Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis

BMC Genomics
Claudia CavaIsabella Castiglioni

Abstract

Modern high-throughput genomic technologies represent a comprehensive hallmark of molecular changes in pan-cancer studies. Although different cancer gene signatures have been revealed, the mechanism of tumourigenesis has yet to be completely understood. Pathways and networks are important tools to explain the role of genes in functional genomic studies. However, few methods consider the functional non-equal roles of genes in pathways and the complex gene-gene interactions in a network. We present a novel method in pan-cancer analysis that identifies de-regulated genes with a functional role by integrating pathway and network data. A pan-cancer analysis of 7158 tumour/normal samples from 16 cancer types identified 895 genes with a central role in pathways and de-regulated in cancer. Comparing our approach with 15 current tools that identify cancer driver genes, we found that 35.6% of the 895 genes identified by our method have been found as cancer driver genes with at least 2/15 tools. Finally, we applied a machine learning algorithm on 16 independent GEO cancer datasets to validate the diagnostic role of cancer driver genes for each cancer. We obtained a list of the top-ten cancer driver genes for each cancer considered in this...Continue Reading

References

Apr 5, 2018·International Journal of Molecular Sciences·Valentina BravatàGiusi Irma Forte
Aug 18, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Mingzhe XuJiayin Wang
Aug 14, 2019·Genes·Shuaichao WangShuangge Ma
Sep 12, 2019·Healthcare Management Forum·Michael Beauvais, Bartha Maria Knoppers
Apr 18, 2020·Frontiers in Pharmacology·Cuicui XiaoQi Zhang
Sep 19, 2018·Cancer Informatics·Abdallah K AlameddineBrian Binnall
Jun 7, 2018·Journal of Translational Medicine·Claudia CavaIsabella Castiglioni
Sep 19, 2019·Scientific Reports·Shuaichao WangShuangge Ma
Feb 26, 2020·Scientific Reports·Gizem GulfidanKazim Yalcin Arga
Jun 1, 2018·Cancer Reports·Abdallah K AlameddineKhaled O Alameddine
May 21, 2019·Frontiers in Immunology·Paola M TricaricoSergio Crovella

Citations

Jan 27, 2000·Cell·D Hanahan, R A Weinberg
May 10, 2000·Nature Genetics·M AshburnerGavin Sherlock
Aug 3, 2004·Nature Medicine·Bert Vogelstein, Kenneth W Kinzler
May 15, 2007·Bioinformatics·Sean Davis, Paul S Meltzer
Dec 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Rameen BeroukhimWilliam R Sellers
Apr 17, 2008·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Kazuhiko InoFumitaka Kikkawa
Oct 25, 2008·Nature·Li DingRichard K Wilson
Apr 11, 2009·Nature·Michael R StrattonP Andrew Futreal
Feb 20, 2010·PloS One·Ethan CeramiChris Sander
Feb 24, 2010·Nature Reviews. Molecular Cell Biology·Simona NegriniThanos D Halazonetis
Jul 8, 2010·Diagnostic Cytopathology·Cristina Aparecida Troques da Silveira MitteldorfLuis Heraldo Camara-Lopes
Dec 21, 2010·Bioinformatics·Ahrim Youn, Richard Simon
Jun 10, 2011·Genome Research·Fabio VandinBenjamin J Raphael
Sep 7, 2011·Cell Research·Zhaoyuan FangHongbin Ji
Sep 13, 2011·Genome Research·Giovanni CirielloNikolaus Schultz
Dec 20, 2011·BMC Bioinformatics·Davide RissoSandrine Dudoit
Aug 21, 2012·Nucleic Acids Research·Abel Gonzalez-Perez, Nuria Lopez-Bigas
Sep 18, 2012·Bioinformatics·Junfei ZhaoXiang-Sun Zhang
Mar 30, 2013·Science·Bert VogelsteinKenneth W Kinzler
Sep 28, 2013·Nature Genetics·Cancer Genome Atlas Research NetworkJoshua M Stuart
Oct 4, 2013·Scientific Reports·Jüri ReimandGary D Bader
Jan 1, 2012·Cancers·Marija MilacicLincoln Stein
Nov 12, 2013·Nucleic Acids Research·Wei-Chung ChengHsei-Wei Wang
Jun 28, 2014·International Journal of Oncology·Dan LiuQing-Lei Gao
Jul 30, 2014·Bioinformatics·Eduard Porta-Pardo, Adam Godzik
Aug 12, 2014·BMC Bioinformatics·Junhua ZhangShihua Zhang
Sep 2, 2014·Genome Medicine·Jack P Hou, Jian Ma
Jan 24, 2015·Science·Mathias UhlénFredrik Pontén
Sep 12, 2015·IEEE Transactions on Visualization and Computer Graphics·Alexander LexHanspeter Pfister
Sep 18, 2015·Vaccines·Jacques C MbongueWilliam H R Langridge
Dec 8, 2015·Scientific Reports·Laura CantiniMichele Caselle
Dec 26, 2015·Nucleic Acids Research·Antonio ColapricoHoutan Noushmehr
Apr 2, 2016·International Journal of Molecular Medicine·Hugo Gomez-RuedaVictor Trevino
Jun 29, 2016·European Journal of Internal Medicine·Chaohui XiongChaozhao Liang
Dec 2, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima

Related Concepts

Study
Biochemical Pathway
Gene Expression Regulation, Neoplastic
Genome
Genes
Regulation of Biological Process
Neoplasms
Tumor Lysis Syndrome
Tumor Markers
Genomics

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.

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.