Identification of genes associated with multiple cancers via integrative analysis.

BMC Genomics
Shuangge MaMeena S Moran

Abstract

Advancement in gene profiling techniques makes it possible to measure expressions of thousands of genes and identify genes associated with development and progression of cancer. The identified cancer-associated genes can be used for diagnosis, prognosis prediction, and treatment selection. Most existing cancer microarray studies have been focusing on the identification of genes associated with a specific type of cancer. Recent biomedical studies suggest that different cancers may share common susceptibility genes. A comprehensive description of the associations between genes and cancers requires identification of not only multiple genes associated with a specific type of cancer but also genes associated with multiple cancers. In this article, we propose the Mc.TGD (Multi-cancer Threshold Gradient Descent), an integrative analysis approach capable of analyzing multiple microarray studies on different cancers. The Mc.TGD is the first regularized approach to conduct "two-dimensional" selection of genes with joint effects on cancer development. Simulation studies show that the Mc.TGD can more accurately identify genes associated with multiple cancers than meta analysis based on "one-dimensional" methods. As a byproduct, identificat...Continue Reading

References

Jan 11, 2000·Nucleic Acids Research·G SherlockJ M Cherry
Sep 13, 2001·Proceedings of the National Academy of Sciences of the United States of America·T SørlieA L Børresen-Dale
Nov 15, 2001·Proceedings of the National Academy of Sciences of the United States of America·A BhattacharjeeM Meyerson
Dec 14, 2001·Proceedings of the National Academy of Sciences of the United States of America·S RamaswamyT R Golub
Jun 12, 2002·Molecular Biology of the Cell·Xin ChenPatrick O Brown
Jun 28, 2002·Cancer Cell·Dinesh SinghWilliam R Sellers
Mar 26, 2003·The American Journal of Pathology·Christine A Iacobuzio-DonahueMichael Goggins
Aug 20, 2003·Molecular Biology of the Cell·Xin ChenPatrick O Brown
Jun 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Daniel R RhodesArul M Chinnaiyan
Jun 23, 2004·Annals of the New York Academy of Sciences·Daniel R Rhodes, Arul M Chinnaiyan
Sep 28, 2004·Nature Genetics·Eran SegalAviv Regev
Nov 3, 2004·Cancer Research·Insoo BaeEliot M Rosen
Mar 16, 2005·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Donghong WangThomas H Haugen
May 11, 2005·Pharmacogenomics·Russell A WilkeMarylyn D Ritchie
Sep 1, 2005·Biomedical Microdevices·Xinan YangRainer Spang
Dec 7, 2005·Environmental Health Perspectives·Zhuowei LiYuh-Chin T Huang
May 10, 2006·Cancer Genetics and Cytogenetics·Marjut PuputtiNina N Nupponen
May 11, 2006·BMC Bioinformatics·Shuangge MaJian Huang
Jul 5, 2006·Cancer Research·Haiyan R QinKay Huebner
Jul 17, 2007·Computational Biology and Chemistry·Yee Leng YapJeffrey Hill
Nov 28, 2007·Annual Review of Pathology·Maggie C U CheangTorsten O Nielsen
Dec 14, 2007·Lung Cancer : Journal of the International Association for the Study of Lung Cancer·Cristina FríasPilar Iniesta
Jun 20, 2008·Briefings in Bioinformatics·Shuangge Ma, Jian Huang
Jan 3, 2009·BMC Bioinformatics·Shuangge Ma, Jian Huang
Jan 1, 2007·Hereditary Cancer in Clinical Practice·Joanne M McKinleyKelly-Anne Phillips

❮ Previous
Next ❯

Citations

Dec 27, 2011·Briefings in Bioinformatics·Jeffrey D AllenGuanghua Xiao
Jun 22, 2013·Briefings in Bioinformatics·Xingjie ShiShuangge Ma
Nov 20, 2012·Genetic Epidemiology·Jin LiuShuangge Ma
Apr 29, 2014·Biometrics·Jin LiuShuangge Ma
Mar 1, 2014·Scandinavian Journal of Statistics, Theory and Applications·Jin LiuShuangge Ma
Jan 2, 2015·Briefings in Bioinformatics·Xingjie ShiShuangge Ma
Aug 17, 2019·Royal Society Open Science·Zhilong MiZhiming Zheng
Nov 30, 2019·Analytical Cellular Pathology (Amsterdam)·Mennatallah Elfar, Asma Amleh
Jan 1, 2012·Statistical Science : a Review Journal of the Institute of Mathematical Statistics·Jian HuangShuangge Ma

❮ Previous
Next ❯

Software Mentioned

Affymetrix

Related Concepts

Related Feeds

Birth Defects

Birth defects encompass structural and functional alterations that occur during embryonic or fetal development and are present since birth. The cause may be genetic, environmental or unknown and can result in physical and/or mental impairment. Here is the latest research on birth defects.

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.

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

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

Breast Cancer: BRCA1 & BRCA2

Mutations involving BRCA1, found on chromosome 17, and BRCA2, found on chromosome 13, increase the risk for specific cancers, such as breast cancer. Discover the last research on breast cancer BRCA1 and BRCA2 here.

Related Papers

Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
Hong LiWei-di You
Clinical Cancer Research : an Official Journal of the American Association for Cancer Research
Junwei FanZhihai Peng
Clinical Cancer Research : an Official Journal of the American Association for Cancer Research
Pornchai O-charoenratBhuvanesh Singh
Ai zheng = Aizheng = Chinese journal of cancer
Xin-Yan ZhangJie Feng
© 2022 Meta ULC. All rights reserved