![\"\u56fe\u7247\u5305\u542b](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-55.png?resize=580%2C322\")
<\/p>\nHello\uff0c\u5404\u4f4d\u5c0f\u4f19\u4f34\u5927\u5bb6\u597d\u54e6\uff0c\u5f88\u9ad8\u5174\u53c8\u5230\u5206\u4eab\u77e5\u8bc6\u7684\u65f6\u95f4\u5566\uff01<\/p>\n
\u4f17\u6240\u5468\u77e5\uff0c\u8f6c\u5f55\u7ec4\u662f\u751f\u7269\u5b66\u9886\u57df\u4e2d\u4e00\u79cd\u7814\u7a76\u57fa\u56e0\u8868\u8fbe\u7684\u65b9\u6cd5\uff0c\u662f\u6307\u57fa\u56e0\u4e2d\u7684\u4fe1\u606f\u88ab\u8f6c\u5f55\u6210RNA\uff0c\u5e76\u5728\u968f\u540e\u7ffb\u8bd1\u6210\u86cb\u767d\u8d28\u7684\u8fc7\u7a0b\u3002\u8f6c\u5f55\u7ec4\u5b66\u80fd\u5e2e\u52a9\u5927\u5bb6\u7406\u89e3\u7ec6\u80de\u6216\u7ec4\u7ec7\u4e2d\u6240\u6709\u57fa\u56e0\u7684\u603b\u4f53\u8f6c\u5f55\u60c5\u51b5\uff0c\u4ece\u800c\u5728\u63ed\u793a\u57fa\u56e0\u7684\u8c03\u63a7\u3001\u53d1\u73b0\u65b0\u7684RNA\u5206\u5b50\u4ee5\u53ca\u7406\u89e3\u57fa\u56e0\u5728\u4e0d\u540c\u751f\u7406\u548c\u75c5\u7406\u6761\u4ef6\u4e0b\u7684\u8868\u8fbe\u53d8\u5316\u6709\u6240\u5e2e\u52a9\u3002<\/p>\n
\u9488\u5bf9\u6709\u53c2\u8f6c\u5f55\u7ec4\uff0c\u5927\u5bb6\u7684\u786e\u53ef\u4ee5\u4f7f\u7528clusterProfiler\u5305\u8fdb\u884cGO\u5bcc\u96c6\u5206\u6790\uff0c\u53ea\u9700\u8981\u83b7\u5f97\u4f60\u60f3\u5bcc\u96c6\u5206\u6790\u7684\u57fa\u56e0\u540d\u79f0\u5c31OK\u4e86\u3002\u4f46\u5982\u679c\u662f\u65e0\u53c2\u8f6c\u5f55\u7ec4\u5462\uff0c\u8be5\u600e\u4e48\u529e\u5462\uff1f\u54b1\u4eec\u6ca1\u6709\u5df2\u7ecf\u786e\u5b9a\u7684gene symbol\uff0c\u53ea\u662f\u62e5\u6709\u516c\u53f8\u7ed9\u51fa\u7684\u7ec4\u88c5\u57fa\u56e0\u7684\u540d\u79f0\uff0c\u8fd9\u5e76\u4e0d\u80fd\u5728\u6570\u636e\u5e93\u4e2d\u88ab\u8bc6\u522b\uff0c\u6240\u4ee5\u6211\u4eec\u53ea\u80fd\u901a\u8fc7\u672c\u5730\u5efa\u5e93\u7684\u65b9\u6cd5\uff0c\u6765\u8fdb\u884c\u65e0\u53c2\u8f6c\u5f55\u7ec4\u7684\u5bcc\u96c6\u5206\u6790\u4e86\u3002<\/p>\n
\u6211\u4eec\u672c\u5730\u5efa\u5e93\u7684\u914d\u7f6e\u6587\u4ef6\u6709\u4e24\u4e2a\uff0c\u4e00\u4e2a\u662f\u5305\u542b\u57fa\u56e0ID\u548c\u57fa\u56e0\u6ce8\u91ca\u7684gene_info\u6587\u4ef6\uff0c\u4e00\u4e2a\u662f\u5305\u542b\u57fa\u56e0ID\u548cGO\u53f7\u53caEVIDENCE\u884c\u7684gene2go\u6587\u4ef6\u3002<\/p>\n
\u54b1\u4eec\u4eca\u5929\u6240\u7528\u6570\u636e\u8f83\u5927\uff0c\u5c0f\u679c\u63a8\u8350\u5927\u5bb6\u4f7f\u7528\u670d\u52a1\u5668\u8fdb\u884c\u5206\u6790\uff0c\u5982\u679c\u5404\u4f4d\u5c0f\u4f19\u4f34\u6ca1\u6709\u670d\u52a1\u5668\u7684\u8bdd\uff0c\u53ef\u4ee5\u8054\u7cfb\u5c0f\u679c\u8fdb\u884c\u79df\u8d41\u54e6~<\/p>\n
\u73b0\u5728\u54b1\u4eec\u5c31\u8fdb\u884c\u4e24\u4e2a\u914d\u7f6e\u6587\u4ef6\u7684\u5236\u4f5c\u5427\uff01\u53e6\u5916\u63d0\u4e00\u53e5\uff0c\u4eca\u5929\u4f7f\u7528\u7684\u6570\u636e\u662f\u7ecf\u8fc7eggNOG\u6ce8\u91ca\u540e\u7684\u6570\u636e\uff0c\u5927\u5bb6\u53ef\u4ee5\u53c2\u7167\u6700\u540e\u7684\u8f93\u51fa\u7ed3\u679c\uff0c\u5bf9\u81ea\u5df1\u7684\u65e0\u53c2\u8f6c\u5f55\u7ec4\u6570\u636e\u8fdb\u884c\u5904\u7406\u54e6~<\/p>\n
#\u8c03\u7528\u5305<\/p>\n
library(clusterProfiler)<\/p>\n
library(pheatmap)<\/p>\n
library(readr)<\/p>\n
library(tidyverse)<\/p>\n
library(org.Hs.eg.db)<\/p>\n
library(pathview)<\/p>\n
#\u5dee\u5f02\u5bcc\u96c6\u5206\u6790\u603b\u6570<\/p>\n
de_result <- read_delim(‘\u7ed3\u679c\u6587\u4ef6.tsv’)<\/p>\n
de_result<\/p>\n
<\/p>\n
#eggnog\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u7b5b\u9009<\/p>\n
emapper <- read_delim(‘query_seqs.fa.emapper.annotations’,<\/p>\n
‘\\t’,escape_double = FALSE,col_names = FALSE,<\/p>\n
comment = “#”,trim_ws = TRUE) %>%<\/p>\n
dplyr::select(GID = X1,<\/p>\n
Gene_symbol = X6,<\/p>\n
GO = X7,<\/p>\n
KO = X9,<\/p>\n
Pathway = X10,<\/p>\n
OG = X21,<\/p>\n
Gene_Name = X22)<\/p>\n
emapper<\/p>\n
![\"\u6587\u672c\n\n\u4e2d\u5ea6\u53ef\u4fe1\u5ea6\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-56.png?resize=640%2C167\")
<\/p>\n
#\u7b5b\u9009\u8981\u5bcc\u96c6\u57fa\u56e0<\/p>\n
gene <- filter(de_result,abs(log2FoldChange) > 2 & padj < 0.01) %>%<\/p>\n
pull(id)<\/p>\n
#\u5c06\u6240\u6709\u57fa\u56e0\u7684log2<\/sub>FC\u4ee5\u57fa\u56e0\u540d\u4e3a\u540d\u79f0\u8f6c\u5316\u6210\u5411\u91cf<\/p>\n #\u57fa\u56e0\u5dee\u5f02\u7684\u5411\u91cf<\/p>\n genelist <- de_result$log2FoldChange<\/p>\n names(genelist) <- de_result$id<\/p>\n genelist <- sort(genelist,decreasing = T)<\/p>\n #\u6784\u5efa\u672c\u5730\u5e93<\/p>\n #\u63d0\u53d6\u57fa\u56e0\u4fe1\u606f<\/p>\n gene_info <- dplyr::select(emapper, GID , Gene_Name) %>%<\/p>\n dplyr::filter(!is.na(Gene_Name))<\/p>\n gene_info<\/p>\n #\u63d0\u53d6go\u4fe1\u606f<\/p>\n gene2go <- dplyr::select(emapper,GID,GO) %>%<\/p>\n separate_rows(GO,sep = ‘,’,convert = F) %>%<\/p>\n filter(!is.na(GO)) %>%<\/p>\n mutate(EVIDENCE = ‘IEA’)<\/p>\n gene2go<\/p>\n setwd(‘C:\/Users\/10395\/Desktop\/’) #\u751a\u81f3\u5305\u7684\u5b89\u88c5\u8def\u5f84<\/p>\n #\u6784\u5efa\u5305<\/p>\n AnnotationForge::makeOrgPackage(gene_info = gene_info,<\/p>\n go = gene2go,<\/p>\n maintainer = ‘xiaoguo <pingguo @genek.tv>’,<\/p>\n author = ‘xiaoguo’,<\/p>\n outputDir = ‘.\/’,<\/p>\n tax_id = 0000,<\/p>\n genus = ‘X’,<\/p>\n species = ‘iaoguo’,<\/p>\n goTable = ‘go’,<\/p>\n version = ‘1.0’)<\/p>\n \u6b64\u65f6\u5728\u684c\u9762\u4e0a\u4f1a\u751f\u6210\u8fd9\u4e2a\u6587\u4ef6\u5939\uff0c\u7136\u540e\u6211\u4eec\u518d\u5bf9\u8be5\u6587\u4ef6\u5939\u8fdb\u884c\u6253\u5305<\/p>\n #\u6253\u5305<\/p>\n pkgbuild::build(‘.\/org.Xiaoguo.eg.db’,dest_path = “C:\/Users\/10395\/Desktop”)<\/p>\n \u968f\u7740\u6253\u5305\u7684\u7ed3\u675f\uff0c\u4f60\u6240\u9009\u7684\u6587\u4ef6\u5939\u5185\u4f1a\u751f\u6210\u4ee5\u4e0a\u7684\u538b\u7f29\u6587\u4ef6\uff0c\u65e2\u662f\u672c\u5730\u7684\u5b89\u88c5R\u5305<\/p>\n #\u65b0\u5efa\u6587\u4ef6\u5939<\/p>\n dir.create(‘R_Library’,recursive =T)<\/p>\n #\u5b89\u88c5\u5305<\/p>\n install.packages(‘ C:\/Users\/10395\/Desktop\/org.Xiaoguo.eg.db_1.0.tar.gz’,<\/p>\n repos = NULL,#\u672c\u5730\u5b89\u88c5<\/p>\n lib = ‘R_Library’) #\u5b89\u88c5\u6587\u4ef6\u5939<\/p>\n #\u52a0\u8f7d\u5305<\/p>\n library(org.Xiaoguo.eg.db_1.0.tar.gz, lib = ‘R_Library’)<\/p>\n #\u5bcc\u96c6\u5206\u6790<\/p>\n de_ego <- enrichGO(gene = gene,<\/p>\n OrgDb = org.Xiaoguo.eg.db,<\/p>\n keyType = ‘GID’,<\/p>\n ont = ‘BP’,<\/p>\n qvalueCutoff = 0.05,<\/p>\n pvalueCutoff = 0.05)<\/p>\n #\u5c06\u7ed3\u679c\u8f6c\u4e3a\u6570\u636e\u6846\u6a21\u5f0f<\/p>\n de_ego_df <- as.data.frame(de_ego)<\/p>\n head(de_ego_df)<\/p>\n #\u53ef\u89c6\u5316<\/p>\n P1 <- barplot(de_ego,showCategory = 10)<\/p>\n P1<\/p>\n P2 <- enrichplot::dotplot(de_ego,showCategory = 10)<\/p>\n P2<\/p>\n P3 <- cnetplot(de_ego,<\/p>\n foldChange = genelist,<\/p>\n showCategory = 5,<\/p>\n node_label = ‘all’ ,#category, gene all none<\/p>\n circular = TRUE,<\/p>\n colorEdge = TRUE)<\/p>\n P3<\/p>\n \u597d\u5566\uff0c\u4ee5\u4e0a\u5c31\u662f\u54b1\u4eec\u65e0\u53c2\u8f6c\u5f55\u7ec4\u4ee5\u53ca\u88abeggNOG\u6ce8\u91ca\u6587\u4ef6\u7684\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u54e6\u3002\u5176\u5b9e\u4ece\u6b65\u9aa4\u6765\u770b\uff0c\u7684\u786e\u4e0d\u662f\u5f88\u96be\uff0c\u4e5f\u4fbf\u4e8e\u7406\u89e3\uff0c\u6211\u4eec\u53ea\u9700\u8981\u901a\u8fc7\u5df2\u6709\u6587\u4ef6\u5c06\u4e24\u4e2a\u914d\u7f6e\u6587\u4ef6\u505a\u597d\u5c31OK\u4e86\u3002\u4f46\u662f\uff0c\u5728\u8fd9\u4e2a\u8fc7\u7a0b\u4e2d\u5927\u5bb6\u4e00\u5b9a\u8981\u6ce8\u610f\u4e24\u4e2a\u4e8b\u60c5\uff0c\u5373\u6211\u4eec\u914d\u7f6e\u6587\u4ef6\u7684\u8868\u5934\u4e00\u5b9a\u8981\u6309\u7167\u6211\u6240\u5199\u7684\u6765\u547d\u540d\uff0c\u56e0\u4e3a\u5728\u8fd9\u4e2a\u5e95\u5c42\u903b\u8f91\u4e0a\uff0c\u5efa\u5e93\u7684\u5305\u53ea\u8ba4\u4ee5\u8be5\u540d\u5b57\u547d\u540d\u7684\u5217\uff1b\u53e6\u5916\u5c31\u662f\u7684\u786e\u6709\u7684\u6570\u636e\u4e0d\u80fd\u88ab\u8f6c\u6362\u6210\u6570\u636e\u6846\u683c\u5f0f\u6216\u8f6c\u6362\u7684\u8fc7\u7a0b\u4e2d\u4ee5NULL\u7ed3\u675f\u8fdb\u7a0b\uff0c\u8fd9\u662f\u56e0\u4e3a\u683c\u5f0f\u95ee\u9898\uff0c\u8fd9\u65f6\u5019\u6211\u4eec\u9700\u8981\u5bf9\u4ed6\u8fdb\u884c\u53e6\u5916\u4e00\u79cd\u5904\u7406\u2014\u7528data.frame\u51fd\u6570\u81ea\u5df1\u62fc\u5efa\u6570\u636e\u6846\u5373\u7ed3\u679c\u6587\u4ef6\uff1a<\/p>\n result <- data.frame(de_ego@result[[“ID”]],<\/p>\n de_ego@result[[“Description”]],<\/p>\n de_ego@result[[“GeneRatio”]],<\/p>\n de_ego@result[[“BgRatio”]],<\/p>\n de_ego@result[[“pvalue”]],de_ego@result[[“p.adjust”]],<\/p>\n de_ego@result[[“qvalue”]],<\/p>\n de_ego@result[[“geneID”]],de_ego@result[[“Count”]])<\/p>\n \u8fd9\u6837\u7684\u8bdd\u4e5f\u4f1a\u751f\u6210\u548c\u4e0a\u8ff0de_ego_df\u76f8\u540c\u7684\u6570\u636e\u6846\u7ed3\u679c\u54e6\uff0c\u4e5f\u4fdd\u8bc1\u4e86\u5404\u4f4d\u5c0f\u4f19\u4f34\u4eec\u5fd9\u788c\u4e86\u534a\u5929\u7684\u6210\u679c\u4e0d\u4f1a\u4ed8\u4e4b\u4e1c\u6d41\u3002<\/p>\n \u53e6\u5916\uff0c\u5982\u679c\u5404\u4f4d\u89c9\u5f97\u76f4\u63a5\u83b7\u5f97\u7684\u53ef\u89c6\u5316\u7ed3\u679c\u4e0d\u597d\u770b\uff0c\u8fd9\u4e9b\u51fd\u6570\u672c\u8eab\u8fd8\u6709\u591a\u4e2a\u53c2\u6570\u53ef\u6539\u53d8\u56fe\u5f62\u7684\u6837\u5f0f\u800c\u4f9b\u5c0f\u4f19\u4f34\u4eec\u4f7f\u7528\u54e6\u3002\u5176\u6b21\u6211\u4eec\u7684\u786e\u8fd8\u53ef\u4ee5\u5229\u7528\u73b0\u6709\u7684\u5df2\u7ecf\u8f93\u51fa\u7684\u7ed3\u679c\u6587\u4ef6\u518d\u6b21\u8fdb\u884c\u4e8c\u6b21\u7ed8\u56fe\uff0c\u76f8\u4fe1\u80af\u5b9a\u4f1a\u6bd4\u5c0f\u679c\u753b\u7684\u66f4\u597d\u770b\u5462\uff01\u6700\u540e\uff0c\u5982\u679c\u5404\u4f4d\u5c0f\u4f19\u4f34\u771f\u7684\u4e0d\u60f3\u5728\u6570\u636e\u53ef\u89c6\u5316\u4e0a\u82b1\u8d39\u592a\u5927\u65f6\u95f4\uff0c\u53ef\u4ee5\u6765\u5c0f\u679c\u7684\u4e91\u751f\u4fe1\u5e73\u53f0\u54e6\uff0c\u91cc\u9762\u6709\u5927\u91cf\u6210\u719f\u7684\u53ef\u89c6\u5316\u4ee3\u7801\uff0c\u53ea\u9700\u8981\u5927\u5bb6\u5c06\u6570\u636e\u8f93\u5165\u5c31\u53ef\u4ee5\u4e86\u54e6\uff0c\u5feb\u6765\u52a0\u5165\u6211\u4eec\u628a\uff01<\/p>\n http:\/\/www.biocloudservice.com\/home.html<\/p>\n","protected":false},"excerpt":{"rendered":" Hello\uff0c\u5404\u4f4d\u5c0f\u4f19\u4f34\u5927\u5bb6\u597d\u54e6\uff0c\u5f88\u9ad8\u5174\u53c8\u5230\u5206\u4eab\u77e5\u8bc6\u7684\u65f6\u95f4\u5566\uff01 \u4f17\u6240\u5468\u77e5\uff0c\u8f6c\u5f55\u7ec4\u662f\u751f\u7269\u5b66\u9886\u57df\u4e2d\u4e00\u79cd\u7814\u7a76\u57fa\u56e0\u8868\u8fbe\u7684 […]<\/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\/28628"}],"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=28628"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/28628\/revisions"}],"predecessor-version":[{"id":28640,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/28628\/revisions\/28640"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=28628"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=28628"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=28628"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}![](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-28628-3.png?resize=640%2C62\")
<\/p>\n![\"\u7535\u8111\u8424\u5e55\u753b\u9762\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-57.png?resize=640%2C168\")
<\/p>\n![\"\u6587\u672c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-58.png?resize=640%2C282\")
<\/p>\n![](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-28628-6.png?resize=640%2C43\")
<\/p>\n![](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-28628-7.png?resize=306%2C30\")
<\/p>\n![\"\u6587\u672c\n\n\u4e2d\u5ea6\u53ef\u4fe1\u5ea6\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-59.png?resize=640%2C181\")
<\/p>\n![\"\u56fe\u8868,](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-60.png?resize=640%2C549\")
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