Title: Finding new Core Promoter Elements using backward-looking strategies

Authors: Yin-Fu Huang, Yi-Chao Jhan, Sing-Wu Liou

Addresses: Graduate School of Computer Science and Information Engineering, National Yunlin University of Science and Technology, 123 University Road, Section 3, Touliu, Yunlin, Taiwan 640, ROC. ' Institute of Electronic and Information Engineering, National Yunlin University of Science and Technology, 123 University Road, Section 3, Touliu, Yunlin, Taiwan 640, ROC. ' Graduate School of Engineering Science and Technology, National Yunlin University of Science and Technology, 123 University Road, Section 3, Touliu, Yunlin, Taiwan 640, ROC

Abstract: Core Promoter Elements (CPEs) were key players in transcription initiation. Identifying CPEs is crucial for understanding gene expression. In this paper, a framework for finding new CPEs was proposed. An experiment was performed on the sequences of Eukaryotic Promoter Database (EPD). From the results, the known CPEs were all recovered; in addition, five new motifs were discovered in Drosophila and three in human. By comparing the results with currently known CPEs, it is shown that the proposed system is feasible and reliable, and these new CPEs are worth of further exploration.

Keywords: CPE; core promoter elements; transcription initiation; PIC; pre-initiation complex; transcription factor binding sites; data mining; bioinformatics; gene expression; sequences; motifs; eukaryotic promoter database.

DOI: 10.1504/IJDMB.2009.023882

International Journal of Data Mining and Bioinformatics, 2009 Vol.3 No.1, pp.23 - 39

Published online: 17 Mar 2009 *

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