Experimental and computational challenges from array-based to sequence-based ChIP techniques

ISSN: 2212-392X (Online)
ISSN: 1574-8936 (Print)


Volume 10, 5 Issues, 2015


Download PDF Flyer




Current Bioinformatics

Aims & ScopeAbstracted/Indexed in


Submit Abstracts Online Submit Manuscripts Online

Editor-in-Chief:
Alessandro Giuliani
Istituto Superiore di Sanit√° (Italian NIH) Environment and Health Dept
Roma
Italy


View Full Editorial Board

Subscribe Purchase Articles Order Reprints

Current: 0.921
5 - Year: 1.045

Experimental and computational challenges from array-based to sequence-based ChIP techniques



Current Bioinformatics, Volume 8 (E-pub ahead of print)

Author(s): Xun Lan and Victor X Jin.


Abstract

Transcriptional regulation is a key step to control the level of mRNA formed. Recent view of transcriptional regulation has evolved from a one-dimensional mode, i.e. RNA Polymerase II assembles with general transcription factors, and cis-regulatory elements (CREs) interact with transcription factors, to a much complex multiple-dimensional mode, involving combinatorial interactions between transcription factors and regulatory sequences, chromatin structure, histone modifications, DNA methylation. High throughput experimental technologies, such as array-based ChIP-chip and sequencing-based ChIP-seq, have been developed to survey in vivo transcription factor binding sites and histone modifications. Despite many efforts have been made to analyze and interpret the data, challenges remain in many aspects of both experimental protocols and computational analyses. For example, how to determine the optimized number of PCR cycles? How to normalize multiple datasets from multiple experiments? How to utilize the large number of unmapped and multiple mapped tags in ChIP-seq experiment? This review focuses on issues emerged in high throughput data processing and discusses advantages and disadvantages of various strategies.


Purchase Online Order Reprints Order Eprints Rights and Permissions




Article Details

Volume: 8
First Page:
Page Count:
DOI: 10.2174/15748936113089990013
Advertisement

Related Journals




Webmaster Contact: urooj@benthamscience.org Copyright © 2015 Bentham Science