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  • Is there a way to get transcription factors from gene list?

    Hello everybody,

    During a RNA-seq experiment analysis I've receiver the request of getting the Transcription factors (TF) associated to the names of the Differentially expressed (DE) genes. I've been trying to fin a tool or R-package to achieve this, but I can't seem to find one.
    I also looked in this forum to see if I could get any help, but the only post I came across was the following one.



    I tried the solution there, but after crossing my DE table with the one mentioned in the post the result was almost useless (only 4 transcription factors seemed to be related with my DE list).

    Briefly, Can anybody shed some light on this issue?

    Thanks in advance

    JL

  • #2
    you may try IPA ,it gives you this kind f TF which associated to your genelist.alternatively you can also gathering some TF data from open database like transfac,this way may take a lot time .

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    • #3
      TRANSFAC is a commercial package as is IPA, some very limited datasets are available from TRANSFAC via a trial. oPossum and JASPAR seem like the best options for 'free' TF analysis.

      I thought about this before; how useful is it to use RNAseq data to determine what TFs may be relevant to your DE genes? Do you have other data which can confirm the presence or absence of TFs? Maybe alternative splicing and SNP analysis is more relevant for RNAseq data (at least this is the conclusion I came to!)

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      • #4
        You could try also to browse GSEA,
        Investigate Gene Sets adn search for TFT: transcription factor targets

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        • #5
          Thank you everybody for your insights

          @bruce01 and @zinky, IPA and TRansfac are commercial as you point out and I don't have the budget to purchase them...

          @bruce I agree with you in the RNAseq data consideration, but it's not my idea, it was the researcher request...

          @paolo.kunder, I've tried to use GSEA but I can't get any input format that make it work...not clear if it's worth to keep on trying to use such tool.

          I'll keep searching...

          Comment


          • #6
            in GSEA you just have to upload offcial gene symbol,
            for instance,

            Gapdh
            Acta1
            Myh7
            Erg

            Comment


            • #7
              @paolo.kunder thank you for this insight I was trying to use GSEA for enrichment analysis instead of TF searches. It seems to work quite nicely

              Comment

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