A graph-based multi-sample test for identifying pathways associated with cancer progression

Computational Biology and Chemistry
Qingyang ZhangHao Chen

Abstract

Cancer is in general not a result of an abnormality of a single gene but a consequence of changes in many genes, it is therefore of great importance to understand the roles of different oncogenic and tumor suppressor pathways in tumorigenesis. In recent years, there have been many computational models developed to study the genetic alterations of different pathways in the evolutionary process of cancer. However, most of the methods are knowledge-based enrichment analyses and inflexible to analyze user-defined pathways or gene sets. In this paper, we develop a nonparametric and data-driven approach to testing for the dynamic changes of pathways over the cancer progression. Our method is based on an expansion and refinement of the pathway being studied, followed by a graph-based multivariate test, which is very easy to implement in practice. The new test is applied to the rich Cancer Genome Atlas data to study the (epi)genetic alterations of 186 KEGG pathways in the development of serous ovarian cancer. To make use of the comprehensive data, we incorporate three data types in the analysis representing gene expression level, copy number and DNA methylation level. Our analysis suggests a list of nine pathways that are closely assoc...Continue Reading

References

May 16, 2002·Journal of Mammary Gland Biology and Neoplasia·S A Eccles
Apr 26, 2003·Proceedings of the National Academy of Sciences of the United States of America·Xiao-Jun MaDennis C Sgroi
Dec 14, 2004·BMC Bioinformatics·Thomas BreslinMorten Krogh
Feb 25, 2005·BioTechniques·Kang TuMingzhu Zhu
Jun 9, 2005·BMC Bioinformatics·Seon-Young Kim, David J Volsky
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Oct 26, 2005·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Dmitri TalantovYixin Wang
Nov 11, 2005·BMC Bioinformatics·Homin K LeePaul Pavlidis
Dec 19, 2006·Nature Genetics·Scott A TomlinsArul M Chinnaiyan
Apr 5, 2007·BMC Bioinformatics·Fátima Al-ShahrourJoaquín Dopazo
May 29, 2007·Nucleic Acids Research·Christina BackesHans-Peter Lenhof
Feb 20, 2008·PLoS Computational Biology·Elena J EdelmanSayan Mukherjee
May 29, 2009·BMC Bioinformatics·Weijun LuoPeter J Woolf
Jul 2, 2011·Nature·UNKNOWN Cancer Genome Atlas Research Network
Feb 22, 2012·The Journal of Cell Biology·Pengfei LuZena Werb
Aug 14, 2012·Pathology Research International·Massimo PancioneVittorio Colantuoni
Sep 11, 2012·Bioinformatics·Enrico GlaabAlfonso Valencia
Sep 25, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Aug 1, 2014·Nature·UNKNOWN Cancer Genome Atlas Research Network
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Aug 19, 2015·Journal of the American Statistical Association·Karl Bruce GregorySoumendra N Lahiri
Dec 5, 2015·Frontiers in Pharmacology·Aline Appert-CollinAmar Bennasroune
Dec 27, 2017·International Journal of Gynecological Cancer : Official Journal of the International Gynecological Cancer Society·Jeremy Chien, Elizabeth M Poole
Mar 27, 2019·Lancet·Stephanie LheureuxAmit M Oza

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