{"id":54672,"date":"2024-06-16T14:23:21","date_gmt":"2024-06-16T06:23:21","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54672"},"modified":"2024-06-16T14:23:21","modified_gmt":"2024-06-16T06:23:21","slug":"tcga%e5%8e%9f%e5%a7%8b%e8%a1%a8%e8%be%be%e8%b0%b1%e6%95%b0%e6%8d%ae%e5%a6%82%e4%bd%95%e5%a4%84%e7%90%86%ef%bc%9f%e4%b8%80%e4%b8%aar%e5%8c%85%e5%b8%ae%e4%bd%a0%e6%90%9e%e5%ae%9a%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54672","title":{"rendered":"TCGA\u539f\u59cb\u8868\u8fbe\u8c31\u6570\u636e\u5982\u4f55\u5904\u7406\uff1f\u4e00\u4e2aR\u5305\u5e2e\u4f60\u641e\u5b9a\uff01"},"content":{"rendered":"


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flex-start;\">\n<section style=\"display: flex;flex-flow: row;margin: -9px 0% 5px;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 0 0 0%;height: auto;line-height: 0;align-self: flex-start;border-width: 0px;margin-top: 5px;margin-left: 7px;\">\n<section style=\"text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 2px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(59, 149, 115);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;margin: -6px 0% 4px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 10px;height: 2px;vertical-align: top;overflow: hidden;background-color: rgb(59, 149, 115);\"><svg viewbox=\"0 0 1 1\" 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115);font-size: 19px;padding-right: 11px;padding-left: 11px;line-height: 1;text-align: justify;\">\n<p style=\"text-align: left;text-wrap: wrap;\"><strong>\u70b9\u51fb\u84dd\u5b57 \u5173\u6ce8\u6211\u4eec<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;line-height: 0;flex: 0 0 0%;height: auto;\">\n<section style=\"text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 16px;height: 12px;vertical-align: top;overflow: hidden;background-color: rgb(59, 149, 115);padding-right: 2px;padding-left: 2px;\">\n<section style=\"justify-content: center;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: 50%;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"margin-top: 4px;margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 3px;height: 3px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 155px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 245, 245);\"><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 style=\"display: inline-block;vertical-align: top;width: 50%;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"margin-top: 4px;margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 3px;height: 3px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 155px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 245, 245);\"><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>\n<\/section>\n<section style=\"text-align: center;transform: translate3d(3px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 0px 0px 4px 4px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(59, 149, 115);\"><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>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><br \/><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u751f\u7269\u4fe1\u606f\u5b66\u6700\u5e38\u7528\u7684\u6570\u636e\u5e93\u6709\u54ea\u4e9b\uff1f\u5927\u6d77\u54e5\u8ba4\u4e3a\uff0c\u4e0d\u7ba1\u6709\u8c01\uff0c\u80af\u5b9a\u4e0d\u80fd\u5c11\u4e86TCGA\uff08The Cancer Genome Atlas\uff09\uff0c\u8d5e\u540c\u7684\u5c0f\u4f19\u4f34\u70b9\u4e2a\u8d5e^-^<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><br \/><\/p>\n<p>TCGA\uff08The Cancer Genome Atlas\uff09\u662f\u4e00\u4e2a\u65e8\u5728\u5e2e\u52a9\u6df1\u5165\u4e86\u89e3\u591a\u79cd\u764c\u75c7\u7c7b\u578b\u7684\u9879\u76ee\uff0c\u901a\u8fc7\u6536\u96c6\u3001\u5206\u6790\u548c\u5206\u4eab\u6765\u81ea\u591a\u79cd\u764c\u75c7\u60a3\u8005\u7684\u5927\u89c4\u6a21\u57fa\u56e0\u7ec4\u6570\u636e\uff0c\u4ee5\u66f4\u597d\u5730\u4e86\u89e3\u764c\u75c7\u7684\u5206\u5b50\u673a\u5236\u3001\u8bca\u65ad\u6807\u5fd7\u7269\u548c\u6cbb\u7597\u65b9\u6cd5\u3002\u8be5\u9879\u76ee\u4f7f\u7528\u4e86\u591a\u79cd\u9ad8\u901a\u91cf\u6280\u672f\uff0c\u5176\u4e2d\u6211\u4eec\u6700\u5e38\u4f7f\u7528\u7684\u662f\u6765\u6e90\u4e8eRNA\u6d4b\u5e8f\uff08RNASeq\uff09\u6280\u672f\u7684\u57fa\u56e0\u8868\u8fbe\u8c31\u6570\u636e\uff0c\u4f46\u4e00\u822c\u7ed9\u51fa\u7684\u6d4b\u5e8f\u6570\u636e\u662f\u5305\u542b\u7f16\u7801\u548c\u975e\u7f16\u7801RNA\u7684\u3002\u5bf9\u4e8e\u4e0d\u540c\u8bfe\u9898\u7ec4\u7ecf\u5e38\u4f1a\u6709\u4e0d\u540c\u7684\u7814\u7a76\u503e\u5411\uff0c\u9700\u8981\u4ece\u6570\u636e\u4e2d\u5c06\u6240\u6709\u975e\u7f16\u7801RNA\u63d0\u53d6\u6216\u5254\u9664\u51fa\u53bb\u3002\u5176\u5b9e\u53ef\u4ee5\u901a\u8fc7Excel\u7b49\u65b9\u5f0f\u6765\u64cd\u4f5c\uff0c\u4f46\u90a3\u6837\u5176\u5b9e\u5f88\u9ebb\u70e6\uff0c\u4eca\u5929\u5927\u6d77\u54e5\u5e26\u5927\u5bb6\u7528R\u8bed\u8a00\u6765\u5b9e\u73b0\uff01<\/p>\n<p><br \/><\/p>\n<p>\u5f00\u59cb\u4e4b\u524d\uff0c\u5927\u5bb6\u5148\u4e86\u89e3\u4e00\u4e0b<span style=\"color: rgb(59, 149, 115);\"><strong>\u4ec0\u4e48\u662fEnsembl ID\u3001Entrez ID\u548cGene symbol\uff1f<\/strong><\/span><\/p>\n<p><span style=\"color: rgb(59, 149, 115);\"><strong><br \/><\/strong><\/span><\/p>\n<p><strong><span style=\"color: rgb(59, 149, 115);\">Gene ID <\/span><\/strong>\u4e5f\u79f0Entrez ID\/EntrezGene ID \uff0c\u662f NCBI \u4f7f\u7528\u7684\u80fd\u591f\u5bf9\u4f17\u591a\u6570\u636e\u5e93\u8fdb\u884c\u8054\u5408\u641c\u7d22\u7684\u641c\u7d22\u5f15\u64ce, \u5176\u5bf9\u4e0d\u540c\u7684 Gene \u8fdb\u884c\u4e86\u7f16\u53f7, \u6bcf\u4e2a gene \u7684\u7f16\u53f7\u5c31\u662f entrez gene id\uff0c\u5c31\u662f\u4e00\u4e32\u6570\u5b57\uff0c\u6bd4\u5982\uff1aTP53 \u7684Gene ID\u662f:7157\u3002\u56e0\u4e3aentrez ID\u76f8\u5bf9\u7a33\u5b9a, \u6240\u4ee5\u4e5f\u88ab\u5176\u4ed6\u6570\u636e\u5e93, \u5982 KEGG \u7b49\u91c7\u7528\u3002\u4e0d\u540c\u7269\u79cd\u7684\u540c\u4e00\u4e2a\u57fa\u56e0\u7684Gene ID\u662f\u4e0d\u540c\u7684\u3002<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><strong><span style=\"color: rgb(59, 149, 115);\">Gene Symbol<\/span><\/strong> \uff0c\u662fHGNC\u6570\u636e\u5e93\u4e3a\u57fa\u56e0\u63d0\u4f9b\u7684\u5b98\u65b9\u540d\u79f0\uff0cHGNC\u662f\u4eba\u7c7b\u57fa\u56e0\u547d\u540d\u59d4\u5458\u4f1a(HUGO Gene Nomenclature Committee);\u4eba\u7c7b\u57fa\u56e0\u7ec4\u547d\u540d\u59d4\u5458\u4f1a\u3002\u6709\u4e13\u95e8\u7684\u6570\u636e\u5e93\uff1ahttps:\/\/www.genenames.org\/\u3002\u4e3b\u8981\u662f\u6309\u57fa\u56e0\u7684\u529f\u80fd\u8d77\u7684\u540d\u5b57\uff0c\u5b57\u6bcd\u4e00\u822c\u4e3a\u82f1\u6587\u5168\u79f0\u7684\u7f29\u5199\uff0c\u7531\u5927\u5199\u5b57\u6bcd\u548c\u6570\u5b57\u7ec4\u6210\uff0c\u5982TP53\u57fa\u56e0\u7684Official Symbol\u5c31\u662f\u7531HGNC\u6240\u63d0\u4f9b\u3002<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><strong><span style=\"color: rgb(59, 149, 115);\">Ensembl ID<\/span><\/strong>\uff0c\u662f\u5728Ensembl\u6570\u636e\u5e93\u4e2d\u5bf9\u57fa\u56e0\u7684\u547d\u540d\uff0c\u5e38\u89c1\u7684\u7269\u79cd\u524d\u7f00\uff1a\u201cENS\u201c\u8868\u793aHomo sapiens (Human)\uff0c\u201dENSMUS\u201c\u8868\u793aMus musculus (Mouse)\uff0c\u201dENSDAR\u201c\u8868\u793aDanio rerio (Zebrafish)\uff1b\u800c\u5e38\u89c1\u7684\u5e8f\u5217\u7c7b\u578b\u7528G\u3001P\u3001T\u3001\u5206\u522b\u8868\u793agene\u3001protein\u548ctranscript\u3002TCGA\u4e0b\u8f7d\u7684\u6570\u636e\u4e00\u822c\u5c31\u662f\u7528\u7684Ensembl ID\u3002<\/p>\n<p><br \/><\/p>\n<p>\u90a3\u4e48\u4e86\u89e3\u5b8c\u57fa\u672c\u6982\u5ff5\u540e\uff0c\u6211\u4eec\u5c31\u4f7f\u7528\u4eca\u5929\u7684\u4e3b\u89d2R\u5305\uff1aBioMart\u6765\u5f00\u59cb\u64cd\u4f5c\u5427\uff01<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u52a0\u8f7d\u6240\u9700R\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">suppressPackageStartupMessages({<\/span><\/code><code><span class=\"code-snippet_outer\">  library(biomaRt)<\/span><\/code><code><span class=\"code-snippet_outer\">  library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\">})<\/span><\/code><code><span class=\"code-snippet_outer\">  <span class=\"code-snippet__comment\">#\u4f7f\u7528biomaRt\u521b\u5efa\u8f6c\u6362\u8868<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">  biomart_table <- getBM(<\/span><\/code><code><span class=\"code-snippet_outer\">  <span class=\"code-snippet__built_in\">attributes<\/span> = <span class=\"code-snippet__built_in\">c<\/span>(<\/span><\/code><code><span class=\"code-snippet_outer\">    <span class=\"code-snippet__string\">\"external_gene_name\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">    <span class=\"code-snippet__string\">\"ensembl_gene_id\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">    <span class=\"code-snippet__string\">\"entrezgene_id\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">    <span class=\"code-snippet__string\">\"gene_biotype\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">  ),<\/span><\/code><code><span class=\"code-snippet_outer\">  mart = useMart(<span class=\"code-snippet__string\">\"ensembl\"<\/span>, dataset = <span class=\"code-snippet__string\">\"hsapiens_gene_ensembl\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">) <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u770b\u770b\u957f\u5565\u6837<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.2490740740740741\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_fXe7JqQUWuCYEEy1d69O8LbACXMibA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQsOLouKj7aN2ybPkPOnaaO27FKS4tqY3jSeWOdiarxWbIo71fXe7JqQUWuCYEEy1d69O8LbACXMibA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#########\u5bf9\u4e8e\u4e0d\u540c\u7269\u79cd\uff0c\u9700\u8981\u4fee\u6539dataset\uff0c\u53ef\u4ee5\u4f7f\u7528\u5982\u4e0b\u4ee3\u7801\u67e5\u770b\uff1a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">##mart = useMart('ensembl')<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">##listDatasets(mart)<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"1.2157407407407408\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-24_\u300c\u8f6c\u300dTCGA\u539f\u59cb\u8868\u8fbe\u8c31\u6570\u636e\u5982\u4f55\u5904\u7406\uff1f\u4e00\u4e2aR\u5305\u5e2e\u4f60\u641e\u5b9a\uff01\/2_bomP9W65WsxE9QKzQBRglUUVzLoEwg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQsOLouKj7aN2ybPkPOnaaOwwgVcGlXLmC2gAic77dz77HEXibomP9W65WsxE9QKzQBRglUUVzLoEwg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/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__comment\">#\u6709\u5f88\u591a\u7269\u79cd\u54e6\uff01\u81ea\u7531\u6311\u9009~<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u4f7f\u7528NA\u4ee3\u66ff\u7a7a\u503c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">biomart_table[biomart_table == <span class=\"code-snippet__string\">\"\"<\/span>] <- <span class=\"code-snippet__literal\">NA<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4fdd\u7559\u51e0\u4e2a\u5173\u952e\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">biomart_table <- biomart_table %>%<\/span><\/code><code><span class=\"code-snippet_outer\">  dplyr::select(<\/span><\/code><code><span class=\"code-snippet_outer\">    <span class=\"code-snippet__string\">\"Symbol\"<\/span>    = external_gene_name,<\/span><\/code><code><span class=\"code-snippet_outer\">    <span class=\"code-snippet__string\">\"Ensembl\"<\/span> = ensembl_gene_id,<\/span><\/code><code><span class=\"code-snippet_outer\">    <span class=\"code-snippet__string\">\"Entrez\"<\/span>  = entrezgene_id,<\/span><\/code><code><span class=\"code-snippet_outer\">    <span class=\"code-snippet__string\">\"Biotype\"<\/span> = gene_biotype<\/span><\/code><code><span class=\"code-snippet_outer\">  ) %>%<\/span><\/code><code><span class=\"code-snippet_outer\">  arrange(Symbol, Ensembl, Entrez, Biotype)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4fdd\u5b58\u7ed3\u679c\u6ce8\u91ca\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">save(biomart_table, <span class=\"code-snippet__string\">\" biomart_table_homo.RData\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6ce8\u91ca\u6587\u4ef6\u7ecf\u8fc7\u5904\u7406\uff0c\u6700\u540e\u5305\u542b\u4ee5\u4e0b\u8fd9\u51e0\u5217<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.33055555555555555\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_aicBzVuibUicatB3TpyCictm7kZzBw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQsOLouKj7aN2ybPkPOnaaOGic7jHpM7eDtcNBy0p39qpJQl6icAUaicBzVuibUicatB3TpyCictm7kZzBw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u81f3\u6b64\uff0c\u5c31\u53ef\u4ee5\u5f97\u5230\u6ce8\u91ca\u6587\u4ef6\uff0c\u63a5\u4e0b\u6765\u7684\u4efb\u52a1\u5c31\u662f\u5339\u914d\uff0c\u53ef\u4ee5\u4f7f\u7528Excel\uff0c\u65b9\u4fbf\u7684\u8bdd\u8fd8\u662f\u7528R\uff1a<\/p>\n<p><br \/><\/p>\n<p>load(“biomart_table_homo.RData”)<\/p>\n<p>results <- read.delim(“diffexpr-results.txt”)  #\u8fd9\u662f\u5927\u6d77\u54e5\u7684\u6570\u636e\u54e6\uff01\u53ea\u7528\u8981\u6c42\u6570\u636e\u7b2c\u4e00\u5217\u4e3aEnsembl ID\u5c31\u53ef\u4ee5\u4e86\uff0c\u5176\u4ed6\u6ca1\u6709\u8981\u6c42<\/p>\n<p>results2 <- merge(results,biomart_table[c(2,1,4)],by = “Ensembl”)<\/p>\n<p>results2 <- merge(biomart_table[c(2,1,4)],by = “Ensembl”,results)<\/p>\n<p>write.csv(results2,”results.csv”)<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.5972222222222222\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_hpxIz8w0CwKj5oicMphufu6JOjuzHw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQsOLouKj7aN2ybPkPOnaaOo1YjCc25mzXsxvcKnmzt4Vd5KhpxIz8w0CwKj5oicMphufu6JOjuzHw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/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<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\">#\u7136\u540e\u53ef\u4ee5\u770b\u5230\u83b7\u5f97\u4e86\u5bf9\u5e94\u7684Symbol\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6b64\u5916\uff0c\u8fd8\u53ef\u4ee5\u6839\u636e\u8fd9\u4e2a\u5305\u8fdb\u884c\u4eba\u9f20\u540c\u6e90\u57fa\u56e0\u540d\u5b57\u8f6c\u5316\uff0c\u4f7f\u7528getLDS\u51fd\u6570\uff0c\u5b83\u662fbiomaRt\u67e5\u8be2\u7684\u4e3b\u8981\u529f\u80fd\uff0c\u8fde\u63a5\u4e24\u4e2a\u6570\u636e\u96c6\uff0c\u5e76\u4ece\u8fd9\u4e9b\u94fe\u63a5\u7684biomaRt\u6570\u636e\u96c6\u68c0\u7d22\u4fe1\u606f\u3002\u5728Ensembl\u4e2d\uff0c\u8fd9\u8f6c\u5316\u4e3a\u540c\u6e90\u6620\u5c04\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f7f\u7528\u4e9a\u6d32\u955c\u50cf<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">human <- useEnsembl(<span class=\"code-snippet__string\">'ensembl'<\/span>,dataset = <span class=\"code-snippet__string\">\"hsapiens_gene_ensembl\"<\/span>, mirror = <span class=\"code-snippet__string\">\"asia\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">mouse <- useEnsembl(<span class=\"code-snippet__string\">'ensembl'<\/span>,dataset = <span class=\"code-snippet__string\">\"mmusculus_gene_ensembl\"<\/span>, mirror = <span class=\"code-snippet__string\">\"asia\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6bd4\u5982\u6211\u6709\u4e00\u7cfb\u5217\u5c0f\u9f20\u57fa\u56e0\uff1a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">mouse.genes <- <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Psme2b\"<\/span>,<span class=\"code-snippet__string\">\"Zfp661\"<\/span>,<span class=\"code-snippet__string\">\"Tsc22d1\"<\/span>,<span class=\"code-snippet__string\">\"Prox2\"<\/span>,<span class=\"code-snippet__string\">\"Eml3\"<\/span>,<span class=\"code-snippet__string\">\"Creb1\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5c06\u5176\u6620\u5c04\u5230\u4eba\u7684\u57fa\u56e0\u4e0a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">MtoH <- getLDS(<span class=\"code-snippet__built_in\">attributes<\/span> = <span class=\"code-snippet__string\">\"mgi_symbol\"<\/span>, <span class=\"code-snippet__comment\"># \u8981\u8f6c\u6362\u7b26\u53f7\u7684\u5c5e\u6027\uff0c\u8fd9\u91cc\u57fa\u56e0\u540d\uff08\u7b2c3\u6b65\u662f\u57fa\u56e0\u540d\uff09<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">               filters = <span class=\"code-snippet__string\">\"mgi_symbol\"<\/span>, <span class=\"code-snippet__comment\">#\u53c2\u6570\u8fc7\u6ee4<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">               mart = mouse, <span class=\"code-snippet__comment\">#\u9700\u8981\u8f6c\u6362\u7684\u57fa\u56e0\u540d\u7684\u79cd\u5c5e\u6765\u6e90\uff0c\u4e5f\u5c31\u662f\u7b2c2\u6b65\u7684mouse<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">               values = mouse.genes, <span class=\"code-snippet__comment\">#\u8981\u8f6c\u6362\u7684\u57fa\u56e0\u96c6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">               attributesL = <span class=\"code-snippet__string\">\"hgnc_symbol\"<\/span>, <span class=\"code-snippet__comment\">#\u8981\u540c\u6e90\u8f6c\u6362\u7684\u76ee\u6807\u5c5e\u6027\uff0c\u8fd9\u91cc\u8fd8\u662f\u8f6c\u4e3a\u57fa\u56e0\u540d\uff0c\u4e5f\u53ef\u52a0\u5176\u4ed6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">               martL = human, <span class=\"code-snippet__comment\">#\u8981\u540c\u6e90\u8f6c\u6362\u7684\u76ee\u6807\u79cd\u5c5e\uff0c\u4e5f\u5c31\u662f\u7b2c2\u6b65\u7684human<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">               uniqueRows = <span class=\"code-snippet__literal\">TRUE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f46\u662f\u76ee\u524d\u597d\u50cf\u8fd9\u4e2agetLDS\u529f\u80fd\u6709\u70b9\u5f02\u5e38\uff0c\u6240\u4ee5\u5927\u6d77\u54e5\u53c8\u60f3\u4e86\u4e2a\u65b0\u529e\u6cd5<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5927\u6d77\u54e5\u4f7f\u7528Orthology.eg.db\u5305\u521b\u5efa\u4e86\u4e00\u4e2a\u6bd4\u5bf9\u51fd\u6570\uff0c\u4e5f\u53ef\u4ee5\u5b9e\u73b0\u4eba\u9f20\u57fa\u56e0\u8f6c\u6362<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">mapfun <- <span class=\"code-snippet__keyword\">function<\/span>(mousegenes){<\/span><\/code><code><span class=\"code-snippet_outer\">    gns <- mapIds(org.Mm.eg.db, mousegenes, <span class=\"code-snippet__string\">\"ENTREZID\"<\/span>, <span class=\"code-snippet__string\">\"SYMBOL\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">    mapped <- select(Orthology.eg.db, gns, <span class=\"code-snippet__string\">\"Homo_sapiens\"<\/span>,<span class=\"code-snippet__string\">\"Mus_musculus\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">    naind <- <span class=\"code-snippet__built_in\">is.na<\/span>(mapped$Homo_sapiens)<\/span><\/code><code><span class=\"code-snippet_outer\">    hsymb <- mapIds(org.Hs.eg.db, <span class=\"code-snippet__built_in\">as.character<\/span>(mapped$Homo_sapiens[!naind]), <span class=\"code-snippet__string\">\"SYMBOL\"<\/span>, <span class=\"code-snippet__string\">\"ENTREZID\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">    out <- data.frame(Mouse_symbol = mousegenes, mapped, Human_symbol = <span class=\"code-snippet__literal\">NA<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">    out$Human_symbol[!naind] <- hsymb<\/span><\/code><code><span class=\"code-snippet_outer\">    out<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u9700\u8981\u5bfc\u5165\u4ee5\u4e0b\u4e09\u4e2a\u5305\u54e6\uff01\u6ca1\u4e0b\u8f7d\u7684\u5c0f\u4f19\u4f34\u4f7f\u7528BiocManager::install(\u201c\u201d)\u53ef\u4ee5\u4e0b\u8f7d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(Orthology.eg.db)<\/span><\/code><code><span class=\"code-snippet_outer\">library(org.Mm.eg.db)<\/span><\/code><code><span class=\"code-snippet_outer\">library(org.Hs.eg.db)<\/span><\/code><code><span class=\"code-snippet_outer\">mapfun(mouse.genes)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" 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