{"id":54861,"date":"2024-06-16T14:31:05","date_gmt":"2024-06-16T06:31:05","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54861"},"modified":"2024-06-16T14:31:05","modified_gmt":"2024-06-16T06:31:05","slug":"go%e5%af%8c%e9%9b%86%e5%88%86%e6%9e%90%e5%82%bb%e7%93%9c%e5%bc%8f%e6%95%99%e7%a8%8b","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54861","title":{"rendered":"GO\u5bcc\u96c6\u5206\u6790\u50bb\u74dc\u5f0f\u6559\u7a0b"},"content":{"rendered":"<p><html><br \/>\n<head><br \/>\n<title><\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 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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<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><span style=\"letter-spacing: 0.034em;\">\u4f17\u6240\u5468\u77e5\uff0c\u5728\u5bcc\u96c6\u5206\u6790\u8fd9\u4e00\u5757\uff0cGO\u548cKEGG\u4e24\u5927\u5de8\u5934\u7262\u7262\u5360\u636e\u7740\u821e\u53f0\u4e2d\u592e\u3002<\/span><span style=\"letter-spacing: 0.034em;\">\u5f53\u5dee\u5f02\u5206\u6790\u83b7\u5f97\u4e86\u5927\u91cf\u7684\u5dee\u5f02\u57fa\u56e0\u6216\u8005\u86cb\u767d\u65f6\uff0c\u5c31\u9700\u8981GO\u5bcc\u96c6\u5206\u6790\u5c06\u57fa\u56e0\u6d3b\u86cb\u767d\u5206\u4e3a\u51e0\u4e2a\u5927\u7c7b\uff0c\u540c\u6545\u5bab\u89c2\u5bdf\u8fd9\u51e0\u5927\u7c7b\u7684\u533a\u522b\uff0c\u76f8\u8f83\u4e8e\u4e0a\u767e\u4e2a\u57fa\u56e0\u6216\u86cb\u767d\u7684\u5dee\u5f02\u8981\u66f4\u52a0\u76f4\u89c2\uff0c\u5206\u6790\u7684\u96be\u5ea6\u4e5f\u4f1a\u964d\u4f4e\uff0c\u8fd9\u4e2a\u8fc7\u7a0b\u5c31\u662f\u5bcc\u96c6\u5206\u6790\u3002<\/span><br  \/><\/p>\n<p style=\"white-space: normal;\"><br  \/><\/p>\n<p style=\"white-space: normal;\">\u597d\u5566\uff0c\u90a3\u4e48\u5e9f\u8bdd\u4e0d\u591a\u8bf4\uff0c\u54b1\u5f00\u59cb\u5b9e\u64cd\u5427\u3002<\/p>\n<p style=\"white-space: normal;\"><br  \/><\/p>\n<p style=\"white-space: normal;\"><strong>\u9996\u5148\u54b1\u5148\u628abioconductor\u548cGO\u76f8\u5173\u5305\u5b89\u88c5\u4e86<\/strong><\/p>\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<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\">options(BioC_mirror=<span class=\"code-snippet__string\">\"http:\/\/mirrors.ustc.edu.cn\/bioc\/\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"DO.db\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"BiocUpgrade\"<\/span>)<\/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\">BiocManager::install(<span class=\"code-snippet__string\">\"fastmatch\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"gridExtra\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"ggraph\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"UpSetR\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"cowplot\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"ggridges\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"org.Hs.eg.db\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"topGO\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"Rgraphviz\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;\" powered-by=\"xiumi.us\"><br  \/><\/p>\n<p style=\"white-space: normal;\" powered-by=\"xiumi.us\"><strong>\u5982\u679c\u62a5\u9519\uff1a<\/strong><\/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\">Warning message: In file(filename, <span class=\"code-snippet__string\">\"r\"<\/span>, encoding = encoding) : InternetOpenUrl failed: <span class=\"code-snippet__string\">'\u64cd\u4f5c\u8d85\u65f6'<\/span>\u3002<\/span><\/code><\/pre>\n<\/section>\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=\"1.16750418760469\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-14_\u300c\u8f6c\u300dGO\u5bcc\u96c6\u5206\u6790\u50bb\u74dc\u5f0f\u6559\u7a0b\/1_3GYIf7PsvWwTZROlUAcPapDlgqK6uQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUZ7dhqcnibiax7ZEsgBTTBGJpRBA1xFfxZgufiaITKceHSvbT3GYIf7PsvWwTZROlUAcPapDlgqK6uQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"597\" style=\"vertical-align: middle;width: 100%;\"  \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u8ddf\u7740\u5c0f\u5e08\u59b9\u628a\u6e90\u4fee\u6539\u4e86\u5373\u53ef\u3002<\/p>\n<p style=\"white-space: normal;\"><br  \/><\/p>\n<p style=\"white-space: normal;\"><strong>\u6216\u8005\u54b1\u6765\u624b\u9ad8\u7ea7\u7684\uff0c\u4fee\u6539Rprofile.site.<\/strong><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">R.home()<span class=\"code-snippet__comment\">#\u67e5\u770bR\u5b89\u88c5\u5728\u54ea<\/span><\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><strong>\u6839\u636e\u4e0a\u8ff0\u547d\u4ee4\u6307\u51fa\u6765\u7684\u8def\u5f84\u4fee\u6539\u955c\u50cf<\/strong><br  \/><\/p>\n<p style=\"white-space: normal;\"><strong>\u67e5\u627eX:XXXR-X.X.Xetc \u8def\u5f84\u4e0b\u7684Rprofile.site\u6587\u4ef6\uff0c\u7528\u8bb0\u4e8b\u672c\u7684\u65b9\u5f0f\u6253\u5f00\uff0c\u5199\u5165\u5982\u4e0b\u547d\u4ee4\uff1a<\/strong><\/p>\n<\/section>\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=\"0.6033653846153846\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-14_\u300c\u8f6c\u300dGO\u5bcc\u96c6\u5206\u6790\u50bb\u74dc\u5f0f\u6559\u7a0b\/2_HKAY96LLRr2qHXia1RvKLH99HcoXVw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUZ7dhqcnibiax7ZEsgBTTBGJ7eMx6ic5c3KHbp0W8VSB4KwdibgHKAY96LLRr2qHXia1RvKLH99HcoXVw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"832\" style=\"vertical-align: middle;width: 100%;\"  \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\"><strong>\u8fd8\u6709\u53ef\u80fd\u62a5\u9519\uff1apackage \u2018XXX\u2019 is not available (for R version X.X.X)<\/strong><br  \/><\/p>\n<p style=\"white-space: normal;\"><strong><br  \/><\/strong><\/p>\n<p style=\"white-space: normal;\">\u8fd9\u4e2a\u62a5\u9519\u7684\u95ee\u9898\u4e00\u822c\u662f\u7248\u672c\u7684\u95ee\u9898\uff0c\u5f88\u5927\u53ef\u80fd\u5c31\u662f\u4f9d\u8d56bioconductor\u7684\u5305\u4f7f\u7528\u4e86r\u547d\u4ee4install.packages\u5b89\u88c5\uff08\u770b\u5565\uff0c\u5c31\u662f\u4f60\uff0c\u8001\u8001\u5b9e\u5b9e\u8ddf\u7740\u5c0f\u5e08\u59b9\u8d70\uff0c\u4ee3\u7801\u90fd\u662f\u6d4b\u8bd5\u8fc7\u7684\uff0c\u51fa\u95ee\u9898\u7684\u6982\u7387\u4e0d\u5927\uff0c\u5c0f\u5e08\u59b9\u53ef\u53ef\u7231\u7231\uff0c\u8fd8\u80fd\u5bb3\u4e86\u4f60\u4e0d\u6210\uff09<\/p>\n<p style=\"white-space: normal;\"><br  \/><\/p>\n<p style=\"white-space: normal;\"><strong>\u5b89\u88c5\u597d\u8f6f\u4ef6\u540e\uff0cgo\u5bcc\u96c6\u5206\u6790\u6b63\u5f0f\u5f00\u59cb\uff1a<\/strong><\/p>\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<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\">install.packages(xlsx)<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(readxl)<\/span><\/code><code><span class=\"code-snippet_outer\">library(xlsx)<\/span><\/code><code><span class=\"code-snippet_outer\">library(readxl)<\/span><\/code><code><span class=\"code-snippet_outer\">model&lt;-read.xlsx(<span class=\"code-snippet__string\">\"F:\/download\/38gene.xlsx\"<\/span>,<span class=\"code-snippet__number\">1<\/span>,header=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">model&lt;-data.frame(model)<\/span><\/code><code><span class=\"code-snippet_outer\">library(clusterProfiler)<\/span><\/code><code><span class=\"code-snippet_outer\">GENEID_model = bitr(model, fromType=<span class=\"code-snippet__string\">\"SYMBOL\"<\/span>, toType=<span class=\"code-snippet__string\">\"ENTREZID\"<\/span>, OrgDb=<span class=\"code-snippet__string\">\"org.Hs.eg.db\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#GENID_LIST=as.vector(t(GENEID_model))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">go_model &lt;- enrichGO(GENEID_model, OrgDb = org.Hs.eg.db, ont=<span class=\"code-snippet__string\">'ALL'<\/span>,pAdjustMethod = <span class=\"code-snippet__string\">'BH'<\/span>,pvalueCutoff = <span class=\"code-snippet__number\">0.05<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; qvalueCutoff = <span class=\"code-snippet__number\">0.2<\/span>,keyType = <span class=\"code-snippet__string\">'ENTREZID'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv((as.data.frame(go_model)),<span class=\"code-snippet__string\">\"F:\/download\/GENEID_model.csv\"<\/span>,row.names =<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">###go\u5bcc\u96c6\u7ed3\u679cbarplot\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">barplot(go_model,showCategory=<span class=\"code-snippet__number\">20<\/span>,drop=<span class=\"code-snippet__built_in\">T<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">####go\u5bcc\u96c6\u7ed3\u679c\u70b9\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">dotplot(go_model,showCategory=<span class=\"code-snippet__number\">50<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">###\u7ed8\u5236GO\u7684\u7f51\u7edc\u5173\u7cfb\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">go.BP &lt;- enrichGO(go_model, OrgDb = org.Hs.eg.db, ont=<span class=\"code-snippet__string\">'CC'<\/span>,pAdjustMethod = <span class=\"code-snippet__string\">'BH'<\/span>, pvalueCutoff = <span class=\"code-snippet__number\">0.05<\/span>, qvalueCutoff = <span class=\"code-snippet__number\">0.2<\/span>, keyType = <span class=\"code-snippet__string\">'ENTREZID'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">plotGOgraph(go.BP)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">###ont='CC'\u4e5f\u53ef\u4ee5\u6539\u4e3aont='BP'\u6216ont='MF'<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;\" powered-by=\"xiumi.us\">\u5c0f\u5e08\u59b9\u8fd9\u5f3a\u8c03\u4e00\u4e0b\uff0c\u4ee5\u4e0a\u6559\u7a0b<strong><span style=\"color: rgb(249, 110, 87);\">\u57fa\u4e8eclusterProfile<\/span><\/strong>\uff0c\u76ee\u524d\u53ea\u652f\u630119\u4e2a\u5e38\u89c1\u7684\u7269\u79cd\uff0c\u5176\u4ed6\u975e\u6a21\u5f0f\u751f\u7269\u7a0d\u5fae\u590d\u6742\u4e9b\uff0c\u5173\u6ce8\u5c0f\u5e08\u59b9\uff0c\u54b1\u4f1a\u5728\u65e5\u540e\u628a\u8fd9\u4e9b\u90fd\u5b89\u6392\u4e0a\u3002<\/p>\n<section style=\"text-align: left;justify-content: center;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;flex: 100 100 0%;height: auto;align-self: center;margin-right: 10px;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><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\/3_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=\"\"  data-recalc-dims=\"1\" \/><\/p>\n<section style=\"background-color: rgb(249, 172, 172);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float: left;line-height: 0;width: 0px;vertical-align: top;text-align: left;\"><\/svg><\/section>\n<\/section>\n<\/section>\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>GO\u5bcc\u96c6\u5206\u6790\u50bb\u74dc\u5f0f\u6559\u7a0b \u5c0f\u5e08\u59b9&nbsp;&nbsp;\u751f\u4fe1\u679c&nbsp;&nbsp;2023-06-14 19 [&hellip;]<\/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\/54861"}],"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=54861"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/54861\/revisions"}],"predecessor-version":[{"id":54865,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/54861\/revisions\/54865"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=54861"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=54861"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=54861"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}