search

LauraPS1 / TFEA.ChIP_downloads

TFEA.ChIP is an R package in developement. Its purpose is to analyze transcription factor enrichment in a set of differentially expressed genes.
5 stars 1 forks source link

TF Peaks & Region Enrichment Support #4

Closed YuanTian1991 closed 2 years ago

YuanTian1991 commented 3 years ago

Hi:

I have two questions related to TFEA.CHIP, I hope you can help me a bit.

  1. Do you know where I can get peaks of each TF from TFEA.CHIP? I checked the .Rdata in this repo, but they are matched result between TF and genes. I want to get original TF peaks' coordinates for some visualisation.
  2. Now TFEA.CHIP seems can only do TFEA on genes, but what I have are regions on the genome, like hypermethylated CpG Islands, 5hmC enriched peaks .etc. Is there any way I use TFEA.CHIP to do enrichment analysis on them?

Best Tian

LauraPS1 commented 3 years ago

Hi,

  1. The ChIP-seq data is from the ReMap colection and is available here.
  2. It's possible make a custom database for TFEA.ChIP with the genomic locations of interest to you. The process to make the custom database is described in the package's vignette.

Cheers

YuanTian1991 commented 3 years ago

Thanks Laura:

I just checked the link you gave me, but it seems remap only provided human and Arabidopsis thaliana. Where did you get the Mouse TF Peaks?

Best

LauraPS1 commented 3 years ago

No problem. The mouse data is from the ENCODE project. It's also available in UCSC's table browser.