Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network

PLoS Computational Biology
Yafei LyuQunhua Li

Abstract

Co-expression network analysis provides useful information for studying gene regulation in biological processes. Examining condition-specific patterns of co-expression can provide insights into the underlying cellular processes activated in a particular condition. One challenge in this type of analysis is that the sample sizes in each condition are usually small, making the statistical inference of co-expression patterns highly underpowered. A joint network construction that borrows information from related structures across conditions has the potential to improve the power of the analysis. One possible approach to constructing the co-expression network is to use the Gaussian graphical model. Though several methods are available for joint estimation of multiple graphical models, they do not fully account for the heterogeneity between samples and between co-expression patterns introduced by condition specificity. Here we develop the condition-adaptive fused graphical lasso (CFGL), a data-driven approach to incorporate condition specificity in the estimation of co-expression networks. We show that this method improves the accuracy with which networks are learned. The application of this method on a rat multi-tissue dataset and Th...Continue Reading

References

Jul 1, 1997·Journal of Neurocytology·A Holz, M E Schwab
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Mar 29, 2000·Proceedings of the National Academy of Sciences of the United States of America·N TamuraM Katsuki
Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
Feb 25, 2005·Annals of Surgery·Mark S DuxburyEdward E Whang
Feb 1, 2007·European Journal of Human Genetics : EJHG·Kate V EverettMark Gardiner
Oct 30, 2007·American Journal of Human Genetics·Kai WangMaja Bucan
Dec 15, 2007·Biostatistics·Jerome FriedmanRobert Tibshirani
Nov 19, 2008·BMC Biology·Zoltán DezsoTatiana Nikolskaya
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Mar 11, 2009·Nature Reviews. Genetics·Juan M VaquerizasNicholas M Luscombe
May 26, 2009·Nucleic Acids Research·Jing ChenAnil G Jegga
Jan 1, 2008·Journal of the Royal Statistical Society. Series B, Statistical Methodology·Hao Helen Zhang
Nov 3, 2009·Journal of the American Statistical Association·Jie PengJi Zhu
Aug 18, 2010·Cell Cycle·Cristian MoiolaAdriana De Siervi
Dec 15, 2010·PLoS Computational Biology·Benjamin A Logsdon, Jason Mezey
Feb 25, 2011·Future Oncology·Sharon B Cantor, Shawna Guillemette
Apr 19, 2011·Briefings in Bioinformatics·Helen E Lockstone
May 7, 2011·Bioinformatics·Arthur LiberzonJill P Mesirov
Jun 24, 2011·PLoS Computational Biology·Wenyuan LiXianghong Jasmine Zhou
Apr 7, 2012·Trends in Genetics : TIG·Vijay K RamananAndrew J Saykin
Aug 10, 2012·The Journal of Biological Chemistry·Yajun LiangYibin Kang
Aug 31, 2012·Frontiers in Physiology·Anna S Blazier, Jason A Papin
Sep 25, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Mar 1, 2011·Biometrika·Jian GuoJi Zhu
Oct 31, 2012·Neuropeptides·Daisuke Kohno, Toshihiko Yada
Feb 20, 2013·Oncology Letters·Guang-Hui WangXue-Min Xu
Feb 5, 2014·Acta Biochimica Et Biophysica Sinica·Yunqiang ZhangMin Yan
Apr 15, 2014·Journal of Theoretical Biology·Y X Rachel Wang, Haiyan Huang
May 13, 2014·Journal of the Royal Statistical Society. Series B, Statistical Methodology·Patrick DanaherDaniela M Witten
Feb 3, 2015·Journal of the American Statistical Association·Yunzhang ZhuWei Pan

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Methods Mentioned

BETA
RNA-seq
xenografts

Software Mentioned

ToppFun
WGCNA
CFGL
rma
R
WGCNA R
R package LIMMA
CFGLO
sketch
Affymetrix Power Tools

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