How to decrease the number of candidate TFs binding to gene promoter region

Question

[Shicheng Guo]

Hi All,

I want to know which transcript factors regulated gene expression of FGF6. Therefore, I used all the ChIP-seq data for 685 TFs from the ENCODE project. However, I found there were more than 101TFs have peaks/signals in the promoter region of FGF6. Is there any other way to decrease the candidate numbers so that I can do some further deep analysis to few of the candidate TFs?

Thanks

[lessismore]

If you find a perturbation experiment for FGF6 gene, you can retrieve all genes that are differentially expressed (DEGs) and overlap the two sets to extract some more biologically relevant conclusions.

Answer 1

[ATpoint]

I would get my hands on RNA-seq data from the cell type you are working on and then eliminate factors lowly-expressed in this cell type. Proteomics data would of course be more precise. You can also try to perform some kind of correlation analysis if you get your hands on larger (many samples) datasets with different cell types and see if expression of these TFs is somewhat linear correlated to FGF6 expression.

[Shicheng Guo]

Great suggestion. Maybe I can use TCGA and GTEx data to do a co-expression analysis. Thanks ATpoint