{"id":1846,"date":"2019-09-23T11:55:40","date_gmt":"2019-09-23T03:55:40","guid":{"rendered":"https:\/\/lsl.sinica.edu.tw\/Blog\/?p=1846"},"modified":"2019-09-23T11:55:40","modified_gmt":"2019-09-23T03:55:40","slug":"20190923","status":"publish","type":"post","link":"https:\/\/lsl.sinica.edu.tw\/Blog\/2019\/09\/20190923\/","title":{"rendered":"DAVID \u751f\u7269\u8cc7\u8a0a\u8cc7\u6599\u5eab"},"content":{"rendered":"

\"ChatRoom20190923\"<\/a><\/p>\n

 <\/p>\n

<\/p>\n

 <\/p>\n

\u6587\uff1a\u5f35\u8000\u660e\u7814\u7a76\u52a9\u6280\u5e2b\/\u751f\u7269\u91ab\u5b78\u79d1\u5b78\u7814\u7a76\u6240<\/span><\/strong><\/h3>\n

 <\/p>\n

\u5982\u679c\u7d93\u904e\u751f\u7269\u5be6\u9a57\u5f8c\u6211\u5011\u6709\u5e7e\u7d44\u300c\u6709\u986f\u8457\u8868\u73fe\u5dee\u7570\u57fa\u56e0(differentially expressed genes, DEGs)\u300d\u7684\u5217\u8868\uff0c\u6211\u5011\u60f3\u8981\u77e5\u9053\u9019\u4e9b\u57fa\u56e0\u53ef\u80fd\u53c3\u8207\u5728\u54ea\u4e9b\u985e\u578b\u7684\u529f\u80fd(gene ontology, GO)\u6216\u662f\u751f\u7269\u9014\u5f91(biological pathway)\u88e1\uff0c\u6709\u4ec0\u9ebc\u514d\u8cbb\u65b9\u4fbf\u7684\u5de5\u5177\u53ef\u4ee5\u5e6b\u6211\u627e\u51fa\u4f86\u5462\uff1f<\/h3>\n

\u4eca\u5929\u6211\u5011\u4ecb\u7d39\u7684\u662f\u4e00\u500b\u597d\u7528\u7684\u7dda\u4e0a\u8cc7\u6599\u5eab\u7db2\u7ad9DAVID<\/a> (The Database for Annotation, Visualization and Integrated Discovery)\uff0c\u96d6\u7136\u5b83\u662f\u4e00\u500b\u514d\u8cbb\u7684\u7db2\u8def\u670d\u52d9\uff0c\u4f46\u5b83\u7684\u529f\u80fd\u5df2\u7d93\u76f8\u7576\u5b8c\u6574\u4e00\u9ede\u4e5f\u4e0d\u8f38\u7d66\u8a31\u591a\u5546\u7528\u8edf\u9ad4\u3002<\/h3>\n

\u9996\u5148\uff0c\u6211\u5011\u8981\u5148\u6e96\u5099\u4e00\u7d44\u57fa\u56e0\u5217\u8868(a list of Gene IDs)\uff0c\u5217\u8868\u4e2d\u901a\u5e38\u662f\u5728\u5be6\u9a57\u7d50\u679c\u4e2d\u6709\u986f\u8457\u5dee\u7570\u7684\u57fa\u56e0(DEGs)\uff0c\u800cDAVID\u7db2\u7ad9\u652f\u63f4\u5f88\u591a\u4e0d\u540c\u8cc7\u6599\u5eab\u7684Gene ID\u683c\u5f0f\uff0c\u5982\u5e38\u7528\u7684ENSEMBL gene ID\u6216\u662fAffymetrix microarray \u7684probe ID\u7b49\u3002\u6b64\u5916\uff0c\u70ba\u4e86\u900f\u904e\u7d71\u8a08\u7684\u65b9\u5f0f\u627e\u51faDEGs\u53c3\u8207\u7684\u751f\u7269\u529f\u80fd(biological functions)\u6216\u662f\u8def\u5f91(pathways)\uff0c\u6211\u5011\u901a\u5e38\u4e5f\u6703\u6e96\u5099\u53e6\u4e00\u7d44\u57fa\u56e0\u5217\u8868\u7576\u4f5c\u80cc\u666f\u8cc7\u6599(background data)\uff0c\u9019\u7d44\u57fa\u56e0\u5217\u8868\u901a\u5e38\u662f\u5be6\u9a57\u4e2d\u300c\u6240\u6709\u8868\u73fe\u57fa\u56e0(all expressed genes)\u300d\u7684\u5217\u8868\u3002\u5982\u679c\u6c92\u6709\uff0cDAVID\u7db2\u7ad9\u4e5f\u6703\u6839\u64da\u4e0d\u540c\u7684\u7269\u7a2e\u63d0\u4f9b\u300c\u6240\u6709\u8a3b\u89e3\u57fa\u56e0(all annotated genes)\u300d\u5217\u8868\u4f86\u7576\u4f5c\u9810\u8a2d\u7684\u80cc\u666f\u8cc7\u6599\u3002<\/h3>\n

\u8cc7\u6599\u6e96\u5099\u597d\u4e4b\u5f8c\u6211\u5011\u63a5\u4e0b\u4f86\u5c31\u4e00\u6b65\u6b65\u544a\u8a34\u5927\u5bb6\u5982\u4f55\u4f7f\u7528\uff1a<\/h3>\n

 <\/p>\n

\u4e00\u3001\u5728\u7db2\u9801\u700f\u89bd\u5668\u4e0a\u958b\u555f\u9023\u7d50\u9032\u5165DAVID<\/a>\u7db2\u7ad9(https:\/\/david.ncifcrf.gov\/home.jsp<\/a>)\uff0c\u63a5\u8457\u5728\u7db2\u9801\u4e0a\u65b9\u7684\u6a6b\u5e45\u529f\u80fd\u9078\u55ae\u4e0a\u9ede\u9078 \u201cStart Analysis\u201d<\/h3>\n

\"2019092301\"<\/a><\/p>\n

\u5716\u4e00\u3001DAVID\u7db2\u7ad9\u9996\u9801<\/h3>\n

<\/h3>\n

\u4e8c\u3001\u5728\u7db2\u9801\u4e0a\u7684\u5de6\u908a\u6703\u51fa\u73fe\u53ef\u4ee5\u8b93\u6211\u5011\u4e0a\u50b3\u57fa\u56e0\u5217\u8868\u7684\u8868\u55ae\uff0c\u6211\u5011\u53ef\u4ee5\u76f4\u63a5\u5229\u7528\u8907\u88fd\u8cbc\u4e0a\u7684\u529f\u80fd\u76f4\u63a5\u5c07\u57fa\u56e0\u5217\u8868\u8cbc\u5728A: Paste a list\u4e0b\u65b9\u7684\u7a7a\u767d\u8655\uff0c\u63a5\u8457\u5728\u8868\u55aeStep 3: List Type\u7684\u5730\u65b9\u8981\u9ede\u9078Gene List\u5f8c\u4e26\u6309\u4e0b \u201cSubmit List\u201d \u6309\u9215\uff08\u5716\u4e8c\u3001\u4e09\uff09\u3002\u53e6\u4e00\u500b\u65b9\u5f0f\u5247\u662f\u5148\u5c07\u57fa\u56e0\u5217\u8868\u5132\u5b58\u6210\u6587\u5b57\u6a94\u6848\uff0c\u5229\u7528B: Choose From a File\u7684\u6309\u9215\u9078\u64c7\u8981\u4e0a\u50b3\u7684\u57fa\u56e0\u5217\u8868\uff08\u4e0b\u4e00\u500b\u6b65\u9a5f\u6703\u793a\u7bc4\uff09\u3002\u4e0a\u50b3\u6210\u529f\u5f8c\uff0c\u539f\u4f86\u7684\u4e0a\u50b3\u8868\u55ae\u6703\u51fa\u73feList Manager\u4e26\u986f\u793a\u4e0a\u50b3\u7684\u57fa\u56e0\u5217\u8868\u7de8\u865f\uff08\u5716\u56db\u4e2d\u7684List_1\uff09\u3002<\/h3>\n

\"2019092302\"<\/a><\/p>\n

\u5716\u4e8c\u3001\u9ede\u9078Start Analysis\u5f8c\uff0c\u756b\u9762\u5de6\u908a\u51fa\u73fe\u53ef\u4e0a\u50b3\u57fa\u56e0\u5217\u8868\u7684\u8868\u55ae<\/h3>\n

\"2019092303\"<\/a><\/p>\n

\u5716\u4e09\u3001\u5c07\u57fa\u56e0\u5217\u8868\u8cbc\u5728A: Paste a list\u4e0b\u65b9\u7684\u7a7a\u767d\u8655<\/h3>\n

\"2019092304\"<\/a><\/p>\n

\u5716\u56db\u3001\u4e0a\u50b3\u5b8c\u6210\u5f8c\uff0cList Manager\u6703\u51fa\u73fe\u4e00\u7b46\u8cc7\u6599(List_1)<\/h3>\n

\u4e09\u3001\u63a5\u8457\u6211\u5011\u518d\u4e0a\u50b3\u4e00\u7d44\u80cc\u666f\u8cc7\u6599\u7528\u7684\u57fa\u56e0\u5217\u8868\u3002\u8acb\u9ede\u9078\u5de6\u908a\u8868\u55ae\u4e2d \u201cUpload\u201d\uff0c\u9019\u6b21\u5229\u7528\u53e6\u4e00\u500b\u4e0a\u50b3\u65b9\u5f0fB. Choose From a List\u4f86\u4e0a\u50b3\u57fa\u56e0\u5217\u8868\u3002\u6309\u4e0b \u201cChoose File\u201d\u6309\u9215\uff0c\u7136\u5f8c\u9078\u53d6\u6211\u5011\u8981\u4e0a\u50b3\u7684\u6a94\u6848\u5f8c\uff0c\u6309\u9215\u65c1\u908a\u6703\u51fa\u73fe\u9078\u64c7\u6a94\u6848\u7684\u540d\u7a31\u3002\u6b64\u6642\u56e0\u70ba\u6211\u5011\u7684\u57fa\u56e0\u5217\u8868\u662f\u8981\u62ff\u4f86\u7576\u4f5c\u80cc\u666f\u8cc7\u6599\uff0c\u6240\u4ee5\u8a18\u5f97\u8981\u5728Step 3: List Type\u7684\u5730\u65b9\u9078\u64c7Background\u5f8c\u6309\u4e0b \u201cSubmit List\u201d \u6309\u9215\uff08\u5716\u4e94\uff09\u3002\u503c\u5f97\u6ce8\u610f\u7684\u662f\uff0c\u56e0\u70ba\u7db2\u8def\u983b\u5bec\u7684\u5927\u5c0f\u56e0\u7d20\uff0c\u6709\u6642\u5019\u6703\u56e0\u70ba\u4e0a\u50b3\u7684\u57fa\u56e0\u6578\u91cf\u592a\u591a\uff0c\u4e0a\u50b3\u7684\u901f\u5ea6\u6703\u6709\u9ede\u6162\uff0c\u8acb\u7a0d\u5fae\u8010\u5fc3\u7b49\u5019\u3002<\/h3>\n

\"2019092305\"<\/a><\/p>\n

\u5716\u4e94\u3001\u5229\u7528\u6a94\u6848\u4f86\u4e0a\u50b3\u57fa\u56e0\u5217\u8868<\/h3>\n

\"2019092306\"<\/a><\/p>\n

\u5716\u516d\u3001\u8cc7\u6599\u4e0a\u50b3\u5b8c\u6210\u5f8c\uff0c\u51fa\u73fe\u958b\u59cb\u5206\u6790\u7684\u756b\u9762<\/h3>\n

 <\/p>\n

\u56db\u3001\u7576\u8cc7\u6599\u90fd\u4e0a\u50b3\u5b8c\u6210\u5f8c\uff0c\u7db2\u9801\u7684\u4e2d\u9593\u90e8\u5206\u6703\u51fa\u73fe\u53ef\u4ee5\u958b\u59cb\u5206\u6790\u7684\u756b\u9762\uff08\u5716\u516d\uff09\uff0c\u9019\u6642\u4f9d\u7167\u7bad\u982d\u6307\u793a\u9ede\u9078 \u201cFunctional Annotation Tool\u201d \u7684\u9023\u7d50\u5373\u53ef\u3002<\/h3>\n

\"2019092307\"<\/a><\/p>\n

\u5716\u4e03\u3001\u5206\u6790\u5b8c\u6210\uff0c\u8b93\u4f7f\u7528\u8005\u9ede\u9078\u7d50\u679c\u985e\u5225\u7684\u756b\u9762<\/h3>\n

 <\/p>\n

\u4e94\u3001\u7576\u5206\u6790\u5b8c\u6210\uff0cDAVID\u53ef\u4ee5\u8b93\u6211\u5011\u9078\u64c7\u6211\u5011\u60f3\u8981\u770b\u54ea\u4e9b\u7d50\u679c\uff08\u5716\u4e03\uff09\u3002\u7531\u65bc\u9810\u8a2d\u7684\u529f\u80fd\u6216\u662f\u8def\u5f91\u985e\u5225\u6709\u76f8\u7576\u591a\uff0c\u4e0d\u4e00\u5b9a\u90fd\u7b26\u5408\u6211\u5011\u60f3\u8981\u770b\u7684\u985e\u5225\uff0c\u6240\u4ee5\u53ef\u4ee5\u5148\u9ede\u9078\u53f3\u4e0a\u89d2 \u201cClear All\u201d \u7684\u6309\u9215\uff0c\u7136\u5f8c\u518d\u4f9d\u7167\u81ea\u5df1\u7684\u9700\u6c42\u9ede\u9078\u985e\u5225\u3002\u4f8b\u5982\u6211\u5011\u95dc\u5fc3\u7684\u662f DEGs\u5217\u8868\u7684\u57fa\u56e0\u5728\u54ea\u4e9bKEGG pathways\u4e2d\u626e\u6f14\u91cd\u8981\u7684\u89d2\u8272\uff1f\u9019\u6642\u6211\u5011\u5c31\u9ede\u9078Pathways\u4e2d\u7684KEGG_PATHWAY \u5f8c\u518d\u6309\u4e0b\u65b9 \u201cFunctional Annotation Chart\u201d \u6309\u9215\u3002<\/h3>\n

\"2019092308\"<\/a><\/p>\n

\u5716\u516b\u3001\u6e05\u9664\u9810\u8a2d\u9078\u64c7\uff0c\u55ae\u7368\u9078\u64c7KEGG_PATHWAY<\/h3>\n

<\/h3>\n

\u516d\u3001\u5206\u6790\u7d50\u679c\u6703\u4ee5\u8868\u683c\u7684\u65b9\u5f0f\u986f\u793a\uff08\u5716\u4e5d\uff09\uff0c\u9664\u4e86\u53c3\u8207\u751f\u7269\u8def\u5f91\u7684\u540d\u7a31\u4e4b\u5916\uff0c\u5404\u9805\u7d71\u8a08\u7684\u8cc7\u6599\u4e5f\u6703\u5217\u51fa\u4f86\u3002\u5982\u679c\u6211\u5011\u8981\u66f4\u5b8c\u6574\u7684\u7d50\u679c\u53ef\u4ee5\u9ede\u9078\u53f3\u4e0a\u89d2 \u201cDownload File\u201d\u7684\u9023\u7d50\u3002<\/h3>\n

\"2019092309\"<\/a><\/p>\n

\u5716\u4e5d\u3001\u7d50\u679c\u986f\u793a\u6211\u5011\u4e0a\u50b3\u7684\u57fa\u56e0\u4e2d\u53c3\u8207\u4e86\u8a31\u591a\u4e0d\u540c\u7684pathways\uff0c\u6bcf\u4e00\u500bpathway\u7684\u7d71\u8a08\u8cc7\u6599\u4e5f\u4e00\u4f75\u5217\u5728\u53f3\u908a\u7684\u6b04\u4f4d\u4e2d\u3002<\/h3>\n

 <\/p>\n

\u4e03\u3001\u540c\u6a23\u7684\uff0c\u5982\u679c\u6211\u5011\u60f3\u8981\u770b\u9019\u4e9b\u57fa\u56e0\u53c3\u8207\u7684GO function\uff0c\u6211\u5011\u4e5f\u53ef\u4ee5\u9078\u64c7\u985e\u5225\u7684\u756b\u9762\u9078\u64c7Gene_Ontology\u4e2dGOTERM_BP_DIRECT\u3001 GOTERM_CC_DIRECT\u4ee5\u53caGOTERM_MF_DIRECT\u985e\u5225\uff08\u5716\u5341\uff09\u4e4b\u5f8c\u518d\u6309\u4e0b\u65b9 \u201cFunctional Annotation Chart\u201d \u6309\u9215\u5373\u53ef\u3002<\/h3>\n

\"2019092310\"<\/a><\/p>\n

\u5716\u5341\u3001\u6e05\u9664\u9810\u8a2d\u9078\u64c7\uff0c\u55ae\u7368\u9078\u64c7Gene_Ontology\u7684\u985e\u5225<\/h3>\n

 <\/p>\n

\u611f\u8b1d\u5f35\u8000\u660e\u7814\u7a76\u52a9\u6280\u5e2b\u5206\u4eab<\/span><\/strong><\/h2>\n
\r\n
\r\n \r\n <\/i>\r\n <\/a>\r\n 0 <\/span>\r\n<\/div><\/div>","protected":false},"excerpt":{"rendered":"

  0<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[18],"tags":[80,16],"class_list":["post-1846","post","type-post","status-publish","format-standard","hentry","category-bioinformatics","tag-david","tag-dr-a-cula-lab"],"_links":{"self":[{"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/posts\/1846","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/comments?post=1846"}],"version-history":[{"count":13,"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/posts\/1846\/revisions"}],"predecessor-version":[{"id":1870,"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/posts\/1846\/revisions\/1870"}],"wp:attachment":[{"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/media?parent=1846"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/categories?post=1846"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/lsl.sinica.edu.tw\/Blog\/wp-json\/wp\/v2\/tags?post=1846"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}