Gene selection in microarray survival studies under possibly non-proportional hazards.

Bioinformatics
Daniela DunklerGeorg Heinze

Abstract

Univariate Cox regression (COX) is often used to select genes possibly linked to survival. With non-proportional hazards (NPH), COX could lead to under- or over-estimation of effects. The effect size measure c=P(T(1)<T(0)), i.e. the probability that a person randomly chosen from group G(1) dies earlier than a person from G(0), is independent of the proportional hazards (PH) assumption. Here we consider its generalization to continuous data c' and investigate the suitability of c' for gene selection. Under PH, c' is most efficiently estimated by COX. Under NPH, c' can be obtained by weighted Cox regression (WHE) or a novel method, concordance regression (CON). The least biased and most stable estimates were obtained by CON. We propose to use c' as summary measure of effect size to rank genes irrespective of different types of NPH and censoring patterns. WHE and CON are available as R packages. georg.heinze@meduniwien.ac.at Supplementary Data are available at Bioinformatics online.

References

Dec 15, 1994·Statistics in Medicine·P J Verweij, H C Van Houwelingen
Feb 28, 1997·Statistics in Medicine·R Tibshirani
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Nov 15, 2001·Proceedings of the National Academy of Sciences of the United States of America·A BhattacharjeeM Meyerson
Jun 21, 2002·The New England Journal of Medicine·Andreas RosenwaldUNKNOWN Lymphoma/Leukemia Molecular Profiling Project
Jul 16, 2002·Nature Medicine·David G BeerSamir Hanash
Aug 10, 2002·Bioinformatics·Peter J ParkIsaac S Kohane
Aug 23, 2003·Biostatistics·R Xu, J O'Quigley
Apr 20, 2004·PLoS Biology·Eric Bair, Robert Tibshirani
Apr 19, 2005·Computational Biology and Chemistry·Jinfeng XuJurg Ott
Feb 16, 2006·Statistics in Medicine·Michal Abrahamowicz, Todd A MacKenzie
Feb 25, 2006·Journal of Applied Physiology·Markus AmannJerome A Dempsey
Nov 10, 2006·Statistics in Medicine·Stephan Lehr, Michael Schemper
Jun 8, 2007·Bioinformatics·H M BøvelstadO C Lingjaerde
Apr 4, 2008·Statistical Applications in Genetics and Molecular Biology·Harald Binder, Martin Schumacher
May 28, 2009·Statistics in Medicine·Michael SchemperGeorg Heinze

❮ Previous
Next ❯

Citations

Oct 30, 2012·Lifetime Data Analysis·Torben Martinussen, Christian Bressen Pipper
Nov 20, 2010·Briefings in Bioinformatics·Shuangge Ma, Xiao Song
Jan 25, 2014·Amyloid : the International Journal of Experimental and Clinical Investigation : the Official Journal of the International Society of Amyloidosis·Tilmann BochtlerStefan O Schönland
Jan 17, 2014·Biometrical Journal. Biometrische Zeitschrift·Holger Fröhlich
May 2, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Herbert PangTiejun Tong
Sep 5, 2013·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Andrea PellagattiJacqueline Boultwood
Jan 29, 2017·Histopathology·Benjamin GoeppertMarcus Renner
Oct 19, 2013·British Journal of Cancer·B GoeppertW Weichert
Mar 11, 2020·Bioinformatics·Lauren Spirko-Burns, Karthik Devarajan
Oct 17, 2015·Oncotarget·Inez YuwanitaEran R Andrechek
Apr 15, 2017·BioMed Research International·Chengqi Sun, Xudong Zhao

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.