<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>

CC BY-SA 4.0
2022-04-30T16:13:39.257Z
What’s your actual question?
user438383
CC BY-SA 4.0
2022-05-02T14:36:28.720Z
@user438383 My question is how do I see which genes are driving those pathways?
mmpp
<single-cell><pathway><go-enrichment><kegg>
What genes are driving a certain pathway
# 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**: @user438383 My question is how do I see which genes are driving those pathways?  

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## 0 answers

