{"id":60939,"date":"2024-10-11T10:22:58","date_gmt":"2024-10-11T02:22:58","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60939"},"modified":"2024-10-11T10:22:58","modified_gmt":"2024-10-11T02:22:58","slug":"%e8%a7%89%e5%be%97%e5%af%8c%e9%9b%86%e5%88%86%e6%9e%90%e5%a4%aa%e9%9a%be%ef%bc%9fclusterprofiler%e5%8c%85%ef%bc%8c%e5%b8%a6%e4%bd%a0%e5%bf%ab%e9%80%9f%e5%8f%91%e7%8e%b0%e9%9a%90%e8%97%8f%e9%80%9a","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60939","title":{"rendered":"\u89c9\u5f97\u5bcc\u96c6\u5206\u6790\u592a\u96be\uff1fclusterProfiler\u5305\uff0c\u5e26\u4f60\u5feb\u901f\u53d1\u73b0\u9690\u85cf\u901a\u8def\uff0c\u8ba9\u4f60\u79d2\u53d8\u751f\u4fe1\u9ad8\u624b\uff01"},"content":{"rendered":"\n
\"\"<\/figure>\n\n\n\n

\u5927\u5bb6\u597d\uff01\u4eca\u5929\u5c0f\u5e08\u59b9\u8981\u5411\u5927\u5bb6\u4ecb\u7ecd\u4e00\u6b3e\u5728\u751f\u7269\u4fe1\u606f\u5b66\u7814\u7a76\u4e2d\u4e0d\u53ef\u6216\u7f3a\u7684\u5de5\u5177\u2014\u2014clusterProfiler\u5305\u3002clusterProfiler\u662f\u4e00\u6b3e\u529f\u80fd\u5f3a\u5927\u7684R\u5305\uff0c\u4e13\u95e8\u7528\u4e8e\u57fa\u56e0\u529f\u80fd\u6ce8\u91ca\u548c\u5bcc\u96c6\u5206\u6790\u3002\u901a\u8fc7\u5b83\uff0c\u6211\u4eec\u53ef\u4ee5\u8f7b\u677e\u5730\u5bf9\u57fa\u56e0\u5217\u8868\u8fdb\u884cGO\u548cKEGG\u901a\u8def\u7684\u5bcc\u96c6\u5206\u6790\uff0c\u751f\u6210\u8be6\u5c3d\u7684\u7edf\u8ba1\u7ed3\u679c\u548c\u4e30\u5bcc\u7684\u53ef\u89c6\u5316\u56fe\u8868\uff0c\u5982GO\u5bcc\u96c6\u7f51\u7edc\u56fe\u3002\u5b83\u4e0d\u4ec5\u80fd\u5e2e\u52a9\u6211\u4eec\u7406\u89e3\u57fa\u56e0\u5728\u751f\u7269\u5b66\u529f\u80fd\u4e0a\u7684\u5206\u5e03\uff0c\u8fd8\u80fd\u63ed\u793a\u57fa\u56e0\u8c03\u63a7\u7f51\u7edc\u548c\u5173\u952e\u7684\u751f\u7269\u5b66\u901a\u8def\u3002<\/p>\n\n\n\n

\u751f\u4fe1\u5206\u6790\u5bf9\u5c0f\u5e08\u59b9\u6765\u8bf4\u53ef\u4e0d\u662f\u96be\u9898\uff01\u5982\u679c\u540c\u5b66\u4eec\u6709\u81ea\u5df1\u505a\u4e0d\u4e86\u7684\u751f\u4fe1\u5206\u6790\uff0c\u6b22\u8fce\u968f\u65f6\u8054\u7cfb\u6211\u4eec\uff01<\/strong><\/strong><\/p>\n\n\n\n

\u5728\u4eca\u5929\u7684\u5b66\u4e60\u4e2d\uff0c\u5c0f\u5e08\u59b9\u5c06\u5e26\u9886\u5927\u5bb6\u4e00\u8d77\u5b66\u4e60\u5982\u4f55\u5b89\u88c5\u548c\u52a0\u8f7dclusterProfiler\u5305\u3001\u8fdb\u884c\u6570\u636e\u9884\u5904\u7406\u3001\u6267\u884c\u8fdb\u884cGO\u548cKEGG\u5bcc\u96c6\u5206\u6790\uff0c\u5e76\u5229\u7528\u53ef\u89c6\u5316\u5de5\u5177\u5c55\u793a\u5206\u6790\u7ed3\u679c\u3002\u901a\u8fc7\u8fd9\u4e9b\u5b66\u4e60\u5185\u5bb9\uff0c\u540c\u5b66\u4eec\u5c06\u80fd\u591f\u638c\u63e1\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u7684\u57fa\u672c\u6280\u80fd\uff0c\u5e76\u4e14\u53ef\u4ee5\u5c06\u8fd9\u4e9b\u65b9\u6cd5\u5e94\u7528\u4e8e\u81ea\u5df1\u7684\u79d1\u7814\u5de5\u4f5c\u4e2d\u3002\u542c\u8d77\u6765\u662f\u4e0d\u662f\u5f88\u6709\u8da3\u5462\uff1f\u90a3\u5c31\u7d27\u8ddf\u5c0f\u5e08\u59b9\u7684\u6b65\u4f10\uff0c\u8ba9\u6211\u4eec\u4e00\u8d77\u5f00\u542f\u5bf9clusterProfiler\u5305\u7684\u5b66\u4e60\u4e4b\u65c5\u5427\uff01<\/p>\n\n\n\n

\u672c\u6b21\u4ecb\u7ecd\u7684<\/strong>R\u5305<\/strong>\u9700\u8981\u8f83\u591a\u7684\u786c\u4ef6\u8d44\u6e90\uff0c\u5728<\/strong>\u670d\u52a1\u5668<\/strong>\u53ef\u4ee5\u66f4\u52a0\u6d41\u7545<\/strong>\u8fd0\u884c\uff0c<\/strong>\u540c\u5b66\u4eec<\/strong>\u5982\u679c\u6ca1\u6709\u81ea\u5df1\u7684\u670d\u52a1\u5668\u6b22\u8fce\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u670d\u52a1\u5668\u79df\u8d41~<\/strong><\/strong><\/p>\n\n\n\n

clusterProfiler\u5305\u7b80\u4ecb<\/p>\n\n\n\n

clusterProfiler\u5305\u662fR\u8bed\u8a00\u4e2d\u7528\u4e8e\u57fa\u56e0\u529f\u80fd\u6ce8\u91ca\u548c\u5bcc\u96c6\u5206\u6790\u7684\u5f3a\u5927\u5de5\u5177\uff0c\u5e7f\u6cdb\u5e94\u7528\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u9886\u57df\u3002\u5b83\u80fd\u591f\u5bf9\u57fa\u56e0\u5217\u8868\u8fdb\u884c\u57fa\u56e0\u672c\u4f53\uff08GO\uff09\u548cKEGG\u901a\u8def\u7684\u5bcc\u96c6\u5206\u6790\uff0c\u5e2e\u52a9\u7814\u7a76\u8005\u8bc6\u522b\u663e\u8457\u5bcc\u96c6\u7684\u751f\u7269\u5b66\u8fc7\u7a0b\u3001\u5206\u5b50\u529f\u80fd\u548c\u7ec6\u80de\u7ec4\u6210\u3002\u9664\u4e86\u57fa\u672c\u7684\u5bcc\u96c6\u5206\u6790\u529f\u80fd\uff0cclusterProfiler\u8fd8\u652f\u6301\u4e30\u5bcc\u7684\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u80fd\u591f\u751f\u6210\u591a\u79cd\u7c7b\u578b\u7684\u56fe\u8868\uff0c\u5982GO\u6761\u5f62\u56fe\u3001\u6c14\u6ce1\u56fe\u548c\u5bcc\u96c6\u7f51\u7edc\u56fe\uff0c\u4f7f\u5f97\u5206\u6790\u7ed3\u679c\u66f4\u76f4\u89c2\u6613\u61c2\u3002\u901a\u8fc7\u7b80\u5316\u590d\u6742\u7684\u57fa\u56e0\u529f\u80fd\u5206\u6790\u6d41\u7a0b\uff0cclusterProfiler\u6781\u5927\u63d0\u5347\u4e86\u6570\u636e\u89e3\u8bfb\u6548\u7387\u3002<\/p>\n\n\n\n

clusterProfiler\u5305\u5b89\u88c5<\/p>\n\n\n\n

\u9700\u8981R\u8bed\u8a00\u7248\u672c\u4e3a4.4\uff0c\u5728\u63a7\u5236\u53f0\u4e2d\u8f93\u5165\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n\n\n\n

if (!require(“BiocManager”, quietly = TRUE))<\/p>\n\n\n\n

    install.packages(“BiocManager”)<\/p>\n\n\n\n

BiocManager::install(“clusterProfiler”) # \u5728BiocManager\u73af\u5883\u4e0b\u5b89\u88c5clusterProfiler\u5305<\/p>\n\n\n\n

\u67e5\u770b\u662f\u5426\u5b89\u88c5\u6210\u529f<\/p>\n\n\n\n

packageVersion(“clusterProfiler”) # \u67e5\u770bclusterProfiler\u7248\u672c<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u663e\u793a\u4e3a4.12.1\u7248\u672c\uff0c\u5219\u8868\u793a\u5df2\u7ecf\u5b89\u88c5\u4e86clusterProfiler\u5305\u3002<\/p>\n\n\n\n

\u9664\u6b64\u4e4b\u5916\uff0c\u540e\u7eed\u793a\u4f8b\u8fd8\u9700\u8981\u4f7f\u7528org.Hs.eg.db\u5305\uff0c\u6211\u4eec\u53ef\u4ee5\u63d0\u524d\u5b89\u88c5\uff0c\u5b89\u88c5\u547d\u4ee4\u5982\u4e0b\uff1a<\/p>\n\n\n\n

if (!requireNamespace(“BiocManager”, quietly = TRUE))<\/p>\n\n\n\n

    install.packages(“BiocManager”)<\/p>\n\n\n\n

BiocManager::install(“org.Hs.eg.db”)# \u5728BiocManager\u73af\u5883\u4e0b\u5b89\u88c5org.Hs.eg.db\u5305<\/p>\n\n\n\n

\u4f7f\u7528clusterProfiler\u5305\u8fdb\u884cGO\u5bcc\u96c6\u5206\u6790<\/p>\n\n\n\n

\u8f7d\u5165\u5305\u548c\u6570\u636e<\/strong><\/strong><\/p>\n\n\n\n

\u60f3\u8981\u8fdb\u884c\u540e\u7eed\u7684GO\u5bcc\u96c6\u5206\u6790\uff0c\u6211\u4eec\u9996\u5148\u9700\u8981\u8f7d\u5165\u9700\u8981\u7684\u5305\u548c\u6570\u636e\uff0c\u5728\u672c\u6587\u4e2d\uff0c\u6211\u4eec\u4f7f\u7528DOSE\u5305\u63d0\u4f9b\u7684genlist\u6570\u636e\u96c6\u4f5c\u4e3a\u793a\u4f8b\u6570\u636e\uff0c\u76f8\u5173\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

library(clusterProfiler) #\u8f7d\u5165clusterProfiler\u5305<\/p>\n\n\n\n

library(org.Hs.eg.db) #\u8f7d\u5165org.Hs.eg.db\u5305<\/p>\n\n\n\n

data(geneList, package=”DOSE”) #\u4eceDOSE\u5bfc\u5165geneList\u6570\u636e<\/p>\n\n\n\n

gene <- names(geneList)[abs(geneList) > 2] #\u7b5b\u9009\u51fa\u4e0e\u7edd\u5bf9\u503c\u5927\u4e8e2\u7684\u5206\u6570\u76f8\u5173\u8054\u7684\u57fa\u56e0<\/p>\n\n\n\n

head(gene) # \u67e5\u770b\u7b5b\u9009\u540e\u7684Entrez\u57fa\u56e0ID<\/p>\n\n\n\n

\u7ed3\u679c\u663e\u793a\u5982\u4e0b\u56fe<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u57fa\u56e0\u672c\u4f53\uff08Gene Ontology\uff0cGO\uff09\u5206\u6790\uff0c\u4e3b\u8981\u5305\u62ec\u4ee5\u4e0b\u4e09\u4e2a\u65b9\u9762\uff1a<\/p>\n\n\n\n

\u751f\u7269\u8fc7\u7a0b\uff08Biological Process\uff09\uff1a\u57fa\u56e0\u4ea7\u54c1\u53c2\u4e0e\u7684\u751f\u7269\u5b66\u4e8b\u4ef6\uff0c\u5982\u7ec6\u80de\u5468\u671f\u3001\u4fe1\u53f7\u4f20\u5bfc\u7b49\u3002\u7ec6\u80de\u7ec4\u5206\uff08Cellular Component\uff09\uff1a\u57fa\u56e0\u4ea7\u54c1\u6240\u5728\u7684\u7ec6\u80de\u90e8\u4f4d\uff0c\u5982\u7ec6\u80de\u6838\u3001\u819c\u3001\u7ec6\u80de\u8d28\u7b49\u3002\u5206\u5b50\u529f\u80fd\uff08Molecular Function\uff09\uff1a\u57fa\u56e0\u4ea7\u54c1\u7684\u57fa\u672c\u6d3b\u52a8\uff0c\u5982\u9176\u6d3b\u6027\u3001\u7ed3\u5408\u6d3b\u6027\u7b49\u3002<\/p>\n\n\n\n

\u5728\u672c\u6587\u4e2d\u6211\u4eec\u4e3b\u8981\u6f14\u793a\u4f7f\u7528clusterProfiler\u5305\u8fdb\u884c\u7ec6\u80de\u7ec4\u5206\uff08Cellular Component\uff09GO\u5bcc\u96c6\u5206\u6790\u7684\u8fc7\u7a0b\uff0c\u5176\u4f59\u4e24\u4e2a\u65b9\u9762\u7684GO\u5206\u6790\u6b65\u9aa4\u4e0e\u7ec6\u80de\u7ec4\u5206\uff08Cellular Component\uff09\u5927\u81f4\u76f8\u540c\uff0c\u540c\u5b66\u4eec\u53ef\u4ee5\u4e3e\u4e00\u53cd\u4e09\u3002<\/p>\n\n\n\n

GO\u5206\u7c7b<\/strong><\/strong><\/p>\n\n\n\n

\u9996\u5148\u6211\u4eec\u9700\u8981\u4f7f\u7528groupGO()\u51fd\u6570\uff0c\u6839\u636e\u7279\u5b9a\u7ea7\u522b\u7684GO\u5206\u5e03\u5bf9\u57fa\u56e0\u8fdb\u884c\u5206\u7c7b\u3002\u4ee5\u4e0b\u662f\u4f7f\u7528DOSE\u63d0\u4f9b\u7684geneList\u6570\u636e\u96c6\u7684\u793a\u4f8b\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

# \u4f7f\u7528groupGO\u51fd\u6570\u5bf9\u7b5b\u9009\u51fa\u7684\u57fa\u56e0\u8fdb\u884cGO\u5206\u7c7b<\/p>\n\n\n\n

ggo <- groupGO(<\/p>\n\n\n\n

  gene     = gene,             # \u8f93\u5165\u7684\u57fa\u56e0ID\u5411\u91cf<\/p>\n\n\n\n

  OrgDb    = org.Hs.eg.db,     # \u4f7f\u7528\u7684\u4eba\u7c7b\u57fa\u56e0\u6ce8\u91ca\u6570\u636e\u5e93<\/p>\n\n\n\n

  ont      = “CC”,             # GO\u5206\u7c7b\u672c\u4f53\uff0c”CC”\u8868\u793a\u7ec6\u80de\u7ec4\u5206\uff08Cellular Component\uff09<\/p>\n\n\n\n

  level    = 3,                # GO\u672f\u8bed\u5c42\u7ea7<\/p>\n\n\n\n

  readable = TRUE              # \u5c06\u57fa\u56e0ID\u8f6c\u6362\u4e3a\u57fa\u56e0\u7b26\u53f7<\/p>\n\n\n\n

)<\/p>\n\n\n\n

head(ggo) #\u663e\u793a\u524d\u516d\u4e2aGO\u5206\u7c7b\u7ed3\u679c<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

GO\u5bcc\u96c6\u5206\u6790<\/strong><\/strong><\/p>\n\n\n\n

\u63a5\u7740\u6211\u4e48\u53ef\u4ee5\u7528clusterProfiler\u5305\u4e2d\u7684enrichGO()\u8fdb\u884cGO\u5bcc\u96c6\u5206\u6790\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

# \u6267\u884cGO\u5bcc\u96c6\u5206\u6790<\/p>\n\n\n\n

ego <- enrichGO(<\/p>\n\n\n\n

    gene = gene,            # \u8981\u5206\u6790\u7684\u57fa\u56e0\u5217\u8868<\/p>\n\n\n\n

    universe= names(geneList), # \u80cc\u666f\u57fa\u56e0\u5217\u8868\uff0c\u7528\u4e8e\u6bd4\u8f83<\/p>\n\n\n\n

    OrgDb= org.Hs.eg.db,    # \u57fa\u56e0\u6ce8\u91ca\u6570\u636e\u5e93\uff0c\u8fd9\u91cc\u662f\u4eba\u7c7b\u7684\u57fa\u56e0\u6ce8\u91ca\u6570\u636e\u5e93<\/p>\n\n\n\n

    ont= “CC”,            # GO\u672c\u4f53\u7c7b\u522b\uff0c\u8fd9\u91cc\u662f\u7ec6\u80de\u7ec4\u5206\uff08Cellular Component\uff09<\/p>\n\n\n\n

    pAdjustMethod = “BH”,            # p\u503c\u8c03\u6574\u65b9\u6cd5\uff0c\u8fd9\u91cc\u4f7f\u7528Benjamini-Hochberg\u65b9\u6cd5<\/p>\n\n\n\n

    pvalueCutoff = 0.01,            # p\u503c\u622a\u65ad\uff0c\u53ea\u6709p\u503c\u5c0f\u4e8e0.01\u7684\u7ed3\u679c\u624d\u4f1a\u88ab\u8fd4\u56de<\/p>\n\n\n\n

    qvalueCutoff = 0.05,            # q\u503c\u622a\u65ad\uff0c\u53ea\u6709q\u503c\u5c0f\u4e8e0.05\u7684\u7ed3\u679c\u624d\u4f1a\u88ab\u8fd4\u56de<\/p>\n\n\n\n

    readable = TRUE             # \u5c06\u57fa\u56e0ID\u8f6c\u6362\u4e3a\u53ef\u8bfb\u7684\u57fa\u56e0\u540d\u79f0<\/p>\n\n\n\n

)<\/p>\n\n\n\n

head(ego) # \u663e\u793a\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u7684\u524d\u51e0\u884c<\/p>\n\n\n\n

\u7ed3\u679c\u663e\u793a\u5982\u4e0b\u56fe\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528goplot()\u51fd\u6570\u53ef\u89c6\u5316enrichGO()\u51fd\u6570\u7684GO\u5bcc\u96c6\u7ed3\u679c,\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

goplot(ego) #\u53ef\u89c6\u5316\u5bcc\u96c6\u7ed3\u679c<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u4e0d\u96be\u770b\u51fa\uff0c\u56fe\u4e2d\u63cf\u8ff0\u4e86\u7ec6\u80de\u7ec4\u4ef6\uff08Cellular Component\uff09\u7c7b\u522b\u4e0b\u7684\u663e\u8457GO\u672f\u8bed\u4e4b\u95f4\u7684\u5173\u7cfb\u7f51\u7edc\u3002\u56fe\u4e2d\u7684\u8282\u70b9\u4ee3\u8868GO\u672f\u8bed\uff0c\u8282\u70b9\u5927\u5c0f\u548c\u989c\u8272\u8868\u793ap\u503c\u7684\u663e\u8457\u6027\uff0c\u989c\u8272\u4ece\u7ea2\u8272\u5230\u84dd\u8272\u4f9d\u6b21\u8868\u793ap\u503c\u4ece\u663e\u8457\u5230\u4e0d\u663e\u8457\u7684\u6e10\u53d8\u3002\u8282\u70b9\u4e4b\u95f4\u7684\u7ebf\u6761\u8868\u793aGO\u672f\u8bed\u4e4b\u95f4\u7684\u5173\u7cfb\uff0c\u201cisa\u201d\u8868\u793a\u5305\u542b\u5173\u7cfb\uff0c\u201cpart of\u201d\u8868\u793a\u90e8\u5206\u5173\u7cfb\u3002\u56fe\u4e2d\u663e\u793a\u4e86\u4e00\u4e9b\u5173\u952e\u7684\u7ec6\u80de\u7ec4\u4ef6\uff0c\u5982\u7ec6\u80de\u5668\uff08organelle\uff09\u3001\u67d3\u8272\u4f53\uff08chromosome\uff09\u3001\u7ec6\u80de\u9aa8\u67b6\uff08cytoskeleton\uff09\u7b49\u3002\u901a\u8fc7\u8fd9\u4e9b\u8282\u70b9\u548c\u8fde\u63a5\u7ebf\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u51fa\u57fa\u56e0\u4ea7\u54c1\u5728\u7ec6\u80de\u5185\u7684\u4f4d\u7f6e\u53ca\u5176\u76f8\u4e92\u5173\u8054\u7684\u7ed3\u6784\u3002\u4f8b\u5982\uff0c\u201c\u67d3\u8272\u4f53\u201d\uff08chromosome\uff09\u4e0e\u201c\u51dd\u7f29\u67d3\u8272\u4f53\u201d\uff08condensed chromosome\uff09\u4e4b\u95f4\u5b58\u5728\u76f4\u63a5\u5173\u7cfb\uff0c\u800c\u201c\u7ec6\u80de\u9aa8\u67b6\u201d\uff08cytoskeleton\uff09\u4e0e\u201c\u5fae\u7ba1\u201d\uff08microtubule\uff09\u4e4b\u95f4\u4e5f\u6709\u76f4\u63a5\u8054\u7cfb\u3002<\/p>\n\n\n\n

<\/a>\u4f7f\u7528clusterProfiler\u5305\u8fdb\u884cKEGG \u5bcc\u96c6\u5206\u6790<\/p>\n\n\n\n

\u8f7d\u5165\u5305\u548c\u6570\u636e<\/strong><\/strong><\/p>\n\n\n\n

\u60f3\u8981\u8fdb\u884c\u540e\u7eed\u7684KEGG\u5bcc\u96c6\u5206\u6790\uff0c\u6211\u4eec\u9996\u5148\u9700\u8981\u8f7d\u5165\u9700\u8981\u7684\u5305\u548c\u6570\u636e\uff0c\u5728\u672c\u6587\u4e2d\uff0c\u6211\u4eec\u5c06\u4f7f\u7528DOSE\u5305\u63d0\u4f9b\u7684genlist\u6570\u636e\u96c6\u4f5c\u4e3a\u793a\u4f8b\u6570\u636e\uff0c\u76f8\u5173\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

library(clusterProfiler) #\u8f7d\u5165clusterProfiler\u5305<\/p>\n\n\n\n

data(geneList, package=”DOSE”) #\u4eceDOSE\u5bfc\u5165geneList\u6570\u636e<\/p>\n\n\n\n

gene <- names(geneList)[abs(geneList) > 2] #\u7b5b\u9009\u51fa\u4e0e\u7edd\u5bf9\u503c\u5927\u4e8e2\u7684\u5206\u6570\u76f8\u5173\u8054\u7684\u57fa\u56e0<\/p>\n\n\n\n

gene # \u67e5\u770b\u7b5b\u9009\u540e\u7684Entrez\u57fa\u56e0ID<\/p>\n\n\n\n

\u7ed3\u679c\u663e\u793a\u5982\u4e0b\u56fe<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u652f\u6301KEGG\u5bcc\u96c6\u5206\u6790\u7684\u751f\u7269\u4f53<\/strong><\/strong><\/p>\n\n\n\n

clusterProfiler\u652f\u6301\u6240\u6709\u5728KEGG\u6570\u636e\u5e93\u4e2d\u5177\u6709\u6ce8\u91ca\u6570\u636e\u7684\u751f\u7269\u4f53\u3002\u7528\u6237\u53ef\u4ee5\u76f4\u63a5\u5411organism\u53c2\u6570\u4f20\u9012kegg_code\uff08\u751f\u7269\u4f53\u540d\u79f0\u7f29\u5199\uff09\u3002\u6211\u4eec\u6240\u4f7f\u7528\u7684\u793a\u4f8b\u6570\u636e\u5747\u4e3a\u4eba\u7c7b\u57fa\u56e0\uff0c\u6240\u4ee5\u5e94\u8be5\u4f7f\u7528\u7f29\u5199\u201chsa\u201d(Homo sapiens)\u3002<\/p>\n\n\n\n

\u5982\u679c\u4f60\u4e0d\u6e05\u695akegg_code\u4e5f\u4e0d\u7528\u62c5\u5fc3\uff0cclusterProfiler\u5305\u63d0\u4f9b\u4e86search_kegg_organism()\u51fd\u6570\u6765\u5e2e\u52a9\u641c\u7d22\u652f\u6301\u7684\u751f\u7269\u4f53\u3002\u4ee5\u6211\u4eec\u9700\u8981\u641c\u7d22\u5927\u80a0\u6746\u83cc\uff08Escherichia coli\uff09\u7684\u76f8\u5173\u4fe1\u606f\u4e3a\u4f8b\uff0c\u76f8\u5173\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

search_result <- search_kegg_organism(‘ece’, by=’kegg_code’) # \u6839\u636e KEGG \u4ee3\u7801 ‘ece’ \u641c\u7d22\u652f\u6301\u7684\u751f\u7269\u4f53<\/p>\n\n\n\n

search_result # \u663e\u793a\u641c\u7d22\u7ed3\u679c<\/p>\n\n\n\n

ecoli <- search_kegg_organism(‘Escherichia coli’, by=’scientific_name’) # \u6839\u636e\u79d1\u5b66\u540d\u79f0 ‘Escherichia coli’ \u641c\u7d22\u652f\u6301\u7684\u751f\u7269\u4f53<\/p>\n\n\n\n

dim(ecoli) # \u663e\u793a\u641c\u7d22\u7ed3\u679c\u7684\u7ef4\u5ea6\uff08\u884c\u6570\u548c\u5217\u6570\uff09<\/p>\n\n\n\n

head(ecoli) # \u663e\u793a\u641c\u7d22\u7ed3\u679c\u7684\u524d\u51e0\u884c<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u7ed3\u679c\u5982\u4e0a\u56fe\uff0c\u53ef\u77e5kegg_code\u4e2d\u5305\u542b\u201cece\u201d\u7684\u751f\u7269\u4f53\u6761\u76ee\u4e3a\u4e24\u4e2a\uff0c\u5b66\u672f\u540d\u79f0\u5305\u542b\u201cEscherichia coli\u201d\u7684\u751f\u7269\u4f53\u6761\u76ee\u4e3a65\u4e2a\u3002<\/p>\n\n\n\n

KEGG\u5bcc\u96c6\u5206\u6790<\/strong><\/strong><\/p>\n\n\n\n

KEGG\u5bcc\u96c6\u901a\u8fc7\u6bd4\u8f83\u8f93\u5165\u7684\u57fa\u56e0\u5217\u8868\u4e0eKEGG\u6570\u636e\u5e93\u4e2d\u7684\u901a\u8def\u4fe1\u606f\uff0c\u6765\u8bc6\u522b\u54ea\u4e9b\u4ee3\u8c22\u901a\u8def\u6216\u4fe1\u53f7\u4f20\u5bfc\u901a\u8def\u5728\u57fa\u56e0\u8868\u8fbe\u53d8\u5316\u4e2d\u663e\u8457\u5bcc\u96c6\u3002\u901a\u8fc7\u4ee5\u4e0a\u7684\u6b65\u9aa4\uff0c\u6211\u4eec\u5df2\u7ecf\u8f7d\u5165\u4e86\u9700\u8981\u7684\u5305\u548c\u793a\u4f8b\u6570\u636e\uff0c\u5e76\u4e14\u901a\u8fc7search_kegg_organism()\u51fd\u6570\u83b7\u5f97\u4e86\u751f\u7269\u4f53\u7684kegg_code\u4e4b\u540e\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4f7f\u7528enrichKEGG()\u51fd\u6570\u8fdb\u884cKEGG\u5bcc\u96c6\u5206\u6790\u4e86\uff0c\u76f8\u5173\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

kk <- enrichKEGG(gene         = gene,<\/p>\n\n\n\n

                 organism     = ‘hsa’,<\/p>\n\n\n\n

                 pvalueCutoff = 0.05)<\/p>\n\n\n\n

# \u4f7f\u7528 enrichKEGG \u51fd\u6570\u8fdb\u884c KEGG \u5bcc\u96c6\u5206\u6790<\/p>\n\n\n\n

# gene: \u8f93\u5165\u7684\u57fa\u56e0\u5217\u8868\uff0c\u901a\u5e38\u662f\u663e\u8457\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u7684 Entrez IDs<\/p>\n\n\n\n

# organism: \u6307\u5b9a\u751f\u7269\u4f53\u7684 KEGG \u7f29\u5199\u4ee3\u7801\uff0c\u8fd9\u91cc ‘hsa’ \u4ee3\u8868\u4eba\u7c7b (Homo sapiens)<\/p>\n\n\n\n

# pvalueCutoff: \u8bbe\u7f6e p \u503c\u7684\u622a\u65ad\u503c\uff0c\u7528\u4e8e\u7b5b\u9009\u663e\u8457\u5bcc\u96c6\u7684\u901a\u8def\uff0c\u8fd9\u91cc\u8bbe\u7f6e\u4e3a 0.05<\/p>\n\n\n\n

kk[]# \u663e\u793a\u5bcc\u96c6\u5206\u6790\u7ed3\u679c<\/p>\n\n\n\n

\u4ee5\u4e0a\u4ee3\u7801\u8fd0\u884c\u65f6\u95f4\u8f83\u957f\uff0c\u540c\u5b66\u4eec\u9700\u8981\u8010\u5fc3\u7b49\u5f85\uff0c\u7ed3\u679c\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u53ef\u77e5\uff0cKEGG\u5bcc\u96c6\u7ed3\u679c\u663e\u793a\uff0c\u793a\u4f8b\u6570\u636e\u4e2d\u7684207\u4e2a\u57fa\u56e0\u5bcc\u96c6\u5230\u4e86\u5305\u62ec\u7ec6\u80de\u5468\u671f\uff08Cell cycle\uff09\u3001\u5375\u6bcd\u7ec6\u80de\u51cf\u6570\u5206\u88c2\uff08Oocyte meiosis\uff09\u3001\u7ec6\u80de\u8870\u8001\uff08Cellular senescence\uff09\u7b497\u4e2a\u4e0d\u540c\u7684\u901a\u8def\u3002<\/p>\n\n\n\n

\u5bcc\u96c6\u7ed3\u679c\u53ef\u89c6\u5316<\/strong><\/strong><\/p>\n\n\n\n

clusterProfiler\u5305\u6709\u591a\u79cd\u65b9\u6cd5\u6765\u53ef\u89c6\u5316\u5bcc\u96c6\u7ed3\u679c\uff0c\u672c\u6587\u4e2d\u6211\u4eec\u5c06\u4ecb\u7ecdbrowseKEGG()\u51fd\u6570\u548cpathview::pathview()\u51fd\u6570\uff0c\u6765\u5bf9KEGG\u5bcc\u96c6\u7ed3\u679c\u8fdb\u884c\u53ef\u89c6\u5316\u3002<\/p>\n\n\n\n

\u4f7f\u7528browseKEGG()\u51fd\u6570\u7684\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

browseKEGG(kk, ‘hsa04110’) #\u4f7f\u7528browseKEGG()\u51fd\u6570\u53ef\u89c6\u5316\u201chsa04110\u201d\u901a\u8def<\/p>\n\n\n\n

\u7ed3\u679c\u5982\u4e0b\u56fe\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u5927\u5bb6\u8fd8\u53ef\u4ee5\u4f7f\u7528pathview\u5305\u4e2d\u7684pathview()\u51fd\u6570\u6765\u53ef\u89c6\u5316clusterProfiler\u5305\u4e2d\u7684KEGG\u5bcc\u96c6\u7ed3\u679c\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

BiocManager::install(“pathview”) # \u5728BiocManager\u73af\u5883\u4e0b\u5b89\u88c5pathview\u5305<\/p>\n\n\n\n

library(“pathview”) # \u8f7d\u5165pathview\u5e93<\/p>\n\n\n\n

hsa04110 <- pathview(<\/p>\n\n\n\n

  gene.data  = geneList,  # \u8f93\u5165\u57fa\u56e0\u6570\u636e\uff0c\u5e94\u4e3a\u4e00\u4e2a\u57fa\u56e0\u5217\u8868\u6216\u8868\u8fbe\u6570\u636e<\/p>\n\n\n\n

  pathway.id = “hsa04110”,  # \u6307\u5b9aKEGG\u901a\u8defID\uff0c\u8fd9\u91cc\u662f\u7ec6\u80de\u5468\u671f\u901a\u8def<\/p>\n\n\n\n

  species    = “hsa”,  # \u6307\u5b9a\u7269\u79cd\uff0c\u8fd9\u91cc\u4f7f\u7528\u4eba\u7c7b\uff08hsa\uff09<\/p>\n\n\n\n

  limit      = list(gene=max(abs(geneList)), cpd=1)  # \u9650\u5236\u663e\u793a\u57fa\u56e0\u548c\u4ee3\u8c22\u7269\u7684\u6570\u91cf<\/p>\n\n\n\n

) # \u4f7f\u7528pathview\u51fd\u6570\u751f\u6210\u901a\u8def\u53ef\u89c6\u5316<\/p>\n\n\n\n

\u7ed3\u679c\u663e\u793a\u5982\u4e0b\u56fe\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u7531\u56fe\u53ef\u77e5\uff0cKEGG\u5bcc\u96c6\u7ed3\u679c\u56fe\u8be6\u7ec6\u63cf\u8ff0\u4e86\u7ec6\u80de\u5468\u671f\u4e2d\u5404\u4e2a\u9636\u6bb5\uff08G1\u3001S\u3001G2\u3001M\uff09\u6d89\u53ca\u7684\u5173\u952e\u57fa\u56e0\u53ca\u5176\u76f8\u4e92\u4f5c\u7528\u5173\u7cfb\u3002\u4e0d\u540c\u989c\u8272\u7684\u6846\u8868\u793a\u57fa\u56e0\u8868\u8fbe\u7684\u53d8\u5316\u60c5\u51b5\uff0c\u7ea2\u8272\u8868\u793a\u57fa\u56e0\u4e0a\u8c03\uff0c\u7eff\u8272\u8868\u793a\u57fa\u56e0\u4e0b\u8c03\uff0c\u7070\u8272\u8868\u793a\u57fa\u56e0\u672a\u663e\u8457\u53d8\u5316\uff0c\u989c\u8272\u6e10\u53d8\u8868\u793a\u53d8\u5316\u7684\u7a0b\u5ea6\u3002\u56fe\u4e2d\u8fd8\u5c55\u793a\u4e86\u591a\u4e2a\u4e0e\u7ec6\u80de\u5468\u671f\u8c03\u63a7\u76f8\u5173\u7684\u4fe1\u53f7\u901a\u8def\u548c\u86cb\u767d\u8d28\u590d\u5408\u7269\uff0c\u5982MAPK\u4fe1\u53f7\u901a\u8def\u3001SCF\u590d\u5408\u7269\u3001APC\/C\u590d\u5408\u7269\u7b49\u3002\u901a\u8fc7\u8fd9\u4e9b\u901a\u8def\u548c\u590d\u5408\u7269\uff0c\u53ef\u4ee5\u770b\u5230\u57fa\u56e0\u5728\u7ec6\u80de\u5468\u671f\u4e2d\u7684\u7cbe\u7ec6\u8c03\u63a7\u8fc7\u7a0b\uff0c\u4ee5\u53ca\u7ec6\u80de\u5982\u4f55\u901a\u8fc7\u4e00\u7cfb\u5217\u4fe1\u53f7\u4f20\u5bfc\u548c\u57fa\u56e0\u8868\u8fbe\u53d8\u5316\u6765\u5b8c\u6210\u7ec6\u80de\u5206\u88c2\u3002<\/p>\n\n\n\n

\u4ee5\u4e0a\u5c31\u662f\u5bf9clusterProfiler\u5305\u7684\u5168\u9762\u4ecb\u7ecd\u4e86\u3002\u901a\u8fc7\u5b66\u4e60\u5982\u4f55\u5b89\u88c5\u548c\u4f7f\u7528clusterProfiler\uff0c\u6211\u4eec\u638c\u63e1\u4e86\u5728\u751f\u7269\u4fe1\u606f\u5b66\u4e2d\u8fdb\u884c\u57fa\u56e0\u672c\u4f53\uff08GO\uff09\u5bcc\u96c6\u5206\u6790\u548cKEGG\u901a\u8def\u5bcc\u96c6\u5206\u6790\u7684\u5173\u952e\u6b65\u9aa4\u548c\u65b9\u6cd5\u3002clusterProfiler\u80fd\u591f\u5e2e\u52a9\u6211\u4eec\u8bc6\u522b\u57fa\u56e0\u5728\u751f\u7269\u5b66\u8fc7\u7a0b\u3001\u7ec6\u80de\u7ec4\u5206\u3001\u5206\u5b50\u529f\u80fd\u4e2d\u7684\u663e\u8457\u5bcc\u96c6\uff0c\u540c\u65f6\u63ed\u793a\u4e0e\u4ee3\u8c22\u548c\u4fe1\u53f7\u4f20\u5bfc\u76f8\u5173\u7684\u91cd\u8981\u901a\u8def\u3002\u501f\u52a9\u5176\u4e30\u5bcc\u7684\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u5982goplot()\u548cpathview()\u51fd\u6570\uff0c\u6211\u4eec\u80fd\u591f\u66f4\u76f4\u89c2\u5730\u89e3\u8bfb\u590d\u6742\u7684\u5bcc\u96c6\u7ed3\u679c\u3002\u5e0c\u671b\u5927\u5bb6\u7ee7\u7eed\u6df1\u5165\u63a2\u7d22\u751f\u7269\u4fe1\u606f\u5b66\u9886\u57df\uff0c\u5145\u5206\u5229\u7528clusterProfiler\u5305\uff0c\u4e3a\u79d1\u7814\u8d21\u732e\u529b\u91cf\uff01<\/p>\n\n\n\n

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