Universität zu Köln

Sikora-Wohlfeld, Weronika, Ackermann, Marit, Christodoulou, Eleni G., Singaravelu, Kalaimathy and Beyer, Andreas ORCID: 0000-0002-3891-2123 (2013). Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data. PLoS Comput. Biol., 9 (11). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1553-7358

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Abstract

Chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) has great potential for elucidating transcriptional networks, by measuring genome-wide binding of transcription factors (TFs) at high resolution. Despite the precision of these experiments, identification of genes directly regulated by a TF (target genes) is not trivial. Numerous target gene scoring methods have been used in the past. However, their suitability for the task and their performance remain unclear, because a thorough comparative assessment of these methods is still lacking. Here we present a systematic evaluation of computational methods for defining TF targets based on ChIP-seq data. We validated predictions based on 68 ChIP-seq studies using a wide range of genomic expression data and functional information. We demonstrate that peak-to-gene assignment is the most crucial step for correct target gene prediction and propose a parameter-free method performing most consistently across the evaluation tests.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Sikora-Wohlfeld, Weronika UNSPECIFIED UNSPECIFIED UNSPECIFIED Ackermann, Marit UNSPECIFIED UNSPECIFIED UNSPECIFIED Christodoulou, Eleni G. UNSPECIFIED UNSPECIFIED UNSPECIFIED Singaravelu, Kalaimathy UNSPECIFIED UNSPECIFIED UNSPECIFIED Beyer, Andreas UNSPECIFIED orcid.org/0000-0002-3891-2123 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-473684
DOI:	10.1371/journal.pcbi.1003342
Journal or Publication Title:	PLoS Comput. Biol.
Volume:	9
Number:	11
Date:	2013
Publisher:	PUBLIC LIBRARY SCIENCE
Place of Publication:	SAN FRANCISCO
ISSN:	1553-7358
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language BIOCONDUCTOR; EXPRESSION; POWERFUL; NETWORK; MODULES; TOOL Multiple languages Biochemical Research Methods; Mathematical & Computational Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/47368