Jump to ContentJump to Main Navigation
Show Summary Details

Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Stumpf, Michael P.H.

6 Issues per year


IMPACT FACTOR increased in 2015: 1.265
5-year IMPACT FACTOR: 1.423
Rank 42 out of 123 in category Statistics & Probability in the 2015 Thomson Reuters Journal Citation Report/Science Edition

SCImago Journal Rank (SJR) 2015: 0.954
Source Normalized Impact per Paper (SNIP) 2015: 0.554
Impact per Publication (IPP) 2015: 1.061

Mathematical Citation Quotient (MCQ) 2015: 0.06

Online
ISSN
1544-6115
See all formats and pricing
Volume 10, Issue 1 (Oct 2011)

Adaptive Elastic-Net Sparse Principal Component Analysis for Pathway Association Testing

Xi Chen
  • Vanderbilt University
Published Online: 2011-10-24 | DOI: https://doi.org/10.2202/1544-6115.1697

Pathway or gene set analysis has become an increasingly popular approach for analyzing high-throughput biological experiments such as microarray gene expression studies. The purpose of pathway analysis is to identify differentially expressed pathways associated with outcomes. Important challenges in pathway analysis are selecting a subset of genes contributing most to association with clinical phenotypes and conducting statistical tests of association for the pathways efficiently. We propose a two-stage analysis strategy: (1) extract latent variables representing activities within each pathway using a dimension reduction approach based on adaptive elastic-net sparse principal component analysis; (2) integrate the latent variables with the regression modeling framework to analyze studies with different types of outcomes such as binary, continuous or survival outcomes. Our proposed approach is computationally efficient. For each pathway, because the latent variables are estimated in an unsupervised fashion without using disease outcome information, in the sample label permutation testing procedure, the latent variables only need to be calculated once rather than for each permutation resample. Using both simulated and real datasets, we show our approach performed favorably when compared with five other currently available pathway testing methods.

Keywords: gene expression; microarray; pathway analysis; sparse principal component analysis

About the article

Published Online: 2011-10-24


Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: https://doi.org/10.2202/1544-6115.1697. Export Citation

Comments (0)

Please log in or register to comment.
Log in