The PinkThing for analysing ChIP profiling data in their genomic context.

ABSTRACT:

Background

Current epigenetic research makes frequent use of whole-genome ChIP profiling for determining the in vivo binding of proteins, e.g. transcription factors and histones, to DNA. Two important and recurrent questions for these large scale analyses are: 1) What is the genomic distribution of a set of binding sites? and 2) Does this genomic distribution differ significantly from another set of sites?

Findings

We exemplify the functionality of the PinkThing by analysing a ChIP profiling dataset of cohesin binding sites. We show the subset of cohesin sites with no CTCF binding have a characteristic genomic distribution different from the set of all cohesin sites.

Conclusions

The PinkThing is a web application for fast and easy analysis of the context of genomic lo

SUBMITTER: Nielsen FG 

PROVIDER: S-EPMC3674928 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature