Transcription factors associated with Differentially Expressed Genes

Question

[kamalika]

Hi,

I have a list of Differentially Expressed Genes , I want to find which transcription factors (TFs) are enriched for these genes. Which tool can be used for this?

Thanks!

Answer 1

[ATpoint]

You could scan their promoter regions (say 1kb upstream of the annotated TSS) for motif enrichment. Tools like Homer or MEME suite can do this. Important is the choice of background. Don't compare with random regions from the genome as this will return general promoter factors. Rather, I would test DEGs versus confident non-DEGs, e.g. pvalue > 0.95 and a good average expression across all samples.

[kamalika]

Thanks a lot for your response. I can see multiple options in the MEME suite for the motif enrichment analysis. Which tool will be the best to use:

[ATpoint]

I usually use AME for such situations.

[kamalika]

Thanks a lot!

[kamalika]

Hi,

Could you please tell me how do you interpret the results obtained from AME? I don't see any log fold change value for the enriched TFs.