PUGSVM: A caBIG analytical tool for multiclass gene selection and predictive classification

Guoqiang Yu, Huai Li, Sook Ha, Ie Ming Shih, Robert Clarke, Eric P. Hoffman, Subha Madhavan, Jianhua Xuan, Yue Wang

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

Summary: Phenotypic Up-regulated Gene Support Vector Machine (PUGSVM) is a cancer Biomedical Informatics Grid (caBIG) analytical tool for multiclass gene selection and classification. PUGSVM addresses the problem of imbalanced class separability, small sample size and high gene space dimensionality, where multiclass gene markers are defined by the union of oneversus-everyone phenotypic upregulated genes, and used by a well-matched one-versus-rest support vector machine. PUGSVM provides a simple yet more accurate strategy to identify statistically reproducible mechanistic marker genes for characterization of heterogeneous diseases.

Original languageEnglish (US)
Article numberbtq721
Pages (from-to)736-738
Number of pages3
JournalBioinformatics
Volume27
Issue number5
DOIs
StatePublished - Mar 2011
Externally publishedYes

Bibliographical note

Funding Information:
Funding: This work is supported in part by the National Institutes of Health, under Contract No. HHSN261200800001E and Grants CA109872, CA149147, CA139246, NS029525.

Copyright:
Copyright 2011 Elsevier B.V., All rights reserved.

Fingerprint Dive into the research topics of 'PUGSVM: A caBIG<sup>™</sup> analytical tool for multiclass gene selection and predictive classification'. Together they form a unique fingerprint.

Cite this