find Overlapping targets.

Question

[Ram]

Hi,

Can anybody suggest how to find overlapping targets from a given list of proteins obtained from ENCODE ?

Thanks

[Devon Ryan]

What exactly is being targeted? Do you just want to find the intersect of two lists of proteins or are you looking for something else entirely?

Answer 1

[seidel]

As worded, your question is almost impossible to understand. It would be really helpful if you could provide some more explanation and context. However, a "list of proteins obtained from ENCODE" could mean ChIP Seq data sets for proteins studied by ENCODE. In that case one could download called peaks or sites, and use BEDTools (intersectBed) to find overlaps, or bring the data into R and use bioconductor tools (i.e. GenomicRanges). There's also a wide variety of tools listed at UCSC.