{"id":61396,"date":"2024-10-30T15:33:46","date_gmt":"2024-10-30T07:33:46","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61396"},"modified":"2024-10-30T15:34:04","modified_gmt":"2024-10-30T07:34:04","slug":"%e8%9b%8b%e7%99%bd%e9%85%b6%e4%bd%9c%e7%94%a8%e6%a8%a1%e5%bc%8f%e9%9a%be%e7%90%86%e8%a7%a3%ef%bc%9fproteasy%e5%8c%85%ef%bc%8c%e8%ae%a9%e5%a4%8d%e6%9d%82%e7%9a%84%e9%85%b6%e5%88%87%e6%95%b0%e6%8d%ae","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61396","title":{"rendered":"\u86cb\u767d\u9176\u4f5c\u7528\u6a21\u5f0f\u96be\u7406\u89e3\uff1fproteasy\u5305\uff0c\u8ba9\u590d\u6742\u7684\u9176\u5207\u6570\u636e\u53d8\u7b80\u5355\uff01"},"content":{"rendered":"\n

<\/p>\n\n\n\n

\u563f\u79d1\u7814\u5c0f\u4f19\u4f34\u4eec\uff01\u4f60\u662f\u5426\u66fe\u5728\u7814\u7a76\u86cb\u767d\u8d28\u6c34\u89e3\u8fc7\u7a0b\u4e2d\u611f\u5230\u8ff7\u832b\uff1f\u662f\u5426\u5728\u5bfb\u627e\u4e00\u79cd\u65b9\u6cd5\u6765\u5206\u6790\u90a3\u4e9b\u590d\u6742\u7684\u9176\u5207\u6570\u636e\uff1f\u522b\u62c5\u5fc3\uff0c\u5c0f\u5e08\u59b9\u4eca\u5929\u5c31\u8981\u7ed9\u5927\u5bb6\u5e26\u6765\u4e00\u4e2a\u6fc0\u52a8\u4eba\u5fc3\u7684\u751f\u7269\u4fe1\u606f\u5b66\u5de5\u5177\u2014\u2014proteasy\u5305\u3002<\/p>\n\n\n\n

\u5728\u8fd9\u4e2a\u9886\u57df\u91cc\uff0c\u86cb\u767d\u9176\uff08protease\uff09\u7684\u5207\u5272\u4f5c\u7528\u5bf9\u8bb8\u591a\u91cd\u8981\u7684\u751f\u7406\u8fc7\u7a0b\u90fd\u6709\u7740\u6df1\u8fdc\u7684\u5f71\u54cd\uff0c\u800cproteasy\u5305\u6b63\u662f\u4e3a\u4e86\u5e2e\u52a9\u6211\u4eec\u66f4\u597d\u5730\u7406\u89e3\u548c\u5206\u6790\u8fd9\u4e9b\u8fc7\u7a0b\u800c\u8bbe\u8ba1\u7684\u3002\u5b83\u80fd\u591f\u8ba9\u6211\u4eec\u8f7b\u677e\u5730\u4eceMEROPS\u6570\u636e\u5e93\u4e2d\u63d0\u53d6\u4fe1\u606f\uff0c\u8bc6\u522b\u7279\u5b9a\u5e95\u7269\u7684\u6f5c\u5728\u9176\u5207\u4f4d\u70b9\uff0c\u5e76\u5bf9\u8fd9\u4e9b\u4f4d\u70b9\u8fdb\u884c\u8be6\u7ec6\u7684\u5206\u6790\u3002<\/p>\n\n\n\n

\u73b0\u5728\uff0c\u5c31\u8ba9\u6211\u4eec\u4e00\u8d77\u6765\u5b66\u4e60\u5982\u4f55\u4f7f\u7528proteasy\u5305\uff0c\u8ba9\u5b83\u6210\u4e3a\u6211\u4eec\u7814\u7a76\u8fc7\u7a0b\u4e2d\u7684\u5f97\u529b\u52a9\u624b\u3002\u6ce8\u610f\u54e6\uff0c<\/strong>\u8fd9\u4e2a<\/strong>R\u5305\u64cd\u4f5c\u5360\u7528\u5185\u5b58\u6bd4\u8f83\u5927\uff0c\u5efa\u8bae\u4f7f\u7528\u670d\u52a1\u5668<\/strong>\u54e6<\/strong>\uff0c\u6b22\u8fce\u8054\u7cfb<\/strong>\u5c0f\u5e08\u59b9<\/strong>\u79df\u8d41\u6027\u4ef7\u6bd4\u9ad8\u7684\u670d\u52a1\u5668<\/strong>~<\/strong><\/strong><\/p>\n\n\n\n

\u51c6\u5907\u597d\u4e86\u5417\uff1f\u8ba9\u6211\u4eec\u5f00\u59cb\u8fd9\u6bb5\u7cbe\u5f69\u7684\u63a2\u7d22\u4e4b\u65c5\uff0c\u4e00\u8d77\u63ed\u5f00\u86cb\u767d\u8d28\u9176\u5207\u7684\u795e\u79d8\u9762\u7eb1\uff01\u5982\u679c\u6709\u4efb\u4f55\u7591\u95ee\uff0c\u5c0f\u5e08\u59b9\u968f\u65f6\u5728\u8fd9\u91cc\u4e3a\u4f60\u89e3\u7b54\u54e6\uff01<\/strong><\/strong><\/p>\n\n\n\n

\u9996\u5148\uff0c\u8ba9\u6211\u4eec\u5b89\u88c5\u548c\u52a0\u8f7dproteasy\u5305\uff1a<\/p>\n\n\n\n

if (!requireNamespace(“BiocManager”, quietly = TRUE))<\/p>\n\n\n\n

   install.packages(“BiocManager”)<\/p>\n\n\n\n

BiocManager::install(“proteasy”)<\/p>\n\n\n\n

library(“proteasy”)<\/p>\n\n\n\n

\u4e00\u3001\u4f7f\u7528\u65b9\u6cd5<\/strong><\/strong><\/p>\n\n\n\n

 <\/strong>1. <\/strong>\u6839\u636e\u5e95\u7269\u67e5\u627e\u86cb\u767d\u9176<\/strong><\/strong><\/p>\n\n\n\n

\u60f3\u8981\u5feb\u901f\u8bc6\u522b\u53ef\u80fd\u5207\u5272\u7279\u5b9a\u5e95\u7269\u7684\u86cb\u767d\u9176\u5417\uff1f\u5c0f\u5e08\u59b9\u6765\u6559\u4f60\u7528`searchSubstrate`\u51fd\u6570\u3002\u8fd9\u4e2a\u51fd\u6570\u80fd\u5e2e\u6211\u4eec\u4eceMEROPS\u6570\u636e\u5e93\u4e2d\u68c0\u7d22\u8bb0\u5f55\u7684\u86cb\u767d\u9176\u3002<\/p>\n\n\n\n

\u7b80\u5355\u4e24\u6b65\uff0c\u8f7b\u677e\u67e5\u627e\uff1a<\/p>\n\n\n\n

\uff081\uff09 \u83b7\u53d6\u86cb\u767d\u9176\u5217\u8868  <\/p>\n\n\n\n

   \u8bbe\u7f6e`summarize = TRUE`\uff0c\u51fd\u6570\u4f1a\u8fd4\u56de\u4e00\u4e2a\u5217\u8868\uff0c\u5305\u542b\u6240\u6709\u5df2\u77e5\u80fd\u5207\u5272\u7279\u5b9a\u5e95\u7269\u7684\u3001\u7ecf\u8fc7\u5ba1\u6838\u7684\u86cb\u767d\u9176\u3002<\/p>\n\n\n\n

      searchSubstrate(protein = “P01042”, summarize = TRUE)<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\uff082\uff09 \u83b7\u53d6\u8be6\u7ec6\u5207\u5272\u4e8b\u4ef6  <\/p>\n\n\n\n

   \u8bbe\u7f6e`summarize = FALSE`\uff0c\u51fd\u6570\u4f1a\u8fd4\u56de\u4e00\u4e2a\u8be6\u7ec6\u7684\u6570\u636e\u8868\uff0c\u5c55\u793a\u6bcf\u4e2a\u5207\u5272\u4e8b\u4ef6\u7684\u4fe1\u606f\u3002<\/p>\n\n\n\n

      searchSubstrate(protein = “P01042”, summarize = FALSE) |> head()<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u5904\u7406\u591a\u4e2a\u5e95\u7269\uff1f\u6ca1\u95ee\u9898\uff01<\/p>\n\n\n\n

\u6ca1\u9519\uff0c\u8fd9\u4e2a\u51fd\u6570\u8fd8\u80fd\u540c\u65f6\u5904\u7406\u591a\u4e2a\u5e95\u7269\uff0c\u5e2e\u4f60\u4e00\u6b21\u6027\u83b7\u53d6\u6240\u6709\u76f8\u5173\u86cb\u767d\u9176\u7684\u4fe1\u606f\u3002<\/p>\n\n\n\n

searchSubstrate(protein = c(“P01042”, “P02461”), summarize = FALSE) |> tail()<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u901a\u8fc7\u8fd9\u79cd\u65b9\u5f0f\uff0c\u6211\u4eec\u4e0d\u4ec5\u80fd\u591f\u4e86\u89e3\u54ea\u4e9b\u86cb\u767d\u9176\u53ef\u80fd\u53c2\u4e0e\u4e86\u7279\u5b9a\u5e95\u7269\u7684\u5207\u5272\uff0c\u8fd8\u80fd\u6df1\u5165\u4e86\u89e3\u6bcf\u4e00\u6b21\u5207\u5272\u4e8b\u4ef6\u7684\u5177\u4f53\u7ec6\u8282\u3002\u8fd9\u5bf9\u4e8e\u7814\u7a76\u86cb\u767d\u9176\u7684\u529f\u80fd\u548c\u5b83\u4eec\u5728\u751f\u7269\u4f53\u5185\u7684\u8c03\u63a7\u673a\u5236\u6765\u8bf4\uff0c\u662f\u975e\u5e38\u6709\u4ef7\u503c\u7684\u4fe1\u606f\u3002<\/p>\n\n\n\n

    \n
  • \u6839\u636e\u86cb\u767d\u9176\u67e5\u627e\u5e95\u7269<\/strong><\/strong><\/li>\n<\/ul>\n\n\n\n

    \u5982\u679c\u4f60\u60f3\u77e5\u9053\u67d0\u4e2a\u7279\u5b9a\u7684\u86cb\u767d\u9176\u80fd\u591f\u5207\u5272\u54ea\u4e9b\u5e95\u7269\uff0c`searchProtease`\u51fd\u6570\u5c31\u662f\u4e3a\u4f60\u51c6\u5907\u7684\u3002\u8fd9\u4e2a\u51fd\u6570\u80fd\u591f\u5e2e\u4f60\u627e\u51fa\u7279\u5b9a\u86cb\u767d\u9176\u7684\u6240\u6709\u5df2\u77e5\u5207\u5272\u5e95\u7269\u3002\u4e0b\u9762\uff0c\u6211\u4eec\u5c06\u4ee5\u57fa\u8d28\u91d1\u5c5e\u86cb\u767d\u9176-12\uff08MMP-12\uff0cP39900\uff09\u4e3a\u4f8b\uff0c\u6f14\u793a\u5982\u4f55\u4f7f\u7528\u8fd9\u4e2a\u51fd\u6570\u3002<\/p>\n\n\n\n

    \u53ea\u9700\u8bbe\u7f6e`summarize = TRUE`\uff0c\u51fd\u6570\u5c31\u4f1a\u8fd4\u56de\u4e00\u4e2a\u5411\u91cf\uff0c\u5217\u51faMMP-12\u80fd\u591f\u5207\u5272\u7684\u6240\u6709\u5e95\u7269\u3002<\/p>\n\n\n\n

    searchProtease(protein = “P39900”, summarize = TRUE)<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u5982\u679c\u4f60\u60f3\u8981\u66f4\u8be6\u7ec6\u7684\u4fe1\u606f\uff0c\u6bd4\u5982\u6bcf\u6b21\u5207\u5272\u7684\u5177\u4f53\u4f4d\u7f6e\u548c\u7c7b\u578b\uff0c\u53ea\u9700\u5c06`summarize`\u8bbe\u7f6e\u4e3a`FALSE`\uff0c\u51fd\u6570\u5c31\u4f1a\u8fd4\u56de\u4e00\u4e2a\u5305\u542b\u8fd9\u4e9b\u8be6\u7ec6\u4fe1\u606f\u7684\u6570\u636e\u8868\u3002<\/p>\n\n\n\n

    searchProtease(protein = “P39900”, summarize = FALSE) |> head()<\/p>\n\n\n\n

    \"\"<\/figure>\n\n\n\n

    \u901a\u8fc7\u8fd9\u4e2a\u529f\u80fd\uff0c\u6211\u4eec\u53ef\u4ee5\u6df1\u5165\u4e86\u89e3\u7279\u5b9a\u86cb\u767d\u9176\u5982\u4f55\u5f71\u54cd\u5404\u79cd\u5e95\u7269\uff0c\u8fd9\u5bf9\u4e8e\u7814\u7a76\u86cb\u767d\u9176\u7684\u529f\u80fd\u548c\u5b83\u4eec\u5728\u75be\u75c5\u4e2d\u7684\u4f5c\u7528\u5c24\u4e3a\u91cd\u8981\u3002\u5c0f\u5e08\u59b9\u63d0\u9192\u4f60\uff0c\u8fd9\u4e2a\u5de5\u5177\u975e\u5e38\u5b9e\u7528\uff0c\u65e0\u8bba\u4f60\u662f\u7814\u7a76\u7279\u5b9a\u86cb\u767d\u9176\u8fd8\u662f\u63a2\u7d22\u86cb\u767d\u9176\u7684\u6f5c\u5728\u5e95\u7269\uff0c\u90fd\u80fd\u6d3e\u4e0a\u5927\u7528\u573a\u54e6\uff01<\/p>\n\n\n\n

      \n
    • \u4e3a\u5207\u5272\u7684\u80bd\u6bb5\u5bfb\u627e\u53ef\u80fd\u7684\u86cb\u767d\u9176<\/strong><\/strong><\/li>\n<\/ul>\n\n\n\n

      \u5f53\u4f60\u624b\u5934\u6709\u4e00\u5806\u5207\u5272\u540e\u7684\u80bd\u6bb5\uff0c\u800c\u4f60\u60f3\u77e5\u9053\u54ea\u4e9b\u86cb\u767d\u9176\u53ef\u80fd\u662f\u201c\u5e55\u540e\u9ed1\u624b\u201d\u65f6\uff0c`findProtease`\u51fd\u6570\u5c31\u80fd\u5927\u663e\u8eab\u624b\u4e86\u3002\u8fd9\u4e2a\u51fd\u6570\u4f1a\u81ea\u52a8\u5c06\u80bd\u6bb5\u5e8f\u5217\u6620\u5c04\u5230\u5b8c\u6574\u7684\u86cb\u767d\u5e8f\u5217\u4e0a\uff0c\u5e76\u83b7\u53d6\u80bd\u6bb5\u7684\u8d77\u59cb\u548c\u7ec8\u6b62\u4f4d\u7f6e\u3002\u7136\u540e\uff0c\u5b83\u4f1a\u5728MEROPS\u6570\u636e\u5e93\u4e2d\u641c\u7d22\u8fd9\u4e9b\u4f4d\u7f6e\uff0c\u8fd4\u56de\u6240\u6709\u5339\u914d\u7684\u86cb\u767d\u9176\u3002<\/p>\n\n\n\n

      \u6b65\u9aa4\u4e00\uff1a\u51c6\u5907\u6570\u636e<\/p>\n\n\n\n

      \u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u51c6\u5907\u4e00\u4e2a\u5305\u542bUniProt ID\u548c\u76f8\u5e94\u80bd\u6bb5\u5e8f\u5217\u7684\u5411\u91cf\u3002<\/p>\n\n\n\n

      protein <- c(“P02671”, “P02671”, “P68871”, “P01011”, “P68133”, “P02461”, “P0DJI8”, “P0DJI8”, “P0DJI8”)<\/p>\n\n\n\n

      peptide <- c(“FEEVSGNVSPGTR”, “FVSETESR”, “LLVVYPW”, “ITLLSAL”, “DSYVGDEAQS”, “AGGFAPYYG”, “FFSFLGEAFDGAR”, “EANYIGSDKY”, “GGVWAAEAISDAR”)<\/p>\n\n\n\n

      # \u6216\u8005\u76f4\u63a5\u52a0\u8f7d\u5c0f\u5e08\u59b9\u51c6\u5907\u7684\u6570\u636e\u54e6~<\/p>\n\n\n\n

      #protein1 <- read.csv(“protein.csv”, header = TRUE, stringsAsFactors = FALSE)[,1]<\/p>\n\n\n\n

      #peptide1 <- read.csv(“peptide.csv”, header = TRUE, stringsAsFactors = FALSE)[,1]<\/p>\n\n\n\n

      \u6b65\u9aa4\u4e8c\uff1a\u81ea\u52a8\u6620\u5c04\u548c\u641c\u7d22<\/p>\n\n\n\n

      \u4f7f\u7528`findProtease`\u51fd\u6570\uff0c\u5982\u679c\u672a\u6307\u5b9a\u80bd\u6bb5\u7684\u8d77\u59cb\u548c\u7ec8\u6b62\u4f4d\u7f6e\uff0c\u51fd\u6570\u5c06\u81ea\u52a8\u901a\u8fc7\u5339\u914d\u5b8c\u6574\u86cb\u767d\u5e8f\u5217\u6765\u786e\u5b9a\u8fd9\u4e9b\u503c\u3002<\/p>\n\n\n\n

      res <- findProtease(protein = protein, peptide = peptide, organism = “Homo sapiens”)<\/p>\n\n\n\n

      \u6b65\u9aa4\u4e09\uff1a\u67e5\u770b\u7ed3\u679c<\/p>\n\n\n\n

      \u6211\u4eec\u53ef\u4ee5\u7528\u4e09\u79cd\u65b9\u5f0f\u67e5\u770b\u7ed3\u679c\uff1a<\/p>\n\n\n\n

      substrates(res) |> head() # \u663e\u793a\u8f93\u5165\u5e8f\u5217\u7684\u6570\u636e<\/p>\n\n\n\n

      \"\"<\/figure>\n\n\n\n

      proteases(res) |> head() # \u663e\u793a\u53ef\u80fd\u5207\u5272\u8be5\u86cb\u767d\u7684\u5df2\u77e5\u86cb\u767d\u9176<\/p>\n\n\n\n

      \"\"<\/figure>\n\n\n\n

      cleavages(res) |> head() # \u663e\u793a\u76f8\u5173\u7684\u86cb\u767d\u6c34\u89e3\u4e8b\u4ef6\u7684\u8be6\u7ec6\u4fe1\u606f<\/p>\n\n\n\n

      \"\"<\/figure>\n\n\n\n

      \u9664\u4e86\u4e0a\u9762\u4e09\u4e2a\u6b65\u9aa4\uff0c\u6211\u4eec\u8fd8\u53ef\u4ee5\u8fdb\u884c\u4e00\u4e9b\u989d\u5916\u5206\u6790\uff1a<\/p>\n\n\n\n

      # \u4e86\u89e3\u7ecf\u8fc7\u5ba1\u6838\u7684\u86cb\u767d\u9176\u5728N\u7aef\u548cC\u7aef\u7684\u5207\u5272\u4e8b\u4ef6\u6bd4\u4f8b\uff1a<\/p>\n\n\n\n

      cl <- cleavages(res)[`Protease status` == “reviewed”]<\/p>\n\n\n\n

      cl$`Cleaved terminus` |> table() |> prop.table() |> round(digits = 2)<\/p>\n\n\n\n

      \"\"<\/figure>\n\n\n\n

      # \u68c0\u67e5\u5207\u5272\u7684\u6c28\u57fa\u9178\u5206\u5e03\u60c5\u51b5\uff1a<\/p>\n\n\n\n

      cl$`Cleaved residue` |> table() |> barplot(cex.names = 2)<\/p>\n\n\n\n

      \"\"<\/figure>\n\n\n\n

      # \u67e5\u627e\u6d89\u53ca\u6700\u591a\u5207\u5272\u4e8b\u4ef6\u7684\u86cb\u767d\u9176\uff1a<\/p>\n\n\n\n

      cl[!duplicated(Peptide), .(count = .N), by = `Protease (Uniprot)`]<\/p>\n\n\n\n

      \"\"<\/figure>\n\n\n\n

      \u6ce8\u610f\u54e6\uff0c\u5982\u679c\u4f60\u6307\u5b9a\u4e86\u8d77\u59cb\u548c\u7ec8\u6b62\u4f4d\u7f6e\uff0c\u51fd\u6570\u5c06\u4e0d\u4f1a\u81ea\u52a8\u67e5\u627e\u6307\u5b9a\u86cb\u767d\/\u80bd\u6bb5\u7684\u5e8f\u5217\u6570\u636e\uff0c\u8fd9\u610f\u5473\u7740\u5e95\u7269\u7684\u5e8f\u5217\u7ec6\u8282\u5c06\u4e0d\u53ef\u7528\u3002<\/p>\n\n\n\n

      cl_by_pos <- findProtease(<\/p>\n\n\n\n

        protein = “P02671”,<\/p>\n\n\n\n

        peptide = “FEEVSGNVSPGTR”,<\/p>\n\n\n\n

        start_pos = 413,<\/p>\n\n\n\n

        end_pos = 425)<\/p>\n\n\n\n

      substrates(cl_by_pos)<\/p>\n\n\n\n

      \"\"<\/figure>\n\n\n\n

      \u901a\u8fc7\u8fd9\u79cd\u65b9\u5f0f\uff0c\u6211\u4eec\u53ef\u4ee5\u6df1\u5165\u4e86\u89e3\u86cb\u767d\u9176\u5982\u4f55\u4f5c\u7528\u4e8e\u7279\u5b9a\u7684\u80bd\u6bb5\uff0c\u4e3a\u7814\u7a76\u86cb\u767d\u9176\u7684\u529f\u80fd\u548c\u8c03\u63a7\u673a\u5236\u63d0\u4f9b\u4e86\u6709\u529b\u7684\u5de5\u5177\u3002<\/p>\n\n\n\n

        \n
      • \u5728MEROPS\u4e2d\u67e5\u627e\u86cb\u767d\u9176\u8be6\u60c5<\/strong><\/strong><\/li>\n<\/ul>\n\n\n\n

        \u5982\u679c\u4f60\u60f3\u8981\u76f4\u63a5\u5728MEROPS\u6570\u636e\u5e93\u4e2d\u67e5\u770b\u67d0\u4e2a\u86cb\u767d\u9176\u7684\u8be6\u7ec6\u4fe1\u606f\uff0c\u53ef\u4ee5\u4f7f\u7528`browseProtease`\u51fd\u6570\u3002\u8fd9\u4e2a\u51fd\u6570\u63a5\u53d7\u4e00\u4e2aUniProt\u6216MEROPS\u7684ID\uff0c\u5e76\u5728\u7f51\u9875\u6d4f\u89c8\u5668\u4e2d\u6253\u5f00\u5bf9\u5e94\u7684MEROPS\u6458\u8981\u9875\u9762\u3002<\/p>\n\n\n\n

        browseProtease(“P07339”, keytype = “UniprotID”) # \uff08\u6253\u5f00\u7f51\u9875\u6d4f\u89c8\u5668\uff09<\/p>\n\n\n\n

        \u5728MEROPS\u6570\u636e\u5e93\u4e2d\u6307\u5b9a\u86cb\u767d\u9176\u7684\u8be6\u7ec6\u9875\u9762\uff0c\u6211\u4eec\u53ef\u4ee5\u627e\u5230\u5173\u4e8e\u8be5\u86cb\u767d\u9176\u7684\u66f4\u591a\u6570\u636e\uff0c\u5305\u62ec\u5b83\u7684\u5206\u7c7b\u3001\u5e95\u7269\u3001\u6291\u5236\u5242\u4ee5\u53ca\u76f8\u5173\u7684\u6587\u732e\u4fe1\u606f\u3002\u5c0f\u5e08\u59b9\u63d0\u9192\u4f60\uff0c\u867d\u7136\u8fd9\u4e2a\u51fd\u6570\u5f88\u65b9\u4fbf\uff0c\u4f46\u8bb0\u5f97\u5728\u6709\u7f51\u7edc\u8fde\u63a5\u7684\u60c5\u51b5\u4e0b\u4f7f\u7528\u54e6\uff01<\/p>\n\n\n\n

          \n
        • \u5e94\u7528\u6848\u4f8b<\/strong><\/strong><\/li>\n\n\n\n
        • \u53ef\u89c6\u5316\u86cb\u767d\u9176\u4f5c\u7528\u7f51\u7edc<\/strong><\/strong><\/li>\n<\/ul>\n\n\n\n

          \u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u53ef\u4ee5\u7528\u4e00\u79cd\u76f4\u89c2\u7684\u65b9\u6cd5\u6765\u63a2\u7a76\u4e24\u79cd\u5e95\u7269\u7684\u86cb\u767d\u9176\u4f5c\u7528\u6a21\u5f0f\uff1a\u5c06\u5b83\u4eec\u5448\u73b0\u4e3a\u4e00\u4e2a\u86cb\u767d-\u86cb\u767d\u76f8\u4e92\u4f5c\u7528\u7f51\u7edc\u56fe\uff0c\u5176\u4e2d\u5e95\u7269\u4ee5\u7ea2\u8272\u8282\u70b9\u8868\u793a\uff0c\u76f8\u5173\u7684\u86cb\u767d\u9176\u5219\u4ee5\u84dd\u8272\u8282\u70b9\u663e\u793a\u3002<\/p>\n\n\n\n

          \u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u52a0\u8f7d\u4e00\u4e9b\u5fc5\u8981\u7684R\u5305\uff0c\u5e76\u5b9a\u4e49\u6211\u4eec\u60f3\u8981\u7814\u7a76\u7684\u5e95\u7269\u5217\u8868\u3002<\/p>\n\n\n\n

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

          library(data.table)<\/p>\n\n\n\n

          # \u5b9a\u4e49\u7814\u7a76\u7684\u5e95\u7269<\/p>\n\n\n\n

          proteins <- c(‘P01011′,’P02671’)<\/p>\n\n\n\n

          \u7136\u540e\uff0c\u6211\u4eec\u5229\u7528`searchSubstrate`\u51fd\u6570\u67e5\u627e\u8fd9\u4e9b\u5e95\u7269\u7684\u5df2\u77e5\u86cb\u767d\u9176\uff0c\u5e76\u7b5b\u9009\u51fa\u72b6\u6001\u4e3a\u201creviewed\u201d\u7684\u86cb\u767d\u9176\u3002<\/p>\n\n\n\n

          # \u67e5\u8be2\u5207\u5272\u8fd9\u4e9b\u5e95\u7269\u7684\u86cb\u767d\u9176<\/p>\n\n\n\n

          res <- searchSubstrate(protein = proteins, summarize = FALSE)<\/p>\n\n\n\n

          # \u7b5b\u9009\u72b6\u6001\u4e3a\u201creviewed\u201d\u7684\u86cb\u767d\u9176<\/p>\n\n\n\n

          res <- res[`Protease status` == “reviewed”]<\/p>\n\n\n\n

          \u4e3a\u4e86\u6784\u5efa\u7f51\u7edc\u56fe\uff0c\u6211\u4eec\u63d0\u53d6\u4e86\u4e0e\u86cb\u767d\u9176\u5bf9\u5e95\u7269\u7684\u5207\u5272\u4f5c\u7528\u76f8\u5173\u7684\u4e24\u5217\u6570\u636e\u3002<\/p>\n\n\n\n

          # \u63d0\u53d6\u6784\u5efa\u7f51\u7edc\u6240\u9700\u7684\u6570\u636e<\/p>\n\n\n\n

          res <- res[, c(“Protease (Uniprot)”, “Substrate (Uniprot)”, “Cleavage type”)]<\/p>\n\n\n\n

          \u4f7f\u7528igraph\u5305\uff0c\u6211\u4eec\u6839\u636e\u8fd9\u4e9b\u6570\u636e\u6784\u5efa\u4e86\u4e00\u4e2a\u6709\u5411\u65e0\u73af\u56fe\uff08DAG\uff09\u3002<\/p>\n\n\n\n

          # \u6784\u5efa\u7f51\u7edc\u56fe<\/p>\n\n\n\n

          g <- igraph::graph_from_data_frame(res,<\/p>\n\n\n\n

                                             directed = TRUE,<\/p>\n\n\n\n

                                             vertices = unique(<\/p>\n\n\n\n

                                                 c(res$`Protease (Uniprot)`,<\/p>\n\n\n\n

                                                   res$`Substrate (Uniprot)`)))<\/p>\n\n\n\n

          \u6700\u540e\uff0c\u6211\u4eec\u7ed8\u5236\u8fd9\u4e2a\u7f51\u7edc\u56fe\uff0c\u5e76\u5bf9\u5176\u8fdb\u884c\u7f8e\u5316\uff0c\u4ee5\u4fbf\u4e8e\u6211\u4eec\u80fd\u66f4\u6e05\u695a\u5730\u770b\u5230\u6bcf\u4e2a\u86cb\u767d\u9176\u548c\u5e95\u7269\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u3002<\/p>\n\n\n\n

          # \u8bbe\u7f6e\u968f\u673a\u79cd\u5b50\u4ee5\u590d\u73b0\u7ed3\u679c<\/p>\n\n\n\n

          set.seed(104)<\/p>\n\n\n\n

          # \u7ed8\u5236\u7f51\u7edc\u56fe<\/p>\n\n\n\n

          plot(g,<\/p>\n\n\n\n

               vertex.label.family = “Helvetica”,<\/p>\n\n\n\n

               vertex.size = 14,<\/p>\n\n\n\n

               vertex.color = ifelse(V(g)$name %in% res$`Protease (Uniprot)`,<\/p>\n\n\n\n

                                     “#377EB8”, “#E41A1C”),<\/p>\n\n\n\n

               vertex.label.cex = 1,<\/p>\n\n\n\n

               vertex.label.color = “white”,<\/p>\n\n\n\n

               edge.arrow.size = .6,<\/p>\n\n\n\n

               edge.color =  ifelse(E(g)$`Cleavage type` == “physiological”,<\/p>\n\n\n\n

                                    “#01665E”, “#8E0152”),<\/p>\n\n\n\n

               layout = igraph::layout.davidson.harel)<\/p>\n\n\n\n

          # \u6dfb\u52a0\u56fe\u4f8b<\/p>\n\n\n\n

          legend(title = “Nodes”, cex = 2, horiz = FALSE,<\/p>\n\n\n\n

                 title.adj = 0.0, inset = c(0.0, 0.2),<\/p>\n\n\n\n

                 “bottomleft”, bty = “n”,<\/p>\n\n\n\n

                 legend = c(“Protease”, “Substrate”),<\/p>\n\n\n\n

                 fill = c(“#377EB8”, “#E41A1C”), border = NA)<\/p>\n\n\n\n

          legend(title = “Edges”, cex = 2, horiz = FALSE,<\/p>\n\n\n\n

                 title.adj = 0.0, inset = c(0.0, 0.0),<\/p>\n\n\n\n

                 “bottomleft”, bty = “n”,<\/p>\n\n\n\n

                 legend = c(“Physiological”, “Non-physiological”),<\/p>\n\n\n\n

                 fill = c(“#01665E”, “#8E0152”), border = NA)<\/p>\n\n\n\n

          \"\"<\/figure>\n\n\n\n

          \u901a\u8fc7\u8fd9\u79cd\u7f51\u7edc\u56fe\uff0c\u6211\u4eec\u53ef\u4ee5\u76f4\u89c2\u5730\u89c2\u5bdf\u5230\u7279\u5b9a\u86cb\u767d\u9176\u4e0e\u5e95\u7269\u4e4b\u95f4\u7684\u6f5c\u5728\u4e92\u4f5c\u5173\u7cfb\uff0c\u8fd9\u5bf9\u4e8e\u7406\u89e3\u86cb\u767d\u8d28\u5728\u751f\u7269\u4f53\u5185\u7684\u529f\u80fd\u548c\u8c03\u63a7\u7f51\u7edc\u975e\u5e38\u6709\u5e2e\u52a9\u3002<\/p>\n\n\n\n