English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

Stegle, O., Parts, L., Piipari, M., Winn, J., & Durbin, R. (2012). Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nature Protocols, 7(3), 500-507. doi:10.1038/nprot.2011.457.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0013-B838-A Version Permalink: http://hdl.handle.net/21.11116/0000-0001-8A09-A
Genre: Journal Article

Files

show Files

Locators

show
hide
Description:
-

Creators

show
hide
 Creators:
Stegle, O1, Author              
Parts, L, Author
Piipari, M, Author
Winn, J, Author
Durbin, R, Author
Affiliations:
1Max Planck Institute for Intelligent Systems, Max Planck Society, Heisenbergstr. 3 70569 Stuttgart , DE, ou_1497638              

Content

show
hide
Free keywords: -
 Abstract: We present PEER (probabilistic estimation of expression residuals), a software package implementing statistical models that improve the sensitivity and interpretability of genetic associations in population-scale expression data. This approach builds on factor analysis methods that infer broad variance components in the measurements. PEER takes as input transcript profiles and covariates from a set of individuals, and then outputs hidden factors that explain much of the expression variability. Optionally, these factors can be interpreted as pathway or transcription factor activations by providing prior information about which genes are involved in the pathway or targeted by the factor. The inferred factors are used in genetic association analyses. First, they are treated as additional covariates, and are included in the model to increase detection power for mapping expression traits. Second, they are analyzed as phenotypes themselves to understand the causes of global expression variability. PEER extends previous related surrogate variable models and can be implemented within hours on a desktop computer.

Details

show
hide
Language(s):
 Dates: 2012-02
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1038/nprot.2011.457
BibTex Citekey: SteglePPWD2012
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Nature Protocols
  Other : Nat. Protoc.
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: London, UK : Nature Publishing Group
Pages: - Volume / Issue: 7 (3) Sequence Number: - Start / End Page: 500 - 507 Identifier: ISSN: 1750-2799
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000223800_1