JSM 2012 Home

JSM 2012 Online Program

The views expressed here are those of the individual authors and not necessarily those of the JSM sponsors, their officers, or their staff.

Online Program Home

Abstract Details

Activity Number: 253
Type: Contributed
Date/Time: Monday, July 30, 2012 : 2:00 PM to 3:50 PM
Sponsor: Biometrics Section
Abstract - #306141
Title: Model-Based Stastical Approach for Paired-End ChIP-Seq
Author(s): Sangsoon Woo*+ and Xuekui Zhang and Raphael Gottardo
Companies: Fred Hutchinson Cancer Research Center and The Johns Hopkins University and Fred Hutchinson Cancer Research Center
Address: Vaccine and Infectious Disease and Public Health Sciences Divisions, Seattle, WA, 98109, United States
Keywords: ChIP-Seq ; Paired-End sequencing ; PING

ChIP-Seq enables to study protein interaction with DNA such as histones,histone modification,nucleosome positioning and transcription binding sites. Several statistical approaches have been developed for single-ended(SE) ChiP-Seq to identify genomic regions showing biological signal. The paired-end(PE) sequencing platform is recently introduced technology, which generates double-end sequencing reads. Compared to SE, PE offers better information of each DNA fragment by providing genome coordinates of both ends. We recently published model-based approach for identifying nucleosome positions(PING) that models bi-directional read densities using mixture models and imputing missing reads. As a modification of PING, we developed a model-based approach for analyzing PE data(PING-PE) by forcing fragment's forward and reverse reads belong to the same mixture component, modifying parameter estimates, imputing missing reads and changing segmentation step. We will discuss about efficiency of PE sequencing compared to SE sequencing and also compare our PING-PE approach to several widely used ChIP-Seq data analysis tools such as MACS, CisGenome and SIPeS using published PE sequencing data.

The address information is for the authors that have a + after their name.
Authors who are presenting talks have a * after their name.

Back to the full JSM 2012 program

2012 JSM Online Program Home

For information, contact jsm@amstat.org or phone (888) 231-3473.

If you have questions about the Continuing Education program, please contact the Education Department.