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Steps I have done

  • I have two cell types to compare one is stem cell and leukemic stem cell
  • Two sets of data for each condition RNA seq and ATAC seq.
  • Did differential expression as well as differential accessibility analysis.
  • From the differential accessibility analysis I'm getting the regions which I used for motif analysis using homer.
  • The result of de novo motif enrichment

motif enrichment

Question

So this results shows possible transcription factor binding motif. Now how do i find the target genes of this putative transcription factor. Do i need to see the literature or what other ways to do it. As of now I don;t have chip seq data. So is it possible to use expression and accessibility data to find out the possible targets of this putative transcription factors, which in turn can give me lead for my downstream validation.

Any suggestion or help would be really appreciated

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