Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer

Genome Medicine
Safiye CelikSu-In Lee

Abstract

Patterns in expression data conserved across multiple independent disease studies are likely to represent important molecular events underlying the disease. We present the INSPIRE method to infer modules of co-expressed genes and the dependencies among the modules from multiple expression datasets that may contain different sets of genes. We show that INSPIRE infers more accurate models than existing methods to extract low-dimensional representation of expression data. We demonstrate that applying INSPIRE to nine ovarian cancer datasets leads to a new marker and potential driver of tumor-associated stroma, HOPX, followed by experimental validation. The implementation of INSPIRE is available at http://inspire.cs.washington.edu .

References

Jan 26, 2002·Briefings in Bioinformatics·G Sherlock
Sep 26, 2002·Cell·Fabian ChenJonathan A Epstein
Nov 13, 2003·Genome Biology·Su-In Lee, Serafim Batzoglou
Dec 19, 2003·Nucleic Acids Research·Minoru KanehisaMasahiro Hattori
Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry
Aug 24, 2005·The Journal of Biological Chemistry·Thomas H BarkerE Helene Sage
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic
Sep 14, 2006·Proceedings of the National Academy of Sciences of the United States of America·Su-In LeeDaphne Koller
Mar 21, 2007·Genome Biology·Imre VastrikLincoln Stein
Oct 5, 2007·Nature·Antoine E KarnoubRobert A Weinberg
Oct 18, 2007·Molecular Systems Biology·Han-Yu ChuangTrey Ideker
Dec 15, 2007·Biostatistics·Jerome FriedmanRobert Tibshirani
Mar 5, 2008·Genes & Development·Jared WelsDavid Lyden
Jun 4, 2008·Cancer Research·Pravin J MishraDebabrata Banerjee
Jun 10, 2008·Developmental Cell·Jing Yang, Robert A Weinberg
Aug 14, 2008·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Richard W TothillDavid D L Bowtell
Sep 11, 2008·Current Cancer Drug Targets·Maria L Macheda, Steven A Stacker
Nov 8, 2008·PLoS Computational Biology·Eunjung LeeDoheon Lee
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Jan 31, 2009·PLoS Genetics·Su-In LeeDaphne Koller
Feb 3, 2009·Nature Biotechnology·Ian W TaylorJeffrey L Wrana
Nov 19, 2009·Cancer Research·Lonneke A M GravendeelPim J French
Jan 6, 2010·EMBO Molecular Medicine·Jose Miguel López-Novoa, M Angela Nieto
Mar 10, 2010·Cell·Timothy RavasiYoshihide Hayashizaki
Jun 16, 2010·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Panagiotis A KonstantinopoulosStephen A Cannistra
Sep 21, 2010·Nucleic Acids Research·Emilie ChautardSylvie Ricard-Blum
Dec 1, 2010·Nucleic Acids Research·Donna MaglottTatiana Tatusova
Dec 7, 2010·Cell·Uri David AkaviaDana Pe'er
Dec 24, 2010·JAMA : the Journal of the American Medical Association·Andrew J GentlesAsh A Alizadeh
Jun 4, 2011·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Jennifer Permuth-WeyOvarian Cancer Association Consortium (OCAC)
Jul 2, 2011·Nature·Cancer Genome Atlas Research Network
Sep 24, 2011·Nature Reviews. Cancer·Sarah Seton-Rogers
Apr 21, 2012·Current Molecular Medicine·R E TamuraL F Zerbini
Apr 26, 2012·Nature Reviews. Immunology·Katarina Le Blanc, Dimitrios Mougiakakos
Jun 30, 2012·Genetics·Gustavo de Los CamposMario P L Calus
Aug 21, 2012·Neoplasia : an International Journal for Oncology Research·Hiroshi KatohMasahiko Watanabe
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva
Apr 19, 2013·Science Translational Medicine·Wei-Yi ChengDimitris Anastassiou
Apr 19, 2013·Science Translational Medicine·Adam A MargolinAnne-Lise Børresen-Dale
Aug 24, 2013·Frontiers in Psychology·Marco ZorziIvilin P Stoianov
Sep 17, 2013·Nature Methods·Matan HofreeTrey Ideker
Sep 26, 2013·Nature Reviews. Cancer·Marie-Pier TetreaultJonathan P Katz
Sep 28, 2013·Nature Genetics·Giovanni CirielloChris Sander
Nov 5, 2013·Cell Death and Differentiation·S MaY Wang
Feb 4, 2014·Genome Biology·Charity W LawGordon K Smyth
Apr 5, 2014·Journal of the National Cancer Institute·Markus RiesterMichael J Birrer
May 31, 2014·Nature Cell Biology·Alain PuisieuxJulie Caramel
Aug 1, 2014·Nature·Cancer Genome Atlas Research Network
Mar 1, 2012·Journal of the Royal Statistical Society. Series B, Statistical Methodology·Robert TibshiraniRyan J Tibshirani
Jan 15, 2015·Nucleic Acids Research·Benjamin A LogsdonSu-In Lee
Apr 14, 2015·Nature Communications·Rajan JainJonathan A Epstein
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Jul 21, 2015·Nature Medicine·Andrew J GentlesAsh A Alizadeh

Citations

Oct 17, 2017·Bioinformatics·Dana FerrantiDavid Craft
Oct 13, 2016·G3 : Genes - Genomes - Genetics·Gregory P WayJennifer A Doherty
Jun 16, 2017·Oncotarget·Jian-Yong WangXiong-Hui Zhou
Dec 29, 2018·BMC Bioinformatics·Saugato Rahman DhrubaRanadip Pal

Related Concepts

HOP protein, human
Unsupervised Machine Learning
Females
Homo sapiens
Malignant Neoplasm of Ovary
Tumor Markers
Gene Expression Regulation, Neoplastic
Homeodomain Proteins
Computational Molecular Biology
MRNA Differential Display

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