Abstract
The stratification of cancer into subtypes that are significantly associated with clinical outcomes is beneficial for targeted prognosis and treatment. In this study, we integrated somatic mutation and gene expression data to identify clusters of patients. In contrast to previous studies, we constructed cancer-type-specific significant co-expression networks (SCNs) rather than using a fixed gene network across all cancers, such as the network-based stratification (NBS) method, which ignores cancer heterogeneity. For each type of cancer, the gene expression data were used to construct the SCN network, while the gene somatic mutation data were mapped onto the network, propagated, and used for further clustering. For the clustering, we adopted an improved network-regularized non-negative matrix factorization (netNMF) (netNMF_HC) for a more precise classification. We applied our method to various datasets, including ovarian cancer (OV), lung adenocarcinoma (LUAD) and uterine corpus endometrial carcinoma (UCEC) cohorts derived from the TCGA (The Cancer Genome Atlas) project. Based on the results, we evaluated the performance of our method to identify survival-relevant subtypes and further compared it to the NBS method, which adopts ...Continue Reading
References
Nov 5, 1999·Nature·D D Lee, H S Seung
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Mar 7, 2006·BMC Genomics·Marc R J CarlsonStanley F Nelson
Mar 14, 2008·Bioinformatics·Cheng-Long ChuangGrace S Shieh
Mar 15, 2008·Cancer Research·Minaxi JhawerJohn M Mariadason
Apr 3, 2008·Genome Research·Trey Ideker, Roded Sharan
Aug 14, 2008·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Richard W TothillDavid D L Bowtell
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Mar 20, 2009·Nucleic Acids Research·Vivek JayaswalYee Hwa Yang
Nov 4, 2010·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Nov 4, 2010·Current Opinion in Oncology·Magali Olivier, Philippe Taniere
May 4, 2011·Genome Research·Insuk LeeEdward M Marcotte
Dec 17, 2011·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Juliann ChmieleckiWilliam Pao
Jun 19, 2013·Nature·Michael S LawrenceGad Getz
Sep 17, 2013·Nature Methods·Matan HofreeTrey Ideker
Jan 7, 2014·Nature·Michael S LawrenceGad Getz
Feb 4, 2014·Nature Communications·Yang YangHan Liang
May 13, 2014·Cell Reports·Valentina PirazzoliKaterina Politi
Aug 12, 2014·Cell·Katherine A HoadleyJoshua M Stuart
Mar 21, 2015·Computational Biology and Chemistry·Amin Ahmadi Adl, Xiaoning Qian
Jun 24, 2015·BMC Genomics·Xue ZhongBingshan Li
Jul 8, 2015·BMC Genomics·Zhaoqi Liu, Shihua Zhang
Sep 3, 2016·Bioinformatics·Thanh Le VanSiegfried Nijssen
Citations
Feb 2, 2019·BMC Medical Genomics·Mark MenorYouping Deng
Jun 15, 2019·BMC Bioinformatics·N Özlem Özcan ŞimşekFikret Gürgen
Apr 25, 2019·BMC Cancer·Matthew Ruffalo, Ziv Bar-Joseph
Feb 5, 2021·Frontiers in Genetics·Zongzhen HeYuanyuan Zhang
Mar 16, 2021·Frontiers in Genetics·Qin Jiang, Min Jin