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            <h1 id="seo-header">clusterProfiler：构建WikiPathways数据库</h1>
            
            
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                <p><a target="_blank" rel="noopener" href="https://www.wikipathways.org/">WikiPathways</a>是一个开放协作平台，旨在促进生物学界对通路信息的贡献和维护。它提供了一种新的模型，可以增强和补充<a target="_blank" rel="noopener" href="http://www.genome.jp/kegg/">KEGG</a>、<a target="_blank" rel="noopener" href="http://www.reactome.org/">Reactome</a>和<a target="_blank" rel="noopener" href="http://www.pathwaycommons.org/pc/">Pathway Commons</a>等正在进行的工作。</p>
<h2 id="安装相应的R包"><a href="#安装相应的R包" class="headerlink" title="安装相应的R包"></a>安装相应的R包</h2><ul>
<li><a target="_blank" rel="noopener" href="https://occdn.limour.top/2126.htm">conda activate clusterprofiler</a></li>
<li>conda install -c bioconda bioconductor-rwikipathways -y</li>
</ul>
<h2 id="初步建立数据库"><a href="#初步建立数据库" class="headerlink" title="初步建立数据库"></a>初步建立数据库</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>rWikiPathways<span class="hljs-punctuation">)</span><br>wp <span class="hljs-operator">&lt;-</span> downloadPathwayArchive<span class="hljs-punctuation">(</span>organism<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Homo sapiens&#x27;</span><span class="hljs-punctuation">,</span> format<span class="hljs-operator">=</span><span class="hljs-string">&#x27;gmt&#x27;</span><span class="hljs-punctuation">)</span><br>text <span class="hljs-operator">&lt;-</span> readLines<span class="hljs-punctuation">(</span>wp<span class="hljs-punctuation">,</span> encoding <span class="hljs-operator">=</span> <span class="hljs-string">&quot;UTF-8&quot;</span><span class="hljs-punctuation">)</span><br>text <span class="hljs-operator">&lt;-</span> strsplit<span class="hljs-punctuation">(</span>text<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;\t&quot;</span><span class="hljs-punctuation">)</span><br>WP <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>TERM2GENE<span class="hljs-operator">=</span>data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> TERM2NAME<span class="hljs-operator">=</span>data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>text<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    line <span class="hljs-operator">&lt;-</span> text<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    gsid <span class="hljs-operator">&lt;-</span> line<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    WP<span class="hljs-operator">$</span>TERM2NAME <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>WP<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>i<span class="hljs-punctuation">,</span>gsid<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>k <span class="hljs-keyword">in</span> <span class="hljs-number">3</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>line<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        WP<span class="hljs-operator">$</span>TERM2GENE <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>WP<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>i<span class="hljs-punctuation">,</span>line<span class="hljs-punctuation">[</span>k<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br>colnames<span class="hljs-punctuation">(</span>WP<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;gsid&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;name&#x27;</span><span class="hljs-punctuation">)</span><br>colnames<span class="hljs-punctuation">(</span>WP<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;gsid&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;gene&#x27;</span><span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> AnnotationDbi<span class="hljs-operator">::</span>select<span class="hljs-punctuation">(</span>org.Hs.eg.db<span class="hljs-operator">::</span>org.Hs.eg.db<span class="hljs-punctuation">,</span>keys<span class="hljs-operator">=</span>WP<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-operator">$</span>gene<span class="hljs-punctuation">,</span>columns<span class="hljs-operator">=</span><span class="hljs-string">&#x27;SYMBOL&#x27;</span><span class="hljs-punctuation">,</span> keytype<span class="hljs-operator">=</span><span class="hljs-string">&#x27;ENTREZID&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="修订部分更新"><a href="#修订部分更新" class="headerlink" title="修订部分更新"></a>修订部分更新</h2><ul>
<li>tmp[is.na(tmp$SYMBOL),] 找到所有转换失败的ENTREZID，比如 388813</li>
<li>访问 <a target="_blank" rel="noopener" href="https://www.ncbi.nlm.nih.gov/gene/">https://www.ncbi.nlm.nih.gov/gene/</a><ENTREZID> 得到更新信息</li>
<li>比如 388813 现在已经更名为 64092，HGNC确认其官方SYMBOL为 SAMSN1</li>
<li>tmp[is.na(tmp$SYMBOL), ‘SYMBOL’] &lt;- c(‘SAMSN1’, rep(‘S1PR3’,3))，手动更新信息</li>
<li>WP$TERM2GENE$gene &lt;- tmp$SYMBOL 更改ENTREZID为SYMBOL</li>
<li>saveRDS(WP,’WP.hsa.rds’) 保存数据库</li>
<li>自定义数据库的使用方法见下面的博文</li>
</ul>
<p><a target="_blank" rel="noopener" href="https://occdn.limour.top/2128.html">https://occdn.limour.top/2128.html</a></p>

                
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