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I have a list of gene names from the analysis of my mouse single seq data. I want to perform a simple grouping of the genes based on the pathways to which they belong or pathways through which they relate. Results from my online searches strongly recommend the ingenuity pathway analysis (IPA) tool. My laboratory has a license for the tool, but I need help with the workflow/steps. I have no prior experience with pathway analysis, and I have a background in R and Python programming. Can anyone also suggest any link which can help me proceed with the required IPA analysis? I will also be very grateful for any other tools (databases, R or Python packages) that can be helpful here.

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  • $\begingroup$ Have you tried watching any of the many videos Qiagen has made for how to use IPA? They're quite helpful. Note that you'll want to upload a list of gene identifiers with fold-changes (and possibly p-values, unless you've already subset them). $\endgroup$
    – Devon Ryan
    Feb 18 '19 at 10:24
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    $\begingroup$ What are you interested in? The title ask one question but the body ask another one. Which is your biological question of interest? Could you also explain what steps have you done to find help with the IPA software? $\endgroup$
    – llrs
    Feb 18 '19 at 10:24
  • $\begingroup$ FYI: Question is also posted on biostars. $\endgroup$
    – finswimmer
    Feb 18 '19 at 10:38
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The DAVID tool is always interesting, and easy to try: https://david.ncifcrf.gov/gene2gene.jsp

You submit a list of genes, it uses several different annotation databases to annotate the gene list, and then it clusters the results and tests for statistical enrichment. You can potentially learn about functional enrichment in your gene list from several different independent annotations.

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