6bd4\u4e0a\u8ff0GO\u5bcc\u96c6\uff0cclusterProfiler\u7684KEGG\u5bcc\u96c6\u5206\u6790\u53ef\u4ee5\u76f4\u63a5\u94fe\u63a5\u5230KEGG\u7684\u5728\u7ebf\u6570\u636e\u5e93\u83b7\u53d6\u5df2\u6709\u7269\u79cd\u7684\u6ce8\u91ca\u3002<\/p>\n<p powered-by=\"xiumi.us\">\u4ee3\u7801\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">getOption(<span class=\"code-snippet__string\">\"clusterProfiler.download.method\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">R.utils::setOption(<span class=\"code-snippet__string\">\"clusterProfiler.download.method\"<\/span>,<span class=\"code-snippet__string\">\"auto\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#KEGG \u5bcc\u96c6\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6bcf\u6b21\u6253\u5f00 R \u8ba1\u7b97\u65f6\uff0c\u5b83\u4f1a\u81ea\u52a8\u8fde\u63a5 KEGG \u5b98\u7f51\u83b7\u5f97\u6700\u8fd1\u7684\u7269\u79cd\u6ce8\u91ca\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">kegg <- enrichKEGG(<\/span><\/code><code><span class=\"code-snippet_outer\"> gene = gene2kegg$ENTREZID, <span class=\"code-snippet__comment\">#\u57fa\u56e0\u5217\u8868\u6587\u4ef6\u4e2d\u7684\u57fa\u56e0\u540d\u79f0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> keyType = <span class=\"code-snippet__string\">'kegg'<\/span>, <span class=\"code-snippet__comment\">#KEGG \u5bcc\u96c6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> organism = <span class=\"code-snippet__string\">\"hsa\"<\/span>, <span class=\"code-snippet__comment\">#\u4f8b\u5982\uff0chsa \u4ee3\u8868\u4eba\u7c7b\uff0c\u5176\u5b83\u7269\u79cd\u66f4\u6539\u8fd9\u884c\u5373\u53ef<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> pAdjustMethod = <span class=\"code-snippet__string\">\"BH\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> pvalueCutoff = <span class=\"code-snippet__number\">0.1<\/span>, <span class=\"code-snippet__comment\">#\u6307\u5b9a p \u503c\u9608\u503c\uff08\u53ef\u6307\u5b9a 1 \u4ee5\u8f93\u51fa\u5168\u90e8\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> qvalueCutoff = <span class=\"code-snippet__number\">0.2<\/span>) <span class=\"code-snippet__comment\">#\u6307\u5b9a q \u503c\u9608\u503c\uff08\u53ef\u6307\u5b9a 1 \u4ee5\u8f93\u51fa\u5168\u90e8\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u7ed3\u679c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">write.table(kegg, <span class=\"code-snippet__string\">'kegg.txt'<\/span>, sep = <span class=\"code-snippet__string\">'t'<\/span>, <span class=\"code-snippet__built_in\">quote<\/span> = <span class=\"code-snippet__literal\">FALSE<\/span>, row.names = <span class=\"code-snippet__literal\">FALSE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\">\u5728\u4e0a\u8ff0\u4ee3\u7801\u4e2d\uff0c\u6211\u4eec\u6307\u5b9a\u4e86\u6ce8\u91ca\u540e\u7684\u57fa\u56e0\uff08gene = gene2kegg$ENTREZID\uff09\uff0c\u9009\u62e9\u4e86\u4eba\u7c7b\uff08organism = “hsa”\uff09\u4f5c\u4e3a\u7814\u7a76\u5bf9\u8c61\uff0c\u5e76\u8bbe\u7f6e\u4e86p\u503c\u548cq\u503c\u7684\u9608\u503c\uff08pvalueCutoff = 0.05, qvalueCutoff = 0.2\uff09\u3002\u53ef\u4ee5\u901a\u8fc7KEGG\u5b98\u7f51\uff08KEGG Organisms: Complete Genomes\uff09\u67e5\u770bKEGG\u6570\u636e\u5e93\u4e2d\u63d0\u4f9b\u7684\u7269\u79cd\u6ce8\u91ca\u5217\u8868\u3002<\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(189, 216, 245);min-width: 5%;height: auto;padding: 6px 15px;\">\n<section style=\"color: rgb(255, 255, 255);text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>5<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: -6px;transform: scale(0.66);transform-origin: left top;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1;transform: translate3d(12px, 0px, 0px);\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.6em solid rgb(247, 221, 223);border-left: 0.6em solid rgb(247, 221, 223);border-bottom: 0.6em solid transparent !important;border-right: 0.6em solid transparent !important;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 100 100 0%;height: auto;align-self: flex-start;background-color: rgb(255, 229, 231);padding: 6px 6px 6px 14px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>\u7ed3\u679c\u89e3\u91ca\u548c\u53ef\u89c6\u5316<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u7ecf\u8fc7KEGG\u5bcc\u96c6\u5206\u6790\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u5bf9\u7ed3\u679c\u8fdb\u884c\u89e3\u91ca\u548c\u53ef\u89c6\u5316\uff0c\u4ee5\u66f4\u597d\u5730\u7406\u89e3\u57fa\u56e0\u96c6\u5408\u4e2d\u5bcc\u96c6\u7684KEGG\u901a\u8def\u3002\u53ef\u4ee5\u4f7f\u7528summary\u51fd\u6570\u548cbarplot\u3001dotplot\u51fd\u6570\u5bf9\u7ed3\u679c\u8fdb\u884c\u6458\u8981\u548c\u53ef\u89c6\u5316\u3002<\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\"><strong>summary\u51fd\u6570\uff1asummary(kegg)<\/strong><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.20277777777777778\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_l3WUaKGDAZibsLLqR9RpJTYT7ZUm2w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicC1M5LbXv3kxNd5ZOl0lzicond9Pl3WUaKGDAZibsLLqR9RpJTYT7ZUm2w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe2 \u67e5\u770b\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u6458\u8981<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"text-indent: 2em;\">\u901a\u8fc7summary\u51fd\u6570\uff0c\u6211\u4eec\u53ef\u4ee5\u67e5\u770bKEGG\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\u6458\u8981\u4fe1\u606f\uff0c\u5305\u62ec\u5bcc\u96c6\u7684KEGG\u901a\u8def\u3001\u8c03\u6574\u7684p\u503c\u3001\u57fa\u56e0\u6570\u7b49\u3002\u8fd9\u4e9b\u4fe1\u606f\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u7406\u89e3\u57fa\u56e0\u96c6\u5408\u5728\u4e0d\u540c\u901a\u8def\u4e2d\u7684\u5bcc\u96c6\u60c5\u51b5\u3002<\/span><\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\"><strong>barplot\u51fd\u6570\uff1abarplot(kegg)<\/strong><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9825581395348837\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_gibBFmZnGj87ZDrs2R7OCib0TEMP7A.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicCicHw6icvCpwr3nuDzzZicHdVbhIkzgibBFmZnGj87ZDrs2R7OCib0TEMP7A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"860\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe3 \u5bcc\u96c6\u67f1\u5f62\u56fe<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\"><strong><span style=\"text-indent: 2em;\">dotplot\u51fd\u6570\uff1adotplot(kegg)<\/span><\/strong><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9905992949471211\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_m8zfbcllMicUQsEq05LzpibZYicDSQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicCmGj76hzhG6gpDZ3oSaVGsQ6qsaem8zfbcllMicUQsEq05LzpibZYicDSQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"851\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe4 \u5bcc\u96c6\u6c14\u6ce1\u56fe<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"text-indent: 2em;\">\u4f7f\u7528barplot\u51fd\u6570\u548cdotplot\u51fd\u6570\uff0c\u6211\u4eec\u53ef\u4ee5\u751f\u6210\u5bcc\u96c6\u7ed3\u679c\u7684\u53ef\u89c6\u5316\u56fe\u8868\uff0c\u4ee5\u66f4\u76f4\u89c2\u5730\u5c55\u793a\u57fa\u56e0\u96c6\u5408\u7684KEGG\u5bcc\u96c6\u60c5\u51b5\u3002\u8be5\u51fd\u6570\u53ef\u4ee5\u751f\u6210\u67f1\u72b6\u56fe\u6216\u6c14\u6ce1\u56fe\uff0c\u5176\u4e2d\u6bcf\u4e2a\u67f1\u5b50\u6216\u6c14\u6ce1\u4ee3\u8868\u4e00\u4e2a\u5bcc\u96c6\u7684KEGG\u901a\u8def\uff0c\u5176\u9ad8\u5ea6\u6216\u5927\u5c0f\u8868\u793a\u5bcc\u96c6\u7a0b\u5ea6\u7684\u6307\u6807\uff08\u5982p\u503c\u3001\u57fa\u56e0\u6570\u7b49\uff09\u3002<\/span><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">pathview\u5305\u53ef\u4ee5\u53ef\u89c6\u5316KEGG \u901a\u8def\uff0c\u6211\u4eec\u53ef\u4ee5\u7528\u5b83\u67e5\u770b\u7279\u5b9a\u901a\u8def\u56fe\u3002<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\">\u4ee3\u7801\uff1a<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"pathview\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">library(pathview)<\/span><\/code><code><span class=\"code-snippet_outer\">hsa04750 <- pathview(gene.data = geneList,<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"> pathway.id = <span class=\"code-snippet__string\">\"hsa04750\"<\/span>, <span class=\"code-snippet__comment\">#\u4e0a\u8ff0\u7ed3\u679c\u4e2d\u7684hsa04750\u901a\u8def<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"> species = <span class=\"code-snippet__string\">\"hsa\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"> limit = <span class=\"code-snippet__built_in\">list<\/span>(gene=<span class=\"code-snippet__built_in\">max<\/span>(<span class=\"code-snippet__built_in\">abs<\/span>(geneList)), cpd=<span class=\"code-snippet__number\">1<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6296296296296297\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_6AmGjkhvaU84Ryj2dd0iaiahrjehGg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUs5CyNWdLD0d3SibfRrNOicCCIPW7O8n02MdzWqpAub8Fr7QNy6AmGjkhvaU84Ryj2dd0iaiahrjehGg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 12px;color: rgb(160, 160, 160);\" powered-by=\"xiumi.us\">\n<p>\u56fe5 \u7279\u5b9a\u901a\u8def\uff08hsa04750\uff09\u56fe<\/p>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\"><span style=\"text-indent: 2em;\">\u9664\u4e86\u4e0a\u8ff0\u57fa\u672c\u7684KEGG\u5bcc\u96c6\u5206\u6790\u5916\uff0cclusterProfiler\u8fd8\u63d0\u4f9b\u4e86\u5176\u4ed6\u529f\u80fd\u548c\u5de5\u5177\uff0c\u4ee5\u8fdb\u4e00\u6b65\u6df1\u5165\u5206\u6790\u548c\u89e3\u91ca\u57fa\u56e0\u96c6\u5408\u7684\u751f\u7269\u5b66\u610f\u4e49\u3002\u4f8b\u5982\uff1a<\/span><\/p>\n<ul style=\"list-style-type: \uf06c;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" 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