NDLI: Development of Two-Stage SVM-RFE Gene Selection Strategy for Microarray Expression Data Analysis

Content Provider	IEEE Xplore Digital Library
Author	Tang, Yuchun Zhang, Yan-Qing Huang, Zhen
Copyright Year	2004
Description	Extracting a subset of informative genes from microarray expression data is a critical data preparation step in cancer classification and other biological function analyses. Though many algorithms have been developed, the Support Vector Machine - Recursive Feature Elimination (SVM-RFE) algorithm is one of the best gene feature selection algorithms. It assumes that a smaller "filter-out" factor in the SVM-RFE, which results in a smaller number of gene features eliminated in each recursion, should lead to extraction of a better gene subset. Because the SVM-RFE is highly sensitive to the "filter-out" factor, our simulations have shown that this assumption is not always correct and that the SVM-RFE is an unstable algorithm. To select a set of key gene features for reliable prediction of cancer types or subtypes and other applications, a new two-stage SVM-RFE algorithm has been developed. It is designed to effectively eliminate most of the irrelevant, redundant and noisy genes while keeping information loss small at the first stage. A fine selection for the final gene subset is then performed at the second stage. The two-stage SVM-RFE overcomes the instability problem of the SVM-RFE to achieve better algorithm utility. We have demonstrated that the two-stage SVM-RFE is significantly more accurate and more reliable than the SVM-RFE and three correlation-based methods based on our analysis of three publicly available microarray expression datasets. Furthermore, the two-stage SVM-RFE is computationally efficient because its time complexity is $O(d * \log{_2d})$, where $d$ is the size of the original gene set.
Sponsorship	IEEE Computer Society
Page Count	17
File Size	4885024
Starting Page	365
Ending Page	381
File Format	PDF
ISSN	15455963
Volume Number	4
Issue Number	3
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-07-01
Publisher Place	U.S.A.
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Data analysis Gene expression Cancer Organisms Bioinformatics DNA Genomics Data mining Support vector machines Support vector machine classification Recursive Feature Elimination Microarray Gene Expression Data Analysis Cancer Classification Support Vector Machines Gene Selection Feature Selection
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Libarray of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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