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data-imgfileid=\"100016196\" data-ratio=\"1\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"430\" style=\"width: 170px;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_f6PG40Qrdu5e9B1iaIMItPiajABYWA-9.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAxqaqPbQprPd4vw8Ytp0cprbzXiakMDdFriaB6B59ibhlBCrNyQFf6PG40Qrdu5e9B1iaIMItPiajABYWA\/640?wx_fmt=jpeg'\" data-recalc-dims=\"1\" \/><\/p>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u5728\u6b63\u5f0f\u5f00\u59cb\u4eca\u5929\u7684\u6587\u732e\u590d\u73b0\u4e4b\u524d\uff0c\u5c0f\u679c\u9700\u8981\u7ed9\u5c0f\u4f19\u4f34\u4eec\u5148\u4ecb\u7ecd\u4e00\u4e0b\u672c\u7bc7\u6559\u7a0b\u6240\u9700\u8981\u7684\u5de5\u5177\uff1alimma\u5206\u6790\u3002<\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u5bf9\u4e8elimma\u5206\u6790\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u7b80\u8981\u7684\u4ecb\u7ecd\u4e00\u4e0b\uff1a limma\u5206\u6790\u662f\u4e00\u79cd\u7528\u4e8e\u5dee\u5f02\u57fa\u56e0\u8868\u8fbe\u5206\u6790\u7684\u7edf\u8ba1\u65b9\u6cd5\uff0c\u57fa\u4e8e\u7ebf\u6027\u6a21\u578b\uff0c\u4f7f\u7528\u52a0\u6743\u6700\u5c0f\u4e8c\u4e58\u6cd5\u6765\u4f30\u8ba1\u57fa\u56e0\u8868\u8fbe\u7684\u5dee\u5f02\uff0c\u5e76\u901a\u8fc7\u7ecf\u9a8c\u8d1d\u53f6\u65af\u65b9\u6cd5\u6765\u6821\u6b63\u591a\u91cd\u68c0\u9a8c\u95ee\u9898\u3002\u53ef\u4ee5\u5904\u7406\u591a\u79cd\u6570\u636e\u7c7b\u578b\u548c\u683c\u5f0f\uff0c\u5982\u57fa\u56e0\u82af\u7247\u6570\u636e\u548cRNA-Seq\u6570\u636e\uff0c\u4e5f\u80fd\u591f\u5f88\u597d\u5730\u63a7\u5236\u5047\u9633\u6027\u7387\u3002\u9664\u4e86\u5e38\u89c4\u7684\u8fdb\u884c\u4e00\u4e9b\u80bf\u7624\u7684\u5dee\u5f02\u5206\u6790\uff0climma\u5206\u6790\u8fd8\u53ef\u4ee5\u7528\u4e8e\u9776\u5411\u6cbb\u7597\u76f8\u5173\u7684\u6570\u636e\u5206\u6790\uff0c\u90a3\u4e48limma\u5206\u6790\u5e94\u8be5\u5982\u4f55\u5728\u9776\u5411\u6cbb\u7597\u7684\u6587\u7ae0\u4e2d\u5e94\u7528\u5462\uff1f\u522b\u6025\uff0c\u5c0f\u679c\u8fd9\u5c31\u624b\u628a\u624b\u7684\u6559\u4f1a\u4f60\uff01<\/span> \u5173\u4e8elimma\u5206\u6790\u7684\u57fa\u7840\u77e5\u8bc6\u4ee5\u53ca\u53ef\u89c6\u5316\u6559\u7a0b\uff0c\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u5173\u6ce8\u5c0f\u679c\u641c\u7d22\u5f80\u671f\u5185\u5bb9\u67e5\u9605\u54e6~<\/span><\/span><span style=\"font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;color: rgb(255, 0, 0);font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"> <o:p> <\/o:p><\/span> <\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><o:page><\/o:page><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">Step 1 \u8bbe\u7f6e\u5de5\u4f5c\u73af\u5883\uff0c\u529f\u80fd\u51fd\u6570\uff0c\u8f93\u5165\u6587\u4ef6<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u9996\u5148\uff0c\u9700\u8981\u5bfc\u5165\u4eca\u5929\u7684\u4e3b\u89d2limma\u5305\uff0c\u8fd8\u6709\u4e00\u4e9b\u76f8\u5173\u7684\u7ed8\u56fe\u5305\uff1asplines\uff0csplines2\uff0cscales\u3002\u7136\u540e\u6784\u5efa\u529f\u80fd\u51fd\u6570\u2014\u2014\u901a\u8fc7\u7ed9\u5b9a\u7684\u7ec6\u80de\u7cfb\u6784\u5efa\u6a21\u578b\u77e9\u9635\uff0c\u901a\u8fc7\u7ed9\u5b9a\u7684GSEA\u7ed3\u679c\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u5c06\u8fd9\u4e24\u4e2a\u4e3b\u8981\u7684\u529f\u80fd\u51fd\u6570\u6784\u5efa\u5b8c\u6210\u540e\uff0c\u5bfc\u5165\u672c\u6b21\u590d\u73b0\u6240\u9700\u7684\u6570\u636e\uff08\u6240\u9700\u6570\u636e\u5c0f\u679c\u5df2\u7ecf\u5e2e\u5927\u5bb6\u6574\u7406\u597d\u4e86\uff0c\u70b9\u51fb\u94fe\u63a5\u5373\u53ef\u4e0b\u8f7d\u54e6\uff09\u3002<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u94fe\u63a5\uff1a<\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">https:\/\/pan.baidu.com\/s\/12BZlryXXmBn_nBgsFxL30w <\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u63d0\u53d6\u7801\uff1a2roq<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span><\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index 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class=\"code-snippet__js\" data-lang=\"bash\"><code>##### \u5bfc\u5165R\u5305 #####<\/span><\/span><\/code><code>library(limma)<\/span><\/code><code>library(splines)<\/span><\/code><code>library(splines2)<\/span><\/code><code>ns<-naturalSpline<\/span><\/code><code>library(scales)<\/span><\/code><code>library(BinfTools)<\/span><\/code><code> <\/span><\/code><code>##### \u6784\u5efa\u529f\u80fd\u51fd\u6570 #####<\/span><\/span><\/code><code>##### \u6839\u636e\u7ed9\u5b9a\u7684\u7ec6\u80de\u7cfb\uff0c\u6784\u5efa\u4e00\u4e2a\u7ebf\u6027\u6a21\u578b\u77e9\u9635\uff0c\u7528\u4e8e\u540e\u7eed\u7684\u5dee\u5f02\u5206\u6790 #####<\/span><\/span><\/code><code>makemodel<-function<\/span>(x, colname, cell.lines){<\/span><\/code><code> cell.lines<-sapply(strsplit(cell.lines, split=\"_\"<\/span>, fixed=T),'[['<\/span>, 1)<\/span><\/code><code> if<\/span>(ncol(x)==1){<\/span><\/code><code> olCells<-rownames(x)[which<\/span>(rownames(x) %in<\/span>% cell.lines)]<\/span><\/code><code> x<-as.data.frame(x[olCells,])<\/span><\/code><code> rownames(x)<-olCells<\/span><\/code><code> colnames(x)<-colname<\/span><\/code><code> } else<\/span> {<\/span><\/code><code> x<-x[which<\/span>(rownames(x) %in<\/span>% cell.lines),]<\/span><\/code><code> }<\/span><\/code><code> sm<-NULL<\/span><\/code><code> if<\/span>(ncol(x)==1){ <\/span><\/code><code> sm<-ns(x[,1])<\/span><\/code><code> } else<\/span> {<\/span><\/code><code> sm<-ns(x[,which<\/span>(colnames(x) %in<\/span>% colname)])<\/span><\/code><code> }<\/span><\/code><code> dm<-model.matrix(~sm)<\/span><\/code><code> return<\/span>(dm)<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>##### \u6839\u636e\u7ed9\u5b9a\u7684\u7ec6\u80de\u7cfb\u548c\u8868\u8fbe\u77e9\u9635\uff0c\u8fd4\u56de\u7b26\u5408\u6761\u4ef6\u7684\u7ec6\u80de\u7cfb\u540d\u79f0 #####<\/span><\/span><\/code><code>olCells<-function<\/span>(cell.lines, x){<\/span><\/code><code> tmp<-sapply(strsplit(cell.lines, split=\"_\"<\/span>, fixed=T),'[['<\/span>,1)<\/span><\/code><code> #return(tmp)<\/span><\/span><\/code><code> return<\/span>(cell.lines[which<\/span>(tmp %in<\/span>% rownames(x))])<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>##### \u6839\u636e\u7ed9\u5b9a\u7684\u4e24\u4e2aGSEA\u7ed3\u679c\uff0c\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u548c\u53ef\u89c6\u5316\uff0c\u6bd4\u8f83\u4e0d\u540c\u7269\u79cd\u6216\u6761\u4ef6\u4e0b\u7684\u57fa\u56e0\u96c6\u5bcc\u96c6\u60c5\u51b5 #####<\/span><\/span><\/code><code>compGSEA<-function<\/span>(x, y, title=\"Comparing GSEA results\"<\/span>, xlab=\"Human\"<\/span>, ylab=\"Mouse\"<\/span>, p=1){<\/span><\/code><code> x<-subset(x, padj <p)<\/span><\/code><code> <\/p)<><\/span><\/code><code> y<-subset(y, padj <p)<\/span><\/code><code> <\/p)<><\/span><\/code><code> x<-x[which<\/span>(x$pathway<\/span> %in<\/span>% y$pathway<\/span>),]<\/span><\/code><code> y<-y[which<\/span>(y$pathway<\/span> %in<\/span>% x$pathway<\/span>),]<\/span><\/code><code> x<-x[order(x$pathway<\/span>),]<\/span><\/code><code> y<-y[order(y$pathway<\/span>),]<\/span><\/code><code> if<\/span>(!all.equal(x$pathway<\/span>, y$pathway<\/span>)){<\/span><\/code><code> stop(\"Check again...\"<\/span>)<\/span><\/code><code> }<\/span><\/code><code> dat<-data.frame(row.names=x$pathway<\/span>,<\/span><\/code><code> x=x$NES<\/span>,<\/span><\/code><code> y=y$NES<\/span>)<\/span><\/code><code> dat$Direction<\/span><-ifelse(dat$x<\/span>*dat$y<\/span>>0, \"Positive\"<\/span>, \"Negative\"<\/span>)<\/span><\/code><code> dat$Trend<\/span><-ifelse(dat$x<\/span>*dat$y<\/span>>0,abs(dat$x<\/span>-dat$y<\/span>), abs(dat$x<\/span>-dat$y<\/span>)*-1)<\/span><\/code><code> #print(head(dat))<\/span><\/span><\/code><code> g<-ggpubr::ggscatter(dat, x=\"x\"<\/span>, y=\"y\"<\/span>, add=\"reg.line\"<\/span>, conf.int=T, color=\"Trend\"<\/span>,<\/span><\/code><code> #palette=c(Negative=\"blue\",Positive=\"red\"),<\/span><\/span><\/code><code> cor.coef=T, add.params=list(color=\"purple\"<\/span>,fill=\"purple\"<\/span>),<\/span><\/code><code> xlab=paste(xlab,\"NES\"<\/span>), ylab=paste(ylab,\"NES\"<\/span>)) + <\/span><\/code><code> ggpubr::gradient_color(c(\"blue\"<\/span>,\"white\"<\/span>,\"red\"<\/span>))<\/span><\/code><code> print<\/span>(g) <\/span><\/code><code> return<\/span>(dat)<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>#### \u63d0\u53d6\u57fa\u56e0\u7684\u7b26\u53f7\u540d\u79f0 ####<\/span><\/span><\/code><code>putSym<-function<\/span>(res){<\/span><\/code><code> res$hgnc_symbol<\/span><-sapply(strsplit(rownames(res), split=\".\"<\/span>, fixed=T),'[['<\/span>,1)<\/span><\/code><code> return<\/span>(res)<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>#### \u89c4\u8303\u5316 ####<\/span><\/span><\/code><code>fixRows<-function<\/span>(x, obtype=c(\"res\"<\/span>,\"counts\"<\/span>), col=NULL){<\/span><\/code><code> if<\/span>(obtype[1]==\"res\"<\/span>){<\/span><\/code><code> x<-x[order(x$baseMean<\/span>, decreasing=T),]<\/span><\/code><code> }<\/span><\/code><code> if<\/span>(obtype[1]==\"counts\"<\/span>){<\/span><\/code><code> x<-x[order(rowMeans(x), decreasing=T),]<\/span><\/code><code> }<\/span><\/code><code> genes<-c()<\/span><\/code><code> if<\/span>(is.null(col)){<\/span><\/code><code> genes<-sapply(strsplit(rownames(x), \".\"<\/span>,T),'[['<\/span>,1)<\/span><\/code><code> } else<\/span> {<\/span><\/code><code> genes<-x[,which<\/span>(colnames(x) %in<\/span>% col)]<\/span><\/code><code> }<\/span><\/code><code> dups<-unique(genes[which<\/span>(duplicated(genes))])<\/span><\/code><code> to_remove <- c()<\/span><\/code><code> for<\/span> (i in<\/span> 1:length(dups)) {<\/span><\/code><code> ind <- which<\/span>(genes %in<\/span>% dups[i], arr.ind = T)<\/span><\/code><code> to_remove <- c(to_remove, ind[-1])<\/span><\/code><code> }<\/span><\/code><code> x <- x[-to_remove, ]<\/span><\/code><code> genes<-genes[-to_remove]<\/span><\/code><code> rownames(x)<-genes<\/span><\/code><code> return<\/span>(x)<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>##### \u5bfc\u5165\u6570\u636e #####<\/span><\/span><\/code><code>#\u8bfb\u53d6CCLE\uff08Cancer Cell Line Encyclopedia\uff09\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u7ec6\u80de\u7cfb\u4fe1\u606f\u6570\u636e<\/span><\/span><\/code><code>CCLE<-read.csv(\"\/data\/CCLE_expression.csv\"<\/span>)<\/span><\/code><code>#\u533a\u5206\u6bcf\u4e2a\u7ec6\u80de\u7cfb <\/span><\/span><\/code><code>info<-read.csv(\"\/data\/sample_info.csv\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>#\u901a\u8fc7 DepMap ID \u548c CCLE \u540d\u79f0\u5339\u914d\u7ec6\u80de\u7cfb\u6807\u8bc6\u7b26<\/span><\/span><\/code><code>CCLE<-merge(CCLE, info[,c(1,4)], by.x=\"X\"<\/span>, by.y=\"DepMap_ID\"<\/span>)<\/span><\/code><code>rownames(CCLE)<-CCLE$CCLE_Name<\/span><\/span><\/code><code>CCLE<-CCLE[,-(which<\/span>(colnames(CCLE) %in<\/span>% c(\"X\"<\/span>,\"DepMap_ID\"<\/span>,\"CCLE_Name\"<\/span>)))]<\/span><\/code><code>CCLE<-t(CCLE)<\/span><\/code><code> <\/span><\/code><code>#\u8bfb\u5165\u7ec6\u80de\u7cfb\u6ce8\u91ca\u6570\u636e\uff08\u8bc6\u522b SCLC \u7ec6\u80de\u7cfb\u2014\u2014\u5c0f\u7ec6\u80de\u80ba\u764c\uff09<\/span><\/span><\/code><code>x<-read.delim(\"\/data\/Cell_lines_annotations_20181226.txt\"<\/span>)<\/span><\/code><code>SCLC<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% x[which<\/span>(x$type_refined<\/span> %in<\/span>% \"lung_small_cell\"<\/span>),]$CCLE_ID<\/span>)]<\/span><\/code><code> <\/span><\/code><code>#\u8bc6\u522bSCLC\u7684\u5b50\u7c7b<\/span><\/span><\/code><code>ATOH1<-c(\"CORL24_LUNG\"<\/span>,\"HCC33_LUNG\"<\/span>)<\/span><\/code><code>POU2F3<-c(\"NCIH1048_LUNG\"<\/span>, \"CORL311_LUNG\"<\/span>,\"NCIH211_LUNG\"<\/span>,\"NCIH526_LUNG\"<\/span>)<\/span><\/code><code>YAP1<-c(\"SW1271_LUNG\"<\/span>,\"NCIH1341_LUNG\"<\/span>,\"DMS114_LUNG\"<\/span>, \"NCIH196_LUNG\"<\/span>, \"NCIH1339_LUNG\"<\/span>, \"SBC5_LUNG\"<\/span>,\"NCIH2286_LUNG\"<\/span>,\"NCIH841_LUNG\"<\/span>)<\/span><\/code><code>YAP1_2<-c(\"SW1271_LUNG\"<\/span>,\"NCIH1341_LUNG\"<\/span>,\"DMS114_LUNG\"<\/span>, \"NCIH1339_LUNG\"<\/span>, \"SBC5_LUNG\"<\/span>,\"NCIH2286_LUNG\"<\/span>,\"NCIH841_LUNG\"<\/span>) #YAP1_2 removes outlier sample NCIH196_LUNG<\/span><\/span><\/code><code>NEUROD1<-c(\"NCIH2066_LUNG\"<\/span>,\"CORL279_LUNG\"<\/span>,\"NCIH1694_LUNG\"<\/span>,\"NCIH524_LUNG\"<\/span>,\"DMS273_LUNG\"<\/span>,\"NCIH446_LUNG\"<\/span>,\"NCIH2171_LUNG\"<\/span>,\"NCIH82_LUNG\"<\/span>,\"SCLC21H_LUNG\"<\/span>)<\/span><\/code><code>ASCL1<-colnames(SCLC)<\/span><\/code><code>ASCL1<-ASCL1[which<\/span>(!ASCL1 %in<\/span>% ATOH1)]<\/span><\/code><code>ASCL1<-ASCL1[which<\/span>(!ASCL1 %in<\/span>% POU2F3)]<\/span><\/code><code>ASCL1<-ASCL1[which<\/span>(!ASCL1 %in<\/span>% YAP1)]<\/span><\/code><code>ASCL1<-ASCL1[which<\/span>(!ASCL1 %in<\/span>% NEUROD1)]<\/span><\/code><code> <\/span><\/code><code>typing<-data.frame(Cell.line=c(ATOH1,POU2F3,YAP1,NEUROD1,ASCL1),<\/span><\/code><code> type<\/span>=c(rep(\"ATOH1\"<\/span>, length(ATOH1)), rep(\"POU2F3\"<\/span>, length(POU2F3)),<\/span><\/code><code> rep(\"YAP1\"<\/span>, length(YAP1)), rep(\"NEUROD1\"<\/span>, length(NEUROD1)), <\/span><\/code><code> rep(\"ASCL1\"<\/span>, length(ASCL1))))<\/span><\/code><code> <\/span><\/code><code>#\u52a0\u8f7d TAK243 \u836f\u7269\u53cd\u5e94\u6570\u636e <\/span><\/span><\/code><code>x<-read.csv(\"\/data\/TAK_final_results.csv\"<\/span>, row.names=1)<\/span><\/code><code> <\/span><\/code><code>#\u6709\u4e9b\u7ec6\u80de\u7cfb\u6211\u4eec\u6709 TAK \u6570\u636e\uff0c\u4f46\u5728\u6570\u636e\u96c6\u4e2d\u6ca1\u6709\u8868\u8fbe\u6570\u636e\uff0c\u6240\u4ee5\u4ec5\u4fdd\u7559\u540c\u65f6\u5177\u6709\u8fd9\u4e24\u79cd\u6570\u636e\u7684\u7ec6\u80de\u7cfb<\/span><\/span><\/code><code>x<-as.data.frame(x[which<\/span>(rownames(x) %in<\/span>% sapply(strsplit(colnames(CCLE), split=\"_\"<\/span>, fixed=T),'[['<\/span>,1)),])<\/span><\/code><code>CCLE<-CCLE[,which<\/span>(sapply(strsplit(colnames(CCLE),\"_\"<\/span>,T),'[['<\/span>,1) %in<\/span>% rownames(x))]<\/span><\/code><code>#\u5c06\u836f\u7269\u53cd\u5e94\u6570\u636e\u4e2d\u7ec6\u80de\u7cfb\u7684\u987a\u5e8f\u4e0e\u8868\u8fbe\u6570\u636e\u5339\u914d\u4ee5\u8fdb\u884c\u8868\u8fbe\u5efa\u6a21<\/span><\/span><\/code><code>x<-x[match(sapply(strsplit(colnames(CCLE), split=\"_\"<\/span>, T),'[['<\/span>,1), rownames(x)),]<\/span><\/code><code>x<-x[complete.cases(x),]<\/span><\/code><code>#\u68c0\u67e5\u6240\u6709\u7ec6\u80de\u7cfb\u7684\u987a\u5e8f\u662f\u5426\u76f8\u540c<\/span><\/span><\/code><code>all.equal(sapply(strsplit(colnames(CCLE), \"_\"<\/span>, T),'[['<\/span>,1), rownames(x))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><span style=\"font-variant: normal;text-transform: none;color: rgb(0, 112, 192);font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"><\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u4e24\u4e2a\u6570\u636e\u5206\u522b\u662fCCLE_expression.csv\u548csample_info.csv\uff0c\u5176\u4e2dCCLE_expression.csv\u662f\u4eceCCLE\uff08Cancer Cell Line Encyclopedia\uff09\u2014\u4e00\u4e2a\u5927\u89c4\u6a21\u7684\u764c\u75c7\u7ec6\u80de\u7cfb\u7684\u9057\u4f20\u548c\u836f\u7269\u654f\u611f\u6027\u7684\u6570\u636e\u5e93\u4e2d\u8bfb\u53d6\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u7ec6\u80de\u7cfb\u4fe1\u606f\u6570\u636e\uff0c\u800c\u5982\u4e0b\u56fe\u6240\u793a\uff0csample_info.csv\u662f\u4e00\u4e2a\u5305\u542b\u6bcf\u4e2a\u7ec6\u80de\u7cfb\u7684\u6807\u8bc6\u7b26\u548c\u6ce8\u91ca\u7684\u6587\u4ef6\uff0c\u4f8b\u5982\u7ec6\u80de\u7cfb\u7684\u540d\u79f0\u3001\u764c\u75c7\u7c7b\u578b\u3001\u7ec4\u7ec7\u6765\u6e90\u7b49\u3002<\/span><\/section>\n<section style=\"text-align: center;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016197\" data-ratio=\"0.7055555555555556\" data-type=\"png\" data-w=\"1080\" height=\"325 .27001953125\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"461 .0099792480469\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_HJKFHmPRLVJZ49tibxKeVfjBRPL7nw.png?resize=461%2C325\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyRia5FrJzkEkJCFDicX4KuiaZmdPA9HJKFHmPRLVJZ49tibxKeVfjBRPL7nw\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/> <\/span> <\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u5728\u5bfc\u5165\u6570\u636e\u540e\uff0c\u8fd8\u9700\u8981\u5bfc\u5165\u7ec6\u80de\u7cfb\u6ce8\u91ca\u6570\u636e\uff0c\u7528\u4e8e\u8bc6\u522b SCLC \uff08\u5c0f\u7ec6\u80de\u80ba\u764c\uff09\u7ec6\u80de\u7cfb\uff0c\u7136\u540e\u5bfc\u5165\u6709 TAK243 \u54cd\u5e94\u6570\u636e\u7684\u7ec6\u80de\u7cfb\uff0c\u8bc6\u522bSCLC\u7684\u5b50\u7c7b\u3002\u6700\u540e\u5bfc\u5165 TAK243 \u836f\u7269\u53cd\u5e94\u6570\u636e\uff0c\u5c06\u836f\u7269\u53cd\u5e94\u6570\u636e\u4e2d\u7ec6\u80de\u7cfb\u7684\u987a\u5e8f\u4e0e\u8868\u8fbe\u6570\u636e\u5339\u914d\u4ee5\u8fdb\u884c\u8868\u8fbe\u5efa\u6a21\uff0c\u68c0\u67e5\u6240\u6709\u7ec6\u80de\u7cfb\u7684\u987a\u5e8f\u662f\u5426\u76f8\u540c\u3002<\/span> <\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;font-weight: bold;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">Step 2 Limma\u5206\u6790<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u9996\u5148\u4e3aLimma \u5236\u4f5c\u8bbe\u8ba1\u6a21\u578b\u77e9\u9635\uff0c\u9700\u8981\u4e3a\u6240\u6709\u7684\u7ec6\u80de\u7cfb\u90fd\u5efa\u7acb\u6a21\u578b\uff0c\u7136\u540e\u4f7f\u7528 Spearman \u76f8\u5173\u6027\u68c0\u67e5\u6837\u672c\u5982\u4f55\u5173\u8054\u548c\u805a\u7c7b\uff1a\u901a\u8fc7\u8fd0\u884c limma \u5206\u6790 – \u62df\u5408\u7ebf\u6027\u56de\u5f52\u6a21\u578b\uff0c\u4f7f\u7528\u5dee\u5f02\u8868\u8fbe\u7684\u7ecf\u9a8c\u8d1d\u53f6\u65af\u6765\u8fdb\u884c\u68c0\u9a8c\uff0c\u63d0\u53d6\u8fd4\u56de\u7684\u6570\u636e\uff0c\u5e76\u8f93\u51faDE\u7ed3\u679c\u3002<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span><\/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<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<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=\"bash\"><code>##### Limma \u5206\u6790 #####<\/span><\/span><\/code><code>#\u4e3a EC50 \u503c\u521b\u5efaspline\u6a21\u578b<\/span><\/span><\/code><code>nsEC50<-ns(x$EC50<\/span>)<\/span><\/code><code>#\u4e3a Limma \u5236\u4f5c\u8bbe\u8ba1\u6a21\u578b\u77e9\u9635<\/span><\/span><\/code><code>dm_EC50<-model.matrix(~nsEC50) #Model for all cell lines<\/span><\/span><\/code><code> <\/span><\/code><code>#\u4f7f\u7528\u81ea\u5b9a\u4e49\u51fd\u6570\u4e3a\u5b50\u7c7b\u578b\u7ec4\u751f\u6210\u8bbe\u8ba1\u6a21\u578b\u77e9\u9635<\/span><\/span><\/code><code>dm_EC50_YAP<-makemodel(x, \"EC50\"<\/span>, YAP1) #All YAP1-high\/Triple Negative<\/span><\/span><\/code><code>dm_EC50_YAP2<-makemodel(x, \"EC50\"<\/span>, YAP1_2) #All YAP1-high except NCIH196_LUNG (outlier)<\/span><\/span><\/code><code>dm_EC50_ND1<-makemodel(x, \"EC50\"<\/span>, NEUROD1) #All NEUROD1-high<\/span><\/span><\/code><code>dm_EC50_ASCL1<-makemodel(x, \"EC50\"<\/span>, ASCL1) #All ASCL1-high<\/span><\/span><\/code><code> <\/span><\/code><code>#\u8868\u8fbe\u77e9\u9635\u5b50\u96c6\u4ec5\u5305\u542b\u6bcf\u6b21\u5206\u6790\u6240\u9700\u7684\u7ec6\u80de\u7cfb<\/span><\/span><\/code><code>CCLE<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(colnames(CCLE), x))] #All cell lines<\/span><\/span><\/code><code>CCLE2<-CCLE[,which<\/span>(!colnames(CCLE) %in<\/span>% \"NCIH196_LUNG\"<\/span>)] #All cell lines except NCIH196_LUNG (outlier)<\/span><\/span><\/code><code>dm_EC50_2<-makemodel(x[which<\/span>(!rownames(x) %in<\/span>% \"NCIH196\"<\/span>),], \"EC50\"<\/span>, colnames(CCLE2)) #Create design model matrix for all SCLC cell lines except NCIH196_LUNG (outlier) <\/span><\/span><\/code><code>CCLE_YAP<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(YAP1, x))]<\/span><\/code><code>CCLE_YAP2<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(YAP1_2, x))]<\/span><\/code><code>CCLE_ND1<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(NEUROD1,x))]<\/span><\/code><code>CCLE_ASCL1<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(ASCL1,x))]<\/span><\/code><code> <\/span><\/code><code>#\u4f7f\u7528\u786e\u5b9a\u7684 SCLC \u4e9a\u578b\uff0c\u4f7f\u5b50\u96c6\u6570\u636e\u6846\u4ec5\u5305\u542b\u5df2\u68c0\u6d4b\u7684 SCLC \u7ec6\u80de\u7cfb<\/span><\/span><\/code><code>subtyping<-subset(typing, Cell.line %in<\/span>% colnames(CCLE))<\/span><\/code><code>subtyping<-subtyping[match(colnames(CCLE), subtyping$Cell<\/span>.line),] #Ensure same order of cell lines<\/span><\/span><\/code><code>all.equal(subtyping$Cell<\/span>.line, colnames(CCLE)) #Check - should return TRUE<\/span><\/span><\/code><code> <\/span><\/code><code>#\u521b\u5efa\u6761\u4ef6\u5411\u91cf<\/span><\/span><\/code><code>subtype<-subtyping$type<\/span><\/span><\/code><code>subtype2<-subtype[-which<\/span>(colnames(CCLE) %in<\/span>% \"NCIH196_LUNG\"<\/span>)]<\/span><\/code><code> <\/span><\/code><code>#\u4f7f\u7528 Spearman \u76f8\u5173\u6027\u68c0\u67e5\u6837\u672c\u5982\u4f55\u5173\u8054\u548c\u805a\u7c7b<\/span><\/span><\/code><code>#corHeat(CCLE, hmcol=colPal(\"Greys\"),annodf=data.frame(row.names=subtyping$Cell.line, Subtype=subtyping$type), showTree=T)<\/span><\/span><\/code><code> <\/span><\/code><code>#\u8fd0\u884c limma \u5206\u6790 - \u62df\u5408\u7ebf\u6027\u56de\u5f52\u6a21\u578b<\/span><\/span><\/code><code>EC50_fit<-lmFit(CCLE, design=dm_EC50)<\/span><\/code><code>EC50_fit2<-lmFit(CCLE2, design=dm_EC50_2)<\/span><\/code><code>EC50_fit_YAP<-lmFit(CCLE_YAP, design=dm_EC50_YAP)<\/span><\/code><code>EC50_fit_YAP2<-lmFit(CCLE_YAP2, design=dm_EC50_YAP2)<\/span><\/code><code>EC50_fit_ND1<-lmFit(CCLE_ND1, design=dm_EC50_ND1)<\/span><\/code><code>EC50_fit_ASCL1<-lmFit(CCLE_ASCL1, design=dm_EC50_ASCL1)<\/span><\/code><code> <\/span><\/code><code>#\u5dee\u5f02\u8868\u8fbe\u7684\u7ecf\u9a8c\u8d1d\u53f6\u65af\u68c0\u9a8c<\/span><\/span><\/code><code>EC50_fit<-eBayes(EC50_fit)<\/span><\/code><code>EC50_fit2<-eBayes(EC50_fit2)<\/span><\/code><code>EC50_fit_YAP<-eBayes(EC50_fit_YAP)<\/span><\/code><code>EC50_fit_YAP2<-eBayes(EC50_fit_YAP2)<\/span><\/code><code>EC50_fit_ND1<-eBayes(EC50_fit_ND1)<\/span><\/code><code>EC50_fit_ASCL1<-eBayes(EC50_fit_ASCL1)<\/span><\/code><code> <\/span><\/code><code>#\u8fd4\u56de\u6240\u6709\u7ed3\u679c\uff08\u6240\u6709\u57fa\u56e0\u7684\u56de\u5f52\u7cfb\u6570\u548c p \u503c\uff09 <\/span><\/span><\/code><code>EC50_res<-topTable(EC50_fit, number=Inf)<\/span><\/code><code>EC50_res2<-topTable(EC50_fit2, number=Inf)<\/span><\/code><code>EC50_res_YAP<-topTable(EC50_fit_YAP, number=Inf)<\/span><\/code><code>EC50_res_YAP2<-topTable(EC50_fit_YAP2, number=Inf)<\/span><\/code><code>EC50_res_ND1<-topTable(EC50_fit_ND1, number=Inf)<\/span><\/code><code>EC50_res_ASCL1<-topTable(EC50_fit_ASCL1, number=Inf)<\/span><\/code><code> <\/span><\/code><code>#\u73b0\u5728\u5c06\u5305\u542b\u57fa\u56e0\u7b26\u53f7\u7684\u5217 (hgnc_symbol) \u6dfb\u52a0\u5230\u7ed3\u679c\u4e2d<\/span><\/span><\/code><code>EC50_res<-putSym(EC50_res)<\/span><\/code><code>EC50_res2<-putSym(EC50_res2)<\/span><\/code><code>EC50_res_ASCL1<-putSym(EC50_res_ASCL1)<\/span><\/code><code>EC50_res_YAP<-putSym(EC50_res_YAP)<\/span><\/code><code>EC50_res_YAP2<-putSym(EC50_res_YAP2)<\/span><\/code><code>EC50_res_ND1<-putSym(EC50_res_ND1)<\/span><\/code><code> <\/span><\/code><code>#\u8f93\u51faDE\u7ed3\u679c<\/span><\/span><\/code><code>limResList<-list(SCLC_w196=EC50_res,<\/span><\/code><code> SCLC_wo196=EC50_res2,<\/span><\/code><code> YAP1_w196=EC50_res_YAP,<\/span><\/code><code> YAP1_wo196=EC50_res_YAP2,<\/span><\/code><code> ASCL1=EC50_res_ASCL1,<\/span><\/code><code> NEUROD1=EC50_res_ND1)<\/span><\/code><code>dir.create(\"\/results\/Limma_Results\"<\/span>)<\/span><\/code><code>mapply(write.table, limResList, file=paste0(\"\/results\/Limma_Results\/\"<\/span>,names(limResList),\".res.txt\"<\/span>),<\/span><\/code><code> quote=F, sep=\"t\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><span style=\"font-variant: normal;text-transform: none;color: rgb(0, 112, 192);font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"><\/span><\/section>\n<section style=\"text-align: center;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;text-indent: 0em;\"> <img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016198\" data-ratio=\"0.17592592592592593\" data-type=\"png\" data-w=\"1080\" height=\"97 .4000244140625\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"553 .739990234375\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_816H60iaWkXmCYZdlI2SUnKjQlM93A.png?resize=553%2C97\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyRHbKDCjrlFv3gY3aMH8mYHlbtr816H60iaWkXmCYZdlI2SUnKjQlM93A\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><o:p> <\/o:p><\/span>\u5982\u4e0b\u56fe\u6240\u793a\u662fDE\u7684\u7ed3\u679c\uff1a\u5c06\u6240\u6709\u7684\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u90fd\u8f93\u51fa\u4e3atxt\u6587\u4ef6\u3002<\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u63a5\u7740\u5c06 limma \u7ed3\u679c\u8868\u8f6c\u6362\u4e3a\u4e0e BinfTools \u5305\u51fd\u6570\u517c\u5bb9\u7684\u683c\u5f0f\uff0c\u7528\u706b\u5c71\u56fe\u663e\u793a\u663e\u8457\u654f\u611f\/\u62b5\u6297\u7684\u57fa\u56e0 (FDR < 0.05)\u3002<\/span><span style=\"font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"> <o:p> <\/o:p><\/span> <\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><o:page><\/o:page><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code>#\u5c06 limma \u7ed3\u679c\u8868\u8f6c\u6362\u4e3a\u4e0e BinfTools \u5305\u51fd\u6570\u517c\u5bb9\u7684\u683c\u5f0f<\/span><\/span><\/code><code>#'fixRows()' will set the rownames to just the HGNC symbol instead of the HGNC.ENTREZID format it currently is<\/span><\/span><\/code><code>bt_EC50<\/span><-fixRows(fromLimma(EC50_res), \"res\"<\/span>)<\/span><\/code><code>bt_EC502<\/span><-fixRows(fromLimma(EC50_res2), \"res\"<\/span>)<\/span><\/code><code>bt_EC50_YAP<\/span><-fixRows(fromLimma(EC50_res_YAP), \"res\"<\/span>)<\/span><\/code><code>bt_EC50_YAP2<\/span><-fixRows(fromLimma(EC50_res_YAP2), \"res\"<\/span>)<\/span><\/code><code>bt_EC50_ASCL1<\/span><-fixRows(fromLimma(EC50_res_ASCL1),\"res\"<\/span>)<\/span><\/code><code>bt_EC50_ND1<\/span><-fixRows(fromLimma(EC50_res_ND1),\"res\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>#\u7528\u706b\u5c71\u56fe\u663e\u793a\u663e\u7740\u7684\u654f\u611f\/\u62b5\u6297\u57fa\u56e0 (FDR < 0.05)<\/span><\/span><\/code><code>#Save sensitizer(down\/negatively correlated)\/resistor(up\/positively correlated) genes<\/span><\/span><\/code><code>pdf<\/span>(\"\/results\/VolcanoPlots.pdf\"<\/span>)<\/span><\/code><code>EC_SCLC<\/span><-volcanoPlot(bt_EC50, \"ALL SCLC\"<\/span>, p=0.05, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>EC_SCLC2<\/span><-volcanoPlot(bt_EC502, \"ALL SCLC - no H196\"<\/span>, p=0.05, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>YAP_EC50<\/span><-volcanoPlot(bt_EC50_YAP, \"YAP1 High\"<\/span>, p=0.05, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>YAP_EC502<\/span><-volcanoPlot(bt_EC50_YAP2, \"YAP1 High - no H196\"<\/span>, pval=0.01, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>ASCL_EC50<\/span><-volcanoPlot(bt_EC50_ASCL1, \"ASCL1 High\"<\/span>, p=0.05, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>ND1_EC50<\/span><-volcanoPlot(bt_EC50_ND1, \"NEUROD1 High\"<\/span>, pval=0.01, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>dev<\/span>.off<\/span>()<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span> <img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016199\" data-ratio=\"1.030195381882771\" data-type=\"png\" data-w=\"563\" height=\"579 .545166015625\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"562 .0119018554688\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_qQtveUXbewgSgT39fA0iaLVzvs6qqQ.png?resize=562%2C579\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyRW9Dy8uSh5eVujLczluIOicm0VuqQtveUXbewgSgT39fA0iaLVzvs6qqQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u4ece\u706b\u5c71\u56fe\u4e2d\u53ef\u4ee5\u770b\u51fa\u56de\u5f52\u5206\u6790\u7ed3\u679c\uff0c\u5176\u4e2dx\u8f74\u8868\u793a\u5206\u914d\u7ed9\u6bcf\u4e2a\u57fa\u56e0\u7684\u56de\u5f52\u7cfb\u6570\uff0cy\u8f74\u8868\u793a\u663e\u8457\u6027\u3002\u84dd\u8272\u7a81\u51fa\u663e\u793a\u7684\u57fa\u56e0\u4ee3\u8868\u663e\u8457\u654f\u611f\u57fa\u56e0(\u8868\u8fbe\u4e0eEC50\u5448\u663e\u8457\u8d1f\u76f8\u5173;FDR < 0.05)\uff0c\u7ea2\u8272\u57fa\u56e0\u4ee3\u8868\u62b5\u6297\u57fa\u56e0(\u8868\u8fbe\u4e0eEC50\u663e\u8457\u6b63\u76f8\u5173;FDR < 0.05)\u3002\u9ed1\u8272\u865a\u7ebf\u4e3a\u663e\u8457\u6027\u9608\u503c(Padj < 0.05)\u3002<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;font-weight: bold;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u7ed8\u5236\u5b8c\u6210\u706b\u5c71\u56fe\u540e\uff0c\u518d\u8f93\u51fa\u7ef4\u6069\u56fe\u5e76\u8fd4\u56de\u91cd\u53e0\u57fa\u56e0\uff0c\u6700\u540e\u5c06\u91cd\u53e0\u5199\u51fa\u4e3a\u57fa\u56e0\u96c6\u6587\u4ef6\u3002<\/span><span style=\"font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"> <o:p> <\/o:p><\/span> <\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><o:page><\/o:page><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span><\/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<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>#\u8f93\u51fa\u7ef4\u6069\u56fe\u5e76\u8fd4\u56de\u91cd\u53e0\u57fa\u56e0<\/span><\/span><\/code><code>pdf(\"\/results\/VennDiagrams.pdf\"<\/span>)<\/span><\/code><code>Sensitizers<-plotVenn(list<\/span>(SCLC=EC_SCLC$Down, YAP1=YAP_EC50$Down,<\/span><\/code><code> ASCL1=ASCL_EC50$Down, NEUROD1=ND1_EC50$Down),<\/span><\/code><code> title=\"Sensitizers\"<\/span>, retVals=T)<\/span><\/code><code> <\/span><\/code><code>Sensitizers2<-plotVenn(list<\/span>(SCLC=EC_SCLC2$Down, YAP1=YAP_EC502$Down,<\/span><\/code><code> ASCL1=ASCL_EC50$Down, NEUROD1=ND1_EC50$Down),<\/span><\/code><code> title=\"Sensitizers - no H196\"<\/span>, retVals=T)<\/span><\/code><code> <\/span><\/code><code>Resistors<-plotVenn(list<\/span>(SCLC=EC_SCLC$Up, YAP1=YAP_EC50$Up,<\/span><\/code><code> ASCL1=ASCL_EC50$Up, NEUROD1=ND1_EC50$Up),<\/span><\/code><code> title=\"Resistors\"<\/span>, retVals=T)<\/span><\/code><code>Resistors2<-plotVenn(list<\/span>(SCLC=EC_SCLC2$Up, YAP1=YAP_EC502$Up,<\/span><\/code><code> ASCL1=ASCL_EC50$Up, NEUROD1=ND1_EC50$Up),<\/span><\/code><code> title=\"Resistors - no H196\"<\/span>, retVals=T)<\/span><\/code><code>dev.off()<\/span><\/code><code> <\/span><\/code><code>#\u91cd\u547d\u540d\u91cd\u53e0\u90e8\u5206\uff0c\u4f7f\u5176\u66f4\u6e05\u6670<\/span><\/span><\/code><code>OLnames<-c(\"SCLC\"<\/span>,\"YAP1\"<\/span>,\"ASCL1\"<\/span>,\"NEUROD1\"<\/span>,\"SCLC_YAP1\"<\/span>, \"SCLC_ASCL1\"<\/span>,\"SCLC_NEUROD1\"<\/span>,<\/span><\/code><code> \"YAP1_ASCL1\"<\/span>,\"YAP1_NEUROD1\"<\/span>,\"ASCL1_NEUROD1\"<\/span>,\"SCLC_YAP1_ASCL1\"<\/span>,\"SCLC_YAP1_NEUROD1\"<\/span>,<\/span><\/code><code> \"SCLC_ASCL1_NEUROD1\"<\/span>,\"YAP1_ASCL1_NEUROD1\"<\/span>,\"All\"<\/span>)<\/span><\/code><code>names(Sensitizers)<-OLnames<\/span><\/code><code>names(Resistors)<-OLnames<\/span><\/code><code>names(Sensitizers2)<-OLnames<\/span><\/code><code>names(Resistors2)<-OLnames<\/span><\/code><code> <\/span><\/code><code>#\u5c06\u91cd\u53e0\u5199\u51fa\u4e3a\u57fa\u56e0\u96c6\u6587\u4ef6<\/span><\/span><\/code><code>dir.create(\"\/results\/gmts\/\"<\/span>)<\/span><\/code><code>write.gmt(Sensitizers, \"\/results\/gmts\/Sensitizer_Genes1.gmt\"<\/span>)<\/span><\/code><code>write.gmt(Sensitizers2, \"\/results\/gmts\/Sensitizer_Genes2.gmt\"<\/span>)<\/span><\/code><code>write.gmt(Resistors, \"\/results\/gmts\/Resistor_Genes1.gmt\"<\/span>)<\/span><\/code><code>write.gmt(Resistors2, \"\/results\/gmts\/Resistor_Genes2.gmt\"<\/span>) <\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"> <\/span> <\/span><\/section>\n<section style=\"text-align: center;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016200\" data-ratio=\"0.36574074074074076\" data-type=\"png\" data-w=\"1080\" height=\"199 .47000122070312\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"545 .6099853515625\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_w60PaibQic76MbDARqZZFMsY5P49DQ.png?resize=545%2C199\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyRyfbm4iagk0DYX1rCp5A7zF3ERh0w60PaibQic76MbDARqZZFMsY5P49DQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/> <\/span><\/section>\n<section style=\"text-align: center;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;text-align: justify;caret-color: transparent;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016201\" data-ratio=\"0.9596153846153846\" data-type=\"png\" data-w=\"520\" height=\"498 .8755798339844\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"519 .0758666992188\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_cp5sVJ5ZaqaYBtq29wuAich9iaVPAA.png?resize=519%2C498\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyR63BdTBPfQDptNibonTp0ks6HZHXicp5sVJ5ZaqaYBtq29wuAich9iaVPAA\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/span><\/section>\n<section style=\"text-align: justify;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;text-align: justify;caret-color: transparent;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;\">\u5982\u56fe\u6240\u793a\uff0c\u7ef4\u6069\u56fe\u663e\u793a\u4e86\u4ece\u56db\u79cd\u56de\u5f52\u5206\u6790\u4e2d\u9274\u5b9a\u51fa\u7684\u654f\u611f\u57fa\u56e0(\u4e0a)\u548c\u62b5\u6297\u57fa\u56e0\uff08\u4e0b\uff09\u7684\u91cd\u53e0:\u6240\u6709SCLC\u7ec6\u80de\u7cfb\uff0c\u4ec5ascl1\u9ad8\u7ec6\u80de\u7cfb\uff0c\u4ec5TN\/ yap1\u9ad8\u7ec6\u80de\u7cfb\u548c\u4ec5neurod1\u9ad8\u7ec6\u80de\u7cfb\uff0c\u8fd9\u6837\u5c31\u6210\u529f\u627e\u5230\u4e86\u53ef\u80fd\u7684\u9776\u5411\u57fa\u56e0~<\/span> <\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u5230\u8fd9\u4e00\u6b65\uff0c\u6211\u4eec\u5c31\u6210\u529f\u7684\u627e\u5230\u654f\u611f\u57fa\u56e0\u4e0e\u62b5\u6297\u57fa\u56e0\u4e86\uff0c\u53ef\u4ee5\u53d1\u73b0\uff0climma\u5206\u6790\u4f5c\u4e3a\u4e00\u79cd\u5e38\u7528\u7684\u5dee\u5f02\u5206\u6790\u7684\u65b9\u6cd5\uff0c\u5728\u9776\u5411\u6cbb\u7597\u65b9\u5411\u5bfb\u627e\u9776\u5411\u57fa\u56e0\u4e5f\u662f\u975e\u5e38\u4fbf\u5229\u7684\uff0c\u901a\u8fc7\u5bfc\u5165\u6570\u636e\uff0c\u6784\u5efa\u77e9\u9635\uff0c\u7ebf\u6027\u62df\u5408\uff0c\u6807\u6ce8\u5dee\u5f02\u57fa\u56e0\uff0c\u5373\u53ef\u627e\u51fa\u914d\u4f53\u76f8\u5173\u7684\u654f\u611f\u57fa\u56e0\u4e0e\u62b5\u6297\u57fa\u56e0\uff0c\u4ece\u800c\u4e3a\u8fdb\u4e00\u6b65\u7684\u9776\u5411\u6cbb\u7597\u63d0\u4f9b\u6307\u5bfc\u3002<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;font-weight: bold;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u4ee5\u4e0a\u5c31\u662f\u5c0f\u679c\u4eca\u5929\u5168\u90e8\u7684\u5206\u4eab\u5566\uff0c\u4e0d\u77e5\u9053\u5c0f\u4f19\u4f34\u4eec\u6709\u6ca1\u6709\u5b66\u4f1alimma\u5206\u6790\u5728\u9776\u5411\u6cbb\u7597\u4e2d\u7684\u5e94\u7528\u5462\uff1f<\/span>\u5982\u679c\u6709\u4efb\u4f55\u7591\u95ee\u6b22\u8fce\u5173\u6ce8\u516c\u4f17\u53f7\u5411\u5c0f\u679c\u63d0\u95ee\uff0c\u6211\u4eec\u6709\u4e13\u95e8\u7684\u751f\u4fe1\u5206\u6790\u670d\u52a1\u54e6\u3002\u540c\u65f6\uff0c\u5982\u679c\u5927\u5bb6\u6ca1\u6709\u505a\u51fa\u6765\u4e5f\u4e0d\u8981\u7070\u5fc3\uff0c\u53ef\u4ee5\u8bd5\u4e00\u8bd5\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177\u54e6\uff0c\u53ea\u8981\u8f93\u5165\u5408\u9002\u7684\u6570\u636e\u4ee5\u53ca\u6307\u4ee4\u5c31\u53ef\u4ee5\u76f4\u63a5\u7ed8\u5236\u60f3\u8981\u7684\u56fe\u5462\uff0c\u94fe\u63a5\uff1a<\/span><\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">http:\/\/www.biocloudservice.com\/home.html\u3002<\/span><\/span> <\/span><\/section>\n\u5c0f\u679c\u8fd8\u63d0\u4f9b\u601d\u8def\u8bbe\u8ba1\u3001\u5b9a\u5236\u751f\u4fe1\u5206\u6790\u3001\u6587\u732e\u601d\u8def\u590d\u73b0\uff1b\u6709\u9700\u8981\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u76f4\u63a5\u626b\u7801\u54a8\u8be2\u5c0f\u679c\uff0c\u7aed\u8bda\u4e3a\u60a8\u7684\u79d1\u7814\u52a9\u529b\uff01<\/span><\/span><\/strong><\/span><\/p>\n <\/p>\n<section style=\"font-size: 15px;padding-right: 2px;padding-left: 2px;margin-bottom: 0px;\">\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;flex: 0 0 auto;height: auto;border-color: rgb(114, 114, 114);border-width: 1px;border-style: solid;box-shadow: rgb(194, 209, 255) -5px 5px 0px;align-self: flex-start;\">\n<section style=\"justify-content: center;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 42.6829%;vertical-align: middle;box-shadow: rgb(43, 65, 110) 0px 0px 0px;flex: 0 0 auto;height: auto;padding-left: 10px;align-self: center;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;line-height: 0;transform: translate3d(20px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 75%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016202\" data-ratio=\"1\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"430\" style=\"vertical-align: middle;width: 100%;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_B2jkicacLzPjw4xMSqVvoucZjonVDA-9.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAxVYfSsM0wdf9d3RpNiaTcHohxPNEVs2VFhPMukpU8lchxrvcB2jkicacLzPjw4xMSqVvoucZjonVDA\/640?wx_fmt=jpeg&from=appmsg'\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 56.9106%;flex: 0 0 auto;height: auto;align-self: center;\">\n<section style=\"line-height: 2;letter-spacing: 1px;color: rgb(43, 65, 110);\" powered-by=\"xiumi.us\">\n\u5b9a\u5236\u751f\u4fe1\u5206\u6790<\/strong><\/p>\n\u670d\u52a1\u5668\u79df\u8d41<\/strong><\/p>\n\u626b\u7801\u54a8\u8be2\u5c0f\u679c<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n <\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247497780&idx=2&sn=7eee90af6f387e4153bba13028e545a1&chksm=cf7f68f1f808e1e7dfb3a0597ef442e5c6e700ecf6ee5a035c766a4c7486c12eabd0ab218ea6&scene=21#wechat_redirect\" textvalue=\"\u4f60\u5df2\u9009\u4e2d\u4e86\u6dfb\u52a0\u94fe\u63a5\u7684\u5185\u5bb9\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"1\" rel=\"noopener\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016203\" data-ratio=\"0.3253333333333333\" data-s=\"300,640\" data-type=\"png\" data-w=\"750\" style=\"vertical-align: middle;width: 100%;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_7TvAyUibd1TPhJmZfialJtv6tu2SEg-15.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxVYfSsM0wdf9d3RpNiaTcHoj9xlsoyiaBvzaezDUFAicibMAF8ts7TvAyUibd1TPhJmZfialJtv6tu2SEg\/640?wx_fmt=png&from=appmsg'\" data-recalc-dims=\"1\" \/><\/span><\/a><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;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 js_insertlocalimg\" data-imgfileid=\"100016204\" data-ratio=\"0.3811111111111111\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"900\" style=\"letter-spacing: 0.578px;text-align: center;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_9N02aBaau07RufXeXRLmvAHsrFZxtw-14.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAz5wg6Ne6sYkannSE9NiatkcPh3icbKanJagacjU6LqJrGAL29N02aBaau07RufXeXRLmvAHsrFZxtw\/640?wx_fmt=jpeg&from=appmsg'\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-right: 0%;margin-left: 0%;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-end;padding-right: 2px;padding-left: 2px;\">\n<section style=\"margin: 10px 0% 2px;transform: translate3d(2px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"font-size: 16px;color: rgb(58, 66, 94);line-height: 1;letter-spacing: 5px;text-align: center;\">\n\u5f80\u671f\u56de\u987e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"height: 3px;background-color: rgb(95, 156, 239);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"margin-top: 2px;margin-right: 0%;margin-left: 0%;text-align: center;line-height: 0.8;font-size: 9px;\" powered-by=\"xiumi.us\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.8em solid rgb(58, 66, 94);border-left: 0.7em solid transparent !important;border-right: 0.7em solid transparent !important;\"><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: bottom;width: auto;flex: 100 100 0%;align-self: flex-end;height: auto;\">\n<section style=\"margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"height: 3px;background-color: rgb(95, 156, 239);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"margin-top: 2px;margin-right: 0%;margin-left: 0%;text-align: center;line-height: 0.8;font-size: 9px;\" powered-by=\"xiumi.us\">\n<section style=\"width: 0px;display: inline-block;border-top: 0.8em solid rgba(255, 255, 255, 0);border-left: 0.7em solid transparent !important;border-right: 0.7em solid transparent !important;\"><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 style=\"min-height: 40px;margin: 10px 0%;\" powered-by=\"xiumi.us\">\n<section style=\"width: 100%;margin-right: auto;margin-bottom: -10px;margin-left: auto;\">\n<table width=\"100%\">\n<tbody>\n<tr opera-tn-ra-comp=\"_$.pages:0.layers:0.comps:4.classicTable1:0\" powered-by=\"xiumi.us\">\n<td colspan=\"1\" rowspan=\"1\" opera-tn-ra-cell=\"_$.pages:0.layers:0.comps:4.classicTable1:0.td@@0\" style=\"border-color: rgb(62, 62, 62);border-style: none;padding: 0px;\" width=\"100.0000%\">\n<section>\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-right: 0%;margin-left: 0%;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 10%;height: auto;flex: 0 0 auto;align-self: center;box-shadow: rgb(0, 0, 0) 0px 0px 0px;\">\n<section style=\"font-size: 19px;color: rgb(95, 156, 239);line-height: 1;\" powered-by=\"xiumi.us\">\n01<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;flex: 100 100 0%;align-self: center;height: auto;\">\n<section style=\"color: rgb(140, 140, 140);\" powered-by=\"xiumi.us\">\n\uff5c<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247497780&idx=2&sn=7eee90af6f387e4153bba13028e545a1&chksm=cf7f68f1f808e1e7dfb3a0597ef442e5c6e700ecf6ee5a035c766a4c7486c12eabd0ab218ea6&scene=21#wechat_redirect\" textvalue=\"1024G\u5b58\u50a8\u7684\u751f\u4fe1\u670d\u52a1\u5668\uff0c\u4e24\u4eba\u6210\u56e2\uff0c1\u4eba\u514d\u5355\uff01\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">1024G\u5b58\u50a8\u7684\u751f\u4fe1\u670d\u52a1\u5668\uff0c\u4e24\u4eba\u6210\u56e2\uff0c1\u4eba\u514d\u5355\uff01<\/a><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 5px 0%;\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(224, 224, 224);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/td>\n<\/tr>\n<tr opera-tn-ra-comp=\"_$.pages:0.layers:0.comps:4.classicTable1:1\" powered-by=\"xiumi.us\">\n<td colspan=\"1\" rowspan=\"1\" opera-tn-ra-cell=\"_$.pages:0.layers:0.comps:4.classicTable1:1.td@@0\" style=\"border-color: rgb(62, 62, 62);border-style: none;padding: 0px;\" width=\"100.0000%\">\n<section>\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-right: 0%;margin-left: 0%;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 10%;height: auto;flex: 0 0 auto;align-self: center;\">\n<section style=\"font-size: 19px;color: rgb(95, 156, 239);line-height: 1;\" powered-by=\"xiumi.us\">\n02<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;flex: 100 100 0%;align-self: center;height: auto;\">\n<section style=\"color: rgb(140, 140, 140);\" powered-by=\"xiumi.us\">\n\uff5c<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247498878&idx=1&sn=fc34ed3f1d15d060bbaf8166adcebd58&chksm=cf7f6cbbf808e5ad0b5417e50ed75cfbd1b3a83ac43b97f1dfa718c822878a9a004990075133&scene=21#wechat_redirect\" textvalue=\"\u5355\u4e2a\u6570\u636e\u5e93\u7528\u817b\u4e86\uff1f\u591a\u6570\u636e\u5e93\u201c\u7ec4\u5408\u62f3\u201d\u5e26\u4f60\u6253\u5f00\u514d\u75ab\u6d78\u6da6\u65b0\u601d\u8def\uff01\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">\u5355\u4e2a\u6570\u636e\u5e93\u7528\u817b\u4e86\uff1f\u591a\u6570\u636e\u5e93\u201c\u7ec4\u5408\u62f3\u201d\u5e26\u4f60\u6253\u5f00\u514d\u75ab\u6d78\u6da6\u65b0\u601d\u8def\uff01<\/a><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 5px 0%;\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(224, 224, 224);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/td>\n<\/tr>\n<tr opera-tn-ra-comp=\"_$.pages:0.layers:0.comps:4.classicTable1:2\" powered-by=\"xiumi.us\">\n<td colspan=\"1\" rowspan=\"1\" opera-tn-ra-cell=\"_$.pages:0.layers:0.comps:4.classicTable1:2.td@@0\" style=\"border-color: rgb(62, 62, 62);border-style: none;padding: 0px;\" width=\"100.0000%\">\n<section>\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-right: 0%;margin-left: 0%;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 10%;height: auto;flex: 0 0 auto;align-self: center;\">\n<section style=\"font-size: 19px;color: rgb(95, 156, 239);line-height: 1;\" powered-by=\"xiumi.us\">\n03<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;flex: 100 100 0%;align-self: center;height: auto;\">\n<section style=\"color: rgb(140, 140, 140);\" powered-by=\"xiumi.us\">\n\uff5c<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247498673&idx=1&sn=1e09b74a836c1e64a62ae1f66eeb3f93&chksm=cf7f6b74f808e262de70be43fd73bf5fefdc0914e525eb2032f741a0152e619689cedc76946f&scene=21#wechat_redirect\" textvalue=\"\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7684\u51c6\u5907\u5de5\u4f5c\uff0cGWAS\u6570\u636e\u7684\u7f51\u7ad9\u4e0b\u8f7d\u65b9\u6cd5\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"11\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7684\u51c6\u5907\u5de5\u4f5c\uff0cGWAS\u6570\u636e\u7684\u7f51\u7ad9\u4e0b\u8f7d\u65b9\u6cd5<\/a><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 5px 0%;\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(224, 224, 224);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/td>\n<\/tr>\n<tr opera-tn-ra-comp=\"_$.pages:0.layers:0.comps:4.classicTable1:3\" powered-by=\"xiumi.us\">\n<td colspan=\"1\" rowspan=\"1\" opera-tn-ra-cell=\"_$.pages:0.layers:0.comps:4.classicTable1:3.td@@0\" style=\"border-color: rgb(62, 62, 62);border-style: none;padding: 0px;\" width=\"100.0000%\">\n<section>\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-right: 0%;margin-left: 0%;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 10%;height: auto;flex: 0 0 auto;align-self: center;\">\n<section style=\"font-size: 19px;color: rgb(95, 156, 239);line-height: 1;\" powered-by=\"xiumi.us\">\n04<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;flex: 100 100 0%;align-self: center;height: 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onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyRuxjwBibr3wX3ThueIbDBtvg0j1NQ56GiaiclNvqqLcXVaktH0RvibMfTUA\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u968f\u7740\u6700\u8fd1\u7684\u533b\u5b66\u671f\u520a\u4e0e\u751f\u7269\u4fe1\u606f\u5b66\u671f\u520a\u4e2d\u9776\u5411\u6cbb\u7597\u7684\u6587\u7ae0\u8d8a\u6765\u8d8a\u591a\uff0c\u540e\u53f0\u6709\u4e0d\u5c11\u7684\u5c0f\u4f19\u4f34\u79c1\u4fe1\u5c0f\u679c\uff0c\u5e0c\u671b\u505a\u4e00\u671f\u548c\u9776\u5411\u6cbb\u7597\u6709\u5173\u7684\u6559\u7a0b\u3002\u54b1\u4eec\u6709\u6c42\u5fc5\u5e94\uff01\u5c0f\u679c\u7279\u5730\u4ece\u5927\u91cf\u7684\u6587\u7ae0\u4e2d\u7b5b\u9009\u4e86\u4e00\u7bc7\u5f71\u54cd\u56e0\u5b50\u9ad8\uff0c\u540c\u65f6\u4e5f\u6613\u4e8e\u590d\u73b0\u7684\u6587\u7ae0\uff1aTargeting the Ubiquitin-Proteasome System Using the UBA1 Inhibitor TAK-243 is a Potential Therapeutic Strategy for Small-Cell Lung Cancer.\u8fd9\u7bc7\u6587\u7ae0\u53d1\u8868\u4e8eClinical cancer research\uff0cIF>11\u3002<\/span>\u672c\u6b21\u4ee3\u7801\u7684\u6570\u636e\u91cf\u504f\u5927\uff0c\u6b22\u8fce\u5927\u5bb6\u6765\u79df\u8d41\u6211\u4eec\u7684\u670d\u52a1\u5668\u54e6\uff0c\u5173\u6ce8\u516c\u4f17\u53f7\u8fd8\u53ef\u4ee5\u83b7\u5f97\u72ec\u7279\u7684\u751f\u4fe1\u5206\u6790\u601d\u8def\u5b9a\u5236~<\/span><\/span><\/section>\n<section style=\"font-size: 15px;padding-right: 2px;padding-left: 2px;margin-bottom: 0px;\">\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;\">\n<section style=\"display: flex;width: 100%;flex-flow: column;\" powered-by=\"xiumi.us\">\n<section style=\"z-index: 1;transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"justify-content: center;display: flex;flex-flow: row;transform: translate3d(4px, 0px, 0px) rotateX(180deg);margin-bottom: -2px;\">\n<section style=\"display: inline-block;vertical-align: top;width: 50%;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 10px;height: 14px;vertical-align: top;overflow: hidden;background-color: rgb(91, 91, 91);border-style: solid;border-width: 2px;border-color: rgb(255, 255, 255);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: 50%;\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 10px;height: 14px;vertical-align: top;overflow: hidden;background-color: rgb(91, 91, 91);border-style: solid;border-width: 2px;border-color: rgb(255, 255, 255);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(194, 209, 255);\">\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row;margin-top: -4px;margin-bottom: 5px;transform: translate3d(5px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(193, 209, 255);padding: 10px 20px;box-shadow: rgb(255, 255, 255) -2px 2px 0px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;align-self: center;flex: 0 0 auto;width: 100%;height: auto;\">\n<section style=\"text-align: center;color: rgb(0, 0, 0);\" powered-by=\"xiumi.us\">\n\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111\u201d<\/strong><\/p>\n\u9886\u53d6\u672c\u7bc7\u4ee3\u7801\u3001\u57fa\u56e0\u96c6\u6216\u793a\u4f8b\u6570\u636e\u7b49\u6587\u4ef6<\/strong><\/p>\n\u6587\u4ef6\u7f16\u53f7\uff1a240115<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n\u9700\u8981\u79df\u8d41\u670d\u52a1\u5668\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u626b\u7801\u6dfb\u52a0\u5c0f\u679c\uff0c\u6b64\u5916\u5c0f\u679c\u8fd8\u63d0\u4f9b\u751f\u4fe1\u5206\u6790\uff0c\u601d\u8def\u8bbe\u8ba1\uff0c\u6587\u732e\u590d\u73b0\u7b49\uff0c\u6709\u9700\u8981\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u64a9~<\/strong><\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100016196\" data-ratio=\"1\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"430\" style=\"width: 170px;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_f6PG40Qrdu5e9B1iaIMItPiajABYWA-9.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAxqaqPbQprPd4vw8Ytp0cprbzXiakMDdFriaB6B59ibhlBCrNyQFf6PG40Qrdu5e9B1iaIMItPiajABYWA\/640?wx_fmt=jpeg'\" data-recalc-dims=\"1\" \/><\/p>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u5728\u6b63\u5f0f\u5f00\u59cb\u4eca\u5929\u7684\u6587\u732e\u590d\u73b0\u4e4b\u524d\uff0c\u5c0f\u679c\u9700\u8981\u7ed9\u5c0f\u4f19\u4f34\u4eec\u5148\u4ecb\u7ecd\u4e00\u4e0b\u672c\u7bc7\u6559\u7a0b\u6240\u9700\u8981\u7684\u5de5\u5177\uff1alimma\u5206\u6790\u3002<\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u5bf9\u4e8elimma\u5206\u6790\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u7b80\u8981\u7684\u4ecb\u7ecd\u4e00\u4e0b\uff1a limma\u5206\u6790\u662f\u4e00\u79cd\u7528\u4e8e\u5dee\u5f02\u57fa\u56e0\u8868\u8fbe\u5206\u6790\u7684\u7edf\u8ba1\u65b9\u6cd5\uff0c\u57fa\u4e8e\u7ebf\u6027\u6a21\u578b\uff0c\u4f7f\u7528\u52a0\u6743\u6700\u5c0f\u4e8c\u4e58\u6cd5\u6765\u4f30\u8ba1\u57fa\u56e0\u8868\u8fbe\u7684\u5dee\u5f02\uff0c\u5e76\u901a\u8fc7\u7ecf\u9a8c\u8d1d\u53f6\u65af\u65b9\u6cd5\u6765\u6821\u6b63\u591a\u91cd\u68c0\u9a8c\u95ee\u9898\u3002\u53ef\u4ee5\u5904\u7406\u591a\u79cd\u6570\u636e\u7c7b\u578b\u548c\u683c\u5f0f\uff0c\u5982\u57fa\u56e0\u82af\u7247\u6570\u636e\u548cRNA-Seq\u6570\u636e\uff0c\u4e5f\u80fd\u591f\u5f88\u597d\u5730\u63a7\u5236\u5047\u9633\u6027\u7387\u3002\u9664\u4e86\u5e38\u89c4\u7684\u8fdb\u884c\u4e00\u4e9b\u80bf\u7624\u7684\u5dee\u5f02\u5206\u6790\uff0climma\u5206\u6790\u8fd8\u53ef\u4ee5\u7528\u4e8e\u9776\u5411\u6cbb\u7597\u76f8\u5173\u7684\u6570\u636e\u5206\u6790\uff0c\u90a3\u4e48limma\u5206\u6790\u5e94\u8be5\u5982\u4f55\u5728\u9776\u5411\u6cbb\u7597\u7684\u6587\u7ae0\u4e2d\u5e94\u7528\u5462\uff1f\u522b\u6025\uff0c\u5c0f\u679c\u8fd9\u5c31\u624b\u628a\u624b\u7684\u6559\u4f1a\u4f60\uff01<\/span> \u5173\u4e8elimma\u5206\u6790\u7684\u57fa\u7840\u77e5\u8bc6\u4ee5\u53ca\u53ef\u89c6\u5316\u6559\u7a0b\uff0c\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u5173\u6ce8\u5c0f\u679c\u641c\u7d22\u5f80\u671f\u5185\u5bb9\u67e5\u9605\u54e6~<\/span><\/span><span style=\"font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;color: rgb(255, 0, 0);font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"> <o:p> <\/o:p><\/span> <\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><o:page><\/o:page><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">Step 1 \u8bbe\u7f6e\u5de5\u4f5c\u73af\u5883\uff0c\u529f\u80fd\u51fd\u6570\uff0c\u8f93\u5165\u6587\u4ef6<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u9996\u5148\uff0c\u9700\u8981\u5bfc\u5165\u4eca\u5929\u7684\u4e3b\u89d2limma\u5305\uff0c\u8fd8\u6709\u4e00\u4e9b\u76f8\u5173\u7684\u7ed8\u56fe\u5305\uff1asplines\uff0csplines2\uff0cscales\u3002\u7136\u540e\u6784\u5efa\u529f\u80fd\u51fd\u6570\u2014\u2014\u901a\u8fc7\u7ed9\u5b9a\u7684\u7ec6\u80de\u7cfb\u6784\u5efa\u6a21\u578b\u77e9\u9635\uff0c\u901a\u8fc7\u7ed9\u5b9a\u7684GSEA\u7ed3\u679c\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u5c06\u8fd9\u4e24\u4e2a\u4e3b\u8981\u7684\u529f\u80fd\u51fd\u6570\u6784\u5efa\u5b8c\u6210\u540e\uff0c\u5bfc\u5165\u672c\u6b21\u590d\u73b0\u6240\u9700\u7684\u6570\u636e\uff08\u6240\u9700\u6570\u636e\u5c0f\u679c\u5df2\u7ecf\u5e2e\u5927\u5bb6\u6574\u7406\u597d\u4e86\uff0c\u70b9\u51fb\u94fe\u63a5\u5373\u53ef\u4e0b\u8f7d\u54e6\uff09\u3002<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u94fe\u63a5\uff1a<\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">https:\/\/pan.baidu.com\/s\/12BZlryXXmBn_nBgsFxL30w <\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u63d0\u53d6\u7801\uff1a2roq<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span><\/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<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<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<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<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=\"bash\"><code>##### \u5bfc\u5165R\u5305 #####<\/span><\/span><\/code><code>library(limma)<\/span><\/code><code>library(splines)<\/span><\/code><code>library(splines2)<\/span><\/code><code>ns<-naturalSpline<\/span><\/code><code>library(scales)<\/span><\/code><code>library(BinfTools)<\/span><\/code><code> <\/span><\/code><code>##### \u6784\u5efa\u529f\u80fd\u51fd\u6570 #####<\/span><\/span><\/code><code>##### \u6839\u636e\u7ed9\u5b9a\u7684\u7ec6\u80de\u7cfb\uff0c\u6784\u5efa\u4e00\u4e2a\u7ebf\u6027\u6a21\u578b\u77e9\u9635\uff0c\u7528\u4e8e\u540e\u7eed\u7684\u5dee\u5f02\u5206\u6790 #####<\/span><\/span><\/code><code>makemodel<-function<\/span>(x, colname, cell.lines){<\/span><\/code><code> cell.lines<-sapply(strsplit(cell.lines, split=\"_\"<\/span>, fixed=T),'[['<\/span>, 1)<\/span><\/code><code> if<\/span>(ncol(x)==1){<\/span><\/code><code> olCells<-rownames(x)[which<\/span>(rownames(x) %in<\/span>% cell.lines)]<\/span><\/code><code> x<-as.data.frame(x[olCells,])<\/span><\/code><code> rownames(x)<-olCells<\/span><\/code><code> colnames(x)<-colname<\/span><\/code><code> } else<\/span> {<\/span><\/code><code> x<-x[which<\/span>(rownames(x) %in<\/span>% cell.lines),]<\/span><\/code><code> }<\/span><\/code><code> sm<-NULL<\/span><\/code><code> if<\/span>(ncol(x)==1){ <\/span><\/code><code> sm<-ns(x[,1])<\/span><\/code><code> } else<\/span> {<\/span><\/code><code> sm<-ns(x[,which<\/span>(colnames(x) %in<\/span>% colname)])<\/span><\/code><code> }<\/span><\/code><code> dm<-model.matrix(~sm)<\/span><\/code><code> return<\/span>(dm)<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>##### \u6839\u636e\u7ed9\u5b9a\u7684\u7ec6\u80de\u7cfb\u548c\u8868\u8fbe\u77e9\u9635\uff0c\u8fd4\u56de\u7b26\u5408\u6761\u4ef6\u7684\u7ec6\u80de\u7cfb\u540d\u79f0 #####<\/span><\/span><\/code><code>olCells<-function<\/span>(cell.lines, x){<\/span><\/code><code> tmp<-sapply(strsplit(cell.lines, split=\"_\"<\/span>, fixed=T),'[['<\/span>,1)<\/span><\/code><code> #return(tmp)<\/span><\/span><\/code><code> return<\/span>(cell.lines[which<\/span>(tmp %in<\/span>% rownames(x))])<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>##### \u6839\u636e\u7ed9\u5b9a\u7684\u4e24\u4e2aGSEA\u7ed3\u679c\uff0c\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u548c\u53ef\u89c6\u5316\uff0c\u6bd4\u8f83\u4e0d\u540c\u7269\u79cd\u6216\u6761\u4ef6\u4e0b\u7684\u57fa\u56e0\u96c6\u5bcc\u96c6\u60c5\u51b5 #####<\/span><\/span><\/code><code>compGSEA<-function<\/span>(x, y, title=\"Comparing GSEA results\"<\/span>, xlab=\"Human\"<\/span>, ylab=\"Mouse\"<\/span>, p=1){<\/span><\/code><code> x<-subset(x, padj <p)<\/span><\/code><code> <\/p)<><\/span><\/code><code> y<-subset(y, padj <p)<\/span><\/code><code> <\/p)<><\/span><\/code><code> x<-x[which<\/span>(x$pathway<\/span> %in<\/span>% y$pathway<\/span>),]<\/span><\/code><code> y<-y[which<\/span>(y$pathway<\/span> %in<\/span>% x$pathway<\/span>),]<\/span><\/code><code> x<-x[order(x$pathway<\/span>),]<\/span><\/code><code> y<-y[order(y$pathway<\/span>),]<\/span><\/code><code> if<\/span>(!all.equal(x$pathway<\/span>, y$pathway<\/span>)){<\/span><\/code><code> stop(\"Check again...\"<\/span>)<\/span><\/code><code> }<\/span><\/code><code> dat<-data.frame(row.names=x$pathway<\/span>,<\/span><\/code><code> x=x$NES<\/span>,<\/span><\/code><code> y=y$NES<\/span>)<\/span><\/code><code> dat$Direction<\/span><-ifelse(dat$x<\/span>*dat$y<\/span>>0, \"Positive\"<\/span>, \"Negative\"<\/span>)<\/span><\/code><code> dat$Trend<\/span><-ifelse(dat$x<\/span>*dat$y<\/span>>0,abs(dat$x<\/span>-dat$y<\/span>), abs(dat$x<\/span>-dat$y<\/span>)*-1)<\/span><\/code><code> #print(head(dat))<\/span><\/span><\/code><code> g<-ggpubr::ggscatter(dat, x=\"x\"<\/span>, y=\"y\"<\/span>, add=\"reg.line\"<\/span>, conf.int=T, color=\"Trend\"<\/span>,<\/span><\/code><code> #palette=c(Negative=\"blue\",Positive=\"red\"),<\/span><\/span><\/code><code> cor.coef=T, add.params=list(color=\"purple\"<\/span>,fill=\"purple\"<\/span>),<\/span><\/code><code> xlab=paste(xlab,\"NES\"<\/span>), ylab=paste(ylab,\"NES\"<\/span>)) + <\/span><\/code><code> ggpubr::gradient_color(c(\"blue\"<\/span>,\"white\"<\/span>,\"red\"<\/span>))<\/span><\/code><code> print<\/span>(g) <\/span><\/code><code> return<\/span>(dat)<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>#### \u63d0\u53d6\u57fa\u56e0\u7684\u7b26\u53f7\u540d\u79f0 ####<\/span><\/span><\/code><code>putSym<-function<\/span>(res){<\/span><\/code><code> res$hgnc_symbol<\/span><-sapply(strsplit(rownames(res), split=\".\"<\/span>, fixed=T),'[['<\/span>,1)<\/span><\/code><code> return<\/span>(res)<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>#### \u89c4\u8303\u5316 ####<\/span><\/span><\/code><code>fixRows<-function<\/span>(x, obtype=c(\"res\"<\/span>,\"counts\"<\/span>), col=NULL){<\/span><\/code><code> if<\/span>(obtype[1]==\"res\"<\/span>){<\/span><\/code><code> x<-x[order(x$baseMean<\/span>, decreasing=T),]<\/span><\/code><code> }<\/span><\/code><code> if<\/span>(obtype[1]==\"counts\"<\/span>){<\/span><\/code><code> x<-x[order(rowMeans(x), decreasing=T),]<\/span><\/code><code> }<\/span><\/code><code> genes<-c()<\/span><\/code><code> if<\/span>(is.null(col)){<\/span><\/code><code> genes<-sapply(strsplit(rownames(x), \".\"<\/span>,T),'[['<\/span>,1)<\/span><\/code><code> } else<\/span> {<\/span><\/code><code> genes<-x[,which<\/span>(colnames(x) %in<\/span>% col)]<\/span><\/code><code> }<\/span><\/code><code> dups<-unique(genes[which<\/span>(duplicated(genes))])<\/span><\/code><code> to_remove <- c()<\/span><\/code><code> for<\/span> (i in<\/span> 1:length(dups)) {<\/span><\/code><code> ind <- which<\/span>(genes %in<\/span>% dups[i], arr.ind = T)<\/span><\/code><code> to_remove <- c(to_remove, ind[-1])<\/span><\/code><code> }<\/span><\/code><code> x <- x[-to_remove, ]<\/span><\/code><code> genes<-genes[-to_remove]<\/span><\/code><code> rownames(x)<-genes<\/span><\/code><code> return<\/span>(x)<\/span><\/code><code>}<\/span><\/code><code> <\/span><\/code><code>##### \u5bfc\u5165\u6570\u636e #####<\/span><\/span><\/code><code>#\u8bfb\u53d6CCLE\uff08Cancer Cell Line Encyclopedia\uff09\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u7ec6\u80de\u7cfb\u4fe1\u606f\u6570\u636e<\/span><\/span><\/code><code>CCLE<-read.csv(\"\/data\/CCLE_expression.csv\"<\/span>)<\/span><\/code><code>#\u533a\u5206\u6bcf\u4e2a\u7ec6\u80de\u7cfb <\/span><\/span><\/code><code>info<-read.csv(\"\/data\/sample_info.csv\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>#\u901a\u8fc7 DepMap ID \u548c CCLE \u540d\u79f0\u5339\u914d\u7ec6\u80de\u7cfb\u6807\u8bc6\u7b26<\/span><\/span><\/code><code>CCLE<-merge(CCLE, info[,c(1,4)], by.x=\"X\"<\/span>, by.y=\"DepMap_ID\"<\/span>)<\/span><\/code><code>rownames(CCLE)<-CCLE$CCLE_Name<\/span><\/span><\/code><code>CCLE<-CCLE[,-(which<\/span>(colnames(CCLE) %in<\/span>% c(\"X\"<\/span>,\"DepMap_ID\"<\/span>,\"CCLE_Name\"<\/span>)))]<\/span><\/code><code>CCLE<-t(CCLE)<\/span><\/code><code> <\/span><\/code><code>#\u8bfb\u5165\u7ec6\u80de\u7cfb\u6ce8\u91ca\u6570\u636e\uff08\u8bc6\u522b SCLC \u7ec6\u80de\u7cfb\u2014\u2014\u5c0f\u7ec6\u80de\u80ba\u764c\uff09<\/span><\/span><\/code><code>x<-read.delim(\"\/data\/Cell_lines_annotations_20181226.txt\"<\/span>)<\/span><\/code><code>SCLC<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% x[which<\/span>(x$type_refined<\/span> %in<\/span>% \"lung_small_cell\"<\/span>),]$CCLE_ID<\/span>)]<\/span><\/code><code> <\/span><\/code><code>#\u8bc6\u522bSCLC\u7684\u5b50\u7c7b<\/span><\/span><\/code><code>ATOH1<-c(\"CORL24_LUNG\"<\/span>,\"HCC33_LUNG\"<\/span>)<\/span><\/code><code>POU2F3<-c(\"NCIH1048_LUNG\"<\/span>, \"CORL311_LUNG\"<\/span>,\"NCIH211_LUNG\"<\/span>,\"NCIH526_LUNG\"<\/span>)<\/span><\/code><code>YAP1<-c(\"SW1271_LUNG\"<\/span>,\"NCIH1341_LUNG\"<\/span>,\"DMS114_LUNG\"<\/span>, \"NCIH196_LUNG\"<\/span>, \"NCIH1339_LUNG\"<\/span>, \"SBC5_LUNG\"<\/span>,\"NCIH2286_LUNG\"<\/span>,\"NCIH841_LUNG\"<\/span>)<\/span><\/code><code>YAP1_2<-c(\"SW1271_LUNG\"<\/span>,\"NCIH1341_LUNG\"<\/span>,\"DMS114_LUNG\"<\/span>, \"NCIH1339_LUNG\"<\/span>, \"SBC5_LUNG\"<\/span>,\"NCIH2286_LUNG\"<\/span>,\"NCIH841_LUNG\"<\/span>) #YAP1_2 removes outlier sample NCIH196_LUNG<\/span><\/span><\/code><code>NEUROD1<-c(\"NCIH2066_LUNG\"<\/span>,\"CORL279_LUNG\"<\/span>,\"NCIH1694_LUNG\"<\/span>,\"NCIH524_LUNG\"<\/span>,\"DMS273_LUNG\"<\/span>,\"NCIH446_LUNG\"<\/span>,\"NCIH2171_LUNG\"<\/span>,\"NCIH82_LUNG\"<\/span>,\"SCLC21H_LUNG\"<\/span>)<\/span><\/code><code>ASCL1<-colnames(SCLC)<\/span><\/code><code>ASCL1<-ASCL1[which<\/span>(!ASCL1 %in<\/span>% ATOH1)]<\/span><\/code><code>ASCL1<-ASCL1[which<\/span>(!ASCL1 %in<\/span>% POU2F3)]<\/span><\/code><code>ASCL1<-ASCL1[which<\/span>(!ASCL1 %in<\/span>% YAP1)]<\/span><\/code><code>ASCL1<-ASCL1[which<\/span>(!ASCL1 %in<\/span>% NEUROD1)]<\/span><\/code><code> <\/span><\/code><code>typing<-data.frame(Cell.line=c(ATOH1,POU2F3,YAP1,NEUROD1,ASCL1),<\/span><\/code><code> type<\/span>=c(rep(\"ATOH1\"<\/span>, length(ATOH1)), rep(\"POU2F3\"<\/span>, length(POU2F3)),<\/span><\/code><code> rep(\"YAP1\"<\/span>, length(YAP1)), rep(\"NEUROD1\"<\/span>, length(NEUROD1)), <\/span><\/code><code> rep(\"ASCL1\"<\/span>, length(ASCL1))))<\/span><\/code><code> <\/span><\/code><code>#\u52a0\u8f7d TAK243 \u836f\u7269\u53cd\u5e94\u6570\u636e <\/span><\/span><\/code><code>x<-read.csv(\"\/data\/TAK_final_results.csv\"<\/span>, row.names=1)<\/span><\/code><code> <\/span><\/code><code>#\u6709\u4e9b\u7ec6\u80de\u7cfb\u6211\u4eec\u6709 TAK \u6570\u636e\uff0c\u4f46\u5728\u6570\u636e\u96c6\u4e2d\u6ca1\u6709\u8868\u8fbe\u6570\u636e\uff0c\u6240\u4ee5\u4ec5\u4fdd\u7559\u540c\u65f6\u5177\u6709\u8fd9\u4e24\u79cd\u6570\u636e\u7684\u7ec6\u80de\u7cfb<\/span><\/span><\/code><code>x<-as.data.frame(x[which<\/span>(rownames(x) %in<\/span>% sapply(strsplit(colnames(CCLE), split=\"_\"<\/span>, fixed=T),'[['<\/span>,1)),])<\/span><\/code><code>CCLE<-CCLE[,which<\/span>(sapply(strsplit(colnames(CCLE),\"_\"<\/span>,T),'[['<\/span>,1) %in<\/span>% rownames(x))]<\/span><\/code><code>#\u5c06\u836f\u7269\u53cd\u5e94\u6570\u636e\u4e2d\u7ec6\u80de\u7cfb\u7684\u987a\u5e8f\u4e0e\u8868\u8fbe\u6570\u636e\u5339\u914d\u4ee5\u8fdb\u884c\u8868\u8fbe\u5efa\u6a21<\/span><\/span><\/code><code>x<-x[match(sapply(strsplit(colnames(CCLE), split=\"_\"<\/span>, T),'[['<\/span>,1), rownames(x)),]<\/span><\/code><code>x<-x[complete.cases(x),]<\/span><\/code><code>#\u68c0\u67e5\u6240\u6709\u7ec6\u80de\u7cfb\u7684\u987a\u5e8f\u662f\u5426\u76f8\u540c<\/span><\/span><\/code><code>all.equal(sapply(strsplit(colnames(CCLE), \"_\"<\/span>, T),'[['<\/span>,1), rownames(x))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><span style=\"font-variant: normal;text-transform: none;color: rgb(0, 112, 192);font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"><\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u4e24\u4e2a\u6570\u636e\u5206\u522b\u662fCCLE_expression.csv\u548csample_info.csv\uff0c\u5176\u4e2dCCLE_expression.csv\u662f\u4eceCCLE\uff08Cancer Cell Line Encyclopedia\uff09\u2014\u4e00\u4e2a\u5927\u89c4\u6a21\u7684\u764c\u75c7\u7ec6\u80de\u7cfb\u7684\u9057\u4f20\u548c\u836f\u7269\u654f\u611f\u6027\u7684\u6570\u636e\u5e93\u4e2d\u8bfb\u53d6\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u548c\u7ec6\u80de\u7cfb\u4fe1\u606f\u6570\u636e\uff0c\u800c\u5982\u4e0b\u56fe\u6240\u793a\uff0csample_info.csv\u662f\u4e00\u4e2a\u5305\u542b\u6bcf\u4e2a\u7ec6\u80de\u7cfb\u7684\u6807\u8bc6\u7b26\u548c\u6ce8\u91ca\u7684\u6587\u4ef6\uff0c\u4f8b\u5982\u7ec6\u80de\u7cfb\u7684\u540d\u79f0\u3001\u764c\u75c7\u7c7b\u578b\u3001\u7ec4\u7ec7\u6765\u6e90\u7b49\u3002<\/span><\/section>\n<section style=\"text-align: center;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016197\" data-ratio=\"0.7055555555555556\" data-type=\"png\" data-w=\"1080\" height=\"325 .27001953125\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"461 .0099792480469\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_HJKFHmPRLVJZ49tibxKeVfjBRPL7nw.png?resize=461%2C325\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyRia5FrJzkEkJCFDicX4KuiaZmdPA9HJKFHmPRLVJZ49tibxKeVfjBRPL7nw\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/> <\/span> <\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u5728\u5bfc\u5165\u6570\u636e\u540e\uff0c\u8fd8\u9700\u8981\u5bfc\u5165\u7ec6\u80de\u7cfb\u6ce8\u91ca\u6570\u636e\uff0c\u7528\u4e8e\u8bc6\u522b SCLC \uff08\u5c0f\u7ec6\u80de\u80ba\u764c\uff09\u7ec6\u80de\u7cfb\uff0c\u7136\u540e\u5bfc\u5165\u6709 TAK243 \u54cd\u5e94\u6570\u636e\u7684\u7ec6\u80de\u7cfb\uff0c\u8bc6\u522bSCLC\u7684\u5b50\u7c7b\u3002\u6700\u540e\u5bfc\u5165 TAK243 \u836f\u7269\u53cd\u5e94\u6570\u636e\uff0c\u5c06\u836f\u7269\u53cd\u5e94\u6570\u636e\u4e2d\u7ec6\u80de\u7cfb\u7684\u987a\u5e8f\u4e0e\u8868\u8fbe\u6570\u636e\u5339\u914d\u4ee5\u8fdb\u884c\u8868\u8fbe\u5efa\u6a21\uff0c\u68c0\u67e5\u6240\u6709\u7ec6\u80de\u7cfb\u7684\u987a\u5e8f\u662f\u5426\u76f8\u540c\u3002<\/span> <\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;font-weight: bold;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">Step 2 Limma\u5206\u6790<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u9996\u5148\u4e3aLimma \u5236\u4f5c\u8bbe\u8ba1\u6a21\u578b\u77e9\u9635\uff0c\u9700\u8981\u4e3a\u6240\u6709\u7684\u7ec6\u80de\u7cfb\u90fd\u5efa\u7acb\u6a21\u578b\uff0c\u7136\u540e\u4f7f\u7528 Spearman \u76f8\u5173\u6027\u68c0\u67e5\u6837\u672c\u5982\u4f55\u5173\u8054\u548c\u805a\u7c7b\uff1a\u901a\u8fc7\u8fd0\u884c limma \u5206\u6790 – \u62df\u5408\u7ebf\u6027\u56de\u5f52\u6a21\u578b\uff0c\u4f7f\u7528\u5dee\u5f02\u8868\u8fbe\u7684\u7ecf\u9a8c\u8d1d\u53f6\u65af\u6765\u8fdb\u884c\u68c0\u9a8c\uff0c\u63d0\u53d6\u8fd4\u56de\u7684\u6570\u636e\uff0c\u5e76\u8f93\u51faDE\u7ed3\u679c\u3002<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span><\/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<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<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=\"bash\"><code>##### Limma \u5206\u6790 #####<\/span><\/span><\/code><code>#\u4e3a EC50 \u503c\u521b\u5efaspline\u6a21\u578b<\/span><\/span><\/code><code>nsEC50<-ns(x$EC50<\/span>)<\/span><\/code><code>#\u4e3a Limma \u5236\u4f5c\u8bbe\u8ba1\u6a21\u578b\u77e9\u9635<\/span><\/span><\/code><code>dm_EC50<-model.matrix(~nsEC50) #Model for all cell lines<\/span><\/span><\/code><code> <\/span><\/code><code>#\u4f7f\u7528\u81ea\u5b9a\u4e49\u51fd\u6570\u4e3a\u5b50\u7c7b\u578b\u7ec4\u751f\u6210\u8bbe\u8ba1\u6a21\u578b\u77e9\u9635<\/span><\/span><\/code><code>dm_EC50_YAP<-makemodel(x, \"EC50\"<\/span>, YAP1) #All YAP1-high\/Triple Negative<\/span><\/span><\/code><code>dm_EC50_YAP2<-makemodel(x, \"EC50\"<\/span>, YAP1_2) #All YAP1-high except NCIH196_LUNG (outlier)<\/span><\/span><\/code><code>dm_EC50_ND1<-makemodel(x, \"EC50\"<\/span>, NEUROD1) #All NEUROD1-high<\/span><\/span><\/code><code>dm_EC50_ASCL1<-makemodel(x, \"EC50\"<\/span>, ASCL1) #All ASCL1-high<\/span><\/span><\/code><code> <\/span><\/code><code>#\u8868\u8fbe\u77e9\u9635\u5b50\u96c6\u4ec5\u5305\u542b\u6bcf\u6b21\u5206\u6790\u6240\u9700\u7684\u7ec6\u80de\u7cfb<\/span><\/span><\/code><code>CCLE<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(colnames(CCLE), x))] #All cell lines<\/span><\/span><\/code><code>CCLE2<-CCLE[,which<\/span>(!colnames(CCLE) %in<\/span>% \"NCIH196_LUNG\"<\/span>)] #All cell lines except NCIH196_LUNG (outlier)<\/span><\/span><\/code><code>dm_EC50_2<-makemodel(x[which<\/span>(!rownames(x) %in<\/span>% \"NCIH196\"<\/span>),], \"EC50\"<\/span>, colnames(CCLE2)) #Create design model matrix for all SCLC cell lines except NCIH196_LUNG (outlier) <\/span><\/span><\/code><code>CCLE_YAP<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(YAP1, x))]<\/span><\/code><code>CCLE_YAP2<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(YAP1_2, x))]<\/span><\/code><code>CCLE_ND1<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(NEUROD1,x))]<\/span><\/code><code>CCLE_ASCL1<-CCLE[,which<\/span>(colnames(CCLE) %in<\/span>% olCells(ASCL1,x))]<\/span><\/code><code> <\/span><\/code><code>#\u4f7f\u7528\u786e\u5b9a\u7684 SCLC \u4e9a\u578b\uff0c\u4f7f\u5b50\u96c6\u6570\u636e\u6846\u4ec5\u5305\u542b\u5df2\u68c0\u6d4b\u7684 SCLC \u7ec6\u80de\u7cfb<\/span><\/span><\/code><code>subtyping<-subset(typing, Cell.line %in<\/span>% colnames(CCLE))<\/span><\/code><code>subtyping<-subtyping[match(colnames(CCLE), subtyping$Cell<\/span>.line),] #Ensure same order of cell lines<\/span><\/span><\/code><code>all.equal(subtyping$Cell<\/span>.line, colnames(CCLE)) #Check - should return TRUE<\/span><\/span><\/code><code> <\/span><\/code><code>#\u521b\u5efa\u6761\u4ef6\u5411\u91cf<\/span><\/span><\/code><code>subtype<-subtyping$type<\/span><\/span><\/code><code>subtype2<-subtype[-which<\/span>(colnames(CCLE) %in<\/span>% \"NCIH196_LUNG\"<\/span>)]<\/span><\/code><code> <\/span><\/code><code>#\u4f7f\u7528 Spearman \u76f8\u5173\u6027\u68c0\u67e5\u6837\u672c\u5982\u4f55\u5173\u8054\u548c\u805a\u7c7b<\/span><\/span><\/code><code>#corHeat(CCLE, hmcol=colPal(\"Greys\"),annodf=data.frame(row.names=subtyping$Cell.line, Subtype=subtyping$type), showTree=T)<\/span><\/span><\/code><code> <\/span><\/code><code>#\u8fd0\u884c limma \u5206\u6790 - \u62df\u5408\u7ebf\u6027\u56de\u5f52\u6a21\u578b<\/span><\/span><\/code><code>EC50_fit<-lmFit(CCLE, design=dm_EC50)<\/span><\/code><code>EC50_fit2<-lmFit(CCLE2, design=dm_EC50_2)<\/span><\/code><code>EC50_fit_YAP<-lmFit(CCLE_YAP, design=dm_EC50_YAP)<\/span><\/code><code>EC50_fit_YAP2<-lmFit(CCLE_YAP2, design=dm_EC50_YAP2)<\/span><\/code><code>EC50_fit_ND1<-lmFit(CCLE_ND1, design=dm_EC50_ND1)<\/span><\/code><code>EC50_fit_ASCL1<-lmFit(CCLE_ASCL1, design=dm_EC50_ASCL1)<\/span><\/code><code> <\/span><\/code><code>#\u5dee\u5f02\u8868\u8fbe\u7684\u7ecf\u9a8c\u8d1d\u53f6\u65af\u68c0\u9a8c<\/span><\/span><\/code><code>EC50_fit<-eBayes(EC50_fit)<\/span><\/code><code>EC50_fit2<-eBayes(EC50_fit2)<\/span><\/code><code>EC50_fit_YAP<-eBayes(EC50_fit_YAP)<\/span><\/code><code>EC50_fit_YAP2<-eBayes(EC50_fit_YAP2)<\/span><\/code><code>EC50_fit_ND1<-eBayes(EC50_fit_ND1)<\/span><\/code><code>EC50_fit_ASCL1<-eBayes(EC50_fit_ASCL1)<\/span><\/code><code> <\/span><\/code><code>#\u8fd4\u56de\u6240\u6709\u7ed3\u679c\uff08\u6240\u6709\u57fa\u56e0\u7684\u56de\u5f52\u7cfb\u6570\u548c p \u503c\uff09 <\/span><\/span><\/code><code>EC50_res<-topTable(EC50_fit, number=Inf)<\/span><\/code><code>EC50_res2<-topTable(EC50_fit2, number=Inf)<\/span><\/code><code>EC50_res_YAP<-topTable(EC50_fit_YAP, number=Inf)<\/span><\/code><code>EC50_res_YAP2<-topTable(EC50_fit_YAP2, number=Inf)<\/span><\/code><code>EC50_res_ND1<-topTable(EC50_fit_ND1, number=Inf)<\/span><\/code><code>EC50_res_ASCL1<-topTable(EC50_fit_ASCL1, number=Inf)<\/span><\/code><code> <\/span><\/code><code>#\u73b0\u5728\u5c06\u5305\u542b\u57fa\u56e0\u7b26\u53f7\u7684\u5217 (hgnc_symbol) \u6dfb\u52a0\u5230\u7ed3\u679c\u4e2d<\/span><\/span><\/code><code>EC50_res<-putSym(EC50_res)<\/span><\/code><code>EC50_res2<-putSym(EC50_res2)<\/span><\/code><code>EC50_res_ASCL1<-putSym(EC50_res_ASCL1)<\/span><\/code><code>EC50_res_YAP<-putSym(EC50_res_YAP)<\/span><\/code><code>EC50_res_YAP2<-putSym(EC50_res_YAP2)<\/span><\/code><code>EC50_res_ND1<-putSym(EC50_res_ND1)<\/span><\/code><code> <\/span><\/code><code>#\u8f93\u51faDE\u7ed3\u679c<\/span><\/span><\/code><code>limResList<-list(SCLC_w196=EC50_res,<\/span><\/code><code> SCLC_wo196=EC50_res2,<\/span><\/code><code> YAP1_w196=EC50_res_YAP,<\/span><\/code><code> YAP1_wo196=EC50_res_YAP2,<\/span><\/code><code> ASCL1=EC50_res_ASCL1,<\/span><\/code><code> NEUROD1=EC50_res_ND1)<\/span><\/code><code>dir.create(\"\/results\/Limma_Results\"<\/span>)<\/span><\/code><code>mapply(write.table, limResList, file=paste0(\"\/results\/Limma_Results\/\"<\/span>,names(limResList),\".res.txt\"<\/span>),<\/span><\/code><code> quote=F, sep=\"t\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><span style=\"font-variant: normal;text-transform: none;color: rgb(0, 112, 192);font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"><\/span><\/section>\n<section style=\"text-align: center;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;text-indent: 0em;\"> <img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016198\" data-ratio=\"0.17592592592592593\" data-type=\"png\" data-w=\"1080\" height=\"97 .4000244140625\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"553 .739990234375\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_816H60iaWkXmCYZdlI2SUnKjQlM93A.png?resize=553%2C97\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyRHbKDCjrlFv3gY3aMH8mYHlbtr816H60iaWkXmCYZdlI2SUnKjQlM93A\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><o:p> <\/o:p><\/span>\u5982\u4e0b\u56fe\u6240\u793a\u662fDE\u7684\u7ed3\u679c\uff1a\u5c06\u6240\u6709\u7684\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u90fd\u8f93\u51fa\u4e3atxt\u6587\u4ef6\u3002<\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u63a5\u7740\u5c06 limma \u7ed3\u679c\u8868\u8f6c\u6362\u4e3a\u4e0e BinfTools \u5305\u51fd\u6570\u517c\u5bb9\u7684\u683c\u5f0f\uff0c\u7528\u706b\u5c71\u56fe\u663e\u793a\u663e\u8457\u654f\u611f\/\u62b5\u6297\u7684\u57fa\u56e0 (FDR < 0.05)\u3002<\/span><span style=\"font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"> <o:p> <\/o:p><\/span> <\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><o:page><\/o:page><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code>#\u5c06 limma \u7ed3\u679c\u8868\u8f6c\u6362\u4e3a\u4e0e BinfTools \u5305\u51fd\u6570\u517c\u5bb9\u7684\u683c\u5f0f<\/span><\/span><\/code><code>#'fixRows()' will set the rownames to just the HGNC symbol instead of the HGNC.ENTREZID format it currently is<\/span><\/span><\/code><code>bt_EC50<\/span><-fixRows(fromLimma(EC50_res), \"res\"<\/span>)<\/span><\/code><code>bt_EC502<\/span><-fixRows(fromLimma(EC50_res2), \"res\"<\/span>)<\/span><\/code><code>bt_EC50_YAP<\/span><-fixRows(fromLimma(EC50_res_YAP), \"res\"<\/span>)<\/span><\/code><code>bt_EC50_YAP2<\/span><-fixRows(fromLimma(EC50_res_YAP2), \"res\"<\/span>)<\/span><\/code><code>bt_EC50_ASCL1<\/span><-fixRows(fromLimma(EC50_res_ASCL1),\"res\"<\/span>)<\/span><\/code><code>bt_EC50_ND1<\/span><-fixRows(fromLimma(EC50_res_ND1),\"res\"<\/span>)<\/span><\/code><code> <\/span><\/code><code>#\u7528\u706b\u5c71\u56fe\u663e\u793a\u663e\u7740\u7684\u654f\u611f\/\u62b5\u6297\u57fa\u56e0 (FDR < 0.05)<\/span><\/span><\/code><code>#Save sensitizer(down\/negatively correlated)\/resistor(up\/positively correlated) genes<\/span><\/span><\/code><code>pdf<\/span>(\"\/results\/VolcanoPlots.pdf\"<\/span>)<\/span><\/code><code>EC_SCLC<\/span><-volcanoPlot(bt_EC50, \"ALL SCLC\"<\/span>, p=0.05, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>EC_SCLC2<\/span><-volcanoPlot(bt_EC502, \"ALL SCLC - no H196\"<\/span>, p=0.05, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>YAP_EC50<\/span><-volcanoPlot(bt_EC50_YAP, \"YAP1 High\"<\/span>, p=0.05, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>YAP_EC502<\/span><-volcanoPlot(bt_EC50_YAP2, \"YAP1 High - no H196\"<\/span>, pval=0.01, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>ASCL_EC50<\/span><-volcanoPlot(bt_EC50_ASCL1, \"ASCL1 High\"<\/span>, p=0.05, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>ND1_EC50<\/span><-volcanoPlot(bt_EC50_ND1, \"NEUROD1 High\"<\/span>, pval=0.01, FC=0, showNum=F, returnDEG=T)<\/span><\/code><code>dev<\/span>.off<\/span>()<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span> <img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016199\" data-ratio=\"1.030195381882771\" data-type=\"png\" data-w=\"563\" height=\"579 .545166015625\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"562 .0119018554688\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_qQtveUXbewgSgT39fA0iaLVzvs6qqQ.png?resize=562%2C579\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyRW9Dy8uSh5eVujLczluIOicm0VuqQtveUXbewgSgT39fA0iaLVzvs6qqQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u4ece\u706b\u5c71\u56fe\u4e2d\u53ef\u4ee5\u770b\u51fa\u56de\u5f52\u5206\u6790\u7ed3\u679c\uff0c\u5176\u4e2dx\u8f74\u8868\u793a\u5206\u914d\u7ed9\u6bcf\u4e2a\u57fa\u56e0\u7684\u56de\u5f52\u7cfb\u6570\uff0cy\u8f74\u8868\u793a\u663e\u8457\u6027\u3002\u84dd\u8272\u7a81\u51fa\u663e\u793a\u7684\u57fa\u56e0\u4ee3\u8868\u663e\u8457\u654f\u611f\u57fa\u56e0(\u8868\u8fbe\u4e0eEC50\u5448\u663e\u8457\u8d1f\u76f8\u5173;FDR < 0.05)\uff0c\u7ea2\u8272\u57fa\u56e0\u4ee3\u8868\u62b5\u6297\u57fa\u56e0(\u8868\u8fbe\u4e0eEC50\u663e\u8457\u6b63\u76f8\u5173;FDR < 0.05)\u3002\u9ed1\u8272\u865a\u7ebf\u4e3a\u663e\u8457\u6027\u9608\u503c(Padj < 0.05)\u3002<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;font-weight: bold;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u7ed8\u5236\u5b8c\u6210\u706b\u5c71\u56fe\u540e\uff0c\u518d\u8f93\u51fa\u7ef4\u6069\u56fe\u5e76\u8fd4\u56de\u91cd\u53e0\u57fa\u56e0\uff0c\u6700\u540e\u5c06\u91cd\u53e0\u5199\u51fa\u4e3a\u57fa\u56e0\u96c6\u6587\u4ef6\u3002<\/span><span style=\"font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-size: 16px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 1px;\"> <o:p> <\/o:p><\/span> <\/span><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><o:page><\/o:page><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"><\/span><\/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<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>#\u8f93\u51fa\u7ef4\u6069\u56fe\u5e76\u8fd4\u56de\u91cd\u53e0\u57fa\u56e0<\/span><\/span><\/code><code>pdf(\"\/results\/VennDiagrams.pdf\"<\/span>)<\/span><\/code><code>Sensitizers<-plotVenn(list<\/span>(SCLC=EC_SCLC$Down, YAP1=YAP_EC50$Down,<\/span><\/code><code> ASCL1=ASCL_EC50$Down, NEUROD1=ND1_EC50$Down),<\/span><\/code><code> title=\"Sensitizers\"<\/span>, retVals=T)<\/span><\/code><code> <\/span><\/code><code>Sensitizers2<-plotVenn(list<\/span>(SCLC=EC_SCLC2$Down, YAP1=YAP_EC502$Down,<\/span><\/code><code> ASCL1=ASCL_EC50$Down, NEUROD1=ND1_EC50$Down),<\/span><\/code><code> title=\"Sensitizers - no H196\"<\/span>, retVals=T)<\/span><\/code><code> <\/span><\/code><code>Resistors<-plotVenn(list<\/span>(SCLC=EC_SCLC$Up, YAP1=YAP_EC50$Up,<\/span><\/code><code> ASCL1=ASCL_EC50$Up, NEUROD1=ND1_EC50$Up),<\/span><\/code><code> title=\"Resistors\"<\/span>, retVals=T)<\/span><\/code><code>Resistors2<-plotVenn(list<\/span>(SCLC=EC_SCLC2$Up, YAP1=YAP_EC502$Up,<\/span><\/code><code> ASCL1=ASCL_EC50$Up, NEUROD1=ND1_EC50$Up),<\/span><\/code><code> title=\"Resistors - no H196\"<\/span>, retVals=T)<\/span><\/code><code>dev.off()<\/span><\/code><code> <\/span><\/code><code>#\u91cd\u547d\u540d\u91cd\u53e0\u90e8\u5206\uff0c\u4f7f\u5176\u66f4\u6e05\u6670<\/span><\/span><\/code><code>OLnames<-c(\"SCLC\"<\/span>,\"YAP1\"<\/span>,\"ASCL1\"<\/span>,\"NEUROD1\"<\/span>,\"SCLC_YAP1\"<\/span>, \"SCLC_ASCL1\"<\/span>,\"SCLC_NEUROD1\"<\/span>,<\/span><\/code><code> \"YAP1_ASCL1\"<\/span>,\"YAP1_NEUROD1\"<\/span>,\"ASCL1_NEUROD1\"<\/span>,\"SCLC_YAP1_ASCL1\"<\/span>,\"SCLC_YAP1_NEUROD1\"<\/span>,<\/span><\/code><code> \"SCLC_ASCL1_NEUROD1\"<\/span>,\"YAP1_ASCL1_NEUROD1\"<\/span>,\"All\"<\/span>)<\/span><\/code><code>names(Sensitizers)<-OLnames<\/span><\/code><code>names(Resistors)<-OLnames<\/span><\/code><code>names(Sensitizers2)<-OLnames<\/span><\/code><code>names(Resistors2)<-OLnames<\/span><\/code><code> <\/span><\/code><code>#\u5c06\u91cd\u53e0\u5199\u51fa\u4e3a\u57fa\u56e0\u96c6\u6587\u4ef6<\/span><\/span><\/code><code>dir.create(\"\/results\/gmts\/\"<\/span>)<\/span><\/code><code>write.gmt(Sensitizers, \"\/results\/gmts\/Sensitizer_Genes1.gmt\"<\/span>)<\/span><\/code><code>write.gmt(Sensitizers2, \"\/results\/gmts\/Sensitizer_Genes2.gmt\"<\/span>)<\/span><\/code><code>write.gmt(Resistors, \"\/results\/gmts\/Resistor_Genes1.gmt\"<\/span>)<\/span><\/code><code>write.gmt(Resistors2, \"\/results\/gmts\/Resistor_Genes2.gmt\"<\/span>) <\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\"> <\/span> <\/span><\/section>\n<section style=\"text-align: center;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016200\" data-ratio=\"0.36574074074074076\" data-type=\"png\" data-w=\"1080\" height=\"199 .47000122070312\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"545 .6099853515625\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_w60PaibQic76MbDARqZZFMsY5P49DQ.png?resize=545%2C199\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyRyfbm4iagk0DYX1rCp5A7zF3ERh0w60PaibQic76MbDARqZZFMsY5P49DQ\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/> <\/span><\/section>\n<section style=\"text-align: center;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;text-align: justify;caret-color: transparent;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100016201\" data-ratio=\"0.9596153846153846\" data-type=\"png\" data-w=\"520\" height=\"498 .8755798339844\" style=\"letter-spacing: 0.578px;white-space: normal;height: auto !important;\" width=\"519 .0758666992188\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_cp5sVJ5ZaqaYBtq29wuAich9iaVPAA.png?resize=519%2C498\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyN4YIVBeicZ0TpQB5pPiclyR63BdTBPfQDptNibonTp0ks6HZHXicp5sVJ5ZaqaYBtq29wuAich9iaVPAA\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/span><\/section>\n<section style=\"text-align: justify;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;text-align: justify;caret-color: transparent;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;\">\u5982\u56fe\u6240\u793a\uff0c\u7ef4\u6069\u56fe\u663e\u793a\u4e86\u4ece\u56db\u79cd\u56de\u5f52\u5206\u6790\u4e2d\u9274\u5b9a\u51fa\u7684\u654f\u611f\u57fa\u56e0(\u4e0a)\u548c\u62b5\u6297\u57fa\u56e0\uff08\u4e0b\uff09\u7684\u91cd\u53e0:\u6240\u6709SCLC\u7ec6\u80de\u7cfb\uff0c\u4ec5ascl1\u9ad8\u7ec6\u80de\u7cfb\uff0c\u4ec5TN\/ yap1\u9ad8\u7ec6\u80de\u7cfb\u548c\u4ec5neurod1\u9ad8\u7ec6\u80de\u7cfb\uff0c\u8fd9\u6837\u5c31\u6210\u529f\u627e\u5230\u4e86\u53ef\u80fd\u7684\u9776\u5411\u57fa\u56e0~<\/span> <\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section style=\"text-align: justify;margin-top: 8px;margin-bottom: 16px;line-height: 1.6em;\">\u5230\u8fd9\u4e00\u6b65\uff0c\u6211\u4eec\u5c31\u6210\u529f\u7684\u627e\u5230\u654f\u611f\u57fa\u56e0\u4e0e\u62b5\u6297\u57fa\u56e0\u4e86\uff0c\u53ef\u4ee5\u53d1\u73b0\uff0climma\u5206\u6790\u4f5c\u4e3a\u4e00\u79cd\u5e38\u7528\u7684\u5dee\u5f02\u5206\u6790\u7684\u65b9\u6cd5\uff0c\u5728\u9776\u5411\u6cbb\u7597\u65b9\u5411\u5bfb\u627e\u9776\u5411\u57fa\u56e0\u4e5f\u662f\u975e\u5e38\u4fbf\u5229\u7684\uff0c\u901a\u8fc7\u5bfc\u5165\u6570\u636e\uff0c\u6784\u5efa\u77e9\u9635\uff0c\u7ebf\u6027\u62df\u5408\uff0c\u6807\u6ce8\u5dee\u5f02\u57fa\u56e0\uff0c\u5373\u53ef\u627e\u51fa\u914d\u4f53\u76f8\u5173\u7684\u654f\u611f\u57fa\u56e0\u4e0e\u62b5\u6297\u57fa\u56e0\uff0c\u4ece\u800c\u4e3a\u8fdb\u4e00\u6b65\u7684\u9776\u5411\u6cbb\u7597\u63d0\u4f9b\u6307\u5bfc\u3002<\/span> <\/span><o:p style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 16px;font-weight: bold;letter-spacing: 1px;\"> <\/o:p><\/section>\n<section 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onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAz5wg6Ne6sYkannSE9NiatkcPh3icbKanJagacjU6LqJrGAL29N02aBaau07RufXeXRLmvAHsrFZxtw\/640?wx_fmt=jpeg&from=appmsg'\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-right: 0%;margin-left: 0%;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-end;padding-right: 2px;padding-left: 2px;\">\n<section style=\"margin: 10px 0% 2px;transform: translate3d(2px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"font-size: 16px;color: rgb(58, 66, 94);line-height: 1;letter-spacing: 5px;text-align: center;\">\n\u5f80\u671f\u56de\u987e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"height: 3px;background-color: 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style=\"border-color: rgb(62, 62, 62);border-style: none;padding: 0px;\" width=\"100.0000%\">\n<section>\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-right: 0%;margin-left: 0%;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;min-width: 10%;height: auto;flex: 0 0 auto;align-self: center;box-shadow: rgb(0, 0, 0) 0px 0px 0px;\">\n<section style=\"font-size: 19px;color: rgb(95, 156, 239);line-height: 1;\" powered-by=\"xiumi.us\">\n01<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;flex: 100 100 0%;align-self: center;height: auto;\">\n<section style=\"color: rgb(140, 140, 140);\" powered-by=\"xiumi.us\">\n\uff5c<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247497780&idx=2&sn=7eee90af6f387e4153bba13028e545a1&chksm=cf7f68f1f808e1e7dfb3a0597ef442e5c6e700ecf6ee5a035c766a4c7486c12eabd0ab218ea6&scene=21#wechat_redirect\" textvalue=\"1024G\u5b58\u50a8\u7684\u751f\u4fe1\u670d\u52a1\u5668\uff0c\u4e24\u4eba\u6210\u56e2\uff0c1\u4eba\u514d\u5355\uff01\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">1024G\u5b58\u50a8\u7684\u751f\u4fe1\u670d\u52a1\u5668\uff0c\u4e24\u4eba\u6210\u56e2\uff0c1\u4eba\u514d\u5355\uff01<\/a><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 5px 0%;\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(224, 224, 224);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/td>\n<\/tr>\n<tr 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