SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: Differential expression analysis for sequence count data. Newsbot! Literature Watch 3 09-25-2012 09:19 AM
A scaling normalization method for differential expression analysis of RNA-seq data severin Literature Watch 1 09-09-2010 11:09 PM
RNA-Seq: Cloud-scale RNA-sequencing differential expression analysis with Myrna. Newsbot! Literature Watch 0 08-13-2010 08:00 AM

Reply
 
Thread Tools
Old 03-28-2013, 02:00 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,443
Default RNA-Seq: Differential expression analysis for paired RNA-seq data.

Syndicated from PubMed RSS Feeds

Differential expression analysis for paired RNA-seq data.

BMC Bioinformatics. 2013 Mar 27;14(1):110

Authors: Chung LM, Ferguson JP, Zheng W, Qian F, Bruno V, Montgomery RR, Zhao H

Abstract
Background RNA-Seq technology measures the transcript abundance by generating sequence reads and counting their frequencies across different biological conditions. To identify differentially expressed genes between two conditions, it is important to consider the experimental design as well as the distributional property of the data. In many RNA-Seq studies, the expression data are obtained as multiple pairs, e.g., pre- vs. post-treatment samples from the same individual. We seek to incorporate paired structure into analysis.Results We present a Bayesian hierarchical mixture model for RNA-Seq data to separately account for the variability within and between individuals from a paired data structure. The method assumes a Poisson distribution for the data mixed with a gamma distribution to account variability between pairs. The effect of differential expression is modeled by two-component mixture model. The performance of this approach is examined by simulated and real data.Conclusions In this setting, our proposed model provides higher sensitivity than existing methods to detect differential expression. Application to real RNA-Seq data demonstrates the usefulness of this method for detecting expression alteration for genes with low average expression levels or shorter transcript length.


PMID: 23530607 [PubMed - as supplied by publisher]



More...
Newsbot! is offline   Reply With Quote
Reply

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 08:57 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO