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:
|
586
|
Type:
|
Invited
|
Date/Time:
|
Thursday, August 2, 2012 : 8:30 AM to 10:20 AM
|
Sponsor:
|
ENAR
|
Abstract - #303844 |
Title:
|
Predicting Functional Targets of Transcription Factors by Coupling CHiP-Seq with Geo
|
Author(s):
|
Hongkai Ji*+ and George Wu
|
Companies:
|
The Johns Hopkins University and The Johns Hopkins University
|
Address:
|
Department of Biostatistics, Baltimore, ,
|
Keywords:
|
ChIP-seq ;
Gene expression ;
Next-generation sequencing ;
Bayesian model ;
Data integration
|
Abstract:
|
Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is increasingly used to study the role of transcription factors (TFs) in gene regulation. A ChIP-seq experiments can identify thousands of target genes, but typically only a fraction of the targets respond to TF binding, while the others are likely to represent non-functional binding. For this reason, ChIP experiments are often coupled with gene expression profiling to more accurately define functional targets. However, we found that a large proportion of studies did not provide corresponding gene expression data. Based on the previously observed correlation between TF and target genes, we hypothesized that publicly available gene expression data can be used to more effectively identify functional ChIP target genes by combining the likelihood of TF binding with the correlation between gene and TF expression. We developed a model to integrate ChIP-seq with data in Gene Expression Omnibus to accomplish this goal. Our test show that this new method can significantly improve functional target prediction.
|
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.