A human DNA methylation site predictor base on SVM

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Accession number:20094712473348

Title: A human DNA methylation site predictor base on SVM Authors: Sun, Yi-Ming (1); Liu, Baw-Jhiune (2); Liao, Wei-Li (1);

Chang, Cheng-Wei (3); Huang, Hsien-Da (4); Horng, Jorng-Tzong (5);

Wu, Li-Ching (6)

Author affiliation:(1) Department of Computer Science and

Information Engineering, National Central University, Jhongli 320, Taiwan; (2) Department of Computer Science and Information Engineering, Yuan-Ze University, Jhongli 320, Taiwan; (3)

Department if Information Management, Hsing Wu College, Taipei 244, Taiwan; (4) Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao-Tung University, Hsinchu 300, Taiwan; (5) Department of Bioinformatics, Asia University, Wufeng 413, Taiwan; (6) Graduate Institute of System Biology and Bioinformatics, National Central University, Jhongli 320, Taiwan

Corresponding author:Sun, Y.-M.

([email protected])

Source title: Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009

Abbreviated source title:Proc. IEEE Int. Conf. Bioinformatics BioEng., BIBE

Monograph title:Proceedings of the 2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009 Issue date:2009

Publication year:2009 Pages:22-29

Article number:5211324 Language:English

ISBN-13:9780769536569

Document type:Conference article (CA)

Conference name:2009 9th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2009

Conference date:June 22, 2009 - June 24, 2009 Conference location:Taichung, Taiwan

Conference code:78002

Sponsor:IEEE Computer Society Asia University; Biological and AI

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Society

Publisher:IEEE Computer Society, 445 Hoes Lane - P.O.Box 1331, Piscataway, NJ 08855-1331, United States

Abstract:During gene expression, transcription factors are unable to bind to a transcription binding site (TFBS) involved in regulation if DNA methylation has occurred at the TFBS. Methyl-CpG-binding proteins may also occupy the TFBS and prevent the functioning of a transcription factor. Thus, the methylation status of CpG sites is an important issue when trying to understand gene regulation and shows strong correlation with the TFBS involved. In addition, CpG islands would seem to undergo cell-specific and tissue-specific methylation. Such differential methylation is presented at numerous genetic loci that are essential for development. Current DNA

methylation site prediction tools need to be improved so that they include TFBS features and have greater accuracy in terms of the DNA region that is involved in methylation. We developed models that compare the differences across these regions and tissues. The TFBSs, DNA properties and DNA distribution were used as features for this classification. From the results, we found some TFBSs that were able to discriminate whether a sequence was methylated or not. The sensitivity, specificity and accuracy estimated using 10-fold cross validation were 90.8%, 80.54%, and 86.07%, respectively.

Thus, for these four regions and twelve tissues, the performance levels (ACC) were all greater than 80%. We propose that the differential features or methylations vary between the different regions because the features common to each DNA region made up only 50% of the top 70 features. An online predictor based on

EpiMeP is available at http://140.115.51.41/EpiMeP/. Supplementary file is available at http://140.115.51.41/EpiMeP/supplementary. doc.

Number of references:26 Main heading:Alkylation

Controlled terms: Binding energy - Binding sites - Bioinformatics - DNA - Genes - Histology - Methylation - Nucleic acids - Transcription - Transcription factors

Uncontrolled terms: CpG islands - Cross validation - Developed model - DNA Methylation - Gene regulations - Genetic locus - Methyl- CpG-binding - Performance level - Prediction tools - Strong

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correlation

Classification code:804.1 Organic Compounds - 802.3 Chemical Operations - 802.2 Chemical Reactions - 801.4 Physical Chemistry - 903 Information Science - 801.2 Biochemistry - 461.8.2

Bioinformatics - 461.8.1 Genetic Engineering - 461.2 Biological Materials and Tissue Engineering - 461.9 Biology

DOI:10.1109/BIBE.2009.22 Database:Compendex