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  • #1

    Gene Family Anaylsis Tools?

    Hi, dears,
    I am analyzing some RNASeq data.
    I have gotten the differential expressed gene lists, which have hundreds or thousands of genes.
    Studying them one by one is just time-consuming and low efficient.
    So I am thinking about pathway analysis and gene family analysis.
    I just searched, but didn't find specific tools for gene family analysis.
    Do you know any available tools for gene family analysis?
    Thank you.
    Tags: None
  • #2
    Be specific in what you mean by gene family analysis

    Comment

    • #3
      Originally posted by JackieBadger View Post
      Be specific in what you mean by gene family analysis
      Most basically, for a given gene list from one species, the analysis can assign the genes to its corresponding gene family, so we can easily group the genes by its gene family. More details such as the chromosome, the loci, its function are better.
      An across species analysis would be great.

      Comment

      • #4
        Hi,

        maybe you wanna check out something like this http://www.bioconductor.org/help/cou...008/labs/GSEA/ which gives you a statistical significance on the way. Else you might want to look for blast2go or any other GO-Term related tool.

        Cheers

        Comment

        • #5
          and this http://prospectus.usherbrooke.ca/cluss/

          Comment

          • #6
            Thanks, sphil.
            This tool seems interesting.
            Try to dig it and see whether it could be used for gene family.

            Originally posted by sphil View Post
            Hi,

            maybe you wanna check out something like this http://www.bioconductor.org/help/cou...008/labs/GSEA/ which gives you a statistical significance on the way. Else you might want to look for blast2go or any other GO-Term related tool.

            Cheers

            Comment

            • #7
              Hi, Jackie,
              a little confused. Isn't it an aligner for protein?

              Originally posted by JackieBadger View Post
              and this http://prospectus.usherbrooke.ca/cluss/

              Comment

              • #8
                Yup.
                Genome-Wide Comparative Gene Family Classification
                http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013409
                Correct classification of genes into gene families is important for understanding gene function and evolution. Although gene families of many species have been resolved both computationally and experimentally with high accuracy, gene family classification in most newly sequenced genomes has not been done with the same high standard. This project has been designed to develop a strategy to effectively and accurately classify gene families across genomes. We first examine and compare the performance of computer programs developed for automated gene family classification. We demonstrate that some programs, including the hierarchical average-linkage clustering algorithm MC-UPGMA and the popular Markov clustering algorithm TRIBE-MCL, can reconstruct manual curation of gene families accurately. However, their performance is highly sensitive to parameter setting, i.e. different gene families require different program parameters for correct resolution. To circumvent the problem of parameterization, we have developed a comparative strategy for gene family classification. This strategy takes advantage of existing curated gene families of reference species to find suitable parameters for classifying genes in related genomes. To demonstrate the effectiveness of this novel strategy, we use TRIBE-MCL to classify chemosensory and ABC transporter gene families in C. elegans and its four sister species. We conclude that fully automated programs can establish biologically accurate gene families if parameterized accordingly. Comparative gene family classification finds optimal parameters automatically, thus allowing rapid insights into gene families of newly sequenced species.

                Comment

                • #9
                  Nice paper! Thanks, Jackie

                  Originally posted by JackieBadger View Post
                  Yup.
                  http://www.plosone.org/article/info:...l.pone.0013409

                  Comment

                  • #10
                    I read the above post and got to ask, if somebody can tell me how can I do pathway analysis with diff_gene values... is there any free tools...
                    thanks in advance

                    Comment

                    • #11
                      Originally posted by jp. View Post
                      I read the above post and got to ask, if somebody can tell me how can I do pathway analysis with diff_gene values... is there any free tools...
                      thanks in advance
                      Hi, jp, I am using AltAnalyze which is an open-source free tool.

                      Comment

                      • #12
                        Thank you for your reply
                        Its is for alt splicing ?
                        Anything for diff_genes ?

                        Originally posted by ZoeG View Post
                        Hi, jp, I am using AltAnalyze which is an open-source free tool.

                        Comment

                        • #13
                          Originally posted by jp. View Post
                          Thank you for your reply
                          Its is for alt splicing ?
                          Anything for diff_genes ?
                          This software can do differential gene expression, alt splicing and also allow you to do pathway analysis.

                          Comment

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