How to infer the target TF gene of ZNF132 without any ChIP-seq knowledge?

Question

[Shicheng Guo]

Hi All,

Any way I can choose to infer the target genes which are regulated by transcript factor gene: ZNF132 without any ChIP-seq result.

By the way, ENCODE didn't include this gene in his ChIP-seq design.

Thanks.

Answer 1

[Alex Reynolds]

Neph et al describes a procedure which involves locating putative TF binding sites in DNaseI-seq footprinted regions. There's a paper by Maurano et al that shows footprint signal have good concordance with ChIP-seq signal. You then do bedops set operations to find overlaps with gene promoter regions, i.e. where a TF can bind to a gene's promoter may indicate a regulatory relationship between the TF and the target gene.

[Shicheng Guo]

Thanks Alex, I found the Chip-seq data for ZNF132 in

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2825467