Body: <p>I've currently run pathway analysis on a set of genes. I'm now trying to figure out how to see which genes are driving each pathway.</p>
  <pre><code>cleaned_ductal_markers &lt;- tumor_markers
  markers15  = cleaned_ductal_markers %&gt;% filter(cluster==&quot;PSEUDOPAPILLARY&quot;, avg_logFC&gt;0.5, p_val_adj&lt;0.01)
  markers15
  
  #head(genes_map)
  markers_entrez = genes_map[which(genes_map<span class="math-container">$SYMBOL %in% markers15$</span>gene),&quot;ENTREZID&quot;]
  kk &lt;- enrichKEGG(gene         = markers_entrez,
                  universe      = genes_map[, &quot;ENTREZID&quot;],
                   organism     = 'hsa',
                   pvalueCutoff = 0.05)
  #head(kk)
  dotplot(kk, showCategory=10)
  options(repr.plot.width=7, repr.plot.height=5)
  emapplot(kk, showCategory=12, font.size =16) + set_graph_style(family = &quot;Arial Narrow&quot;, face = &quot;plain&quot;,  text_size = 15, text_colour = &quot;black&quot;)
  </code></pre>
  <p>I'm now given a list of pathways but now I'm trying to see which genes are driving those pathways.</p>
  <p>How do I see the genes?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-30T16:13:39.257Z
Comments.Text: What’s your actual question?
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-02T14:36:28.720Z
Comments.Text: @user438383 My question is how do I see which genes are driving those pathways?
Comments.UserDisplayName: mmpp
Tags: <single-cell><pathway><go-enrichment><kegg>
Title: What genes are driving a certain pathway
ThreadText: # What genes are driving a certain pathway
  
  (Asked by: username_0 on 2022-04-30)
  
  I've currently run pathway analysis on a set of genes. I'm now trying to figure out how to see which genes are driving each pathway.
  
  ```
  cleaned_ductal_markers <- tumor_markers
  markers15  = cleaned_ductal_markers %>% filter(cluster=="PSEUDOPAPILLARY", avg_logFC>0.5, p_val_adj<0.01)
  markers15
  
  #head(genes_map)
  markers_entrez = genes_map[which(genes_map$SYMBOL %in% markers15$gene),"ENTREZID"]
  kk <- enrichKEGG(gene         = markers_entrez,
                  universe      = genes_map[, "ENTREZID"],
                   organism     = 'hsa',
                   pvalueCutoff = 0.05)
  #head(kk)
  dotplot(kk, showCategory=10)
  options(repr.plot.width=7, repr.plot.height=5)
  emapplot(kk, showCategory=12, font.size =16) + set_graph_style(family = "Arial Narrow", face = "plain",  text_size = 15, text_colour = "black")
  
  ```
  
  I'm now given a list of pathways but now I'm trying to see which genes are driving those pathways.
  
  How do I see the genes?
  
  **Tags:** single-cell, pathway, go-enrichment, kegg
  
  > **Comments:**
  > **username_1**: What’s your actual question?  
  > **username_0**: @username_1 My question is how do I see which genes are driving those pathways?  
  
  ---
  
  ## 0 answers
  
  