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

doi:10.1186/s13073-016-0319-7

PMID: 27287041DOI: 10.1186/s13073-016-0319-7Jun 12, 2016

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

Get PDF

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

Reduced cell motility and enhanced focal adhesion contact formation in cells from FAK-deficient mice

Oct 12, 1995·Nature·D IlićT Yamamoto

Multivariable prognostic models: issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors

Feb 28, 1996·Statistics in Medicine·F E HarrellD B Mark

The zinc-finger protein slug causes desmosome dissociation, an initial and necessary step for growth factor-induced epithelial-mesenchymal transition

Jun 16, 1997·The Journal of Cell Biology·P SavagnerJ P Thiery

Analysis of large-scale gene expression data

Jan 26, 2002·Briefings in Bioinformatics·G Sherlock

Hop is an unusual homeobox gene that modulates cardiac development

Sep 26, 2002·Cell·Fabian ChenJonathan A Epstein

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

May 13, 2003·Nature Genetics·Eran SegalNir Friedman

Cardiac hypertrophy and histone deacetylase-dependent transcriptional repression mediated by the atypical homeodomain protein Hop

Sep 17, 2003·The Journal of Clinical Investigation·Hyun KookJonathan A Epstein

Application of independent component analysis to microarrays

Nov 13, 2003·Genome Biology·Su-In Lee, Serafim Batzoglou

The KEGG resource for deciphering the genome

Dec 19, 2003·Nucleic Acids Research·Minoru KanehisaMasahiro Hattori

affy--analysis of Affymetrix GeneChip data at the probe level

Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry

VEGF-null cells require PDGFR alpha signaling-mediated stromal fibroblast recruitment for tumorigenesis

Jul 2, 2004·The EMBO Journal·Jianying DongNapoleone Ferrara

Mechanisms regulating the constitutive activation of the extracellular signal-regulated kinase (ERK) signaling pathway in ovarian cancer and the effect of ribonucleic acid interference for ERK1/2 on cancer cell proliferation

Jul 10, 2004·Molecular Endocrinology·Rosemary SteinmetzOra H Pescovitz

SPARC regulates extracellular matrix organization through its modulation of integrin-linked kinase activity

Aug 24, 2005·The Journal of Biological Chemistry·Thomas H BarkerE Helene Sage

Nucleotide modification at the gamma-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase

Sep 6, 2005·Nucleic Acids Research·Brent A MulderSusan H Hardin

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data

Nov 15, 2005·Nucleic Acids Research·Manhong DaiFan Meng

Fibroblast growth factor 9 has oncogenic activity and is a downstream target of Wnt signaling in ovarian endometrioid adenocarcinomas

Feb 3, 2006·Cancer Research·Neali D HendrixKathleen R Cho

Adjusting batch effects in microarray expression data using empirical Bayes methods

Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic

Clustering microarray gene expression data using weighted Chinese restaurant process

Jun 13, 2006·Bioinformatics·Zhaohui S Qin

Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification

Sep 14, 2006·Proceedings of the National Academy of Sciences of the United States of America·Su-In LeeDaphne Koller

Enhancer of polycomb1, a novel homeodomain only protein-binding partner, induces skeletal muscle differentiation

Dec 29, 2006·The Journal of Biological Chemistry·Hae Jin KeeHyun Kook

Reactome: a knowledge base of biologic pathways and processes

Mar 21, 2007·Genome Biology·Imre VastrikLincoln Stein

Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors

May 12, 2007·Genome Biology·Jason I HerschkowitzCharles M Perou

Mesenchymal stem cells within tumour stroma promote breast cancer metastasis

Oct 5, 2007·Nature·Antoine E KarnoubRobert A Weinberg

Network-based classification of breast cancer metastasis

Oct 18, 2007·Molecular Systems Biology·Han-Yu ChuangTrey Ideker

Sparse inverse covariance estimation with the graphical lasso

Dec 15, 2007·Biostatistics·Jerome FriedmanRobert Tibshirani

Migratory neighbors and distant invaders: tumor-associated niche cells

Mar 5, 2008·Genes & Development·Jared WelsDavid Lyden

Carcinoma-associated fibroblast-like differentiation of human mesenchymal stem cells

Jun 4, 2008·Cancer Research·Pravin J MishraDebabrata Banerjee

Epithelial-mesenchymal transition: at the crossroads of development and tumor metastasis

Jun 10, 2008·Developmental Cell·Jing Yang, Robert A Weinberg

A gene signature predicting for survival in suboptimally debulked patients with ovarian cancer

Jul 3, 2008·Cancer Research·Tomas BonomeMichael J Birrer

Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome

Aug 14, 2008·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Richard W TothillDavid D L Bowtell

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

Sep 6, 2008·Nature·Cancer Genome Atlas Research Network

Importance of Wnt signaling in the tumor stroma microenvironment

Sep 11, 2008·Current Cancer Drug Targets·Maria L Macheda, Steven A Stacker

Inferring pathway activity toward precise disease classification

Nov 8, 2008·PLoS Computational Biology·Eunjung LeeDoheon Lee

WGCNA: an R package for weighted correlation network analysis

Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath

Learning a prior on regulatory potential from eQTL data

Jan 31, 2009·PLoS Genetics·Su-In LeeDaphne Koller

Dynamic modularity in protein interaction networks predicts breast cancer outcome

Feb 3, 2009·Nature Biotechnology·Ian W TaylorJeffrey L Wrana

A prognostic gene expression index in ovarian cancer - validation across different independent data sets

Mar 19, 2009·The Journal of Pathology·Carsten DenkertHermann Lage

A pluripotency signature predicts histologic transformation and influences survival in follicular lymphoma patients

Jul 29, 2009·Blood·Andrew J GentlesSylvia K Plevritis

Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology

Nov 19, 2009·Cancer Research·Lonneke A M GravendeelPim J French

A gene signature predictive for outcome in advanced ovarian cancer identifies a survival factor: microfibril-associated glycoprotein 2

Dec 8, 2009·Cancer Cell·Samuel C MokMichael J Birrer

Inflammation and EMT: an alliance towards organ fibrosis and cancer progression

Jan 6, 2010·EMBO Molecular Medicine·Jose Miguel López-Novoa, M Angela Nieto

An atlas of combinatorial transcriptional regulation in mouse and man

Mar 10, 2010·Cell·Timothy RavasiYoshihide Hayashizaki

A genomic and transcriptomic approach for a differential diagnosis between primary and secondary ovarian carcinomas in patients with a previous history of breast cancer

May 25, 2010·BMC Cancer·Jean-Philippe MeynielXavier Sastre-Garau

EMT, cancer stem cells and drug resistance: an emerging axis of evil in the war on cancer

Jun 10, 2010·Oncogene·A Singh, J Settleman

Gene expression profile of BRCAness that correlates with responsiveness to chemotherapy and with outcome in patients with epithelial ovarian cancer

Jun 16, 2010·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Panagiotis A KonstantinopoulosStephen A Cannistra

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

Aug 17, 2010·Bioinformatics·Alexander LachmannAvi Ma'ayan

MatrixDB, the extracellular matrix interaction database

Sep 21, 2010·Nucleic Acids Research·Emilie ChautardSylvie Ricard-Blum

Entrez Gene: gene-centered information at NCBI

Dec 1, 2010·Nucleic Acids Research·Donna MaglottTatiana Tatusova

An integrated approach to uncover drivers of cancer

Dec 7, 2010·Cell·Uri David AkaviaDana Pe'er

Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia

Dec 24, 2010·JAMA : the Journal of the American Medical Association·Andrew J GentlesAsh A Alizadeh

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

Apr 30, 2011·Genome Biology·Craig H MermelGad Getz

MicroRNA processing and binding site polymorphisms are not replicated in the Ovarian Cancer Association Consortium

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)

Integrated genomic analyses of ovarian carcinoma

Jul 2, 2011·Nature·Cancer Genome Atlas Research Network

Layers of regulation

Sep 24, 2011·Nature Reviews. Cancer·Sarah Seton-Rogers

Multi-gene expression predictors of single drug responses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resistance

Feb 22, 2012·PloS One·J Stuart FerrissJae K Lee

Therapeutic potential of perineural invasion, hypoxia and desmoplasia in pancreatic cancer

Mar 1, 2012·Current Pharmaceutical Design·Han LiuErxi Wu

GADD45 proteins: central players in tumorigenesis

Apr 21, 2012·Current Molecular Medicine·R E TamuraL F Zerbini

Multipotent mesenchymal stromal cells and the innate immune system

Apr 26, 2012·Nature Reviews. Immunology·Katarina Le Blanc, Dimitrios Mougiakakos

Whole-genome regression and prediction methods applied to plant and animal breeding

Jun 30, 2012·Genetics·Gustavo de Los CamposMario P L Calus

Epigenetic silencing of HOPX promotes cancer progression in colorectal cancer

Aug 21, 2012·Neoplasia : an International Journal for Oncology Research·Hiroshi KatohMasahiko Watanabe

Cancer specific promoter CpG Islands hypermethylation of HOP homeobox (HOPX) gene and its potential tumor suppressive role in pancreatic carcinogenesis

Sep 11, 2012·BMC Cancer·Mina WarayaMasahiko Watanabe

NCBI GEO: archive for functional genomics data sets--update

Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva

Patient-tailored modulation of the immune system may revolutionize future lung cancer treatment

Dec 12, 2012·BMC Cancer·Marlies E HeuversJoost P Hegmans

Development of a prognostic model for breast cancer survival in an open challenge environment

Apr 19, 2013·Science Translational Medicine·Wei-Yi ChengDimitris Anastassiou

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer

Apr 19, 2013·Science Translational Medicine·Adam A MargolinAnne-Lise Børresen-Dale

Modeling language and cognition with deep unsupervised learning: a tutorial overview

Aug 24, 2013·Frontiers in Psychology·Marco ZorziIvilin P Stoianov

Network-based stratification of tumor mutations

Sep 17, 2013·Nature Methods·Matan HofreeTrey Ideker

Krüppel-like factors in cancer

Sep 26, 2013·Nature Reviews. Cancer·Marie-Pier TetreaultJonathan P Katz

Emerging landscape of oncogenic signatures across human cancers

Sep 28, 2013·Nature Genetics·Giovanni CirielloChris Sander

Immunobiology of mesenchymal stem cells

Nov 5, 2013·Cell Death and Differentiation·S MaY Wang

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts

Feb 4, 2014·Genome Biology·Charity W LawGordon K Smyth

Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples

Apr 5, 2014·Journal of the National Cancer Institute·Markus RiesterMichael J Birrer

Oncogenic roles of EMT-inducing transcription factors

May 31, 2014·Nature Cell Biology·Alain PuisieuxJulie Caramel

Comprehensive molecular profiling of lung adenocarcinoma

Aug 1, 2014·Nature·Cancer Genome Atlas Research Network

HOPX is methylated and exerts tumour-suppressive function through Ras-induced senescence in human lung cancer

Oct 28, 2014·The Journal of Pathology·Yuan ChenIver Petersen

Single-cell analysis of proxy reporter allele-marked epithelial cells establishes intestinal stem cell hierarchy

Nov 25, 2014·Stem Cell Reports·Ning LiChristopher J Lengner

Strong rules for discarding predictors in lasso-type problems

Mar 1, 2012·Journal of the Royal Statistical Society. Series B, Statistical Methodology·Robert TibshiraniRyan J Tibshirani

Sparse expression bases in cancer reveal tumor drivers

Jan 15, 2015·Nucleic Acids Research·Benjamin A LogsdonSu-In Lee

Regulation of mesenchymal stromal cells through fine tuning of canonical Wnt signaling

Apr 13, 2015·Stem Cell Research·Jin-A KimIl-Hoan Oh

Plasticity of Hopx(+) type I alveolar cells to regenerate type II cells in the lung

Apr 14, 2015·Nature Communications·Rajan JainJonathan A Epstein

Deep learning

May 29, 2015·Nature·Yann LeCunGeoffrey Hinton

HEART DEVELOPMENT. Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts

Jun 27, 2015·Science·Rajan JainJonathan A Epstein

The prognostic landscape of genes and infiltrating immune cells across human cancers

Jul 21, 2015·Nature Medicine·Andrew J GentlesAsh A Alizadeh

Citations

The value of prior knowledge in machine learning of complex network systems

Oct 17, 2017·Bioinformatics·Dana FerrantiDavid Craft

A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia

Jan 5, 2018·Nature Communications·Su-In LeePamela S Becker

Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes

Oct 13, 2016·G3 : Genes - Genomes - Genetics·Gregory P WayJennifer A Doherty

Identifying prognostic signature in ovarian cancer using DirGenerank

Jun 16, 2017·Oncotarget·Jian-Yong WangXiong-Hui Zhou

Application of transfer learning for cancer drug sensitivity prediction

Dec 29, 2018·BMC Bioinformatics·Saugato Rahman DhrubaRanadip Pal

Assessing reproducibility of matrix factorization methods in independent transcriptomes

Apr 3, 2019·Bioinformatics·Laura CantiniAndrei Zinovyev

Differential gene expression and gene-set enrichment analysis in Caco-2 monolayers during a 30-day timeline with Dexamethasone exposure

Aug 24, 2019·Tissue Barriers·J M RobinsonW A Henderson

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

Related Feeds

Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.

Breast Invasive Carcinoma (Keystone)

Invasive breast cancers indicate a spread into breast tissues and lymph nodes. Here are the latest discoveries pertaining to breast invasive carcinomas.

Adult Stem Cells

Adult stem cells reside in unique niches that provide vital cues for their survival, self-renewal, and differentiation. They hold great promise for use in tissue repair and regeneration as a novel therapeutic strategies. Here is the latest research.

Breast Invasive Carcinoma

Invasive breast cancers indicate a spread into breast tissues and lymph nodes. Here are the latest discoveries pertaining to breast invasive carcinomas.

Cancer Genomics

Cancer genomics employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research here.

Cadherins and Catenins

Cadherins (named for "calcium-dependent adhesion") are a type of cell adhesion molecule (CAM) that is important in the formation of adherens junctions to bind cells with each other. Catenins are a family of proteins found in complexes with cadherin cell adhesion molecules of animal cells: alpha-catenin can bind to β-catenin and can also bind actin. β-catenin binds the cytoplasmic domain of some cadherins. Discover the latest research on cadherins and catenins here.

Breast Cancer: Risk Factors

Breast cancer is a multifactorial disease that is influenced by both environmental and genetic factors. Discover the latest research on the environmental and genetic risk factors for breast cancer here.