Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq: PeakAnalyzer: Genome-wide annotation of chromatin binding and modification Newsbot! Literature Watch 4 01-21-2017 12:50 AM
Tools for finding differential histone modification sites? asiangg Bioinformatics 27 04-09-2013 05:32 AM
ChIP-Seq: Identifying Differential Histone Modification Sites from ChIP-seq Data. Newsbot! Literature Watch 0 12-02-2011 05:51 AM
ChIP-Seq: Genome-wide analysis of the relationships between DNaseI HS, histone modifi Newsbot! Literature Watch 0 06-21-2011 03:00 AM
PubMed: Genome-wide histone methylation profile for heart failure. Newsbot! Epigenetics 0 12-17-2008 06:03 AM

Thread Tools
Old 08-06-2008, 07:54 AM   #1
Location: FL

Join Date: Jun 2008
Posts: 19
Default An HMM approach to genome-wide identification of differential histone modification si

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.
Xu H, Wei CL, Lin F, Sung WK.


MOTIVATION: Epigenetic modifications are one of the critical factors to regulate gene expression and genome function. Among different epigenetic modifications, the differential histone modification sites (DHMSs) are of great interest to study the dynamic nature of epigenetic and gene expression regulations among various cell-types, stages or environ-mental responses. To capture the histone modifications at whole genome scale, ChIP-seq technology is becoming a robust and comprehensive approach. Thus the DHMSs are potentially identifiable by comparing two ChIP-seq libraries. However, little has been addressed on this issue in literature. RESULTS: Aiming at identifying DHMSs, we propose an approach called ChIPDiff for the genome-wide comparison of histone modification sites identified by ChIP-seq. Based on the observations of ChIP fragment counts, the proposed approach employs a Hidden Markov Model (HMM) to infer the states of histone modification changes at each genomic location. We evaluated the performance of ChIPDiff by com-paring the H3K27me3 modification sites between mouse embryonic stem cell (ESC) and neural progenitor cell (NPC). We demonstrated that the H3K27me3 DHMSs identified by our approach are of high sensitivity, specificity and technical reproducibility. ChIPDiff was further applied to uncover the differential H3K4me3 and H3K36me3 sites between different cell states. Interesting biological discoveries were achieved from such comparison in our study. AVAILABILITY: CONTACT:, SUPPLEMENTARY INFORMATION: Supplementary methods and data are available at Bioinformatics online.
jlli is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:00 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO