{"id":61158,"date":"2024-10-17T13:50:03","date_gmt":"2024-10-17T05:50:03","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61158"},"modified":"2024-10-17T13:50:03","modified_gmt":"2024-10-17T05:50:03","slug":"%e4%b8%89%e5%88%86%e9%92%9f%e6%8b%bf%e4%b8%8bgo%e5%92%8ckegg-pathway%ef%bc%81%e6%89%8b%e6%8a%8a%e6%89%8b%e6%95%99%e4%bd%a0%e8%bd%bb%e6%9d%be%e7%8e%a9%e8%bd%ac%e4%b8%80%e7%ab%99%e5%bc%8f%e7%bd%91","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61158","title":{"rendered":"\u4e09\u5206\u949f\u62ff\u4e0bGO\u548cKEGG pathway\uff01\u624b\u628a\u624b\u6559\u4f60\u8f7b\u677e\u73a9\u8f6c\u4e00\u7ad9\u5f0f\u7f51\u7edc\u836f\u7406\u5b66\u5206\u6790\u5e73\u53f0BATMAN-TCM\uff01"},"content":{"rendered":"\n

\u54c8\u55bd\u5c0f\u4f19\u4f34\u4eec\u5927\u5bb6\u597d~\u5c0f\u679c\u5728\u4e4b\u524d\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e86\u4f7f\u7528TCMSP\u548cBATMAN-TCM\u83b7\u53d6\u836f\u7269\u4e3b\u8981\u6210\u5206\u53ca\u9776\u70b9\u7684\u64cd\u4f5c\uff0c\u90a3\u4e48\u4eca\u5929\u5c0f\u679c\u5c31\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e0bBATMAN-TCM\u7684\u6269\u5c55\u7528\u6cd5\uff0c\u56e0\u4e3aBATMAN-TCM\u4e0d\u4ec5\u4ec5\u662f\u4e00\u4e2a\u6570\u636e\u5e93\uff0c\u66f4\u662f\u4e00\u4e2a\u5f88\u597d\u7528\u7684\u5206\u6790\u5de5\u5177\uff0c\u5982\u679c\u4f7f\u7528\u5f97\u5f53\u751a\u81f3\u53ef\u4ee5\u5e2e\u52a9\u5927\u5bb6\u4e00\u7ad9\u5f0f\u89e3\u51b3\u7f51\u7edc\u836f\u7406\u5b66\u5206\u6790\u54e6\u3002\u5728\u8fd9\u91cc\u5c0f\u679c\u4e5f\u8981\u4ecb\u7ecd\u4e00\u4e0b\uff0c\u5c0f\u679c\u81ea\u5df1\u5f00\u53d1\u7684\u751f\u4fe1\u5de5\u5177http:\/\/www.biocloudservice.com\/home.html<\/a>\u4e5f\u662f\u975e\u5e38\u65b9\u4fbf\u597d\u7528\u7684\u4e00\u7ad9\u5f0f\u7ed8\u56fe\u80fd\u624b\uff0c\u6b22\u8fce\u5c0f\u4f19\u4f34\u4eec\u524d\u6765\u4f7f\u7528\u54e6~\u5e9f\u8bdd\u4e0d\u591a\u8bf4\uff0c\u6211\u4eec\u8d76\u7d27\u5f00\u59cb\u5427~\uff08\u5982\u679c\u5c0f\u4f19\u4f34\u4eec\u6709\u4ec0\u4e48\u66f4\u52a0\u7ec6\u8282\u7684\u95ee\u9898\u6b22\u8fce\u968f\u65f6\u6765\u627e\u5c0f\u679c\u54e6~\u5c0f\u679c\u5728\u751f\u4fe1\u8015\u8018\u5341\u4f59\u5e74\uff0c\u975e\u5e38\u4e50\u610f\u5e2e\u52a9\u751f\u4fe1\u8def\u4e0a\u65b0\u7684\u5c0f\u4f19\u4f34\u4eec~\u9700\u8981\u670d\u52a1\u5668\u7684\u5c0f\u4f19\u4f34\u4eec\u4e5f\u53ef\u4ee5\u6765\u627e\u5c0f\u679c\u79df\uff0c\u5c0f\u679c\u4e13\u95e8\u642d\u5efa\u7684\u7528\u4e8e\u751f\u4fe1\u5206\u6790\u7684\u670d\u52a1\u5668\u6027\u4ef7\u6bd4\u62c9\u6ee1\u54e6\uff09<\/p>\n\n\n\n

\u5728BATMAN\u5206\u6790\u5b8c\u6210\u540e\u6211\u4eec\u53ef\u4ee5\u770b\u5230\u4e00\u5171\u6709\u4e09\u4e2a\u7ed3\u679c\u754c\u9762\uff1atarget prediction result(\u76ee\u6807\u9884\u6d4b\u7ed3\u679c)\u3001bioinformatics analyses of potential targets(\u6f5c\u5728\u9776\u70b9\u7684\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790)\u3001network visualization(\u7f51\u7edc\u53ef\u89c6\u5316)\u3002\u5728\u4e0a\u4e00\u7ae0\u8282\u6211\u4eec\u4ecb\u7ecd\u8fc7\u4e86\u7b2c\u4e00\u4e2a\u754c\u9762target prediction result\uff0c\u90a3\u4e48\u5c0f\u679c\u4eca\u5929\u5c31\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u5176\u4ed6\u4e24\u4e2a\u754c\u9762\u3002<\/p>\n\n\n\n

<\/a>bioinformatics analyses of potential targets<\/strong><\/strong><\/h3>\n\n\n\n

\u9488\u5bf9target prediction result\u754c\u9762\u4e2d\u663e\u793a\u6f5c\u5728\u7684\u4e2d\u533b\u9776\u70b9\uff0cBATMAN-TCM\u63d0\u4f9b\u4e86\u4e09\u79cd\u5bcc\u96c6\u5206\u6790\uff0c\u5305\u62ecKEGG\u751f\u7269\u901a\u8def\u3001OMIM\/TTD\u75be\u75c5\u5bcc\u96c6\u5206\u6790\u548cGO\u529f\u80fd\u6ce8\u91ca\u3002bioinformatics analyses of potential targets\u754c\u9762\u4e2d\u5c06\u663e\u8457\u5bcc\u96c6\u7684KEGG\u751f\u7269\u901a\u8def\u3001OMIM\u75be\u75c5\u8868\u578b\/TTD\u75be\u75c5\u548cGO\u529f\u80fd\u672f\u8bed\uff08\u5305\u62ec\u751f\u7269\u8fc7\u7a0b\u3001\u5206\u5b50\u529f\u80fd\u548c\u7ec6\u80de\u6210\u5206\uff09\uff0c\u4ee5\u53ca\u76f8\u5e94\u7684P\u503c\u548c\u9776\u70b9\u663e\u793a\u5728\u8fd9\u91cc\u3002<\/p>\n\n\n\n

<\/a>KEGG pathway<\/h5>\n\n\n\n

KEGG Pathway\u662f\u4eac\u90fd\u57fa\u56e0\u4e0e\u57fa\u56e0\u7ec4\u767e\u79d1\u5168\u4e66\uff08Kyoto Encyclopedia of Genes and Genomes\uff0cKEGG\uff09\u4e2d\u7684\u4e00\u4e2a\u91cd\u8981\u7ec4\u6210\u90e8\u5206\uff0c\u5b83\u5305\u62ec\u4e86\u4ee3\u8c22\u3001\u8c03\u63a7\u3001\u901a\u8def\u3001\u751f\u5316\u3001\u75be\u75c5\u3001\u836f\u7269\u7b49\u76f8\u5173\u7684\u5206\u5b50\u76f8\u4e92\u4f5c\u7528\u548c\u5173\u7cfb\u7f51\u7edc\u3002KEGG Pathway\u6570\u636e\u5e93\u5c06\u751f\u7269\u4ee3\u8c22\u901a\u8def\u5212\u5206\u4e3a7\u7c7b\uff0c\u5305\u62ec\u65b0\u9648\u4ee3\u8c22\u3001\u9057\u4f20\u4fe1\u606f\u5904\u7406\u3001\u73af\u5883\u4fe1\u606f\u5904\u7406\u3001\u7ec6\u80de\u8fc7\u7a0b\u3001\u751f\u7269\u7cfb\u7edf\u3001\u4eba\u7c7b\u75be\u75c5\u548c\u836f\u7269\u5f00\u53d1\u3002\u5176\u4e2d\uff0c\u65b0\u9648\u4ee3\u8c22\u901a\u8def\u56fe\u662f\u901a\u8fc7\u624b\u5de5\u7ed8\u5236\u7684\u3002<\/p>\n\n\n\n

KEGG Pathway\u5171\u5305\u542b5\u4e2a\u5927\u7c7b\uff0c\u5177\u4f53\u4e3a\u7269\u79cd\u7279\u5f02\u7684\u901a\u8def\u56fe\uff08org-organism-specific pathway maps for “org” linked to gene entries\uff09\uff0c\u8fd9\u4e9b\u901a\u8def\u56fe\u4ee5\u7eff\u8272\u6846\u7684\u5f62\u5f0f\u5c55\u793a\u3002<\/p>\n\n\n\n

\u5728adjusted p-value\u680f\u4e2d\u8d8a\u5c0f\u7684\u503c\u8d8a\u53ef\u4fe1\uff0c\u975e\u5e38\u53ef\u4fe1\u7684\u503c\u4f1a\u7528\u7ea2\u8272\u6807\u51fa\uff0c\u540e\u9762\u7684targets\u680f\u6807\u51fa\u4e86\u5bf9\u5e94\u7684\u9776\u70b9\u6570\u91cf\u3002\u70b9\u51fbKEGG pathway ID\u53ef\u4ee5\u8fdb\u5165KEGG\u4e2d\u76f8\u5e94\u7684\u901a\u8def\u56fe\u4e86\uff1b\u70b9\u51fbPathway Graph\u53ef\u76f4\u89c2\u663e\u793a\u901a\u8def\u5bcc\u96c6\u60c5\u51b5\uff1b\u70b9\u51fbTargets\u5217\u84dd\u8272\u6570\u5b57\u53ef\u663e\u793a\u5bcc\u96c6\u5230\u8be5\u6761\u76ee\u7684\u57fa\u56e0\u3002<\/p>\n\n\n\n

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

\u901a\u8fc7select table view \u53ef\u4ee5\u66f4\u6539\u89c6\u56fe\uff0cKEGG hierarchy\u53ef\u4ee5\u4f7f\u7528\u6811\u89c6\u56fe\u6765\u663e\u793a\u8def\u5f84\u7684\u5c42\u6b21\u7ed3\u6784\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n
<\/a>Disease<\/h5>\n\n\n\n

OMIM\uff08Online Mendelian Inheritance in Man\uff0c\u4eba\u7c7b\u5728\u7ebf\u5b5f\u5fb7\u5c14\u9057\u4f20\u6570\u636e\u5e93\uff09\u662f\u4e00\u4e2a\u4e0d\u65ad\u66f4\u65b0\u7684\u4eba\u7c7b\u5b5f\u5fb7\u5c14\u9057\u4f20\u75c5\u7684\u6570\u636e\u5e93\u3002\u8be5\u6570\u636e\u5e93\u7531\u7ea6\u7ff0\u65af\u00b7\u970d\u666e\u91d1\u65af\u5927\u5b66\u533b\u5b66\u9662\u8d1f\u8d23\u7f16\u64b0\u4e0e\u7ef4\u62a4\uff0c\u4e3b\u8981\u5173\u6ce8\u4eba\u7c7b\u57fa\u56e0\u53d8\u5f02\u548c\u8868\u578b\u6027\u72b6\u4e4b\u95f4\u7684\u5173\u7cfb\uff0c\u5bf9\u5e94\u7684\u7b49\u4f4d\u57fa\u56e0\u4f1a\u6709\u7279\u5b9a\u7684MIM\u7f16\u53f7\u3002OMIM\u6570\u636e\u5e93\u4e2d\u7684\u6570\u636e\u8bb0\u5f55\u88ab\u5206\u4e3a\u4e0d\u540c\u7684\u7c7b\u522b\uff0c\u4ee5\u4fbf\u7528\u6237\u80fd\u591f\u66f4\u65b9\u4fbf\u5730\u68c0\u7d22\u548c\u67e5\u8be2\u3002<\/p>\n\n\n\n

TTD\u6570\u636e\u5e93\uff08Therapeutic Target Database\uff0c\u6cbb\u7597\u9776\u70b9\u6570\u636e\u5e93\uff09\u662f\u4e00\u4e2a\u4e13\u6ce8\u4e8e\u836f\u7269\u7814\u53d1\u9886\u57df\u7684\u6570\u636e\u5e93\uff0c\u5b83\u4e3b\u8981\u63d0\u4f9b\u5173\u4e8e\u836f\u7269\u9776\u70b9\u4e0e\u75be\u75c5\u5173\u7cfb\u7684\u8be6\u7ec6\u4fe1\u606f\u3002TTD\u6570\u636e\u5e93\u6536\u96c6\u5e76\u6838\u5b9e\u4e86\u836f\u7269\u7684\u7597\u6548\u836f\u9776\uff0c\u8fd9\u4e9b\u7597\u6548\u836f\u9776\u5305\u62ec\u6210\u529f\u9776\u6807\uff08\u5bf9\u5e94\u81f3\u5c11\u4e00\u79cd\u5df2\u6279\u51c6\u7684\u836f\u7269\uff09\u3001\u4e34\u5e8a\u8bd5\u9a8c\u9776\u6807\uff08\u5bf9\u5e94\u4e34\u5e8a\u8bd5\u9a8c\u836f\u7269\uff0c\u4f46\u5c1a\u672a\u83b7\u5f97\u6279\u51c6\u7684\u836f\u7269\uff09\u3001\u4e13\u5229\u8bb0\u5f55\u9776\u6807\uff08\u5728\u4e13\u5229\u548c\u540e\u7eed\u6587\u732e\u4e2d\u5f15\u7528\u7684\u9776\u6807\uff09\u548c\u6587\u732e\u62a5\u9053\u7684\u9776\u6807\u3002<\/p>\n\n\n\n

Disease\u754c\u9762\u663e\u793a\u57fa\u4e8eOMIM\u6216\u8005TTD\u6570\u636e\u5e93\u75be\u75c5\u57fa\u56e0\u5173\u8054\u7684\u75be\u75c5\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n
<\/a>Gene Ontology<\/h5>\n\n\n\n

Gene Ontology\uff08GO\uff09\u662f\u4e00\u4e2a\u5728\u751f\u7269\u4fe1\u606f\u5b66\u9886\u57df\u4e2d\u5e7f\u6cdb\u4f7f\u7528\u7684\u672c\u4f53\uff0c\u6db5\u76d6\u4e86\u751f\u7269\u5b66\u7684\u4e09\u4e2a\u65b9\u9762\uff1a\u7ec6\u80de\u7ec4\u5206\uff08Cellular Component\uff0cCC\uff09\u3001\u5206\u5b50\u529f\u80fd\uff08Molecular Function\uff0cMF\uff09\u548c\u751f\u7269\u8fc7\u7a0b\uff08Biological Process\uff0cBP\uff09\u3002<\/p>\n\n\n\n

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

GO\u662f\u4e00\u4e2a\u6709\u5411\u65e0\u73af\u56fe\uff08DAG\uff09\u578b\u7684\u672c\u4f53\uff0c\u4f7f\u7528\u4e86is_a\u3001part_of\u548cregulates\u4e09\u79cd\u5173\u7cfb\u3002\u5b83\u4f7f\u7528\u6709\u63a7\u5236\u7684\u8bcd\u6c47\u8868\u548c\u4e25\u683c\u5b9a\u4e49\u7684\u6982\u5ff5\u5173\u7cfb\uff0c\u4ee5\u6709\u5411\u65e0\u73af\u56fe\u7684\u5f62\u5f0f\u7edf\u4e00\u8868\u793a\u5404\u7269\u79cd\u7684\u57fa\u56e0\u529f\u80fd\u5206\u7c7b\u4f53\u7cfb\uff0c\u4ece\u800c\u8f83\u5168\u9762\u5730\u6982\u62ec\u4e86\u57fa\u56e0\u7684\u529f\u80fd\u4fe1\u606f\uff0c\u7ea0\u6b63\u4e86\u4f20\u7edf\u529f\u80fd\u5206\u7c7b\u4f53\u7cfb\u4e2d\u5e38\u89c1\u7684\u7ef4\u5ea6\u6df7\u6dc6\u95ee\u9898\u3002<\/p>\n\n\n\n

\u5728\u57fa\u56e0\u8868\u8fbe\u8c31\u5206\u6790\u4e2d\uff0cGO\u5e38\u7528\u4e8e\u63d0\u4f9b\u57fa\u56e0\u529f\u80fd\u5206\u7c7b\u6807\u7b7e\u548c\u57fa\u56e0\u529f\u80fd\u7814\u7a76\u7684\u80cc\u666f\u77e5\u8bc6\u3002\u901a\u8fc7GO\u5206\u6790\uff0c\u53ef\u4ee5\u53d1\u6398\u4e0e\u57fa\u56e0\u5dee\u5f02\u8868\u8fbe\u73b0\u8c61\u5173\u8054\u7684\u5355\u4e2a\u7279\u5f81\u57fa\u56e0\u529f\u80fd\u7c7b\u6216\u591a\u4e2a\u7279\u5f81\u529f\u80fd\u7c7b\u7684\u7ec4\u5408\u3002\u6b64\u5916\uff0cGO\u8fd8\u5e7f\u6cdb\u5e94\u7528\u4e8e\u529f\u80fd\u6ce8\u91ca\u3001\u6570\u636e\u89e3\u91ca\u3001\u6bd4\u8f83\u57fa\u56e0\u7ec4\u5b66\u548c\u4ee3\u8c22\u91cd\u5efa\u7b49\u9886\u57df\u3002<\/p>\n\n\n\n

\u5728\u6b64\u9875\u9762\u4e0aGO\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u4ee5\u6811\u72b6\u7ed3\u6784\u5448\u73b0\uff0c\u663e\u793a\u4e86GO\u9879\u4e4b\u95f4\u7684\u5c42\u6b21\u5173\u7cfb\u3002<\/p>\n\n\n\n

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

<\/a>Network visualization<\/strong><\/strong><\/h3>\n\n\n\n

\u4e2d\u836f\u662f\u5178\u578b\u7684\u201c\u591a\u7ec4\u5206\u3001\u591a\u9776\u70b9\u201d\u836f\u5242\uff0c\u5176\u5206\u5b50\u673a\u7406\u7279\u522b\u9002\u5408\u901a\u8fc7\u7f51\u7edc\u5206\u6790\u8fdb\u884c\u7814\u7a76\uff0c\u8fd9\u6837\u53ef\u4ee5\u7b80\u5355\u76f4\u89c2\u5730\u6355\u6349\u4e2d\u836f\u7684\u590d\u6742\u6027\u3002\u201c\u6210\u5206-\u9776\u70b9-\u901a\u8def\/\u75be\u75c5\u201d\u5173\u8054\u7f51\u7edc\uff0c\u6709\u52a9\u4e8e\u76f4\u89c2\u4e86\u89e3\u4e2d\u533b\u836f\u201c\u591a\u7ec4\u5206\u3001\u591a\u9776\u70b9\u3001\u591a\u901a\u8def\u201d\u7684\u8054\u5408\u6cbb\u7597\u673a\u5236\u548c\u6f5c\u5728\u7684\u75be\u75c5\u6cbb\u7597\u673a\u5236\u3002<\/p>\n\n\n\n

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

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\u7f51\u7edc\u56fe\u662f\u6839\u636e\u9884\u6d4b\u7684\u5019\u9009\u9776\u86cb\u767d\u7ed8\u5236\u7684\uff0c\u6bcf\u4e2a\u67e5\u8be2 TCM \u6210\u5206\u7684\u5206\u6570>=Score_cutoff\uff08\u7528\u6237\u5b9a\u4e49\uff09\u3002<\/p>\n\n\n\n

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

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