Predicting transcription factor target genes from ChIP-seq data

Date

Feb 16, 2012

Time

2:30 PM - 3:30 PM

Speaker

Weronika Sikora-Wohlfeld

Affiliation

Biotec Dresden, group Andreas Beyer

Series

IMB - Seminar

Language

en

Main Topic

Informatik

Other Topics

Biologie, Informatik

Description

Chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) has been instrumental for measuring genome-wide binding locations of transcription factors (TFs). Whereas a lot of effort has been put into development of peak-calling methods, prediction of TF targets from ChIP-seq data is still an open problem. In particular, there is a lack of systematic comparisons of existing TF-target assignment methods. Here we present an evaluation of TF-target assignment algorithms that uses independent functional assays for scoring the performance of the methods. We applied the TF-target prediction methods on two datasets of ChIP-seq experiments conducted in mouse hematopoietic ('HemoChIP') and embryonic stem cells ('EsChIP'), covering jointly 42 different TFs and we evaluated them against over 20 expression datasets. Our analysis shows that considering both, the density of the peaks around the TSS and their distance to the TSS, gives best results. We propose a TF-target scoring method which is based on the TF-specific distribution of peak-TSS distances and thus is adaptable to 'new' TFs without prior knowledge.

Last modified: Jan 30, 2012, 5:36:07 PM