NDLI: SVMotif: A Machine Learning Motif Algorithm

Content Provider	IEEE Xplore Digital Library
Author	Kon, M. Yue Fan Holloway, D. DeLisi, C.
Copyright Year	2007
Description	Author affiliation: Boston Univ., Boston (Kon, M.)
Abstract	We describe SVMotif, a support vector machine-based learning algorithm for identification of cellular DNA transcription factor (TF) motifs extrapolated from known TF-gene interactions. An important aspect of this procedure is its ability to utilize negative target information (examples of likely non-targets) as well as positive information. Applications involve situations where clusters of genes are distinguished in experiments with known transcription factors without known binding locations. We apply this to yeast TF data with target identifications from ChlP-chip and other sources, and compare performance with Gibbs sampling methods such as BioProspector. We verify that in yeast this method implies well-defined and cross-validated statistical correlations between TF binding and secondary motifs whose binding properties (either with the primary TF or other possible promoters) are not certain, and discuss some implications of this. SVMotif can be a useful standalone method or a complement to existing techniques, and it will be made publicly available.
Starting Page	573
Ending Page	580
File Size	589284
Page Count	8
File Format	PDF
ISBN	9780769530697
DOI	10.1109/ICMLA.2007.105
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-12-13
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Fungi Learning systems Proteins Machine learning algorithms Regulators DNA Machine learning Sampling methods Gene expression Bioinformatics
Content Type	Text
Resource Type	Article

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
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