{"id":375,"date":"2024-12-31T09:14:41","date_gmt":"2024-12-31T01:14:41","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=375"},"modified":"2025-01-02T17:08:41","modified_gmt":"2025-01-02T09:08:41","slug":"dn-ds-%e7%9a%84%e8%ae%a1%e7%ae%97%e5%8f%8a%e5%85%b6%e6%a0%b8%e5%bf%83%e7%90%86%e5%bf%b5","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2024\/12\/31\/dn-ds-%e7%9a%84%e8%ae%a1%e7%ae%97%e5%8f%8a%e5%85%b6%e6%a0%b8%e5%bf%83%e7%90%86%e5%bf%b5\/","title":{"rendered":"dN\/dS \u7684\u8ba1\u7b97\uff0c\u6838\u5fc3\u7406\u5ff5\u53ca\u5e94\u7528"},"content":{"rendered":"<h4><a href=\"https:\/\/biojuse.com\/2023\/12\/30\/dNdS%20%E7%9A%84%E8%AE%A1%E7%AE%97%E5%8F%8A%E5%85%B6%E6%A0%B8%E5%BF%83%E7%90%86%E5%BF%B5\/\">\u6838\u5fc3\u7406\u5ff5\u539f\u6587\u94fe\u63a5<\/a><\/h4>\n<h2>dN\/dS \u662f\u4ec0\u4e48<\/h2>\n<p>\u8fd9\u91cc\u7684 S \u5373 Synonymous\uff0cN \u5373 Nonsynonymous\u3002<\/p>\n<p>dN \u6307\u7684\u662f\u975e\u540c\u4e49\u66ff\u6362\u7387\uff0cdS \u6307\u7684\u662f\u540c\u4e49\u66ff\u6362\u7387\u3002\u4f46\u6211\u8ba4\u4e3a\u53e6\u4e00\u4e2a\u77e5\u4e4e\u535a\u4e3b\u6587\u7ae0\u91cc\u7684\u8bf4\u6cd5\u4f1a\u66f4\u52a0\u76f4\u89c2\u4e00\u4e9b\uff1a<\/p>\n<ul>\n<li>dN: \u6bcf\u4e2a\u975e\u540c\u4e49\u4f4d\u70b9\u4e0a\u53d1\u751f\u7684\u975e\u540c\u4e49\u7a81\u53d8\u7684\u6570\u91cf\u3002<\/li>\n<li>dS: \u6bcf\u4e2a\u540c\u4e49\u4f4d\u70b9\u4e0a\u53d1\u751f\u7684\u540c\u4e49\u7a81\u53d8\u7684\u6570\u91cf\u3002<\/li>\n<\/ul>\n<h2>\u8ba1\u7b97\u539f\u7406<\/h2>\n<p>\u9996\u5148\uff0c\u7b80\u5355\u6765\u8bf4\uff0cdN \u548c dS \u7684\u8ba1\u7b97\u6d89\u53ca\u5230\u56db\u4e2a\u53d8\u91cf\uff0c\u5206\u522b\u4e3a\u540c\u4e49\u7a81\u53d8\u6570\u91cf\uff08S\uff09\u3001\u975e\u540c\u4e49\u7a81\u53d8\u6570\u91cf\uff08N\uff09\u4ee5\u53ca\u540c\u4e49\u4f4d\u70b9\u6570\u91cf\uff08Ssite\uff09\u548c\u975e\u540c\u4e49\u4f4d\u70b9\u6570\u91cf\uff08Nsite\uff09\u3002<br \/>\n<img decoding=\"async\" src=\"https:\/\/www.kz-hub.tech\/wp-content\/uploads\/2025\/01\/dnds_formula-300x89.jpg\" alt=\"\" \/><br \/>\n\u524d\u4e24\u4e2a\u53d8\u91cf N \u548c S \u975e\u5e38\u597d\u7406\u89e3\uff0c\u6240\u4ee5\u8fd9\u91cc\u9700\u8981\u91cd\u70b9\u5173\u6ce8\u7684\u662f\u540e\u4e24\u4e2a\u53d8\u91cf Nsite \u548c Ssite\uff0c\u5373\u6bcf\u79cd\u7c7b\u578b\u7684\u4f4d\u70b9\u6570\u91cf\u662f\u4ec0\u4e48\uff1f\u5b83\u4eec\u662f\u5982\u4f55\u5f97\u5230\u7684\uff1f\u4f46\u5728\u8fd9\u4e4b\u524d\uff0c\u6211\u4eec\u5148\u7b80\u5355\u56de\u987e\u4e00\u4e0b\u4e00\u4e9b\u5e38\u89c1\u7684\u7a81\u53d8\u7c7b\u578b\u3002<\/p>\n<h2>\u7a81\u53d8\u7c7b\u578b<\/h2>\n<p>\u6211\u4eec\u90fd\u77e5\u9053\uff0c\u4e00\u4e2a\u5bc6\u7801\u5b50\u5728\u53d1\u751f\u7a81\u53d8\u65f6\uff0c\u5176\u6027\u8d28\u53ef\u80fd\u53d1\u751f\u4ee5\u4e0b\u51e0\u79cd\u53d8\u5316\uff0c\u4ee5\u5bc6\u7801\u5b50 TTT \u4e3a\u4f8b\uff08\u5176\u7f16\u7801\u82ef\u4e19\u6c28\u9178 Phe\uff09\uff1a<\/p>\n<ul>\n<li>\u9519\u4e49\u7a81\u53d8\uff1a\u7531\u7f16\u7801\u4e00\u4e2a\u6c28\u57fa\u9178\u53d8\u4e3a\u7f16\u7801\u53e6\u4e00\u4e2a\u6c28\u57fa\u9178\uff0c\u4f8b\u5982 TTT(\u82ef\u4e19\u6c28\u9178)&gt;ATT(\u5f02\u4eae\u6c28\u9178)\u3002<\/li>\n<li>\u540c\u4e49\u7a81\u53d8\uff1a\u7a81\u53d8\u8fc7\u540e\uff0c\u4ecd\u7f16\u7801\u76f8\u540c\u6c28\u57fa\u9178\uff0c\u4f8b\u5982 TTT(\u82ef\u4e19\u6c28\u9178)&gt;TTC(\u82ef\u4e19\u6c28\u9178)\u3002\u540c\u4e49\u7a81\u53d8\u901a\u5e38\u53d1\u751f\u5728\u5bc6\u7801\u5b50\u7684\u7b2c\u4e09\u4e2a\u78b1\u57fa\u4e0a\uff08\u6709\u65f6\u7b2c\u4e00\u4e2a\u78b1\u57fa\u4e5f\u53ef\u4ee5\uff0c\u4f8b\u5982 AGA&gt;CGA \u7686\u7f16\u7801\u7cbe\u6c28\u9178\uff09\uff0c\u6b64\u65f6\u6211\u4eec\u79f0\u8fd9\u4e2a\u4f4d\u70b9\u5177\u6709\u7b80\u5e76\u6027\u3002\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0c\u5728\u67d0\u4e9b\u60c5\u51b5\u4e0b\uff0c\u7ec8\u6b62\u5bc6\u7801\u5b50\u7a81\u53d8\u4e3a\u7ec8\u6b62\u5bc6\u7801\u5b50\uff08\u4f8b\u5982 TAA&gt;TAG\uff09\u4e5f\u88ab\u89c6\u4e3a\u4e00\u79cd\u540c\u4e49\u7a81\u53d8\u3002<\/li>\n<\/ul>\n<p>\u9664\u4e86\u8fd9\u4e00\u4e9b\u53ef\u80fd\u7684\u7a81\u53d8\u4ee5\u5916\uff0c\u8fd8\u6709\u4e00\u4e9b\u5176\u4ed6\u7684\u60c5\u51b5\uff0c\u4f8b\u5982\uff0cTAT(\u916a\u6c28\u9178) \u53ef\u80fd\u53d8\u4e3a\u4e00\u4e2a\u7ec8\u6b62\u5bc6\u7801\u5b50\uff08TAA\uff09\uff0c\u8fd9\u65f6\u6211\u4eec\u79f0\u5176\u4e3a\u65e0\u4e49\u7a81\u53d8\uff0c\u5728\u67d0\u4e9b\u60c5\u666f\u4e0b\uff0c\u8fd9\u4e5f\u53ef\u4ee5\u88ab\u79f0\u4e3a\u622a\u65ad\u7a81\u53d8 (protein-truncating variant\uff0cPTV)\u3002<\/p>\n<p>\u4ee5\u4e0a\u7a81\u53d8\u7c7b\u578b\u5e76\u4e0d\u6db5\u76d6\u5168\u90e8\u60c5\u51b5\uff0c\u4f46\u8fd9\u4e9b\u7a81\u53d8\u662f\u5927\u591a dN\/dS \u7b97\u6cd5\u7684\u5173\u6ce8\u5bf9\u8c61\u3002<\/p>\n<p>\u90e8\u5206\u60c5\u51b5\u4e0b\uff0c\u9519\u4e49\u7a81\u53d8\u548c\u65e0\u4e49\u7a81\u53d8\u4f1a\u88ab\u7edf\u4e00\u89c6\u4e3a\u975e\u540c\u4e49\u7a81\u53d8\uff0c\u5f53\u7136\u5728\u4e00\u4e9b\u7b97\u6cd5\u4e2d\uff0c\u65e0\u4e49\u7a81\u53d8\u5e76\u4e0d\u88ab\u8003\u8651\u3002\u8fd9\u4e5f\u53d6\u51b3\u4e8e\u5177\u4f53\u7684\u7814\u7a76\u76ee\u7684\u548c\u9700\u8981\u3002<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.kz-hub.tech\/wp-content\/uploads\/2025\/01\/type_of_mut-300x169.jpeg\" alt=\"\" \/><\/p>\n<h2>\u4f4d\u70b9\u7c7b\u578b<\/h2>\n<p>\u73b0\u5728\u6211\u4eec\u77e5\u9053\uff0c\u4e00\u4e2a\u4f4d\u70b9\u7684\u7a81\u53d8\u53ef\u80fd\u5e26\u6765\u7684\u7ed3\u679c\u4e5f\u4e0d\u540c\uff0c\u8fd9\u4e5f\u662f\u8ba1\u7b97 Ssite \u548c Nsite \u7684\u5173\u952e\u6240\u5728\u3002<\/p>\n<p>\u9996\u5148\u5bf9\u4e8e\u4efb\u4f55\u60c5\u51b5\u4e0b\u7684 Nsite \u548c Ssite \u8ba1\u7b97\u7ed3\u679c\uff0c\u6211\u4eec\u90fd\u6709\uff1a<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.kz-hub.tech\/wp-content\/uploads\/2025\/01\/Nsite_Ssite-300x64.jpg\" alt=\"\" \/><\/p>\n<p>\u4f8b\u5982\uff0c\u5bf9\u4e8e\u4e00\u4e2a\u957f\u5ea6\u4e3a 3 \u7684\u5bc6\u7801\u5b50\uff0c\u5b83\u6240\u8ba1\u7b97\u51fa\u6765\u7684 Nsite \u548c Ssite \u603b\u548c\u4e5f\u5fc5\u5b9a\u4e3a 3\u3002<\/p>\n<p>\u63a5\u4e0b\u6765\u5c31\u662f\u8ba1\u7b97\u8fc7\u7a0b\uff0c\u6700\u7b80\u5355\u7684\u8ba1\u7b97\u5373\u904d\u5386\u6bcf\u4e2a\u4f4d\u70b9\u7684\u6bcf\u79cd\u7a81\u53d8\u60c5\u51b5\u53ef\u80fd\u5bfc\u81f4\u7684\u7a81\u53d8\u7c7b\u578b\uff0c\u5bf9\u4e8e TTT\uff0c\u6211\u4eec\u53ef\u4ee5\u5217\u4e3e\u51fa\u5b83\u7684\u6240\u6709\u53ef\u80fd\u7a81\u53d8\u60c5\u51b5\uff0c\u8fd9\u91cc\u76f4\u63a5\u7528\u6768\u5b50\u6052\u300a\u8ba1\u7b97\u5206\u5b50\u8fdb\u5316\u300b\u4e2d\u7684\u4e00\u5f20\u56fe\u4f5c\u4e3a\u793a\u4f8b\uff1a<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.kz-hub.tech\/wp-content\/uploads\/2025\/01\/TTTtable-300x215.jpg\" alt=\"\" \/><\/p>\n<p>\u6211\u4eec\u5148\u4ec5\u8003\u8651 k=1 \u4e00\u680f\uff0ck=2 \u5728\u540e\u6587\u4e2d\u6211\u4eec\u4f1a\u62d3\u5c55\u8ba8\u8bba\u3002<\/p>\n<p>\u5176\u4e2d\uff0c\u5bf9\u4e8e\u4e00\u4e2a\u5bc6\u7801\u5b50\u7684\u6bcf\u4e00\u4e2a\u4f4d\u70b9\uff0c\u5b83\u90fd\u53ef\u4ee5\u7a81\u53d8\u6210\u9664\u5b83\u81ea\u8eab\u4e4b\u5916\u7684\u78b1\u57fa\uff0c\u56e0\u6b64\u6bcf\u4e2a\u4f4d\u70b9\u90fd\u6709\u4e09\u4e2a Target codon\uff0c\u5176\u4e2d\u540c\u4e49\u7a81\u53d8\u7684\u60c5\u51b5\u4ec5\u6709 TTT&gt;TTC\uff0c\u800c\u5176\u4ed6\u90fd\u4e3a\u975e\u540c\u4e49\u7a81\u53d8\u3002<\/p>\n<p>\u56e0\u6b64\uff0c\u8fd9\u91cc\u5171\u6709 9 \u4e2a\u60c5\u51b5\uff0c\u5176\u4e2d\u540c\u4e49\u7a81\u53d8\u5360 1 \u4e2a\uff0c\u975e\u540c\u4e49\u7a81\u53d8\u5360 8 \u4e2a\u3002\u56e0\u6b64\uff0c\u540c\u4e49\u4f4d\u70b9\u6570\u91cf\u4e3a 1\/9 <em> 3\uff083 \u5373\u5bc6\u7801\u5b50\u957f\u5ea6\uff09\uff0c\u975e\u540c\u4e49\u4f4d\u70b9\u6570\u91cf\u4e3a 8\/9 <\/em> 3\u3002\u6700\u540e\u5219\u5206\u522b\u4e3a\u8868\u4e2d\u7684 1\/3 \u548c 8\/3\u3002<\/p>\n<h2>\u7a81\u53d8\u8ba1\u6570\u53ca dN\/dS \u8ba1\u7b97<\/h2>\n<p>\u77e5\u9053\u4f4d\u70b9\u6570\u91cf\u540e\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u8ba1\u7b97\u4e86\uff0c\u4f9d\u7136\u4ee5\u4e00\u4e2a\u6700\u7b80\u5355\u7684\u60c5\u51b5\u4f5c\u4e3a\u793a\u4f8b\uff0c\u5047\u8bbe\u6211\u4eec\u6709\u4e00\u4e2a\u5305\u542b\u4e5d\u4e2a TTT \u7684 CDS\uff1a<\/p>\n<ul>\n<li>\n<p>TTTTTTTTTTTTTTTTTTTTTTTTTTT<br \/>\n\u901a\u8fc7\u8ba1\u7b97\u6211\u4eec\u53ef\u4ee5\u77e5\u9053\uff0c\u5b83\u5177\u6709 3 \u4e2a\u540c\u4e49\u4f4d\u70b9\u548c 24 \u4e2a\u975e\u540c\u4e49\u4f4d\u70b9\uff0c\u5047\u8bbe\u8fd9\u91cc\u5728\u4e24\u4e2a\u5bc6\u7801\u5b50\u4e0a\u6211\u4eec\u89c2\u5bdf\u5230\u4e86\u4e00\u4e2a\u540c\u4e49\u7a81\u53d8\u548c\u4e00\u4e2a\u975e\u540c\u4e49\u7a81\u53d8\uff1a<\/p>\n<\/li>\n<li>\n<p>TTCTTTTTTTTTTTTTTTTTTTTTTAT<br \/>\n\u90a3\u4e48\u6b64\u65f6\uff0c\u5176 dN = 1\/24\uff0cdS = 1\/3\uff0c\u8ba1\u7b97\u5f97\u5230 dN\/dS = 1\/8\u3002<\/p>\n<\/li>\n<\/ul>\n<p>\u5f53\u7136\uff0c\u5728\u7a81\u53d8\u8ba1\u6570\u6b65\u9aa4\u4e2d\u4e5f\u53ef\u80fd\u51fa\u73b0\u66f4\u52a0\u590d\u6742\u7684\u60c5\u51b5\uff0c\u4f8b\u5982\u540c\u4e00\u4e2a\u5bc6\u7801\u5b50\u4e0a\u51fa\u73b0\u4e86\u4e24\u4e2a\u7a81\u53d8\uff0c\u4f8b\u5982 TTT \u53d8\u4e3a\u4e86 TCA\uff0c\u8fd9\u79cd\u60c5\u51b5\u5c31\u8981\u8003\u8651\u591a\u6761\u8fdb\u5316\u9014\u5f84\uff1a<\/p>\n<ul>\n<li>TTT &gt; TTA &gt; TCA\uff08\u82ef\u4e19\u6c28\u9178 &gt; \u4eae\u6c28\u9178 &gt; \u4e1d\u6c28\u9178\uff09\uff0c\u8fd9\u6761\u9014\u5f84\u6d89\u53ca\u5230\u4e24\u4e2a\u975e\u540c\u4e49\u7a81\u53d8\u3002<\/li>\n<li>TTT &gt; TCT &gt; TCA\uff08\u82ef\u4e19\u6c28\u9178 &gt; \u4e1d\u6c28\u9178 &gt; \u4e1d\u6c28\u9178\uff09\uff0c\u8fd9\u6761\u9014\u5f84\u6d89\u53ca\u5230\u4e00\u4e2a\u975e\u540c\u4e49\u7a81\u53d8\u548c\u4e00\u4e2a\u540c\u4e49\u7a81\u53d8\u3002<\/li>\n<\/ul>\n<p>\u5bf9\u4e8e\u8fd9\u79cd\u60c5\u51b5\uff0c\u5e38\u89c1\u7684\u505a\u6cd5\u6709\u5bf9\u4e0d\u540c\u7684\u9014\u5f84\u8d4b\u4e88\u5408\u9002\u7684\u6743\u91cd\u7b49\uff0c\u66f4\u591a\u7ec6\u8282\u5982\u679c\u770b\u5ba2\u611f\u5174\u8da3\u53ef\u81ea\u884c\u6df1\u5165\u4e86\u89e3\u3002<\/p>\n<h2>dN\/dS \u5e94\u8be5\u662f\u591a\u5c11<\/h2>\n<p>\u5728\u6700\u7b80\u5355\u7684 dN\/dS \u8ba1\u7b97\u4e2d\uff08\u524d\u6587\u4e2d\u7684 k=1\uff09\uff0c\u5176\u4e2d\u6709\u4e00\u4e2a\u9690\u6027\u7684\u5047\u8bbe\uff1a\u6211\u4eec\u8ba4\u4e3a\u6bcf\u4e00\u4e2a\u4f4d\u70b9\u4e0a\u6bcf\u4e00\u4e2a\u7a81\u53d8\u60c5\u51b5\u53d1\u751f\u7684\u6982\u7387\u90fd\u662f\u76f8\u7b49\u7684\u3002<\/p>\n<p>\u90a3\u4e48\uff0c\u6211\u4eec\u7ee7\u7eed\u4ee5 TTT \u4f5c\u4e3a\u4f8b\u5b50\uff0c\u5982\u679c\u6bcf\u4e00\u4e2a\u7a81\u53d8\u60c5\u51b5\u53d1\u751f\u7684\u6982\u7387\u90fd\u662f\u76f8\u7b49\u7684\uff0c\u7406\u60f3\u60c5\u51b5\u4e0b\uff08\u65e0\u9009\u62e9\u538b\u529b\uff09\u6211\u4eec\u4f1a\u83b7\u5f97\u7684 dN\/dS \u503c\u4f1a\u662f\u591a\u5c11\uff1f<\/p>\n<p>\u5f88\u7b80\u5355\uff0c\u53d1\u751f\u540c\u4e49\u7a81\u53d8\u7684\u6982\u7387\u662f 1\/9\uff0c\u53d1\u751f\u975e\u540c\u4e49\u7a81\u53d8\u7684\u6982\u7387\u662f 8\/9\uff0c\u5047\u8bbe\u53d1\u751f\u7a81\u53d8\u7684\u6570\u91cf\u4e3a x\uff0c\u5219\u901a\u8fc7\u8ba1\u7b97\u548c\u7ea6\u5206\u540e\u6211\u4eec\u53ef\u4ee5\u53d1\u73b0\uff0cdN\/dS \u503c\u5e94\u8be5\u662f 1\u3002<\/p>\n<p>\u5f53\u7136\uff0c\u5728\u73b0\u5b9e\u6761\u4ef6\u4e2d\uff0c\u6bcf\u4e00\u4e2a\u7a81\u53d8\u60c5\u51b5\u53d1\u751f\u7684\u6982\u7387\u5e76\u4e0d\u4e00\u5b9a\u76f8\u7b49\uff0c\u4f8b\u5982\uff0c\u8f6c\u6362\uff08transition\uff09\u53d1\u751f\u7684\u6982\u7387\u5c31\u8981\u6bd4\u98a0\u6362\uff08transversion\uff09\u66f4\u9ad8\uff0c\u800c\u5f88\u591a\u540c\u4e49\u7a81\u53d8\u90fd\u662f\u8f6c\u6362\u4e8b\u4ef6\uff0c\u56e0\u6b64\u5982\u679c\u6211\u4eec\u5ffd\u7565\u8f6c\u6362\u548c\u98a0\u6362\u4e4b\u95f4\u7684\u53d1\u751f\u6982\u7387\u5dee\u5f02\uff0c\u5c31\u4f1a\u5bfc\u81f4 Ssite \u4f4e\u4f30\u548c Nsite \u7684\u9ad8\u4f30\uff0c\u4ece\u800c\u5bfc\u81f4\u8ba1\u7b97\u7684 dN\/dS \u504f\u4f4e\u3002<\/p>\n<p>\u5bf9\u4e8e\u4e0a\u9762\u8fd9\u79cd\u60c5\u51b5\uff0c\u4e00\u79cd\u53ef\u884c\u7684\u65b9\u6cd5\u5c31\u662f\u5728\u8ba1\u7b97\u8f6c\u6362\u4e8b\u4ef6\u65f6\uff0c\u7ed9\u5b83\u63d0\u4f9b\u7684\u4f4d\u70b9\u6570\u91cf\u8fdb\u884c\u76f8\u5e94\u52a0\u6743\uff0c\u4e5f\u5c31\u6709\u4e86\u8fd9\u4e2a\u8868\u683c\u4e2d k=2 \u7684\u60c5\u51b5\uff1a<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.kz-hub.tech\/wp-content\/uploads\/2025\/01\/TTTtable-300x215.jpg\" alt=\"\" \/><\/p>\n<p>\u76f8\u4f3c\u7684\u4e8b\u60c5\u8fd8\u53d1\u751f\u5728\u5bc6\u7801\u5b50\u504f\u597d\u7b49\u56e0\u7d20\u4e0a\uff0c\u800c\u5f88\u591a\u65b9\u6cd5\u4e5f\u9488\u5bf9\u8fd9\u4e9b\u70b9\u8fdb\u884c\u4e86\u6539\u8fdb\u3002\u4f8b\u5982\u4e00\u7bc7 <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0092867417311364\">17 \u5e74\u7684 cell \u6587\u7ae0<\/a>\u4e2d\uff0c\u4f5c\u8005\u4f7f\u7528 192 \u4e2a rate parameters (\u5305\u62ec\u4e0d\u540c\u7684\u66ff\u6362\u7c7b\u578b\u548c\u94fe\u5c5e\u6027\uff0c\u6709\u4e9b\u7c7b\u4f3c 3-mer \u7684\u7a81\u53d8\u7387\u6a21\u578b) \u6765\u8ba1\u7b97 dN\/dS\uff0c\u5e76\u53d1\u73b0\u5176\u4ed6\u65b9\u6cd5\u8981\u4e48\u9ad8\u4f30\u8981\u4e48\u4f4e\u4f30\u4e86 dN\/dS\u3002<\/p>\n<p>\u6240\u4ee5\uff0cdN\/dS \u6709\u4e00\u4e2a\u5f88\u5173\u952e\u7684\u8bbe\u8ba1\u7406\u5ff5\uff0c\u5c31\u662f\u5728\u5b8c\u5168\u6ca1\u6709\u9009\u62e9\u7684\u60c5\u51b5\u4e0b\uff0c\u8fd9\u4e2a\u503c\u5e94\u5f53\u7b49\u4e8e 1\uff0c\u5373\u540c\u4e49\u66ff\u4ee3\u7387\u548c\u975e\u540c\u4e49\u66ff\u4ee3\u7387\u5e94\u5f53\u662f\u76f8\u7b49\u7684\u3002\u8fd9\u4e2a\u6982\u5ff5\u5bf9\u4e8e\u540e\u7eed\u7684\u4e00\u7cfb\u5217\u5f15\u7533\u4e5f\u5f88\u91cd\u8981\u3002<\/p>\n<h2>dN\/dS \u6709\u4ec0\u4e48\u7528<\/h2>\n<p>\u73b0\u5728\u6211\u4eec\u80fd\u591f\u77e5\u9053\uff0c\u5982\u679c\u5b8c\u5168\u8003\u8651\u4e86\u4e0d\u540c\u66ff\u6362\u53d1\u751f\u6982\u7387\u7684\u5dee\u5f02\u5e76\u9488\u5bf9\u5b83\u4eec\u77eb\u6b63 Nsite \u548c Ssite \u7684\u8ba1\u7b97\uff0c\u90a3\u4e48 dN\/dS \u5728\u6ca1\u6709\u9009\u62e9\u7684\u60c5\u51b5\u4e0b\u5e94\u8be5\u662f\u7b49\u4e8e 1 \u7684\u3002<\/p>\n<p>\u5728\u5f88\u591a\u5730\u65b9\u6211\u4eec\u4e5f\u53ef\u4ee5\u770b\u5230\u8fd9\u4e48\u4e00\u4e2a\u7ed3\u8bba\uff1a<\/p>\n<ul>\n<li>dN\/dS &lt; 1\uff0c\u8868\u660e\u5b58\u5728\u7eaf\u5316\u9009\u62e9\u3002<\/li>\n<li>dN\/dS = 1\uff0c\u8868\u660e\u5904\u5728\u4e2d\u6027\u9009\u62e9\u4e0b\u3002<\/li>\n<li>dN\/dS &gt; 1\uff0c\u8868\u660e\u5b58\u5728\u6b63\u9009\u62e9\u3002<\/li>\n<\/ul>\n<p>\u4e5f\u5c31\u662f\u8bf4\uff0cdN\/dS \u8fd8\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u786e\u8ba4\u4e00\u4e2a\u57fa\u56e0\u6240\u5904\u7684\u72b6\u6001\uff0c\u5e76\u636e\u6b64\u63a8\u65ad\u51fa\u5176\u9009\u62e9\u7684\u673a\u5236\uff0c\u4e3a\u6211\u4eec\u7406\u89e3\u5176\u8fdb\u5316\u8fc7\u7a0b\u63d0\u4f9b\u4fe1\u606f\u3002<\/p>\n<p>\u90a3\u4e48\u4e3a\u4ec0\u4e48\u8bf4 dN\/dS = 1 \u65f6\uff0c\u57fa\u56e0\u5904\u4e8e\u4e2d\u6027\u9009\u62e9\u4e0b\u5462\uff1f\u8fd9\u91cc\u9996\u5148\u6211\u4eec\u8981\u660e\u786e\u4e00\u4e2a\u6982\u5ff5\uff0c\u4e2d\u6027\u9009\u62e9\u5e76\u4e0d\u610f\u5473\u7740\u4e0d\u5b58\u5728\u9009\u62e9\uff0c\u53ea\u662f\u5b83\u5bf9\u751f\u7269\u4f53\u7684\u9002\u5e94\u6027\u548c\u751f\u5b58\u51e0\u7387\u6ca1\u6709\u6b63\u9762\u6216\u8d1f\u9762\u7684\u5f71\u54cd\uff0c\u56e0\u6b64\u5b83\u5e76\u4e0d\u56e0\u81ea\u7136\u9009\u62e9\u800c\u9891\u7387\u589e\u52a0\u6216\u4e0b\u964d\uff0c\u5728\u79cd\u7fa4\u5185\u7684\u9891\u7387\u53d8\u5316\u5168\u7531\u9057\u4f20\u6f02\u53d8\u51b3\u5b9a\u3002\u5f53\u7136\u4e3a\u4e86\u65b9\u4fbf\u7406\u89e3\uff0c\u53ef\u4ee5\u5c06\u5176\u89c6\u4e3a\u548c \u201c\u6ca1\u6709\u9009\u62e9\u201d \u7b49\u6548\u3002<\/p>\n<p>\u540c\u6837\uff0c\u4e2d\u6027\uff08neutral\uff09\u7684\u6982\u5ff5\u4e5f\u662f\u5982\u6b64\uff0c\u4e00\u4e2a\u4e2d\u6027\u7a81\u53d8\u5c31\u662f\u5bf9\u751f\u7269\u65e2\u65e0\u76ca\u5904\u4e5f\u65e0\u5bb3\u5904\u7684\u7a81\u53d8\uff08\u4ea6\u6216\u662f\u5e26\u6765\u7684\u76ca\u5bb3\u76f8\u62b5\u6d88\uff09\u3002<\/p>\n<p>\u7136\u540e\u8981\u660e\u786e\u4e00\u4e2a\u6982\u5ff5\uff0cdN\/dS = 1 \u63a8\u5bfc\u51fa\u4e2d\u6027\u9009\u62e9\u7684\u524d\u63d0\u5047\u8bbe\u662f \u2014\u2014 \u540c\u4e49\u7a81\u53d8\u90fd\u662f\u4e2d\u6027\u7684\u3002<\/p>\n<p>\u4e0d\u59a8\u8bbe\u60f3\u4e00\u4e0b\uff0c\u5982\u679c\u540c\u4e49\u7a81\u53d8\u548c\u975e\u540c\u4e49\u7a81\u53d8\u90fd\u53d7\u5230\u76f8\u540c\u5f3a\u5ea6\u7684\u5f3a\u7eaf\u5316\u9009\u62e9\uff0c\u5bfc\u81f4\u5176\u7a81\u53d8\u6570\u91cf\u51cf\u5c11 50%\uff0c\u90a3\u4e48\u6700\u540e\u7b97\u51fa\u6765\u7684 dN\/dS \u4f9d\u7136\u7b49\u4e8e 1\u3002<\/p>\n<p>\u90a3\u4e48\u8fd9\u4e2a\u5047\u8bbe\u5230\u5e95\u6210\u4e0d\u6210\u7acb\u5462\uff1f\u5f88\u663e\u7136\u4e0d\u6210\u7acb\u3002\u8fd9\u4e2a\u5047\u8bbe\u4e3b\u8981\u7684\u6839\u57fa\u5728\u4e8e\u540c\u4e49\u7a81\u53d8\u5e76\u4e0d\u4f1a\u6539\u53d8\u86cb\u767d\u8d28\u7684\u7ec4\u6210\u548c\u7ed3\u6784\uff0c\u56e0\u6b64\u4ece\u86cb\u767d\u7684\u89d2\u5ea6\u51fa\u53d1\u5b83\u4e0d\u4f1a\u5bf9\u751f\u7269\u4f53\u7684\u8868\u578b\u4ea7\u751f\u5f71\u54cd\u3002\u4f46\u662f\u5728\u8f6c\u5f55\u7ffb\u8bd1\u9636\u6bb5\uff0c\u5df2\u7ecf\u6709\u5f88\u591a\u7814\u7a76\u53d1\u73b0\uff0c\u4e0d\u540c\u5bc6\u7801\u5b50\u5c31\u7b97\u7f16\u7801\u540c\u4e00\u6c28\u57fa\u9178\uff0c\u4e5f\u4f1a\u5b58\u5728\u6548\u7387\u548c\u8d28\u91cf\u4e0a\u7684\u4e0d\u540c\uff08\u8fd9\u4e5f\u662f\u5bc6\u7801\u5b50\u504f\u597d\u7684\u539f\u56e0\u4e4b\u4e00\uff09\uff0c\u6240\u4ee5\u5927\u591a\u6570\u540c\u4e49\u7a81\u53d8\u5176\u5b9e\u5f52\u6839\u7ed3\u5e95\u662f\u6709\u5bb3\u7684\uff08\u53ef\u89c1 <a href=\"https:\/\/www.nature.com\/articles\/s41586-022-04823-w\">Shen et al. 2022, Nature<\/a> \uff09\u3002<\/p>\n<p>\u4f46\u662f\u8fd9\u5f71\u4e0d\u5f71\u54cd\u6211\u4eec\u4f7f\u7528\u540c\u4e49\u7a81\u53d8\u4f5c\u4e3a\u4e2d\u6027\u7684 Proxy\uff1f\u5176\u5b9e\u8fd9\u662f\u4e2a\u5f88\u6709\u4e89\u8bae\u7684\u95ee\u9898\uff0c\u56e0\u4e3a\u5373\u4f7f\u540c\u4e49\u7a81\u53d8\u6709\u5bb3\uff0c\u4e5f\u5f88\u96be\u53bb\u91cf\u5316\u540c\u4e49\u7a81\u53d8\u5230\u5e95 \u201c\u591a\u6709\u5bb3\u201d\u3002\u4eca\u5e74 4 \u6708\u4efd\uff0c\u9488\u5bf9\u5f97\u51fa \u201c\u5927\u591a\u6570\u540c\u4e49\u7a81\u53d8\u90fd\u6709\u5bb3\u201d \u7684\u6587\u7ae0\u6709\u4eba\u4ea7\u751f\u4e86<a href=\"https:\/\/www.nature.com\/articles\/s41586-023-05865-4\">\u8d28\u7591<\/a>\u3002\u540c\u6837\uff0c\u5f88\u591a\u5176\u4ed6\u7684\u7814\u7a76\u8868\u660e\u540c\u4e49\u7a81\u53d8\u53ef\u80fd\u4ea7\u751f\u5f71\u54cd\u7684\u6982\u7387\u6bd4\u975e\u540c\u4e49\u5c0f\u5f97\u591a\u3002<\/p>\n<p>\u8fdd\u53cd\u4e00\u4e2a\u5047\u8bbe\u7684\u4e25\u91cd\u6027\uff0c\u4e00\u8981\u770b\u8fdd\u53cd\u7684\u7a0b\u5ea6\uff0c\u4e8c\u8981\u770b\u7406\u8bba\u5bf9\u6b64\u7684\u9c81\u68d2\u6027\u3002\u5c31\u4ee5\u6211\u4e2a\u4eba\u76ee\u524d\u8fdb\u884c\u7684\u5206\u6790\u6765\u770b\uff0c\u540c\u4e49\u7a81\u53d8\u53d7\u5230\u7684\u5f71\u54cd\u5e94\u8be5\u8f83\u4e3a\u8f7b\u5fae\u3002\u4ece\u5404\u79cd\u4f7f\u7528 dN\/dS \u8fdb\u884c\u9009\u62e9\u63a8\u65ad\u7684\u5206\u6790\u6765\u770b\uff0c\u4f3c\u4e4e\u5176\u7ed3\u679c\u90fd \u201c\u5408\u4e4e\u60c5\u7406\u201d\u3002\u5f53\u7136\uff0c\u5177\u4f53\u60c5\u51b5\u5982\u4f55\u4e5f\u6709\u5f85\u66f4\u8be6\u5c3d\u7684\u63a2\u8ba8\u3002<\/p>\n<h2>\u539f\u7406\u603b\u7ed3<\/h2>\n<ol>\n<li>\u8ba1\u7b97 Nsite \u548c Ssite \u65f6\uff0c\u5bf9\u4e8e\u7a81\u53d8\u7387\u9ad8\u7684\u7a81\u53d8\u7c7b\u578b\uff0c\u9700\u8981\u5bf9\u5176\u8fdb\u884c\u4e00\u5b9a\u7684\u52a0\u6743\u4ee5\u5e73\u8861\u5176\u5bf9 dN \u548c dS \u8ba1\u7b97\u7684\u8d21\u732e\u3002\u4ee5\u5f80\u7684\u8ba1\u7b97\u4e2d\uff0c\u8f6c\u6362-\u98a0\u6362\u6bd4\u7387 \u548c \u5bc6\u7801\u5b50\u504f\u597d \u7b49\u90fd\u662f\u57fa\u4e8e\u8be5\u70b9\u8003\u8651\u5bf9\u8ba1\u7b97\u8fdb\u884c\u4fee\u6b63\u3002<\/li>\n<li>\u57fa\u4e8e\u7a81\u53d8\u53d1\u751f\u6982\u7387\u77eb\u6b63\u540e\u8ba1\u7b97\u7684 dN\/dS \u53ef\u4ee5\u4f5c\u4e3a\u9009\u62e9\u60c5\u51b5\u7684\u53c2\u8003\u3002\u5982\u679c\u540c\u4e49\u7a81\u53d8\u7684\u4e2d\u6027\u5047\u8bbe\u662f\u6b63\u786e\u7684\u6216\u8005\u51e0\u8fd1\u6b63\u786e\u7684\uff0c\u5219\u5f53 dN\/dS \u7b49\u4e8e 1 \u65f6\u6211\u4eec\u53ef\u4ee5\u8ba4\u4e3a\u8be5\u86cb\u767d\u7f16\u7801\u57fa\u56e0\u5904\u4e8e\u4e2d\u6027\u9009\u62e9\u4e0b\u3002<\/li>\n<\/ol>\n<h2>\u8f6f\u4ef6\u8ba1\u7b97dN\/dS<\/h2>\n<p><a href=\"https:\/\/github.com\/im3sanger\/dndscv\">dndscv Github \u7f51\u5740<\/a><br \/>\n<a href=\"https:\/\/www.jianshu.com\/p\/81c65cb69f42\">\u8fd0\u884c\u53c2\u8003\u94fe\u63a5<\/a><\/p>\n<h3>\u5b89\u88c5<\/h3>\n<pre><code class=\"language-R\">library(devtools)\ninstall_github(&quot;im3sanger\/dndscv&quot;)<\/code><\/pre>\n<h3>\u4e0b\u8f7d\u6240\u9700\u7684\u53c2\u8003\u6587\u4ef6(dndscv \u9ed8\u8ba4hg19)<\/h3>\n<pre><code class=\"language-bash\">wget https:\/\/codeload.github.com\/im3sanger\/dndscv_data\/zip\/refs\/heads\/master<\/code><\/pre>\n<h3>\u52a0\u8f7dR\u5305<\/h3>\n<pre><code class=\"language-R\">library(vcfR)\nlibrary(dndscv)\nlibrary(IRanges)\nlibrary(dplyr)<\/code><\/pre>\n<h3>vcf \u6587\u4ef6\u5904\u7406<\/h3>\n<pre><code class=\"language-R\">vcf &lt;- read.vcfR(&quot;\/data\/shumin\/software\/snpEff\/Somatic\/CC56tissueA_snpEff_annotated.vcf&quot;)\n\n# \u63d0\u53d6\u4f4d\u7f6e\u4fe1\u606f\npos_info &lt;- as.data.frame(getFIX(vcf))\n\n# \u63d0\u53d6INFO\u5b57\u6bb5\u4e2d\u7684ANN\u4fe1\u606f\nann_info &lt;- extract.info(vcf, element = &quot;ANN&quot;)\n\n# \u63d0\u53d6\u5fc5\u8981\u7684\u5217\nvariants_1 &lt;- data.frame(\n  chr = pos_info$CHROM,\n  pos = pos_info$POS,\n  ref = pos_info$REF,\n  mut = pos_info$ALT\n)\n\n# \u89e3\u6790\u6ce8\u91ca\u4fe1\u606f\u6761\u76ee\nparsed_annotations &lt;- lapply(ann_info, function(ann_info) {\n  # \u6839\u636e | \u5206\u5272\u6ce8\u91ca\u4fe1\u606f\n  fields &lt;- unlist(strsplit(ann_info, &quot;|&quot;, fixed = TRUE))\n\n  # \u8fd4\u56de\u9700\u8981\u7684\u5b57\u6bb5\uff0c\u4f8b\u5982\u57fa\u56e0\u540d\u548c\u53d8\u5f02\u7c7b\u578b\n  gene_name &lt;- fields[4]  # \u57fa\u56e0\u540d\u5728\u7b2c\u56db\u4e2a\u4f4d\u7f6e\n  variant_type &lt;- fields[2]  # \u53d8\u5f02\u7c7b\u578b\u5728\u7b2c\u4e8c\u4e2a\u4f4d\u7f6e\n  impact &lt;- fields[3]  # \u5f71\u54cd\u7a0b\u5ea6\u901a\u5e38\u5728\u7b2c\u4e09\u4e2a\u4f4d\u7f6e\n  return(list(Gene = gene_name, Variant_Type = variant_type, Impact = impact))\n})\n\n# \u5c06\u5217\u8868\u8f6c\u6362\u4e3a\u6570\u636e\u6846\nvariants_2 &lt;- do.call(rbind, parsed_annotations)\n\n# \u5408\u5e76\u6570\u636e\nvariants &lt;- cbind(variants_1, variants_2)\n\n# \u5c06\u5c5e\u6027\u4e3alist\u7684\u5217\u8f6c\u6362\u4e3a\u5b57\u7b26\u4e32\nvariants$Gene &lt;- sapply(variants$Gene, function(x) paste(x, collapse = &quot;&quot;))\nvariants$Variant_Type &lt;- sapply(variants$Variant_Type, function(x) paste(x, collapse = &quot;, &quot;))\nvariants$Impact &lt;- sapply(variants$Impact, function(x) paste(x, collapse = &quot;&quot;))\n\n# \u5904\u7406\u7f3a\u5931\u503c\uff1a\u8fd9\u91cc\u5047\u8bbe\u76f4\u63a5\u5220\u9664\u542b\u6709NA\u503c\u7684\u884c\nvariants &lt;- na.omit(variants)\n\n# \u786e\u4fdd\u6bcf\u5217\u7684\u6570\u636e\u7c7b\u578b\u6b63\u786e\nvariants$chr &lt;- as.character(variants$chr)  # \u67d3\u8272\u4f53\u7f16\u53f7\nvariants$pos &lt;- as.integer(variants$pos)    # \u4f4d\u7f6e\uff0c\u8f6c\u6362\u4e3a\u6574\u6570\u7c7b\u578b\nvariants$ref &lt;- as.character(variants$ref)  # \u53c2\u8003\u78b1\u57fa\nvariants$mut &lt;- as.character(variants$mut)  # \u7a81\u53d8\u78b1\u57fa\nvariants$SampleID &lt;- &quot;CC56tissue&quot;  # \u6dfb\u52a0\u6837\u672c\u540d\u4e00\u5217\n\n# \u79fb\u9664 &quot;chr&quot; \u524d\u7f00\nvariants$chr &lt;- gsub(&quot;^chr&quot;, &quot;&quot;, variants$chr)\n\n# \u8fc7\u6ee4\u51fa\u5355\u78b1\u57fa\u7a81\u53d8\uff08SNPs\uff09\nvariants &lt;- variants %&gt;%\n  filter(nchar(ref) == 1 &amp; nchar(mut) == 1)\n\nstr(variants)\n## &#039;data.frame&#039;:    1624817 obs. of  8 variables:\n##  $ chr         : chr  &quot;1&quot; &quot;1&quot; &quot;1&quot; &quot;1&quot; ...\n##  $ pos         : int  13273 14653 14677 14717 16495 16875 17365 17538 17588 17614 ...\n##  $ ref         : chr  &quot;G&quot; &quot;C&quot; &quot;G&quot; &quot;G&quot; ...\n##  $ mut         : chr  &quot;C&quot; &quot;T&quot; &quot;A&quot; &quot;A&quot; ...\n##  $ Gene        : chr  &quot;WASH7P&quot; &quot;DDX11L1&quot; &quot;DDX11L1&quot; &quot;DDX11L1&quot; ...\n##  $ Variant_Type: chr  &quot;downstream_gene_variant&quot; &quot;downstream_gene_variant&quot; &quot;downstream_gene_variant&quot; &quot;downstream_gene_variant&quot; ...\n##  $ Impact      : chr  &quot;MODIFIER&quot; &quot;MODIFIER&quot; &quot;MODIFIER&quot; &quot;MODIFIER&quot; ...\n##  $ SampleID    : chr  &quot;CC56tissue&quot; &quot;CC56tissue&quot; &quot;CC56tissue&quot; &quot;CC56tissue&quot; ...\n\n# \u7b5b\u9009\u5f71\u54cd\u7a0b\u5ea6\u201cHIGH&quot;\u7684\u6570\u636e\u8fdb\u884c\u540e\u7eed\u5206\u6790\nvariants_sel &lt;- subset(x=variants, variants$Impact==c(&#039;HIGH&#039;)) %&gt;% .[,c(8,1:4)]<\/code><\/pre>\n<h3>\u8fd0\u884cdndscv<\/h3>\n<pre><code class=\"language-R\">dndsout &lt;- dndscv(variants_sel, refdb=&quot;\/usr\/local\/lib\/R\/library\/dndscv\/data\/RefCDS_human_GRCh38_GencodeV18_recommended.rda&quot;, cv=NULL)<\/code><\/pre>\n<h3>\u7ed3\u679c\u89e3\u8bfb<\/h3>\n<ol>\n<li>\n<p>\u5168\u5c40\u7ed3\u679c\uff08$globaldnds\uff09\uff1a\u8fd9\u4e2a\u8868\u5305\u542b\u4e86\u6240\u6709\u57fa\u56e0\u5168\u5c40\u7684dN\/dS\u503c\uff0c\u7528\u4e8e\u8bc4\u4f30\u6b63\u9009\u62e9\u3001\u8d1f\u9009\u62e9\u6216\u4e2d\u6027\u8fdb\u5316<\/p>\n<ul>\n<li>name: \u9009\u62e9\u6a21\u5f0f\u7684\u540d\u79f0\uff08\u5982wmis\u3001wnon\u3001wspl\u3001wtru\u3001wall\uff09\u3002<\/li>\n<li>mle: \u6700\u5927\u4f3c\u7136\u4f30\u8ba1\uff08maximum likelihood estimate\uff09\u7684dN\/dS\u503c\u3002<\/li>\n<li>cilow: dN\/dS\u503c\u7684\u4e0b\u965095%\u7f6e\u4fe1\u533a\u95f4\u3002<\/li>\n<li>cihigh: dN\/dS\u503c\u7684\u4e0a\u965095%\u7f6e\u4fe1\u533a\u95f4\n<pre><code>dndsout[[&quot;globaldnds&quot;]]\n##      name        mle      cilow    cihigh\n## wmis wmis  0.6447645  0.3704856  1.122098\n## wnon wnon 32.2041125 18.5571570 55.887055\n## wspl wspl 17.5535865  9.1980014 33.499495\n## wtru wtru 26.4194841 15.9302538 43.815318\n## wall wall  3.4408418  2.1853716  5.417565<\/code><\/pre>\n<\/li>\n<\/ul>\n<\/li>\n<li>\n<p>\u57fa\u56e0\u7ed3\u679c\uff08$sel_cv\uff09\uff1a\u8fd9\u4e2a\u8868\u663e\u793a\u4e86\u6bcf\u4e2a\u57fa\u56e0\u7684\u9009\u62e9\u4fe1\u53f7\uff0c\u7528\u4e8e\u786e\u5b9a\u54ea\u4e9b\u57fa\u56e0\u53ef\u80fd\u5728\u764c\u75c7\u4e2d\u8d77\u4f5c\u7528<\/p>\n<ul>\n<li>gene_name: \u57fa\u56e0\u7684\u540d\u79f0\u3002<\/li>\n<li>n_syn: \u540c\u4e49\u7a81\u53d8\u7684\u6570\u91cf\u3002<\/li>\n<li>n_mis: \u9519\u4e49\u7a81\u53d8\u7684\u6570\u91cf\u3002<\/li>\n<li>n_non: \u65e0\u4e49\u7a81\u53d8\u7684\u6570\u91cf\u3002<\/li>\n<li>n_spl: \u526a\u63a5\u4f4d\u70b9\u7a81\u53d8\u7684\u6570\u91cf\u3002<\/li>\n<li>n_ind: \u63d2\u5165\/\u7f3a\u5931\u7a81\u53d8\u7684\u6570\u91cf\u3002<\/li>\n<li>wmis_cv: \u9519\u4e49\u7a81\u53d8\u7684dN\/dS\u6bd4\u503c\uff08\u6700\u5927\u4f3c\u7136\u4f30\u8ba1\uff09\u3002<\/li>\n<li>wnon_cv: \u65e0\u4e49\u7a81\u53d8\u7684dN\/dS\u6bd4\u503c\uff08\u6700\u5927\u4f3c\u7136\u4f30\u8ba1\uff09\u3002<\/li>\n<li>wspl_cv: \u526a\u63a5\u4f4d\u70b9\u7a81\u53d8\u7684dN\/dS\u6bd4\u503c\uff08\u6700\u5927\u4f3c\u7136\u4f30\u8ba1\uff09\u3002<\/li>\n<li>pmis_cv: \u9519\u4e49\u7a81\u53d8\u7684P\u503c\uff0c\u8868\u793a\u8be5\u57fa\u56e0\u4e2d\u9519\u4e49\u7a81\u53d8\u7684\u9009\u62e9\u538b\u529b\u7684\u663e\u8457\u6027\u3002<\/li>\n<li>ptrunc_cv: \u622a\u65ad\u7a81\u53d8\uff08\u65e0\u4e49\u548c\u526a\u63a5\u4f4d\u70b9\u7a81\u53d8\uff09\u7684P\u503c\uff0c\u8868\u793a\u8be5\u57fa\u56e0\u4e2d\u622a\u65ad\u7a81\u53d8\u7684\u9009\u62e9\u538b\u529b\u7684\u663e\u8457\u6027\u3002<\/li>\n<li>pallsubs_cv: \u6240\u6709\u975e\u540c\u4e49\u7a81\u53d8\uff08\u9519\u4e49\u3001\u65e0\u4e49\u548c\u526a\u63a5\u4f4d\u70b9\u7a81\u53d8\uff09\u7684P\u503c\uff0c\u8868\u793a\u8be5\u57fa\u56e0\u4e2d\u6240\u6709\u975e\u540c\u4e49\u7a81\u53d8\u7684\u9009\u62e9\u538b\u529b\u7684\u663e\u8457\u6027\u3002<\/li>\n<li>qmis_cv: \u9519\u4e49\u7a81\u53d8\u7684q\u503c\uff08FDR\u6821\u6b63\u540e\u7684P\u503c\uff09\u3002<\/li>\n<li>qtrunc_cv: \u622a\u65ad\u7a81\u53d8\uff08\u65e0\u4e49\u548c\u526a\u63a5\u4f4d\u70b9\u7a81\u53d8\uff09\u7684q\u503c\uff08FDR\u6821\u6b63\u540e\u7684P\u503c\uff09\u3002<\/li>\n<li>qallsubs_cv: \u6240\u6709\u975e\u540c\u4e49\u7a81\u53d8\uff08\u9519\u4e49\u3001\u65e0\u4e49\u548c\u526a\u63a5\u4f4d\u70b9\u7a81\u53d8\uff09\u7684q\u503c\uff08FDR\u6821\u6b63\u540e\u7684P\u503c\uff09\u3002\n<pre><code>dndsout[[&quot;sel_cv&quot;]]\n##       gene_name n_syn n_mis n_non n_spl wmis_cv    wnon_cv    wspl_cv   pmis_cv    ptrunc_cv  pallsubs_cv   qmis_cv    qtrunc_cv  qallsubs_cv\n## 15213    SLC9B1     0     0     3     0       0 10531.6440 10531.6440 0.9443649 2.092424e-10 1.611936e-09 0.9855767 4.020802e-06 3.097496e-05\n## 17932  USP17L22     0     0     2     0       0  9729.2562  9729.2562 0.9446037 6.287852e-08 4.273784e-07 0.9855767 5.973446e-04 3.980201e-03\n## 11565    PABPC3     0     0     2     0       0  8019.2737  8019.2737 0.9377189 9.325738e-08 6.213885e-07 0.9855767 5.973446e-04 3.980201e-03\n## 18196     WDPCP     0     0     2     0       0  3805.0805  3805.0805 0.9349721 4.351865e-07 2.744960e-06 0.9855767 2.090636e-03 1.318679e-02\n## 9776     MROH2A     0     0     1     1       0  1761.9124  1761.9124 0.8956018 2.096382e-06 1.176643e-05 0.9855767 8.056814e-03 4.522073e-02\n## 8301      KMT2C     0     0     1     1       0   716.5142   716.5142 0.8386098 1.257247e-05 5.867674e-05 0.9855767 2.906275e-02 1.557393e-01\n## ......<\/code><\/pre>\n<\/li>\n<\/ul>\n<\/li>\n<li>\n<p>\u7a81\u53d8\u6ce8\u91ca\uff08$annotmuts\uff09\uff1a\u8fd9\u4e2a\u8868\u5305\u542b\u4e86\u6240\u6709\u8f93\u5165\u7684\u7a81\u53d8\u53ca\u5176\u6ce8\u91ca\u4fe1\u606f<\/p>\n<ul>\n<li>sampleID: \u6837\u672c\u7684ID\u3002<\/li>\n<li>chr: \u7a81\u53d8\u6240\u5728\u7684\u67d3\u8272\u4f53\u3002<\/li>\n<li>pos: \u7a81\u53d8\u7684\u4f4d\u7f6e\u3002<\/li>\n<li>ref: \u53c2\u8003\u78b1\u57fa\u3002<\/li>\n<li>mut: \u7a81\u53d8\u78b1\u57fa\u3002<\/li>\n<li>gene: \u7a81\u53d8\u6240\u5728\u7684\u57fa\u56e0\u3002<\/li>\n<li>ref_cod: \u53c2\u8003\u5e8f\u5217\u7684\u4e09\u8054\u5bc6\u7801\u5b50\uff08codon\uff09\u3002<\/li>\n<li>mut_cod: \u7a81\u53d8\u540e\u7684\u4e09\u8054\u5bc6\u7801\u5b50\uff08codon\uff09\u3002<\/li>\n<li>strand: \u57fa\u56e0\u6240\u5728\u7684\u94fe\uff08\u6b63\u94fe\u6216\u8d1f\u94fe\uff09\u3002<\/li>\n<li>ref3_cod: \u53c2\u8003\u5e8f\u5217\u7684\u4e09\u8054\u5bc6\u7801\u5b50\uff08codon\uff09\u53ca\u5176\u4e0a\u4e0b\u6e38\u6838\u82f7\u9178\u5e8f\u5217\u3002<\/li>\n<li>mut3_cod: \u7a81\u53d8\u540e\u7684\u4e09\u8054\u5bc6\u7801\u5b50\uff08codon\uff09\u53ca\u5176\u4e0a\u4e0b\u6e38\u6838\u82f7\u9178\u5e8f\u5217\u3002<\/li>\n<li>aachange: \u6c28\u57fa\u9178\u53d8\u5316\uff08\u4ece\u53c2\u8003\u6c28\u57fa\u9178\u5230\u7a81\u53d8\u540e\u7684\u6c28\u57fa\u9178\uff09\u3002<\/li>\n<li>ntchange: \u6838\u82f7\u9178\u53d8\u5316\uff08\u4ece\u53c2\u8003\u6838\u82f7\u9178\u5230\u7a81\u53d8\u540e\u7684\u6838\u82f7\u9178\uff09\u3002<\/li>\n<li>impact: \u7a81\u53d8\u7684\u5f71\u54cd\uff08\u5982synonymous\u3001missense\u3001nonsense\u7b49\uff09\u3002\n<pre><code class=\"language-R\">dndsout[[&quot;annotmuts&quot;]]\n##           sampleID chr       pos ref mut geneind      gene ref_cod mut_cod strand ref3_cod mut3_cod aachange ntchange           impact             pid\n## 204     CC56tissue   1    924949   G   A   14271    SAMD11       G       A      1      GGT      GAT        -        - Essential_Splice ENSP00000480678\n## 10550   CC56tissue   1  12716215   C   A      12   AADACL3       C       A      1      GCG      GAG     C13*     C39A         Nonsense ENSP00000352268\n## 12672   CC56tissue   1  15626753   C   T    4093      DDI2       C       T      1      ACG      ATG     R75*    C223T         Nonsense ENSP00000417748\n## 22914   CC56tissue   1  26553429   T   C   14086   RPS6KA1       T       C      1      CTG      CCG    A169A    T507C       Synonymous ENSP00000363283\n## 34888   CC56tissue   1  44941527   G   A    4826    EIF2B3       C       T     -1      TCA      TTA    Q145*    C433T         Nonsense ENSP00000353575\n## 35452   CC56tissue   1  46032703   A   G    9269     MAST2       A       G      1      TAG      TGG   V1031V   A3093G       Synonymous ENSP00000501318\n## ......<\/code><\/pre>\n<\/li>\n<\/ul>\n<\/li>\n<li>\n<p>\u5c40\u90e8\u4e2d\u6027\u6d4b\u8bd5\uff08$sel_loc\uff09\uff1a\u5305\u542b\u4e86\u5c40\u90e8\u9009\u62e9\u5206\u6790\u7684\u7ed3\u679c\uff0c\u7528\u4e8e\u8bc6\u522b\u57fa\u56e0\u4e2d\u7279\u5b9a\u4f4d\u7f6e\u7684\u7a81\u53d8\u662f\u5426\u663e\u793a\u51fa\u663e\u8457\u7684\u9009\u62e9\u4fe1\u53f7\u3002\u8fd9\u5728\u8bc6\u522b\u53ef\u80fd\u5177\u6709\u529f\u80fd\u6027\u5f71\u54cd\u7684\u70ed\u70b9\u533a\u57df\u65f6\u975e\u5e38\u6709\u7528<\/p>\n<pre><code class=\"language-R\">dndsout[[&quot;sel_loc&quot;]]\n##       gene_name n_syn n_mis n_non n_spl wmis_loc wnon_loc wspl_loc  pmis_loc     pall_loc  qmis_loc     qall_loc\n## 15213    SLC9B1     0     0     8     0        0    10000        0 0.9999991 8.466339e-12 0.9999998 1.626892e-07\n## 11565    PABPC3     0     0     6     0        0    10000        0 0.9999989 5.799150e-08 0.9999998 5.571824e-04\n## 2129     CALHM4     0     0     0     3        0        0    10000 0.9999993 1.035322e-06 0.9999998 6.631585e-03\n## 6152      GCNT7     0     0     0     3        0        0    10000 0.9999991 7.769189e-06 0.9999998 3.732318e-02\n## 18819    ZNF419     0     0     0     3        0        0    10000 0.9999991 3.321557e-05 0.9999998 1.276541e-01\n## 17350  TRIM51GP     0     0     0     3        0        0    10000 0.9999991 7.640284e-05 0.9999998 1.503908e-01\n## ......\nsignif_genes_localmodel = as.vector(dndsout$sel_loc$gene_name[dndsout$sel_loc$qall_loc&lt;0.1])\nprint(signif_genes_localmodel)\n## [1] &quot;SLC9B1&quot; &quot;PABPC3&quot; &quot;CALHM4&quot; &quot;GCNT7&quot; \n## \u8be5\u6a21\u578b\u68c0\u6d4b\u51faSLC9B1, PABPC3, CALHM4, GCNT7\u6709\u663e\u8457\u7a81\u53d8\u3002<\/code><\/pre>\n<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>\u6838\u5fc3\u7406\u5ff5\u539f\u6587\u94fe\u63a5 dN\/dS \u662f\u4ec0\u4e48 \u8fd9\u91cc\u7684 S \u5373 Synonymous\uff0cN \u5373 Nonsynonymous&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-375","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/375","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/comments?post=375"}],"version-history":[{"count":4,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/375\/revisions"}],"predecessor-version":[{"id":387,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/375\/revisions\/387"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=375"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=375"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=375"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}