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  • Cluster genes based on the Gene Ontology

    Hi

    we have a dataset consisted of a lot of genes and their respective information (like expression). We would like to make a picture to cluster those genes first on their GO terms (gene function) and then on our expression input that we have. Hence, how can I cluster those genes based on their GO terms? Do you have any suggestion?

    We are currently programming in R and we would like a R package to solve the problem. We have looked at topGO but that does not give the information we are looking for. Since only uses a small set of the total number of genes.

    thanks in advance for your help

  • #2
    Maybe BinGO in Cytoscape can help you.

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    • #3
      You can try Blast2GO, it assigns GO terms to your sequences by first performing a blast.

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      • #4
        Gene enrichment analysis for Human - with list of GeneID (Entrez) and Gene Symbols.

        If you have list of Gene ID's or Gene Symbols. I have written a simple perl script to find enriched terms from your list of provided genes. The GO terms are updated till 2014 January. You can download the tool from the following link:

        https://github.com/santhilalsubhash/geneSCF.git

        Please feel free to contact me. If you need further clarification.
        Last edited by santhilalsubhash; 08-05-2014, 07:17 AM.

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