{"id":27241,"date":"2024-01-31T16:49:41","date_gmt":"2024-01-31T08:49:41","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27241"},"modified":"2024-01-31T16:49:42","modified_gmt":"2024-01-31T08:49:42","slug":"%e7%94%a8r%e8%af%ad%e8%a8%80%e5%8c%85gsva%ef%bc%8c%e5%b0%86%e6%95%b0%e6%8d%ae%e8%bd%ac%e5%8c%96%e4%b8%ba%e6%a0%b7%e6%9c%ac%e4%b8%8e%e5%9f%ba%e5%9b%a0%e5%85%b3%e8%81%94%e7%9f%a9%e9%98%b5%ef%bc%8c","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27241","title":{"rendered":"\u7528R\u8bed\u8a00\u5305GSVA\uff0c\u5c06\u6570\u636e\u8f6c\u5316\u4e3a\u6837\u672c\u4e0e\u57fa\u56e0\u5173\u8054\u77e9\u9635\uff0c\u5e2e\u52a9\u4f60\u66f4\u76f4\u89c2\u4e14\u9ad8\u6548\u7684\u5206\u6790"},"content":{"rendered":"

\u5728\u751f\u7269\u5b66\u7814\u7a76\u4e2d\uff0c\u9ad8\u7ef4\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u5206\u6790\u662f\u4e00\u9879\u91cd\u8981\u4e14\u6311\u6218\u6027\u7684\u4efb\u52a1\u3002\u4e3a\u4e86\u63ed\u793a\u57fa\u56e0\u8868\u8fbe\u5728\u4e0d\u540c\u751f\u7269\u5b66\u8fc7\u7a0b\u4e2d\u7684\u6f5c\u5728\u529f\u80fd\u548c\u751f\u7269\u5b66\u610f\u4e49\uff0c\u7814\u7a76\u4eba\u5458\u9700\u8981\u4f7f\u7528\u4e13\u4e1a\u7684\u751f\u7269\u4fe1\u606f\u5b66\u5de5\u5177\u548c\u65b9\u6cd5\u3002\u5176\u4e2d\uff0cGSVA\uff08Gene Set Variation Analysis\uff09\u662f\u4e00\u79cd\u5e38\u7528\u7684R\u8bed\u8a00\u5305\uff0c\u5b83\u88ab\u5e7f\u6cdb\u5e94\u7528\u4e8e\u751f\u7269\u5b66\u7814\u7a76\uff0c\u5c24\u5176\u662f\u8f6c\u5f55\u7ec4\u5b66\u9886\u57df\u3002<\/p>\n

GSVA\u662f\u4e00\u79cd\u65e0\u53c2\u6570\u65b9\u6cd5\uff0c\u7528\u4e8e\u5bf9\u57fa\u56e0\u96c6\uff08Gene Set\uff09\u5728\u6837\u672c\u4e2d\u7684\u8868\u8fbe\u6a21\u5f0f\u8fdb\u884c\u63a8\u65ad\u3002\u5728\u8f6c\u5f55\u7ec4\u6570\u636e\u5206\u6790\u4e2d\uff0c\u4e00\u4e2a\u57fa\u56e0\u96c6\u662f\u6307\u4e00\u7ec4\u5728\u7279\u5b9a\u751f\u7269\u8fc7\u7a0b\u3001\u751f\u7406\u529f\u80fd\u6216\u75be\u75c5\u72b6\u6001\u4e2d\u5171\u540c\u53c2\u4e0e\u7684\u57fa\u56e0\u3002\u8fd9\u4e9b\u57fa\u56e0\u96c6\u901a\u5e38\u6765\u81ea\u516c\u5171\u6570\u636e\u5e93\uff0c\u5982\u57fa\u56e0\u672c\u4f53\uff08Gene Ontology\uff09\u3001KEGG\u901a\u8def\u3001\u751f\u7269\u5b66\u8fc7\u7a0b\u7b49\u3002GSVA\u7684\u6838\u5fc3\u601d\u60f3\u662f\u5c06\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u8f6c\u6362\u4e3a\u6837\u672c\u548c\u57fa\u56e0\u96c6\u4e4b\u95f4\u7684\u5173\u8054\u77e9\u9635\uff0c\u4ece\u800c\u4e3a\u540e\u7eed\u7684\u751f\u7269\u5b66\u89e3\u91ca\u63d0\u4f9b\u4fbf\u5229\u3002<\/p>\n

GSVA\u901a\u8fc7\u5bf9\u6bcf\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u79ef\u5206\uff0c\u5c06\u8fde\u7eed\u7684\u57fa\u56e0\u8868\u8fbe\u8c31\u8f6c\u5316\u4e3a\u79bb\u6563\u7684\u6837\u672c\u548c\u57fa\u56e0\u96c6\u7684\u5173\u8054\u7a0b\u5ea6\u3002\u8fd9\u79cd\u8f6c\u6362\u6d88\u9664\u4e86\u5bf9\u57fa\u56e0\u8868\u8fbe\u91cf\u8fdb\u884c\u622a\u65ad\u6216\u4e8c\u503c\u5316\u5904\u7406\u7684\u9700\u8981\uff0c\u4ece\u800c\u907f\u514d\u4fe1\u606f\u4e22\u5931\u3002\u901a\u8fc7\u5e94\u7528\u6838\u5bc6\u5ea6\u4f30\u8ba1\u65b9\u6cd5\uff0cGSVA\u8fd8\u53ef\u4ee5\u4f30\u7b97\u57fa\u56e0\u96c6\u7684\u8868\u8fbe\u5206\u5e03\uff0c\u4ece\u800c\u63d0\u4f9b\u5173\u4e8e\u57fa\u56e0\u96c6\u5728\u4e0d\u540c\u6837\u672c\u4e2d\u7684\u8868\u8fbe\u5dee\u5f02\u7a0b\u5ea6\u7684\u4fe1\u606f\u3002<\/p>\n

\u8981\u4f7f\u7528GSVA\u5305\uff0c\u53ef\u4ee5\u5728R\u4e2d\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/p>\n

> install.packages(“GSVA”) #\u5b89\u88c5GSVA\u8bed\u8a00\u5305<\/p>\n

> library(GSVA) #\u52a0\u8f7d\u8bed\u8a00\u5305<\/p>\n

GSVA\u7684\u5e94\u7528\u5728\u751f\u7269\u5b66\u7814\u7a76\u4e2d\u5177\u6709\u5e7f\u6cdb\u7684\u610f\u4e49\u3002\u9996\u5148\uff0cGSVA\u53ef\u4ee5\u7528\u4e8e\u5bcc\u96c6\u5206\u6790\uff0c\u5373\u786e\u5b9a\u5728\u4e0d\u540c\u751f\u7269\u5b66\u6761\u4ef6\u4e0b\u7279\u5b9a\u57fa\u56e0\u96c6\u7684\u663e\u8457\u6027\u5bcc\u96c6\u60c5\u51b5\u3002\u8fd9\u6709\u52a9\u4e8e\u8bc6\u522b\u4e0e\u7279\u5b9a\u751f\u7269\u5b66\u8fc7\u7a0b\u6216\u75be\u75c5\u76f8\u5173\u7684\u57fa\u56e0\u96c6\uff0c\u4e3a\u540e\u7eed\u7814\u7a76\u63d0\u4f9b\u91cd\u8981\u7ebf\u7d22\u3002\u5176\u6b21\uff0cGSVA\u53ef\u4ee5\u7528\u4e8e\u5206\u7c7b\u5668\u6784\u5efa\uff0c\u901a\u8fc7\u57fa\u56e0\u96c6\u7684\u8868\u8fbe\u6a21\u5f0f\u6765\u533a\u5206\u4e0d\u540c\u751f\u7269\u5b66\u72b6\u6001\u6216\u9884\u6d4b\u6837\u672c\u7684\u751f\u7269\u5b66\u7279\u6027\u3002\u8fd9\u5728\u764c\u75c7\u5206\u7c7b\u548c\u9884\u540e\u8bc4\u4f30\u7b49\u7814\u7a76\u4e2d\u5c24\u4e3a\u91cd\u8981\u3002\u6b64\u5916\uff0cGSVA\u8fd8\u53ef\u4ee5\u7528\u4e8e\u6316\u6398\u8f6c\u5f55\u7ec4\u6570\u636e\u4e2d\u7684\u6f5c\u5728\u751f\u7269\u5b66\u6a21\u5f0f\uff0c\u5982\u57fa\u56e0\u8c03\u63a7\u7f51\u7edc\u548c\u4fe1\u53f7\u901a\u8def\u3002<\/p>\n

\u793a\u4f8b\uff1a<\/p>\n

# \u5bfc\u5165\u6240\u9700\u5305<\/p>\n

> install.packages(“GSVA”)<\/p>\n

> install.packages(“limma”)<\/p>\n

> library(GSVA)<\/p>\n

> library(limma)<\/p>\n

# \u5bfc\u5165\u793a\u4f8b\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff0c\u8fd9\u91cc\u5047\u8bbe\u6709\u4e00\u4e2a\u57fa\u56e0\u8868\u8fbe\u77e9\u9635data_matrix\uff0c\u884c\u8868\u793a\u57fa\u56e0\uff0c\u5217\u8868\u793a\u6837\u672c<\/p>\n

# \u5047\u8bbe\u8fd8\u6709\u4e00\u4e2a\u57fa\u56e0\u96c6\u5217\u8868gene_sets_list\uff0c\u5305\u542b\u82e5\u5e72\u4e2a\u57fa\u56e0\u96c6\uff0c\u6bcf\u4e2a\u57fa\u56e0\u96c6\u662f\u4e00\u4e2a\u5b57\u7b26\u5411\u91cf\uff0c\u8868\u793a\u57fa\u56e0\u7684Symbol\u6216Entrez ID<\/p>\n

# \u5047\u8bbe\u8fd8\u6709\u4e00\u4e2a\u5bf9\u5e94\u6837\u672c\u7684\u7c7b\u522b\u6807\u7b7egroup_labels\uff0c\u7528\u4e8e\u533a\u5206\u4e0d\u540c\u751f\u7269\u5b66\u72b6\u6001\u6216\u6761\u4ef6<\/p>\n

# \u751f\u6210\u793a\u4f8b\u6570\u636e\uff0c\u8fd9\u91cc\u4f7f\u7528R\u7684\u5185\u7f6e\u6570\u636e\u96c6iris<\/p>\n

> data_matrix <- as.matrix(iris[, 1:4])<\/p>\n

> gene_sets_list <- list(<\/p>\n

+ upregulated_genes = c(“geneA”, “geneB”, “geneC”),<\/p>\n

+ downregulated_genes = c(“geneX”, “geneY”, “geneZ”)<\/p>\n

+)<\/p>\n

> group_labels <- factor(iris$Species)<\/p>\n

# \u8fd0\u884cGSVA\u7b97\u6cd5<\/p>\n

> gsva_result <- gsva(data_matrix, gene_sets_list, method = “gsva”, mx.diff = FALSE)<\/p>\n

# \u53ef\u89c6\u5316\u7ed3\u679c<\/p>\n

# \u53ef\u4ee5\u4f7f\u7528heatmap\u5c55\u793a\u57fa\u56e0\u96c6\u5728\u6837\u672c\u4e2d\u7684\u8868\u8fbe\u6a21\u5f0f<\/p>\n

> heatmap(gsva_result$es.obs, Rowv = NA, Colv = NA, col = colorRampPalette(c(“blue”, “white”, “red”))(100))<\/p>\n

\"Screenshot<\/p>\n

# \u4f7f\u7528boxplot\u6216violinplot\u5c55\u793a\u4e0d\u540c\u57fa\u56e0\u96c6\u5728\u4e0d\u540c\u751f\u7269\u5b66\u6761\u4ef6\u4e0b\u7684\u5f97\u5206\u5206\u5e03<\/p>\n

> boxplot(gsva_result$es.obs ~ group_labels, col = rainbow(nlevels(group_labels)))<\/p>\n

\"12859_2012_Article_5762_Fig4_HTML\"<\/p>\n

# \u6216\u8005\u4f7f\u7528violinplot<\/p>\n

> vioplot(gsva_result$es.obs ~ group_labels, col = rainbow(nlevels(group_labels)))<\/p>\n

\"violin-plot-jitter-ggplot2\"<\/p>\n

# \u4f7f\u7528PCA\u6216t-SNE\u7b49\u964d\u7ef4\u65b9\u6cd5\uff0c\u5c06\u6837\u672c\u6295\u5f71\u5230\u4f4e\u7ef4\u7a7a\u95f4\uff0c\u5e76\u6839\u636eGSVA\u5f97\u5206\u8fdb\u884c\u7740\u8272<\/p>\n

> pca_result <- prcomp(t(gsva_result$es.obs))<\/p>\n

> plot(pca_result$x[, 1], pca_result$x[, 2], col = group_labels)<\/p>\n

\"15-Figure7-1\"<\/p>\n

\u8fd9\u4e2a\u7b80\u5355\u7684\u793a\u4f8b\u5c55\u793a\u4e86GSVA\u5305\u7684\u57fa\u672c\u7528\u6cd5\u3002\u6211\u4eec\u5bfc\u5165\u4e86\u4e00\u4e2a\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u548c\u4e00\u4e9b\u57fa\u56e0\u96c6\uff0c\u5e76\u6839\u636e\u8fd9\u4e9b\u57fa\u56e0\u96c6\u5728\u6837\u672c\u4e2d\u7684\u8868\u8fbe\u6a21\u5f0f\u8fdb\u884c\u4e86GSVA\u5206\u6790\u3002\u7136\u540e\uff0c\u901a\u8fc7\u53ef\u89c6\u5316\u56fe\u8868\uff08heatmap\u3001boxplot\u3001violinplot\u548cPCA\u56fe\uff09\u5c55\u793a\u4e86\u7ed3\u679c\u3002\u5728\u5b9e\u9645\u5e94\u7528\u4e2d\uff0c\u53ef\u4ee5\u6839\u636e\u5177\u4f53\u7684\u751f\u7269\u5b66\u95ee\u9898\u548c\u6570\u636e\u7ed3\u6784\u8fdb\u884c\u66f4\u590d\u6742\u7684GSVA\u5206\u6790\u548c\u53ef\u89c6\u5316\u3002<\/p>\n

\u4ee5\u4e0a\u5c31\u662f\u5bf9R\u8bed\u8a00\u5305GSVA\u7684\u7b80\u5355\u4ecb\u7ecd\u5566\uff0cGSVA\u4f5c\u4e3a\u4e00\u79cd\u65e0\u53c2\u6570\u7684\u57fa\u56e0\u96c6\u5206\u6790\u5de5\u5177\uff0c\u5728\u751f\u7269\u5b66\u7814\u7a76\u4e2d\u53d1\u6325\u7740\u91cd\u8981\u4f5c\u7528\u3002\u901a\u8fc7\u5c06\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8f6c\u6362\u4e3a\u6837\u672c\u548c\u57fa\u56e0\u96c6\u4e4b\u95f4\u7684\u5173\u8054\u77e9\u9635\uff0cGSVA\u4e3a\u751f\u7269\u5b66\u5bb6\u63d0\u4f9b\u4e86\u4e00\u79cd\u76f4\u89c2\u3001\u9ad8\u6548\u7684\u5206\u6790\u624b\u6bb5\uff0c\u6709\u52a9\u4e8e\u63ed\u793a\u57fa\u56e0\u96c6\u5728\u4e0d\u540c\u751f\u7269\u5b66\u8fc7\u7a0b\u4e2d\u7684\u6f5c\u5728\u529f\u80fd\u548c\u751f\u7269\u5b66\u610f\u4e49\u3002\u672a\u6765\u968f\u7740\u6280\u672f\u7684\u4e0d\u65ad\u53d1\u5c55\uff0cGSVA\u5c06\u7ee7\u7eed\u5728\u751f\u7269\u5b66\u7814\u7a76\u4e2d\u53d1\u6325\u91cd\u8981\u4f5c\u7528\uff0c\u5e76\u4e3a\u6211\u4eec\u6df1\u5165\u7406\u89e3\u57fa\u56e0\u8868\u8fbe\u8c03\u63a7\u548c\u751f\u7269\u5b66\u8fc7\u7a0b\u7684\u5965\u79d8\u63d0\u4f9b\u6709\u529b\u652f\u6301\u3002<\/p>\n

\u5c0f\u4f19\u4f34\u4eec\uff0c\u4eca\u5929\u6709\u6ca1\u6709\u5b66\u5230\u65b0\u77e5\u8bc6\u5462\uff0c\u60f3\u8981\u7ee7\u7eed\u4e86\u89e3R\u8bed\u8a00\u5185\u5bb9\u53ef\u4ee5\u6301\u7eed\u5173\u6ce8\u5c0f\u679c\u54e6\uff5e\uff5e\u6216\u8005\u4e5f\u53ef\u4ee5\u5173\u6ce8\u6211\u4eec\u7684\u5b98\u7f51\u4e5f\u4f1a\u6301\u7eed\u66f4\u65b0\u7684\u54e6\uff5e http:\/\/www.biocloudservice.com\/home.html<\/a><\/p>\n

References:<\/p>\n

    \n
  1. https:\/\/www.google.com\/url?sa=i&url=https%3A%2F%2Fwww.biostars.org%2Fp%2F277664%2F&psig=AOvVaw35RMgFKfm_Tz9dJdnKa7Ig&ust=1691471195197000&source=images&cd=vfe&opi=89978449&ved=0CBAQjRxqFwoTCOi3_6_jyYADFQAAAAAdAAAAABAR<\/a><\/li>\n
  2. https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-7\/figures\/4<\/a><\/li>\n
  3. https:\/\/www.google.com\/url?sa=i&url=https%3A%2F%2Fr-charts.com%2Fdistribution%2Fviolin-plot-points-ggplot2%2F&psig=AOvVaw1YO7RId_KFGME_vX6xNsc6&ust=1691471467596000&source=images&cd=vfe&opi=89978449&ved=0CBAQjRxqFwoTCLik1bDkyYADFQAAAAAdAAAAABAJ<\/a><\/li>\n
  4. https:\/\/www.google.com\/url?sa=i&url=https%3A%2F%2Fwww.semanticscholar.org%2Fpaper%2FGSVA%253A-The-Gene-Set-Variation-Analysis-package-for-Sonja-Castelo%2Fef4971c3d7185ef9be4778b9d0807f21276366e8%2Ffigure%2F6&psig=AOvVaw3qe6dwq_va1M7x89N4CJ52&ust=1691471632107000&source=images&cd=vfe&opi=89978449&ved=0CBAQjRxqFwoTCIC__v7kyYADFQAAAAAdAAAAABAJ<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    \u5728\u751f\u7269\u5b66\u7814\u7a76\u4e2d\uff0c\u9ad8\u7ef4\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u5206\u6790\u662f\u4e00\u9879\u91cd\u8981\u4e14\u6311\u6218\u6027\u7684\u4efb\u52a1\u3002\u4e3a\u4e86\u63ed\u793a\u57fa\u56e0\u8868\u8fbe\u5728\u4e0d\u540c\u751f\u7269\u5b66\u8fc7\u7a0b\u4e2d\u7684\u6f5c\u5728\u529f\u80fd\u548c […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27241"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=27241"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27241\/revisions"}],"predecessor-version":[{"id":27246,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27241\/revisions\/27246"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=27241"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=27241"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=27241"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}