{"id":26092,"date":"2024-01-24T17:17:48","date_gmt":"2024-01-24T09:17:48","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26092"},"modified":"2024-01-24T17:17:50","modified_gmt":"2024-01-24T09:17:50","slug":"%e4%bf%9d%e5%a7%86%e7%ba%a7%e6%95%99%e7%a8%8b%ef%bc%81%ef%bc%81%e5%b0%8f%e6%9e%9c%e6%95%99%e4%bd%a0%e5%a6%82%e4%bd%95%e4%bd%bf%e7%94%a8david%e6%95%b0%e6%8d%ae%e5%ba%93%e5%b9%b6%e5%8f%af%e8%a7%86","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26092","title":{"rendered":"\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\u5c0f\u679c\u6559\u4f60\u5982\u4f55\u4f7f\u7528DAVID\u6570\u636e\u5e93\u5e76\u53ef\u89c6\u5316\u7ed3\u679c\uff01\uff01\uff01"},"content":{"rendered":"

\u5c0f\u4f19\u4f34\u4eec\u5728\u505aGO\u529f\u80fd\u5bcc\u96c6\u548cKEGG\u901a\u8def\u5bcc\u96c6\u5206\u6790\u65f6\u5019\uff0c\u9047\u89c1\u8fc7\u5f88\u591a\u56f0\u96be\uff0c\u5176\u4e2d\u4e4b\u4e00\u5c31\u662f\u5728\u7528R\u505aKEGG\u5206\u6790\u65f6\u5019\uff0cKEGG\u6570\u636e\u5e93\u56e0\u4e3a\u7f51\u7edc\u8fdb\u4e0d\u53bb\u5bfc\u81f4KEGG\u901a\u8def\u5bcc\u96c6\u5931\u8d25\u3002\u8fd8\u6709\u7684\u5c0f\u4f19\u4f34\u60f3\u505a\u5bcc\u96c6\u5206\u6790\uff0c\u4f46\u662f\u53ea\u6709\u57fa\u56e0\u540d\uff0c\u5c11\u4e86logFC\u503c\uff0c\u5bfc\u81f4\u60f3\u505a\u5bcc\u96c6\u5206\u6790\u5f88\u82e6\u607c\u3002\u5c0f\u679c\u5728\u8fd9\u91cc\u6559\u5927\u5bb6\u4e00\u4e2a\u65b9\u5f0f\uff0c\u4f7f\u7528DAVID\u6570\u636e\u53bb\u5206\u6790\u3002<\/p>\n

\u76ee\u524d\u6765\u8bf4DAVID\u6570\u636e\u5e93\u57282022\u5e74\u66f4\u65b0\u4e86\uff0c\u90a3\u5c31\u610f\u5473\u7740\u6211\u4eec\u53c8\u53ef\u4ee5\u4f7f\u7528\u4e86\uff0c\u4e4b\u524d\u56e0\u4e3a\u957f\u65f6\u95f4\u6ca1\u8ddf\u65b0\uff0c\u5bfc\u81f4\u8bb8\u591a\u7684\u6570\u636e\u8ddf\u4e0d\u4e0a\u65f6\u4ee3\u3002\u73b0\u5728\u5c0f\u679c\u5e26\u5927\u5bb6\u624b\u628a\u624b\u6559\u5927\u5bb6\u5982\u4f55\u4f7f\u7528DAVID\u6570\u636e\u53bb\u505a\u5bcc\u96c6\u5206\u6790\uff01\uff01<\/p>\n

\u6211\u4eec\u5148\u8fdb\u5165\u6570\u636e\u5e93\u5b98\u7f51\uff08https:\/\/david.ncifcrf.gov\/\uff09<\/p>\n

<\/p>\n

\u4e0a\u9762\u6709\u5f88\u591a\u7684\u529f\u80fd\uff0c\u6211\u4eec\u53ea\u9700\u8981\u70b9\u51fbstart Analysis\u5c31\u53ef\u4ee5\u4e86<\/p>\n

<\/p>\n

\u5728 \u8f93\u5165\u6211\u4eec\u60f3\u8981\u5206\u6790\u7684\u57fa\u56e0\u540d\u6216\u8005\u5bfc\u5165\u6587\u4ef6\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u7ed9\u5927\u5bb6\u6f14\u793a\uff0c\u4f7f\u7528\u7684\u793a\u4f8b\u6570\u636e\u3002 \u63a5\u4e0b\u6765\u8981\u6ce8\u610f\u6211\u4eec\u5728\u7b2c\u4e8c\u90e8\u8981\u9009\u62e9 \uff0c\u56e0\u4e3a\u6211\u4eec\u7684\u57fa\u56e0\u662f\u901a\u8fc7SYMBOL\u8f6c\u6362\u8fc7\u6765\u7684\uff0c\u5c0f\u4f19\u4f34\u4e0d\u8981\u9009\u9519\u4e86<\/p>\n

\u63a5\u4e0b\u6765 \u9009\u62e9\u6211\u4eec\u7684\u4eba\u7c7b\uff0c\u4ee5\u53ca\u7b2c\u4e09\u6b65\uff0c\u7c7b\u578b\uff0c\u662f\u57fa\u56e0\u5217\u8868\u3002<\/p>\n

\u7136\u540e\u6211\u4eec\u5f00\u59cb\u5206\u6790\u5427 \uff0c\u70b9\u51fbSubmit List<\/p>\n

\u7b49\u5f85\u51e0\u79d2\u949f\uff1a<\/p>\n

<\/p>\n

\u5c31\u51fa\u73b0\u8fd9\u6837\u7684\u754c\u9762\uff0c\u53f3\u4fa7\u662f\u5728\u4eba\u7c7b\u6570\u636e\u5e93\u4e2d\u627e\u5230\u4e8697\u4e2aGene\u6211\u4eec\u53ea\u8981\u8fd997\u4e2aUse\u5b83<\/p>\n

\u7136\u540e\u6211\u4eec\u67e5\u770b\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\uff1a<\/p>\n

\u70b9\u51fb\u8fd9\u4e2a\uff1a<\/p>\n

<\/p>\n

<\/p>\n

\u6211\u4eec\u67e5\u770b\u7ed3\u679c\u6211\u4eec\u5148\u6253\u5f00\u901a\u8def\u5bcc\u96c6\u7ed3\u679c\uff1a<\/p>\n

KEGG\u901a\u8def\u662f\u6211\u4eec\u9700\u8981\u7684\uff0c\u6211\u4eec\u70b9\u51fbKEGG\u7ed3\u679c\u7684Chart\uff1a<\/p>\n

\u7136\u540e\u6211\u4eec\u70b9\u53f3\u4e0a\u89d2\u7684\u4e0b\u8f7d<\/p>\n

\u4f46\u662f\u4e0b\u8f7d\u7684\u7ed3\u679c\u662f<\/p>\n

\u8fd9\u5c31\u9700\u8981\u6211\u4eec\u65b0\u5efa\u4e00\u4e2atxt\u6587\u4ef6\uff0c\u6211\u4eec\u628a\u7ed3\u679c\u4fdd\u5b58\u8fdb\u53bb<\/p>\n

\u5c0f\u4f19\u4f34\u81ea\u884c\u4fdd\u5b58\uff0c\u53ef\u4ee5\u770b\u5230\u5bcc\u96c6\u7684\u901a\u8def\u4ee5\u53ca\u5176\u4ed6\u4fe1\u606f\u3002<\/p>\n

\u63a5\u4e0b\u6765\u6211\u4eec\u53bb\u53ef\u89c6\u5316KEGG\u5bcc\u96c6\u7684\u7ed3\u679c\u3002<\/p>\n

\u6211\u4eec\u5148\u8bfb\u5165\u6570\u636e\uff1a<\/p>\n

library(stringi)<\/p>\n

library(ggplot2)<\/p>\n

library(dplyr)<\/p>\n

##\u8bfb\u53d6\u548c\u6574\u7406KEGG\u7684\u7ed3\u679c<\/p>\n

downgokegg<-read.delim(“E:\\\\\u751f\u4fe1\u679c\\\\KEGG.txt<\/a>“)<\/p>\n

\u63a5\u4e0b\u6765\u5bf9\u6570\u636e\u5904\u7406\uff0c\u9009\u62e9\u9700\u8981\u53ef\u89c6\u5316\u7684\u6570\u636e\uff1a<\/p>\n

enrich<-downgokegg<\/p>\n

enrich_signif=enrich[which(enrich$PValue<0.05),]<\/p>\n

enrich_signif=enrich_signif[,c(1:3,5)]<\/p>\n

head(enrich_signif)<\/p>\n

enrich_signif=data.frame(enrich_signif)<\/p>\n

KEGG=enrich_signif<\/p>\n

KEGG$Term<-stri_sub(KEGG$Term,10,100)<\/p>\n

<\/p>\n

\u6700\u540e\u53ef\u89c6\u5316\uff1a<\/p>\n

ggplot(KEGG,aes(x=Count,y=Term))+geom_point(aes(color=PValue,size=Count))+scale_color_gradient(low=’slateblue4′,high=’firebrick3′)+theme_bw()+theme(panel.grid.minor = element_blank(),panel.grid.major = element_blank())<\/p>\n

\u6211\u4eec\u4ee5\u6c14\u6ce1\u56fe\u7684\u5f62\u5f0f\u5c55\u793a\uff0c\u4ee5Count\u503c\u4e3a\u6a2a\u5750\u6807\u3002<\/p>\n

\u63a5\u4e0b\u6765\u6211\u4eec\u53bb\u5206\u6790GO\u5bcc\u96c6\u7ed3\u679c<\/p>\n

<\/p>\n

\u6211\u4eec\u5728\u8fd9\u91cc\u627e\u5230GO\u5bcc\u96c6\u7684\u7ed3\u679c\uff0c\u5176\u4e2d\u6709BP,CC,MF\u3002\u548c\u4e0a\u8ff0KEGG\u7ed3\u679c\u4e00\u6837\u628a\u7ed3\u679c\u4fdd\u5b58\u5230txt\u6587\u4ef6\u4e2d\u3002\u5c0f\u679c\u5728\u8fd9\u91cc\u63d0\u524d\u4fdd\u5b58\u597d\u4e86\uff0c\u5c0f\u4f19\u4f34\u81ea\u884c\u53bb\u4fdd\u5b58\u3002<\/p>\n

\u628a\u7ed3\u679c\u5206\u6210\u4e09\u4e2a\u6587\u4ef6\u5939\u3002\u63a5\u4e0b\u6765\u6211\u4eec\u53bb\u5206\u6790\u5427\uff1a<\/p>\n

\u6211\u4eec\u628a\u6570\u636e\u4e00\u4e00\u5bfc\u5165\u8fdb\u53bb\uff0c\u7136\u540e\u5728\u5408\u5e76\u6570\u636e<\/p>\n

GO_CC<-read.delim(‘E:\\\\\u751f\u4fe1\u679c\\\\CC.txt’)<\/p>\n

GO_CC_signif=GO_CC[which(GO_CC$PValue<0.05),]<\/p>\n

GO_CC_signif=GO_CC[,c(1:3,5)]<\/p>\n

head(GO_CC_signif)<\/p>\n

GO_CC_signif=data.frame(GO_CC_signif)<\/p>\n

GO_CC_signif$Term<-stri_sub(GO_CC_signif$Term,12,100)<\/p>\n

GO_BP<-read.delim(‘E:\\\\\u751f\u4fe1\u679c\\\\BP.txt’)<\/p>\n

GO_BP_signif=GO_BP[which(GO_BP$PValue<0.05),]<\/p>\n

GO_BP_signif=GO_BP_signif[,c(1:3,5)]<\/p>\n

head(GO_BP_signif)<\/p>\n

GO_BP_signif=data.frame(GO_BP_signif)<\/p>\n

GO_BP_signif$Term<-stri_sub(GO_BP_signif$Term,12,100)<\/p>\n

GO_MF<-read.delim(‘E:\\\\\u751f\u4fe1\u679c\\\\MF.txt’)<\/p>\n

GO_MF_signif=GO_MF[which(GO_MF$PValue<0.05),]<\/p>\n

GO_MF_signif=GO_MF_signif[,c(1:3,5)]<\/p>\n

head(GO_MF_signif)<\/p>\n

GO_MF_signif=data.frame(GO_MF_signif)<\/p>\n

GO_MF_signif$Term<-stri_sub(GO_MF_signif$Term,12,100)<\/p>\n

enrich_signif=rbind(GO_BP_signif,rbind(GO_CC_signif,GO_MF_signif))<\/p>\n

go=enrich_signif<\/p>\n

go=arrange(go,go$Category,go$PValue)<\/p>\n

\u5bf9\u4e8e\u8bfb\u53d6\u7684\u6570\u636e\u5c0f\u4f19\u4f34\u53ef\u4ee5\u5728\u53c2\u6570\u8bbe\u7f6e\u9009\u62e9\u81ea\u5df1\u60f3\u53ef\u89c6\u5316\u7684\u6570\u636e\u7ed3\u679c\u3002\u63a5\u4e0b\u6765\u6211\u4eec\u8bbe\u7f6e\u4e00\u4e0b\u56fe\u4f8b\u7684\u540d\u79f0\uff1a<\/p>\n

##\u56fe\u4f8b\u540d\u79f0\u8bbe\u7f6e<\/p>\n

m=go$Category<\/p>\n

m=gsub(“TERM”,””,m)<\/p>\n

m=gsub(“_DIRECT”,””,m)<\/p>\n

go$Category=m<\/p>\n

GO_term_order=factor(as.integer(rownames(go)),labels = go$Term)<\/p>\n

COLS<-c(“#66C3A5″,”#8DA1CB”,”#FD8D62″)<\/p>\n

\u6709\u7684\u5c0f\u4f19\u4f34\u60f3\u7528Count\u503c\u53bb\u5c55\u793a\uff0c\u4e5f\u662f\u53ef\u4ee5\u7684\uff0c\u770b\u5c0f\u4f19\u4f34\u7684\u9700\u6c42\u3002\u6700\u540e\u6211\u4eec\u5f00\u59cb\u753b\u56fe\uff1a<\/p>\n

###\u5f00\u59cb\u753b\u56fe<\/p>\n

ggplot(data=go,aes(x=GO_term_order,y=Count,fill=Category))+<\/p>\n

geom_bar(stat = “identity”,width = 0.8)+<\/p>\n

scale_fill_manual(values = COLS)+<\/p>\n

theme_bw()+<\/p>\n

xlab(“Terms”)+<\/p>\n

ylab(“Gene_counts”)+<\/p>\n

labs()+<\/p>\n

theme(axis.text.x = element_text(face = “bold”,color = “black”,angle = 90,vjust = 1,hjust = 1)) <\/p>\n

\u8fd9\u6837\u6211\u4eec\u7684\u7ed3\u679c\u5c31\u5c55\u793a\u51fa\u6765\u4e86\uff0c\u5305\u542bBP CC MF \u6211\u4eec\u4ee5\u67f1\u72b6\u56fe\u7684\u5f62\u5f0f\u5c55\u793a\uff0c\u4e0d\u8fc7\u6709\u7684\u5c0f\u4f19\u4f34\u60f3\u4ee5\u5176\u4ed6\u7684\u5f62\u5f0f\uff0c\u6bd4\u5982\u6c14\u6ce1\u4e4b\u7c7b\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u5c31\u4e0d\u4e00\u4e00\u6559\u5b66\u4e86\u3002\u611f\u5174\u8da3\u7684\u5c0f\u670b\u53cb\u53ef\u4ee5\u81ea\u884c\u53bb\u8bbe\u7f6e\u3002\u6700\u4e3b\u8981\u7684\u6211\u4eec\u7684\u7ed3\u679c\u5df2\u7ecf\u51fa\u6765\uff0c\u5c0f\u4f19\u4f34\u53ef\u4ee5\u6839\u636e\u7ed3\u679c\u53bb\u53ef\u89c6\u5316\u3002<\/p>\n

\u5feb\u53bb\u8bd5\u8bd5\u5427\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"

\u5c0f\u4f19\u4f34\u4eec\u5728\u505aGO\u529f\u80fd\u5bcc\u96c6\u548cKEGG\u901a\u8def\u5bcc\u96c6\u5206\u6790\u65f6\u5019\uff0c\u9047\u89c1\u8fc7\u5f88\u591a\u56f0\u96be\uff0c\u5176\u4e2d\u4e4b\u4e00\u5c31\u662f\u5728\u7528R\u505aKEGG\u5206\u6790\u65f6\u5019\uff0cKE […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","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\/26092"}],"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=26092"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26092\/revisions"}],"predecessor-version":[{"id":26111,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26092\/revisions\/26111"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26092"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26092"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26092"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}