Get cell-tpe-specific TF-gene regulatory relations

[Ying-Lab]

Hi there!

Thanks for the excellent work!

I am interested in getting the cell-type-specific TF-gene regulations. However, in the taget gene module, I find that all the potential target genes are provided for a certain TF. In the Peak-Browser, the cell-type-specific TF ChIP-seq bed file can be downloaded. I tried to process the bed file via annotatePeak function of ChIPseeker package, while some errors always ocurred,indicating that 'start' or 'end' cannot contain NAs.

Therefore, I was wondering if there is a more convenient way to get the cell-cell-specific TF-gene regulations according to all the cell-type-specific ChIP-seq data?

I look forward to your reply. Thanks in advance for your time and help!

Best, Scotty

[zouzhaonan]

Hi,

To achieve your goal, the window subcommand of bedtools should be useful.

Here’s an example command: bedtools window -a $A_Bed -b $B_Bed -w $width

In this command:

• $A_Bed represents a cell-type-specific TF ChIP-seq BED file that you can download from Peak Browser.
• $B_Bed is a BED file containing the transcription start sites (TSS) of all genes.
• $width specifies the distance range from the TSS, for example, 5000.

You can obtain the appropriate $B_Bed files (originally sourced from the UCSC Genome Browser) from here. Please feel free to reach out if you need any further assistance.

BR, Zhaonan

[Ying-Lab]

Thank you so much! I tried the pipeline and it worked well.