Analysis of computational footprinting methods for DNase sequencing experiments.
Nat Methods
; 13(4): 303-9, 2016 Apr.
Article
in En
| MEDLINE
| ID: mdl-26901649
ABSTRACT
DNase-seq allows nucleotide-level identification of transcription factor binding sites on the basis of a computational search of footprint-like DNase I cleavage patterns on the DNA. Frequently in high-throughput methods, experimental artifacts such as DNase I cleavage bias affect the computational analysis of DNase-seq experiments. Here we performed a comprehensive and systematic study on the performance of computational footprinting methods. We evaluated ten footprinting methods in a panel of DNase-seq experiments for their ability to recover cell-specific transcription factor binding sites. We show that three methods--HINT, DNase2TF and PIQ--consistently outperformed the other evaluated methods and that correcting the DNase-seq signal for experimental artifacts significantly improved the accuracy of computational footprints. We also propose a score that can be used to detect footprints arising from transcription factors with potentially short residence times.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Transcription Factors
/
Software
/
Sequence Analysis, DNA
/
DNA Footprinting
/
Computational Biology
/
High-Throughput Nucleotide Sequencing
Type of study:
Prognostic_studies
Limits:
Humans
Language:
En
Journal:
Nat Methods
Journal subject:
TECNICAS E PROCEDIMENTOS DE LABORATORIO
Year:
2016
Type:
Article
Affiliation country:
Germany