EnrichR parameters used for transcription factors enrichment

Question

[mozart.marins12]

Please, I using EnrichR to find enriched transcription factors in a set of down and up regulated genes. It gives me back mice results but I woudl like to know which are the parameters used such as the region around TSS (-2000/200?), the lenght of the motifs analyzed (8.10. 12?), is there a GC correction? The conservation between motifs in the background and target sequences?

Thanks, Mozart

Answer 1

[WouterDeCoster]

I think for most of those databases (ChEA, TargetScan, Transfac, jaspar, ENCODE,...) Enrichr just uses the annotation provided by those databases without any post processing. You would need to look into each data source separately to determine how their parameters were defined.

You can most likely find more information about data processing in the Enrichr publications: https://www.ncbi.nlm.nih.gov/pubmed/27141961 and https://www.ncbi.nlm.nih.gov/pubmed/23586463

[mozart.marins12]

When you use other tools such as opossum and homer, you have to define the region around the tss you want to be analyzed. And in enrichR this is not possible. It seems to be a fixed parameter. Iwould like to know thisbfor rwsults comparison.

[WouterDeCoster]

Have you read my post?

[mozart.marins12]

Dear DeCoster,

  Thanks . I've read your post and read the papers but this info is not there. And in the enrichR site there's no explanation for this. Thank you for your reply. I will try contact withe the authors.