Classifying gene expression profiles from pairwise mRNA comparisons.

Statistical Applications in Genetics and Molecular Biology
Donald GemanRaimond L Winslow

Abstract

We present a new approach to molecular classification based on mRNA comparisons. Our method, referred to as the top-scoring pair(s) (TSP) classifier, is motivated by current technical and practical limitations in using gene expression microarray data for class prediction, for example to detect disease, identify tumors or predict treatment response. Accurate statistical inference from such data is difficult due to the small number of observations, typically tens, relative to the large number of genes, typically thousands. Moreover, conventional methods from machine learning lead to decisions which are usually very difficult to interpret in simple or biologically meaningful terms. In contrast, the TSP classifier provides decision rules which i) involve very few genes and only relative expression values (e.g., comparing the mRNA counts within a single pair of genes); ii) are both accurate and transparent; and iii) provide specific hypotheses for follow-up studies. In particular, the TSP classifier achieves prediction rates with standard cancer data that are as high as those of previous studies which use considerably more genes and complex procedures. Finally, the TSP classifier is parameter-free, thus avoiding the type of over-fit...Continue Reading

References

Aug 1, 1989·British Journal of Haematology·K F BradstockW G Hughes
Jun 24, 2000·Nature·D J Lockhart, E A Winzeler
Aug 10, 2000·Cell·T R HughesS H Friend
Apr 5, 2001·The New England Journal of Medicine·M J Walport
Jun 1, 2001·Nature Medicine·S H Leppla
Jul 27, 2001·Bioinformatics·C H YeangT Golub
Aug 11, 2001·Cellular and Molecular Life Sciences : CMLS·V Pancholi
Sep 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·M WestJ R Nevins
May 16, 2002·Proceedings of the National Academy of Sciences of the United States of America·Robert TibshiraniGilbert Chu
Jun 28, 2002·Cancer Cell·Dinesh SinghWilliam R Sellers
Dec 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ker-Chau Li
Jan 2, 2003·Journal of the National Cancer Institute·Richard SimonLisa M McShane
Jan 7, 2003·Biotechnology and Bioengineering·Silvio BicciatoCarlo Di Bello
Mar 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Heping ZhangBurton Singer
Jun 13, 2003·Bioinformatics·Marcel Dettling, Peter Bühlmann
Jul 2, 2003·Current Opinion in Structural Biology·Gustavo Stolovitzky
Dec 12, 2003·Bioinformatics·Anne-Laure BoulesteixKorbinian Strimmer
Dec 26, 2003·The American Journal of Pathology·Greg BloomTimothy J Yeatman
Feb 13, 2004·Bioinformatics·Ulisses M Braga-Neto, Edward R Dougherty

❮ Previous
Next ❯

Citations

May 15, 2013·Computers in Biology and Medicine·Muchenxuan TongWenbin Ju
Nov 15, 2012·BMC Bioinformatics·Hongyan ZhangZheming Yuan
Aug 13, 2013·PLoS Computational Biology·Jaeyun SungNathan D Price
Mar 8, 2013·Cancer Informatics·Benjamin UlfenborgBjörn Olsson
Jun 17, 2014·Journal of Theoretical Biology·Wanwei ZhangLuonan Chen
Apr 13, 2011·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·Thomas J Fuchs, Joachim M Buhmann
Jan 29, 2011·European Urology·Youssef M YoussefGeorge M Yousef
Aug 15, 2015·Diagnostic Microbiology and Infectious Disease·Cynthia J CarlynDavid A Lawrence
Nov 23, 2007·Journal of Cellular and Molecular Medicine·Nathan D PriceQiang Tian
Aug 14, 2012·Journal of Applied Toxicology : JAT·Tessa E PronkJeroen L A Pennings
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Lucas B EdelmanNathan D Price
Feb 22, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Cosmin LazarAnn Nowé
Nov 8, 2006·Mathematical Biosciences·Gilles GuillotMats Rudemo
Apr 11, 2015·International Journal of Cancer. Journal International Du Cancer·Daria A GaykalovaJoseph A Califano
Aug 8, 2015·Journal of Theoretical Biology·Shiguo DengHuijie Yang
Jul 6, 2015·Methods : a Companion to Methods in Enzymology·Antonio ScialdoneFlorian Buettner
Oct 31, 2009·BMC Medical Genomics·Xiaosheng Wang, Osamu Gotoh
Feb 1, 2008·Journal of Biomedical Informatics·Hsi-Che LiuChih-Jen Lin
Dec 6, 2011·Genomics·Xiaosheng Wang
Oct 25, 2016·Journal of Biomedical Informatics·Radhakrishnan Nagarajan, Meenakshi Upreti
Nov 1, 2016·Bioinformatics·Roman HornungAnne-Laure Boulesteix
Jan 5, 2011·PloS One·Pankaj ChopraSunwon Lee
Sep 30, 2014·Bioinformatics·Bahman AfsariLuigi Marchionni

❮ Previous
Next ❯

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.