{"id":2342,"date":"2025-11-07T21:53:37","date_gmt":"2025-11-07T13:53:37","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=2342"},"modified":"2025-11-18T16:17:57","modified_gmt":"2025-11-18T08:17:57","slug":"%e6%80%8e%e4%b9%88%e4%bb%a5%e6%af%94%e8%be%83%e8%bd%ac%e5%bd%95%e7%bb%84%e7%9a%84%e5%88%86%e6%9e%90%e6%96%b9%e5%bc%8f%e5%88%86%e6%9e%90%e5%ae%8f%e5%9f%ba%e5%9b%a0%e7%bb%84","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/11\/07\/%e6%80%8e%e4%b9%88%e4%bb%a5%e6%af%94%e8%be%83%e8%bd%ac%e5%bd%95%e7%bb%84%e7%9a%84%e5%88%86%e6%9e%90%e6%96%b9%e5%bc%8f%e5%88%86%e6%9e%90%e5%ae%8f%e5%9f%ba%e5%9b%a0%e7%bb%84\/","title":{"rendered":"\u600e\u4e48\u4ee5\u6bd4\u8f83\u8f6c\u5f55\u7ec4\u7684\u5206\u6790\u65b9\u5f0f\u5206\u6790\u5b8f\u57fa\u56e0\u7ec4"},"content":{"rendered":"\t\t
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1. \u524d\u8a00\n<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\u6bd4\u8f83\u8f6c\u5f55\u7ec4\u4f5c\u4e3a\u751f\u4fe1\u5206\u6790\u4e2d\u6700\u5e38\u89c4\u7684\u5206\u6790\uff0c\u5e95\u5c42\u903b\u8f91\u662f\u901a\u8fc7\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\uff0c\u7b5b\u9009\u5dee\u5f02\u57fa\u56e0\uff0c\u968f\u540e\u8fdb\u884c\u4e0b\u6e38\u7684\u5bcc\u96c6\u5206\u6790\u3002\u4e5f\u53ef\u4ee5\u901a\u8fc7\u8868\u8fbe\u91cf\u77e9\u9635\u8fdb\u884c\u65f6\u5e8f\u5206\u6790\u548cWGCNA\u5206\u6790\u3002\u90a3\u4e48\uff0c\u8fd9\u79cd\u5206\u6790\u6a21\u5f0f\u53ef\u4e0d\u53ef\u4ee5\u7528\u5728\u5176\u4ed6\u5206\u6790\u4e2d\u5462\uff0c\u6211\u4e2a\u4eba\u8ba4\u4e3a\u662f\u53ef\u4ee5\u7684\u3002\u56e0\u6b64\u4eca\u5929\u5c31\u628a\u8fd9\u5957\u6d41\u7a0b\u5e94\u7528\u5728\u5b8f\u57fa\u56e0\u7ec4\u5206\u6790\u4e2d\uff0c\u7528\u57fa\u56e0\u7684\u4e30\u5ea6\u4ee3\u66ff\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\uff0c\u6765\u8fdb\u884c\u4e00\u4e9b\u5206\u6790\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2. \u5206\u6790<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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2.1 DESeq2\u5dee\u5f02\u5206\u6790<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\u901a\u8fc7\u57fa\u56e0\u7684\u4e30\u5ea6\u6570\u636e\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u9700\u8981\u6ce8\u91ca\u7684\u662f\uff0c\u4e30\u5ea6\u8981\u662f\u539f\u59cb\u7684Count\uff0c\u4e0d\u80fd\u662f\u6807\u51c6\u5316\u540e\u7684TMP\u548cFPKM\u3002\u8fd9\u4e00\u6b65\u7684\u8f93\u5165\u6587\u4ef6\u662f\uff081\uff09\u57fa\u56e0\u4e30\u5ea6\uff082\uff09\u6837\u54c1\u5206\u7ec4\u4fe1\u606f<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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sample<\/th>condition<\/th>\n<\/tr>\n<\/thead>\n
J1<\/td>J<\/td>\n<\/tr>\n
J2<\/td>J<\/td>\n<\/tr>\n
J3<\/td>J<\/td>\n<\/tr>\n
J4<\/td>J<\/td>\n<\/tr>\n
F1<\/td>F<\/td>\n<\/tr>\n
F2<\/td>F<\/td>\n<\/tr>\n
F3<\/td>F<\/td>\n<\/tr>\n
F4<\/td>F<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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GeneID<\/th>F2<\/th>J1<\/th>J4<\/th>J3<\/th>J2<\/th>F4<\/th>F1<\/th>F3<\/th>Total<\/th>\n<\/tr>\n<\/thead>\n
J2_k97_737169_1<\/td>298<\/td>318<\/td>4<\/td>2<\/td>8<\/td>90<\/td>20<\/td>30<\/td>770<\/td>\n<\/tr>\n
J2_k97_737170_1<\/td>0<\/td>0<\/td>2<\/td>2<\/td>6<\/td>0<\/td>0<\/td>0<\/td>10<\/td>\n<\/tr>\n
J2_k97_105311_1<\/td>0<\/td>0<\/td>2<\/td>0<\/td>2<\/td>0<\/td>0<\/td>0<\/td>4<\/td>\n<\/tr>\n
J2_k97_1684952_1<\/td>0<\/td>0<\/td>8<\/td>0<\/td>6<\/td>0<\/td>0<\/td>0<\/td>14<\/td>\n<\/tr>\n
J2_k97_1369023_1<\/td>0<\/td>0<\/td>2<\/td>0<\/td>2<\/td>0<\/td>0<\/td>2<\/td>6<\/td>\n<\/tr>\n
J2_k97_1369023_2<\/td>0<\/td>0<\/td>2<\/td>4<\/td>10<\/td>0<\/td>0<\/td>2<\/td>18<\/td>\n<\/tr>\n
J2_k97_631861_1<\/td>0<\/td>0<\/td>0<\/td>2<\/td>0<\/td>0<\/td>0<\/td>0<\/td>2<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\n\t\t\t\t\n\t\t\t\t\t\n\n# --- 1. \u8bbe\u7f6e\u5de5\u4f5c\u73af\u5883 ---\n\n# \u52a0\u8f7d\u6240\u9700\u7684R\u5305\n# \u5982\u679c\u60a8\u5c1a\u672a\u5b89\u88c5\u8fd9\u4e9b\u5305\uff0c\u8bf7\u5148\u8fd0\u884c install.packages(\"\u5305\u540d\") \u8fdb\u884c\u5b89\u88c5\n# \u4f8b\u5982: install.packages(\"DESeq2\")\nsuppressPackageStartupMessages({\n  library(DESeq2)\n  library(readr)\n  library(dplyr)\n})\n\n# --- 2. \u8bbe\u7f6e\u8f93\u5165\u548c\u8f93\u51fa\u6587\u4ef6 ---\n# \u8bf7\u6839\u636e\u60a8\u7684\u6587\u4ef6\u4f4d\u7f6e\u4fee\u6539\u4ee5\u4e0b\u8def\u5f84\n\n# \u8bbe\u7f6e\u539f\u59cb\u57fa\u56e0count\u77e9\u9635\u6587\u4ef6\u7684\u8def\u5f84 (\u4f8b\u5982: \"data\/reads_number.xls\")\n# \u6587\u4ef6\u5e94\u4e3a\u5236\u8868\u7b26\u5206\u9694\uff0c\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0ID\uff0c\u540e\u7eed\u5217\u4e3a\u6837\u672c\u7684count\u503c\u3002\ncount_file <- \"reads_number.xls\"\n\n# \u8bbe\u7f6e\u6837\u672c\u4fe1\u606f\u6587\u4ef6\u7684\u8def\u5f84 (\u4f8b\u5982: \"data\/sample_info.csv\")\n# \u6587\u4ef6\u5e94\u4e3a\u9017\u53f7\u5206\u9694\uff0c\u5305\u542b\u4e24\u5217: \"sample\" (\u6837\u672c\u540d\u79f0) \u548c \"condition\" (\u5206\u7ec4\u4fe1\u606f)\u3002\nsample_info_file <- \"sample_info.csv\"\n\n# \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00 (\u4f8b\u5982: \"results\/deseq2_output\")\n# \u811a\u672c\u5c06\u751f\u6210\u4e00\u4e2a\u540d\u4e3a <output_prefix>_diff_expression.csv \u7684\u7ed3\u679c\u6587\u4ef6\u3002\noutput_prefix <- \"deseq2_results\"\n\n\n# --- 3. \u8bfb\u53d6\u5e76\u9884\u5904\u7406\u6570\u636e ---\n\n# \u8bfb\u53d6\u539f\u59cb\u57fa\u56e0count\u77e9\u9635\n# \u5047\u8bbe\u6587\u4ef6\u662f\u5236\u8868\u7b26\u5206\u9694\u7684\uff0c\u7b2c\u4e00\u5217\u662f\u57fa\u56e0ID\ncat(paste0(\"\u6b63\u5728\u8bfb\u53d6count\u6587\u4ef6: \", count_file, \"\\n\"))\ncount_data <- read.delim(count_file, row.names = 1, sep = \"\\t\", check.names = FALSE)\n\n# \u5220\u9664count\u6570\u636e\u4e2d\u7684\u6700\u540e\u4e00\u5217\n# \u539f\u59cb\u811a\u672c\u4f4d\u7f6e: \/home\/majunpeng\/sda2\/Lishuyan_Kuozangzi_sequence\/Metagenome\/Gemini\/deseq2_analysis_rstudio_1.R\ncount_data <- count_data[, -ncol(count_data)]\n\n# \u8bfb\u53d6\u6837\u672c\u4fe1\u606f\u6587\u4ef6\n# \u5047\u8bbe\u6587\u4ef6\u662f\u9017\u53f7\u5206\u9694\u7684\ncat(paste0(\"\u6b63\u5728\u8bfb\u53d6\u6837\u672c\u4fe1\u606f\u6587\u4ef6: \", sample_info_file, \"\\n\"))\nsample_info <- read_csv(sample_info_file, show_col_types = FALSE)\n\n# \u786e\u4fddcount\u6570\u636e\u662f\u6574\u6570\u7c7b\u578b\uff0cDESeq2\u8981\u6c42\u8f93\u5165\u4e3a\u6574\u6570\ncount_data <- round(count_data)\n\n# \u786e\u4fdd\u6837\u672c\u4fe1\u606f\u4e2d\u7684\u6837\u672c\u540d\u79f0\u4e0ecount\u6570\u636e\u4e2d\u7684\u5217\u540d\u4e00\u81f4\u4e14\u987a\u5e8f\u4e00\u81f4\n# \u7b5b\u9009\u51fa\u5728count\u6570\u636e\u4e2d\u5b58\u5728\u7684\u6837\u672c\nsample_info <- sample_info %>%\n  filter(sample %in% colnames(count_data)) %>%\n  arrange(match(sample, colnames(count_data))) # \u6309\u7167count\u6570\u636e\u7684\u5217\u987a\u5e8f\u6392\u5e8f\n\n# \u68c0\u67e5\u6837\u672c\u6570\u91cf\u662f\u5426\u5339\u914d\nif (ncol(count_data) != nrow(sample_info)) {\n  stop(\"\u9519\u8bef: count\u6570\u636e\u4e2d\u7684\u6837\u672c\u5217\u6570\u4e0e\u6837\u672c\u4fe1\u606f\u6587\u4ef6\u4e2d\u7684\u6837\u672c\u884c\u6570\u4e0d\u5339\u914d\u3002\u8bf7\u68c0\u67e5\u60a8\u7684\u8f93\u5165\u6587\u4ef6\u3002\\n\")\n}\n\n# \u786e\u4fddcount\u6570\u636e\u7684\u5217\u540d\u548csample_info\u7684sample\u5217\u987a\u5e8f\u4e00\u81f4\ncount_data <- count_data[, sample_info$sample]\n\n# \u5c06condition\u5217\u8f6c\u6362\u4e3a\u56e0\u5b50\uff0c\u5e76\u8bbe\u7f6e\u6bd4\u8f83\u7ec4\u548c\u5bf9\u7167\u7ec4\n# DESeq2\u9ed8\u8ba4\u6309\u5b57\u6bcd\u987a\u5e8f\u786e\u5b9a\u5bf9\u7167\u7ec4\uff0c\u4f8b\u5982'F'\u548c'J'\u4e2d\uff0c'F'\u4f1a\u6210\u4e3a\u5bf9\u7167\u7ec4\u3002\n# \u4e3a\u4e86\u660e\u786e\u6307\u5b9a\u5bf9\u7167\u7ec4\uff0c\u6211\u4eec\u4f7f\u7528relevel()\u51fd\u6570\u3002\n# \u8fd9\u91cc\u6211\u4eec\u5c06'J'\u8bbe\u7f6e\u4e3a\u5bf9\u7167\u7ec4(reference level)\u3002\nunique_conditions <- unique(sample_info$condition)\nif (length(unique_conditions) < 2) {\n  stop(\"\u9519\u8bef: \u6837\u672c\u4fe1\u606f\u4e2d\u81f3\u5c11\u9700\u8981\u4e24\u4e2a\u4e0d\u540c\u7684\u6761\u4ef6\u624d\u80fd\u8fdb\u884c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u3002\\n\")\n}\n# \u5047\u8bbe\u60a8\u60f3\u6bd4\u8f83 F\u7ec4 vs J\u7ec4\uff0cJ\u7ec4\u662f\u5bf9\u7167\u7ec4\nsample_info$condition <- factor(sample_info$condition)\nsample_info$condition <- relevel(sample_info$condition, ref = \"F\")\n\n\n# --- 4. \u6784\u5efaDESeqDataSet\u5bf9\u8c61 ---\n\n# \u521b\u5efaDESeqDataSet\u5bf9\u8c61\n# design\u516c\u5f0f\u6307\u5b9a\u4e86\u5982\u4f55\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u8fd9\u91cc\u662f\u6839\u636econdition\u8fdb\u884c\u6bd4\u8f83\ndds <- DESeqDataSetFromMatrix(countData = count_data,\n                              colData = sample_info,\n                              design = ~ condition)\n\n# \u8fc7\u6ee4\u4f4e\u8868\u8fbe\u57fa\u56e0 (\u53ef\u9009\uff0c\u4f46\u63a8\u8350)\n# \u8fc7\u6ee4\u6389\u5728\u6240\u6709\u6837\u672c\u4e2dcount\u603b\u548c\u8fc7\u4f4e\u7684\u57fa\u56e0\uff0c\u4ee5\u51cf\u5c11\u8ba1\u7b97\u91cf\u548c\u63d0\u9ad8\u7edf\u8ba1\u529f\u6548\n# \u8fd9\u91cc\u4fdd\u7559\u90a3\u4e9b\u5728\u81f3\u5c11\u4e00\u4e2a\u6837\u672c\u4e2dcount\u5927\u4e8e\u7b49\u4e8e10\u7684\u57fa\u56e0\nkeep <- rowSums(counts(dds) >= 10) >= 1\ndds <- dds[keep,]\n\n# --- 5. \u8fd0\u884cDESeq2\u6838\u5fc3\u5206\u6790 ---\n\ncat(\"\u6b63\u5728\u8fd0\u884cDESeq2\u5dee\u5f02\u8868\u8fbe\u5206\u6790...\\n\")\ndds <- DESeq(dds)\n\n# --- 6. \u63d0\u53d6\u548c\u4fdd\u5b58\u7ed3\u679c ---\n\n# \u63d0\u53d6\u5dee\u5f02\u8868\u8fbe\u7ed3\u679c\n# resultsNames(dds) \u53ef\u4ee5\u67e5\u770b\u6240\u6709\u53ef\u7528\u7684\u6bd4\u8f83\u540d\u79f0\n# \u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u5b83\u4f1a\u6bd4\u8f83\u5904\u7406\u7ec4\u4e0e\u60a8\u8bbe\u5b9a\u7684\u5bf9\u7167\u7ec4\nres <- results(dds)\n\n# \u60a8\u4e5f\u53ef\u4ee5\u4f7f\u7528 contrast \u53c2\u6570\u660e\u786e\u6307\u5b9a\u6bd4\u8f83\uff0c\u4f8b\u5982\u6bd4\u8f83'F'\u7ec4\u76f8\u5bf9\u4e8e'J'\u7ec4\u7684\u5dee\u5f02\n# res <- results(dds, contrast = c(\"condition\", \"F\", \"J\"))\n\n# \u5bf9\u7ed3\u679c\u8fdb\u884c\u6392\u5e8f (\u4f8b\u5982\uff0c\u6309\u8c03\u6574\u540e\u7684p\u503c(padj)\u4ece\u5c0f\u5230\u5927\u6392\u5e8f)\nres_ordered <- res[order(res$padj),]\n\n# \u5c06\u7ed3\u679c\u8f6c\u6362\u4e3a\u6570\u636e\u6846\nres_df <- as.data.frame(res_ordered)\n\n# \u6dfb\u52a0\u57fa\u56e0ID\u5217\nres_df <- tibble::rownames_to_column(res_df, var = \"gene_id\")\n\n# \u4fdd\u5b58\u7ed3\u679c\u5230CSV\u6587\u4ef6\noutput_file <- paste0(output_prefix, \"_diff_expression.csv\")\ncat(paste0(\"\u6b63\u5728\u4fdd\u5b58\u5dee\u5f02\u8868\u8fbe\u7ed3\u679c\u5230: \", output_file, \"\\n\"))\nwrite_csv(res_df, output_file)\n\ncat(\"DESeq2\u5206\u6790\u5b8c\u6210\uff01\\n\")\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d7d8d19 elementor-widget elementor-widget-text-editor\" data-id=\"d7d8d19\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u6700\u540e\uff0c\u6211\u4eec\u5c31\u4e00\u5b9a\u62ff\u5230\u4e86\u5dee\u5f02\u5206\u6790\u7684\u7ed3\u679c\uff0c\u63a5\u4e0b\u6765\u6211\u4eec\u4ee5P\u503c\u5c0f\u4e8e\u7b49\u4e8e0.05\uff0cLog2FC\u7684\u7edd\u5bf9\u503c\u5927\u4e8e\u7b49\u4e8e1.5\u8fdb\u884c\u5dee\u5f02\u57fa\u56e0\u7684\u7b5b\u9009\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ffbdedf elementor-widget elementor-widget-shortcode\" data-id=\"ffbdedf\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"shortcode.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-shortcode\">\n<table id=\"tablepress-20\" class=\"tablepress tablepress-id-20\">\n<thead>\n<tr class=\"row-1 odd\">\n\t<th class=\"column-1\">gene_id<\/th><th class=\"column-2\">baseMean<\/th><th class=\"column-3\">log2FoldChange<\/th><th class=\"column-4\">lfcSE<\/th><th class=\"column-5\">stat<\/th><th class=\"column-6\">pvalue<\/th><th class=\"column-7\">padj<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-hover\">\n<tr class=\"row-2 even\">\n\t<td class=\"column-1\">J3_k97_1869542_48<\/td><td class=\"column-2\">719.9416276<\/td><td class=\"column-3\">26.53634325<\/td><td class=\"column-4\">2.584192382<\/td><td class=\"column-5\">10.26871816<\/td><td class=\"column-6\">9.75E-25<\/td><td class=\"column-7\">1.10E-18<\/td>\n<\/tr>\n<tr class=\"row-3 odd\">\n\t<td class=\"column-1\">J3_k97_1869542_49<\/td><td class=\"column-2\">505.5442894<\/td><td class=\"column-3\">26.1670583<\/td><td class=\"column-4\">2.571273542<\/td><td class=\"column-5\">10.17669177<\/td><td class=\"column-6\">2.52E-24<\/td><td class=\"column-7\">1.42E-18<\/td>\n<\/tr>\n<tr class=\"row-4 even\">\n\t<td class=\"column-1\">J3_k97_1869542_3<\/td><td class=\"column-2\">502.7114513<\/td><td class=\"column-3\">26.08115486<\/td><td class=\"column-4\">2.581835499<\/td><td class=\"column-5\">10.101788<\/td><td class=\"column-6\">5.42E-24<\/td><td class=\"column-7\">1.53E-18<\/td>\n<\/tr>\n<tr class=\"row-5 odd\">\n\t<td class=\"column-1\">J3_k97_1869542_47<\/td><td class=\"column-2\">495.3948077<\/td><td class=\"column-3\">25.74264487<\/td><td class=\"column-4\">2.546306163<\/td><td class=\"column-5\">10.10979954<\/td><td class=\"column-6\">5.00E-24<\/td><td class=\"column-7\">1.53E-18<\/td>\n<\/tr>\n<tr class=\"row-6 even\">\n\t<td class=\"column-1\">J3_k97_1869542_33<\/td><td class=\"column-2\">623.4655207<\/td><td class=\"column-3\">26.26834756<\/td><td class=\"column-4\">2.607327384<\/td><td class=\"column-5\">10.0748175<\/td><td class=\"column-6\">7.14E-24<\/td><td class=\"column-7\">1.61E-18<\/td>\n<\/tr>\n<tr class=\"row-7 odd\">\n\t<td class=\"column-1\">J3_k97_1869542_67<\/td><td class=\"column-2\">311.7707339<\/td><td class=\"column-3\">25.4921083<\/td><td class=\"column-4\">2.547029189<\/td><td class=\"column-5\">10.00856543<\/td><td class=\"column-6\">1.40E-23<\/td><td class=\"column-7\">2.63E-18<\/td>\n<\/tr>\n<tr class=\"row-8 even\">\n\t<td class=\"column-1\">J3_k97_1869542_32<\/td><td class=\"column-2\">554.8218292<\/td><td class=\"column-3\">26.2904605<\/td><td class=\"column-4\">2.632630124<\/td><td class=\"column-5\">9.986385957<\/td><td class=\"column-6\">1.75E-23<\/td><td class=\"column-7\">2.82E-18<\/td>\n<\/tr>\n<tr class=\"row-9 odd\">\n\t<td class=\"column-1\">J3_k97_1869542_14<\/td><td class=\"column-2\">377.7311327<\/td><td class=\"column-3\">25.44960062<\/td><td class=\"column-4\">2.552398401<\/td><td class=\"column-5\">9.970857455<\/td><td class=\"column-6\">2.04E-23<\/td><td class=\"column-7\">2.89E-18<\/td>\n<\/tr>\n<tr class=\"row-10 even\">\n\t<td class=\"column-1\">J3_k97_1869542_8<\/td><td class=\"column-2\">404.1818614<\/td><td class=\"column-3\">25.85406933<\/td><td class=\"column-4\">2.612079894<\/td><td class=\"column-5\">9.89788612<\/td><td class=\"column-6\">4.25E-23<\/td><td class=\"column-7\">4.23E-18<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-20 from cache --><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-52f684a elementor-widget elementor-widget-heading\" data-id=\"52f684a\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">2.2 \u5bcc\u96c6\u5206\u6790<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7573dab elementor-widget elementor-widget-text-editor\" data-id=\"7573dab\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u5bcc\u96c6\u5206\u6790\u4e3b\u8981\u5206\u4e3a\u4e24\u90e8\u5206\uff0c\u5e38\u89c4\u7684KEGG\u548cGO\u5bcc\u96c6\u5206\u6790\u548cGSEA\u5bcc\u96c6\u5206\u6790\u3002\u7b2c\u4e00\u6b65\u5c31\u662f\u8981\u901a\u8fc7Eggnog\u7684\u6ce8\u91ca\u7ed3\u679c\u6784\u5efa\u4e00\u4e2aOrgdb\u5e93\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-260c91c elementor-widget elementor-widget-code-highlight\" data-id=\"260c91c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>emapper \nRscript \/pub\/software\/emcp\/emapperx.R out.emapper.annotations proteins.fa<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-22c122c elementor-widget elementor-widget-text-editor\" data-id=\"22c122c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u968f\u540e\u8fdb\u884c\u5e38\u89c4\u7684KEGG\u548cGO\u5bcc\u96c6\u5206\u6790\uff0c\u8fd9\u4e00\u6b65\u6211\u4f7f\u7528\u7684\u662fTBtools\uff0c\u5728\u8fd9\u91cc\u5c31\u4e0d\u8be6\u7ec6\u89e3\u91ca\u600e\u4e48\u7528\u4e86\uff0c\u8bf7\u81ea\u884c\u641c\u7d22\u5b66\u4e60\u3002\u5b8c\u6210\u5bcc\u96c6\u5206\u6790\u540e\uff0c\u6309\u7167\u4e0b\u9762\u7684\u8f93\u5165\u6587\u4ef6\u683c\u5f0f\u7b80\u5355\u7684\u6574\u7406\u4e00\u4e0b\uff0c\u4e0b\u9762\u7684\u662f\u4e00\u4e2aKEGG\u548cGO\u5bcc\u96c6\u53ef\u89c6\u5316\u7684\u4ee3\u7801\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-45d1c41 elementor-widget elementor-widget-shortcode\" data-id=\"45d1c41\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"shortcode.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-shortcode\">\n<table id=\"tablepress-22\" class=\"tablepress tablepress-id-22\">\n<thead>\n<tr class=\"row-1 odd\">\n\t<th class=\"column-1\">ONTOLOGY<\/th><th class=\"column-2\">Description<\/th><th class=\"column-3\">p.adjust<\/th><th class=\"column-4\">Count<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-hover\">\n<tr class=\"row-2 even\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Metabolism<\/td><td class=\"column-3\">4.30E-14<\/td><td class=\"column-4\">412<\/td>\n<\/tr>\n<tr class=\"row-3 odd\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Starch and sucrose metabolism<\/td><td class=\"column-3\">2.42E-10<\/td><td class=\"column-4\">943<\/td>\n<\/tr>\n<tr class=\"row-4 even\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Carbohydrate metabolism<\/td><td class=\"column-3\">8.78E-09<\/td><td class=\"column-4\">124<\/td>\n<\/tr>\n<tr class=\"row-5 odd\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Staurosporine biosynthesis<\/td><td class=\"column-3\">1.11E-08<\/td><td class=\"column-4\">66<\/td>\n<\/tr>\n<tr class=\"row-6 even\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Fructose and mannose metabolism<\/td><td class=\"column-3\">1.56E-08<\/td><td class=\"column-4\">559<\/td>\n<\/tr>\n<tr class=\"row-7 odd\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Biosynthesis of type II polyketide products<\/td><td class=\"column-3\">1.68E-08<\/td><td class=\"column-4\">30<\/td>\n<\/tr>\n<tr class=\"row-8 even\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Tetracycline biosynthesis<\/td><td class=\"column-3\">2.21E-08<\/td><td class=\"column-4\">18<\/td>\n<\/tr>\n<tr class=\"row-9 odd\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Biosynthesis of enediyne antibiotics<\/td><td class=\"column-3\">2.91E-08<\/td><td class=\"column-4\">63<\/td>\n<\/tr>\n<tr class=\"row-10 even\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Biosynthesis of other secondary metabolites<\/td><td class=\"column-3\">3.49E-08<\/td><td class=\"column-4\">415<\/td>\n<\/tr>\n<tr class=\"row-11 odd\">\n\t<td class=\"column-1\">KEGG<\/td><td class=\"column-2\">Biosynthesis of vancomycin group antibiotics<\/td><td class=\"column-3\">9.06E-08<\/td><td class=\"column-4\">87<\/td>\n<\/tr>\n<tr class=\"row-12 even\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">catalytic activity<\/td><td class=\"column-3\">3.33E-16<\/td><td class=\"column-4\">414<\/td>\n<\/tr>\n<tr class=\"row-13 odd\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">magnesium ion binding<\/td><td class=\"column-3\">4.44E-16<\/td><td class=\"column-4\">331<\/td>\n<\/tr>\n<tr class=\"row-14 even\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">manganese ion binding<\/td><td class=\"column-3\">4.66E-15<\/td><td class=\"column-4\">148<\/td>\n<\/tr>\n<tr class=\"row-15 odd\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">obsolete cofactor binding<\/td><td class=\"column-3\">4.13E-14<\/td><td class=\"column-4\">524<\/td>\n<\/tr>\n<tr class=\"row-16 even\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">metal ion binding<\/td><td class=\"column-3\">1.55E-10<\/td><td class=\"column-4\">782<\/td>\n<\/tr>\n<tr class=\"row-17 odd\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">zymogen binding<\/td><td class=\"column-3\">2.49E-10<\/td><td class=\"column-4\">42<\/td>\n<\/tr>\n<tr class=\"row-18 even\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">cation binding<\/td><td class=\"column-3\">4.05E-10<\/td><td class=\"column-4\">845<\/td>\n<\/tr>\n<tr class=\"row-19 odd\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">tripeptide aminopeptidase activity<\/td><td class=\"column-3\">1.10E-08<\/td><td class=\"column-4\">8<\/td>\n<\/tr>\n<tr class=\"row-20 even\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">tripeptidase activity<\/td><td class=\"column-3\">1.10E-08<\/td><td class=\"column-4\">8<\/td>\n<\/tr>\n<tr class=\"row-21 odd\">\n\t<td class=\"column-1\">MF<\/td><td class=\"column-2\">obsolete coenzyme binding<\/td><td class=\"column-3\">1.84E-08<\/td><td class=\"column-4\">351<\/td>\n<\/tr>\n<tr class=\"row-22 even\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">cell periphery<\/td><td class=\"column-3\">1.11E-16<\/td><td class=\"column-4\">197<\/td>\n<\/tr>\n<tr class=\"row-23 odd\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">cell wall<\/td><td class=\"column-3\">1.11E-16<\/td><td class=\"column-4\">894<\/td>\n<\/tr>\n<tr class=\"row-24 even\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">membrane<\/td><td class=\"column-3\">1.11E-16<\/td><td class=\"column-4\">452<\/td>\n<\/tr>\n<tr class=\"row-25 odd\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">oxidoreductase complex<\/td><td class=\"column-3\">5.77E-06<\/td><td class=\"column-4\">129<\/td>\n<\/tr>\n<tr class=\"row-26 even\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">cell envelope<\/td><td class=\"column-3\">1.03E-05<\/td><td class=\"column-4\">221<\/td>\n<\/tr>\n<tr class=\"row-27 odd\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">pyruvate dehydrogenase complex<\/td><td class=\"column-3\">5.25E-05<\/td><td class=\"column-4\">25<\/td>\n<\/tr>\n<tr class=\"row-28 even\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">alpha-ketoacid dehydrogenase complex<\/td><td class=\"column-3\">8.13E-05<\/td><td class=\"column-4\">33<\/td>\n<\/tr>\n<tr class=\"row-29 odd\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">outer membrane-bounded periplasmic space<\/td><td class=\"column-3\">9.59E-05<\/td><td class=\"column-4\">137<\/td>\n<\/tr>\n<tr class=\"row-30 even\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">respiratory chain complex II (succinate dehydrogenase)<\/td><td class=\"column-3\">0.000151272<\/td><td class=\"column-4\">17<\/td>\n<\/tr>\n<tr class=\"row-31 odd\">\n\t<td class=\"column-1\">CC<\/td><td class=\"column-2\">obsolete plasma membrane respiratory chain complex II<\/td><td class=\"column-3\">0.000192509<\/td><td class=\"column-4\">16<\/td>\n<\/tr>\n<tr class=\"row-32 even\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">growth<\/td><td class=\"column-3\">7.77E-16<\/td><td class=\"column-4\">136<\/td>\n<\/tr>\n<tr class=\"row-33 odd\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">response to host<\/td><td class=\"column-3\">8.88E-15<\/td><td class=\"column-4\">95<\/td>\n<\/tr>\n<tr class=\"row-34 even\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">response to host immune response<\/td><td class=\"column-3\">2.95E-14<\/td><td class=\"column-4\">88<\/td>\n<\/tr>\n<tr class=\"row-35 odd\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">response to defenses of other organism<\/td><td class=\"column-3\">5.51E-14<\/td><td class=\"column-4\">90<\/td>\n<\/tr>\n<tr class=\"row-36 even\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">response to host defenses<\/td><td class=\"column-3\">5.51E-14<\/td><td class=\"column-4\">90<\/td>\n<\/tr>\n<tr class=\"row-37 odd\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">peptidoglycan-based cell wall biogenesis<\/td><td class=\"column-3\">1.84E-11<\/td><td class=\"column-4\">95<\/td>\n<\/tr>\n<tr class=\"row-38 even\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">obsolete growth involved in symbiotic interaction<\/td><td class=\"column-3\">2.59E-11<\/td><td class=\"column-4\">67<\/td>\n<\/tr>\n<tr class=\"row-39 odd\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">peptidoglycan metabolic process<\/td><td class=\"column-3\">4.20E-11<\/td><td class=\"column-4\">95<\/td>\n<\/tr>\n<tr class=\"row-40 even\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">obsolete pathogenesis<\/td><td class=\"column-3\">1.12E-10<\/td><td class=\"column-4\">99<\/td>\n<\/tr>\n<tr class=\"row-41 odd\">\n\t<td class=\"column-1\">BP<\/td><td class=\"column-2\">cell wall biogenesis<\/td><td class=\"column-3\">1.61E-10<\/td><td class=\"column-4\">107<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-22 from cache --><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-54a59d0 elementor-widget elementor-widget-code-highlight\" data-id=\"54a59d0\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-r line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-r\">\n\t\t\t\t\t<xmp>rm(list = ls())\n\n\n####----load R Package----####\nlibrary(tidyverse)\nlibrary(ggh4x)\nlibrary(ggfun)\nlibrary(clusterProfiler)\nlibrary(org.Hs.eg.db)\n\n####----load Result----####\n\nplot_df <- read.csv(\"KEGG_GO\u5bcc\u96c6\u7ed8\u56fe.csv\")\n####----Plot----####\nplot <- plot_df %>%\n  ggplot() + \n  geom_bar(aes(x = -log10(p.adjust), y = interaction(Description, ONTOLOGY), fill = ONTOLOGY), stat = \"identity\") + \n  geom_text(aes(x = 0.1, y = interaction(Description, ONTOLOGY), label = Description), size = 6, hjust = \"left\", color = \"#000000\") + \n  geom_point(aes(x = 20, y = interaction(Description, ONTOLOGY), size = Count, fill = ONTOLOGY), shape = 21) + \n  geom_text(aes(x = 20, y = interaction(Description, ONTOLOGY), label = Count)) + \n  scale_x_continuous(expand = expansion(mult = c(0, 0.2))) + \n  scale_fill_manual(values = c(\"#74c476\", \"#41b6c4\", \"#f46d43\", \"#9e9ac8\")) + \n  scale_size(range = c(5, 8.5),\n             guide = guide_legend(override.aes = list(fill = \"#000000\"))) + \n  guides(y = \"axis_nested\",\n         fill = guide_legend(reverse = T)) +\n  labs(x = \"-log10(p.adjust)\", y = \"Description\") + \n  ggtitle(label = \"GO and KEGG Enrichment\") + \n  theme_bw() + \n  theme(\n    ggh4x.axis.nestline.y = element_line(size = 3, color = c(\"#74c476\", \"#41b6c4\", \"#f46d43\", \"#9e9ac8\")),\n    ggh4x.axis.nesttext.y = element_text(colour = c(\"#74c476\", \"#41b6c4\", \"#f46d43\", \"#9e9ac8\")),\n    legend.background = element_roundrect(color = \"#969696\"),\n    panel.border = element_rect(linewidth = 1),\n    plot.margin = margin(t = 1, r = 1, b = 1, l = 1, unit = \"cm\"),\n    axis.text = element_text(color = \"#000000\", size = 20),\n    axis.text.y = element_text(color = rep(c(\"#41ae76\", \"#225ea8\", \"#fc4e2a\", \"#88419d\"), each = 10)),\n    axis.text.y.left = element_blank(),\n    axis.ticks.length.y.left = unit(10, \"pt\"),\n    axis.ticks.y.left = element_line(color = NA),\n    axis.title = element_text(color = \"#000000\", size = 15),\n    plot.title = element_text(color = \"#000000\", size = 20, hjust = 0.5)\n  ) \n\nplot\n\nggsave(filename = \"GO_KEGG_Lishuyan.pdf\",\n       plot = plot,\n       height = 15,\n       width = 12)\n\n####----sessionInfo----####\nsessionInfo()\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-cb8c771 elementor-widget elementor-widget-image\" data-id=\"cb8c771\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"819\" height=\"1024\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/GO_KEGG_Lishuyan_1-819x1024.png\" class=\"attachment-large size-large wp-image-2403\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/GO_KEGG_Lishuyan_1-819x1024.png 819w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/GO_KEGG_Lishuyan_1-240x300.png 240w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/GO_KEGG_Lishuyan_1-768x960.png 768w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/GO_KEGG_Lishuyan_1-1228x1536.png 1228w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/GO_KEGG_Lishuyan_1-1638x2048.png 1638w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/GO_KEGG_Lishuyan_1-scaled.png 2047w\" sizes=\"(max-width: 819px) 100vw, 819px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d4f701b elementor-widget elementor-widget-shortcode\" data-id=\"d4f701b\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"shortcode.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-shortcode\">\n<table id=\"tablepress-21\" class=\"tablepress tablepress-id-21\">\n<thead>\n<tr class=\"row-1 odd\">\n\t<th class=\"column-1\">gene_id<\/th><th class=\"column-2\">log2FoldChange<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-hover\">\n<tr class=\"row-2 even\">\n\t<td class=\"column-1\">J3_k97_1869542_48_1<\/td><td class=\"column-2\">26.53634325<\/td>\n<\/tr>\n<tr class=\"row-3 odd\">\n\t<td class=\"column-1\">J3_k97_1869542_32_1<\/td><td class=\"column-2\">26.2904605<\/td>\n<\/tr>\n<tr class=\"row-4 even\">\n\t<td class=\"column-1\">J3_k97_1869542_33_1<\/td><td class=\"column-2\">26.26834756<\/td>\n<\/tr>\n<tr class=\"row-5 odd\">\n\t<td class=\"column-1\">J3_k97_1869542_49_1<\/td><td class=\"column-2\">26.1670583<\/td>\n<\/tr>\n<tr class=\"row-6 even\">\n\t<td class=\"column-1\">J3_k97_1869542_3_1<\/td><td class=\"column-2\">26.08115486<\/td>\n<\/tr>\n<tr class=\"row-7 odd\">\n\t<td class=\"column-1\">J3_k97_1869542_45_1<\/td><td class=\"column-2\">25.94958501<\/td>\n<\/tr>\n<tr class=\"row-8 even\">\n\t<td class=\"column-1\">J3_k97_1869542_8_1<\/td><td class=\"column-2\">25.85406933<\/td>\n<\/tr>\n<tr class=\"row-9 odd\">\n\t<td class=\"column-1\">J3_k97_1869542_23_1<\/td><td class=\"column-2\">25.82508916<\/td>\n<\/tr>\n<tr class=\"row-10 even\">\n\t<td class=\"column-1\">J3_k97_1869542_47_1<\/td><td class=\"column-2\">25.74264487<\/td>\n<\/tr>\n<tr class=\"row-11 odd\">\n\t<td class=\"column-1\">J3_k97_1869542_75_1<\/td><td class=\"column-2\">25.69997138<\/td>\n<\/tr>\n<tr class=\"row-12 even\">\n\t<td class=\"column-1\">J3_k97_1869542_60_1<\/td><td class=\"column-2\">25.6210279<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-21 from cache --><\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7cc0bcd elementor-widget elementor-widget-text-editor\" data-id=\"7cc0bcd\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u63a5\u4e0b\u6765\u8fdb\u884cGSEA\u5bcc\u96c6\u5206\u6790\uff0c\u540c\u6837\uff0c\u9700\u8981\u6309\u7167\u4e0b\u9762\u7684\u683c\u5f0f\u6574\u7406\u7684\u4e00\u4e2a\u8f93\u5165\u6587\u4ef6\uff0c\u5305\u542b\u57fa\u56e0ID\u548cLog2FC\u503c\u4fe1\u606f\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-35cb407 elementor-widget elementor-widget-code-highlight\" data-id=\"35cb407\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-r line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-r\">\n\t\t\t\t\t<xmp>library(magrittr)\nlibrary(readr)\nlibrary(clusterProfiler)\nlibrary(tidyr)\nlibrary(tibble)\nlibrary(stringr)\nlibrary(GseaVis)\n\n\n\nget_path2name <- function(){\n  keggpathid2name.df <- clusterProfiler:::kegg_list(\"pathway\")\n  keggpathid2name.df[,1] %<>% gsub(\"path:map\", \"\", .)\n  colnames(keggpathid2name.df) <- c(\"path_id\",\"path_name\")\n  return(keggpathid2name.df)\n}\npathway2name <- get_path2name()\npathway2name$path_id <- gsub(\"map\", \"\", pathway2name$path_id, ignore.case = TRUE)\n\nemapper <- read_delim(\"..\/EGGNOG.emapper.annotations\",\n                      \"\\t\", escape_double = FALSE, col_names = FALSE,\n                      comment = \"#\", trim_ws = TRUE) %>%\n  dplyr::select(GID = X1,\n                COG = X7,\n                Gene_Name = X8,\n                Gene_Symbol = X9,\n                GO = X10,\n                KO = X12,\n                Pathway = X13\n  )\n\npathway2gene <- dplyr::select(emapper, Pathway, GID) %>%\n  separate_rows(Pathway, sep = ',', convert = F) %>%\n  filter(str_detect(Pathway, 'ko')) %>%\n  mutate(Pathway = str_remove(Pathway, 'ko'))\n\n\ngene_data <- read.csv(\"\u5dee\u5f02\u57fa\u56e0\u8868\u8fbe\u91cf.csv\")\n\ngeneList <- setNames(gene_data$log2FoldChange, gene_data$gene_id)\n\ngeneList <- sort(geneList, decreasing = TRUE)\n\nhead(geneList)\n\nekp2 = GSEA(\n  geneList,\n  TERM2GENE = pathway2gene,\n  TERM2NAME = pathway2name,\n  minGSSize = 10,\n  maxGSSize = 500,\n  pvalueCutoff = 0.05)\n\nekp2_df <- as.data.frame(ekp2)\nwrite.csv(as.data.frame(ekp2), \"GSEA_analysis_KEGG.csv\", row.names = FALSE)\n\ngseaNb(object = ekp2,\n       geneSetID = '00523',\n       addPval = T,\n       rankSeq = 20000)\n       \nGSEA_fig <- gseaNb(object = ekp2,\n       geneSetID = c('00523',\"01059\", \"00404\"),\n       addPval = T,\n       rankSeq = 20000,\n       pvalX = 0.15,pvalY = 0.15)\n\nggsave(\"GSEA.pdf\", GSEA_fig, width = 8, height = 6, dpi = 300)\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ba1859c elementor-widget elementor-widget-image\" data-id=\"ba1859c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img decoding=\"async\" width=\"825\" height=\"750\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/Cyanoamino-acid-metabolism.png\" class=\"attachment-large size-large wp-image-2385\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/Cyanoamino-acid-metabolism.png 825w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/Cyanoamino-acid-metabolism-300x273.png 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/Cyanoamino-acid-metabolism-768x698.png 768w\" sizes=\"(max-width: 825px) 100vw, 825px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fd3f9e9 elementor-widget elementor-widget-heading\" data-id=\"fd3f9e9\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">2.3 WGCNA\u5206\u6790<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-10f4513 elementor-widget elementor-widget-text-editor\" data-id=\"10f4513\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u540c\u6837WGCNA\u4e5f\u53ef\u4ee5\u505a\uff0c\u627e\u5230\u548c\u67d0\u4e2aASV\u76f8\u5173\u6027\u6700\u9ad8\u7684\u57fa\u56e0\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-db3e74b elementor-widget elementor-widget-code-highlight\" data-id=\"db3e74b\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-r line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-r\">\n\t\t\t\t\t<xmp>library(WGCNA)\nlibrary(tidyverse)\n\n# \u8bfb\u53d6\u57fa\u56e0\u4e30\u5ea6\u6587\u4ef6\ngene_exp <- read.csv(file = '\u5dee\u5f02\u57fa\u56e0_TPM.csv',\n                     row.names = 1)\n\n# \u8bfb\u53d6\u6269\u589e\u5b50ASV\u98ce\u5ea6\u6587\u4ef6\nsample_info <- read.table(file = 'ASV_Count.txt',\n                        row.names = 1, header = TRUE )\n\n{\n  # \u8f6c\u7f6e\n  datExpr0 <- t(gene_exp)\n  \n  # \u7f3a\u5931\u6570\u636e\u53ca\u65e0\u6ce2\u52a8\u6570\u636e\u8fc7\u6ee4\n  gsg <- goodSamplesGenes(\n    datExpr0, \n    minFraction = 1\/2 #\u57fa\u56e0\u7684\u7f3a\u5931\u6570\u636e\u6bd4\u4f8b\u9608\u503c\n  )\n  datExpr <- datExpr0[gsg$goodSamples, gsg$goodGenes]\n  \n  # \u901a\u8fc7\u805a\u7c7b\uff0c\u67e5\u770b\u662f\u5426\u6709\u660e\u663e\u5f02\u5e38\u6837\u672c, \u5982\u679c\u6709\u9700\u8981\u5254\u9664\u6389\n  plot(hclust(dist(datExpr)),\n       cex.lab = 1.5,\n       cex.axis = 1.5,\n       cex.main = 2)\n  \n  \n  # \u5982\u679c\u5269\u4f59\u57fa\u56e0\u4ecd\u7136\u592a\u591a(\u5982 5 \u523010\u4e07\u6761)\uff0c\n  ##\u800c\u7535\u8111\u914d\u7f6e\u5185\u5b58\u4e0d\u591f\uff0c\u53ef\u4ee5\u8fdb\u4e00\u6b65\u8fc7\u6ee4\u6389\n  ##\u6ce2\u52a8\u5c0f\u7684\u57fa\u56e0\u3002\u4e0d\u8981\u53ea\u7528\u5dee\u5f02\u57fa\u56e0\u505a\u3002\n  # library(genefilter)\n  # var_gene_exp <- varFilter(\n  #   as.matrix(t(datExpr)),\n  #   var.func = IQR,\n  #   var.cutoff = 0.5, # \u5b9e\u9645\u9879\u76ee\u4e2d\u8bbe\u7f6e 0.5 \u4ee5\u4e0b\n  #   filterByQuantile = TRUE)\n  # \n  # datExpr <- t(var_gene_exp)\n  datExpr[1:4,1:4]\n}\n\n{\n  datTraits <- sample_info\n}\n\n{\n  library(WGCNA)\n  # \u591a\u7ebf\u7a0b\n  enableWGCNAThreads(nThreads = 80)\n  ## disableWGCNAThreads()\n  \n  # \u901a\u8fc7\u5bf9 power \u7684\u591a\u6b21\u8fed\u4ee3\uff0c\u786e\u5b9a\u6700\u4f73 power\n  sft <- pickSoftThreshold(\n    datExpr,\n    powerVector = 1:20, # \u5c1d\u8bd5 1 \u5230 20\n    networkType = \"unsigned\"\n  )\n}\n\n{\n  # \u753b\u56fe\n  library(ggplot2)\n  library(ggrepel)\n  library(cowplot)\n  library(ggthemes)\n  \n  fig_power1 <- ggplot(data = sft$fitIndices,\n                       aes(x = Power,\n                           y = SFT.R.sq)) +\n    geom_point(color = 'red') +\n    geom_text_repel(aes(label = Power)) +\n    geom_hline(aes(yintercept = 0.85), color = 'red') +\n    labs(title = 'Scale independence',\n         x = 'Soft Threshold (power)',\n         y = 'Scale Free Topology Model Fit,signed R^2') +\n    theme_few() +\n    theme(plot.title = element_text(hjust = 0.5))\n  \n  fig_power2 <- ggplot(data = sft$fitIndices,\n                       aes(x = Power,\n                           y = mean.k.)) +\n    geom_point(color = 'red') +\n    geom_text_repel(aes(label = Power)) +\n    labs(title = 'Mean connectivity',\n         x = 'Soft Threshold (power)',\n         y = 'Mean Connectivity') +\n    theme_few()+\n    theme(plot.title = element_text(hjust = 0.5))\n  \n  plot_grid(fig_power1, fig_power2)\n}\n\n{\n  net <- blockwiseModules(\n    # 0.\u8f93\u5165\u6570\u636e\n    datExpr,\n    \n    # 1. \u8ba1\u7b97\u76f8\u5173\u7cfb\u6570\n    corType = \"pearson\", # \u76f8\u5173\u7cfb\u6570\u7b97\u6cd5\uff0cpearson|bicor\n    \n    # 2. \u8ba1\u7b97\u90bb\u63a5\u77e9\u9635\n    power = 6, # \u524d\u9762\u5f97\u5230\u7684 soft power\n    networkType = \"unsigned\", # unsigned | signed | signed hybrid\n    \n    # 3. \u8ba1\u7b97 TOM \u77e9\u9635\n    TOMType = \"unsigned\", # none | unsigned | signed\n    saveTOMs = TRUE,\n    saveTOMFileBase = \"blockwiseTOM\",\n    \n    # 4. \u805a\u7c7b\u5e76\u5212\u5206\u6a21\u5757\n    deepSplit = 2, # 0|1|2|3|4, \u503c\u8d8a\u5927\u5f97\u5230\u7684\u6a21\u5757\u5c31\u8d8a\u591a\u8d8a\u5c0f\n    minModuleSize = 30,\n    \n    # 5. \u5408\u5e76\u76f8\u4f3c\u6a21\u5757\n    ## 5.1 \u8ba1\u7b97\u6a21\u5757\u7279\u5f81\u5411\u91cf\uff08module eigengenes\uff0c MEs\uff09\uff0c\u5373 PC1\n    ## 5.2 \u8ba1\u7b97 MEs \u4e0e datTrait \u4e4b\u95f4\u7684\u76f8\u5173\u6027\n    ## 5.3 \u5bf9\u8ddd\u79bb\u5c0f\u4e8e mergeCutHeight \uff081-cor\uff09\u7684\u6a21\u5757\u8fdb\u884c\u5408\u5e76\n    mergeCutHeight = 0.25,\n    \n    # \u5176\u4ed6\u53c2\u6570\n    numericLabels = FALSE, # \u4ee5\u6570\u5b57\u547d\u540d\u6a21\u5757\n    nThreads = 0, # 0 \u5219\u4f7f\u7528\u6240\u6709\u53ef\u7528\u7ebf\u7a0b\n    maxBlockSize = 200000 # \u9700\u8981\u5927\u4e8e\u57fa\u56e0\u7684\u6570\u76ee\n  )\n  # \u67e5\u770b\u6bcf\u4e2a\u6a21\u5757\u5305\u542b\u57fa\u56e0\u6570\u76ee\n  table(net$colors)\n}\n\n{\n  # \u540c\u65f6\u7ed8\u5236\u805a\u7c7b\u56fe\u548c\u6a21\u5757\u989c\u8272\n  plotDendroAndColors(\n    dendro = net$dendrograms[[1]],\n    colors = net$colors,\n    groupLabels = \"Module colors\",\n    dendroLabels = FALSE,\n    addGuide = TRUE)\n}\n\n{\n  # \u8ba1\u7b97\u76f8\u5173\u6027\n  moduleTraitCor <- cor(\n    net$MEs,\n    datTraits,\n    use = \"p\",\n    method = 'spearman' # \u6ce8\u610f\u76f8\u5173\u7cfb\u6570\u8ba1\u7b97\u65b9\u5f0f\n  )\n  \n  # \u8ba1\u7b97 Pvalue\n  moduleTraitPvalue <- corPvalueStudent(\n    moduleTraitCor,\n    nrow(datExpr))\n}\n\n{\n  # \u76f8\u5173\u6027 heatmap\n  sizeGrWindow(10,6)\n  \n  # \u8fde\u63a5\u76f8\u5173\u6027\u548c pvalue\n  textMatrix <- paste(signif(moduleTraitCor, 2), \"\\n(\",\n                      signif(moduleTraitPvalue, 1), \")\", sep = \"\");\n  dim(textMatrix) <- dim(moduleTraitCor)\n  \n  \n  # heatmap \u753b\u56fe \n  par(mar = c(6, 8.5, 3, 3))\n  labeledHeatmap(Matrix = moduleTraitCor,\n                 xLabels = names(datTraits),\n                 yLabels = names(net$MEs),\n                 ySymbols = names(net$MEs),\n                 colorLabels = FALSE,\n                 colors = blueWhiteRed(50),\n                 textMatrix = textMatrix,\n                 setStdMargins = FALSE,\n                 cex.text = 0.5,\n                 zlim = c(-1,1),\n                 main = paste(\"Module-trait relationships\"))\n}\n\n{\n  # \u521b\u5efa\u7b80\u5316\u7248\u7684 WGCNA \u7ed3\u679c\uff08\u4e0d\u9700\u8981 gene_info\uff09\n  wgcna_result <- data.frame(\n    gene_id = names(net$colors),\n    module = net$colors,\n    stringsAsFactors = FALSE\n  )\n  \n  # \u67e5\u770b\u7ed3\u679c\n  head(wgcna_result)\n  table(wgcna_result$module)\n}\n\n{\n  # \u9700\u8981\u5bfc\u51fa\u7684\u6a21\u5757\n  my_modules <- c('brown')\n  \n  # \u63d0\u53d6\u8be5\u6a21\u5757\u7684\u8868\u8fbe\u77e9\u9635\n  m_wgcna_result <- filter(wgcna_result, module %in% my_modules)\n  m_datExpr <- datExpr[, m_wgcna_result$gene_id]\n  \n  # \u8ba1\u7b97\u8be5\u6a21\u5757\u7684 TOM \u77e9\u9635  \n  m_TOM <- TOMsimilarityFromExpr(\n    m_datExpr,\n    power = 6,\n    networkType = \"unsigned\",\n    TOMType = \"unsigned\")\n  \n  dimnames(m_TOM) <- list(colnames(m_datExpr), colnames(m_datExpr))\n  \n  # \u5bfc\u51fa Cytoscape \u8f93\u5165\u6587\u4ef6\n  cyt <- exportNetworkToCytoscape(\n    m_TOM,\n    edgeFile = \"CytoscapeInput-network.txt\",\n    weighted = TRUE,\n    threshold = 0.2)\n}\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8d3b113 elementor-widget elementor-widget-image\" data-id=\"8d3b113\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img decoding=\"async\" width=\"839\" height=\"512\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/Heatmap.png\" class=\"attachment-large size-large wp-image-2421\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/Heatmap.png 839w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/Heatmap-300x183.png 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/11\/Heatmap-768x469.png 768w\" sizes=\"(max-width: 839px) 100vw, 839px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5eb846e elementor-widget elementor-widget-text-editor\" data-id=\"5eb846e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u901a\u8fc7\u6bcf\u4e2a\u6a21\u5757\u4e0a\u65b9\u663e\u8457\u6027\u548c\u4e0b\u65b9\u7684p\u503c\u6765\u7b5b\u9009\u663e\u8457\u7684\u6a21\u5757\uff0c\u6bd4\u5982\u548cASV\u5448\u73b0\u6b63\u76f8\u5173\u7684\u4e3abrown\uff0c\u8d1f\u76f8\u5173\u7684\u4e3ablue\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>1. \u524d\u8a00 \u6bd4\u8f83\u8f6c\u5f55\u7ec4\u4f5c\u4e3a\u751f\u4fe1\u5206\u6790\u4e2d\u6700\u5e38\u89c4\u7684\u5206\u6790\uff0c\u5e95\u5c42\u903b\u8f91\u662f\u901a\u8fc7\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\uff0c\u7b5b\u9009\u5dee\u5f02\u57fa\u56e0\uff0c\u968f\u540e\u8fdb\u884c\u4e0b\u6e38\u7684\u5bcc\u96c6 &#8230; <a title=\"\u600e\u4e48\u4ee5\u6bd4\u8f83\u8f6c\u5f55\u7ec4\u7684\u5206\u6790\u65b9\u5f0f\u5206\u6790\u5b8f\u57fa\u56e0\u7ec4\" class=\"read-more\" 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