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Published online 29 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 6 1948-1956
© 2004 Oxford University Press

Identifying transcriptional regulatory sites in the human genome using an integrated system

Hsien-Da Huang, Jorng-Tzong Horng*,1,2, Yi-Ming Sun1, Ann-Ping Tsou3 and Shir-Ly Huang2

Department of Biological Science and Technology and Institute of Bioinformatics, National Chiao-Tung University, Hsin-Chu 300, Taiwan, 1 Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan, 2 Department of Life Science, National Central University, Chung-Li 320, Taiwan and 3 Insititute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan

*To whom correspondence should be addressed at Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan. Tel: +886 3 4227151; Fax: +886 3 4273485; Email: horng{at}db.csie.ncu.edu.tw
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received November 17, 2003; Revised January 1, 2004; Accepted March 1, 2004

This work develops an integrated system which, after a set of genes are inputted, is able to predict transcriptional regulatory sites and to detect the co-occurrence of these regulatory sites. The system integrates several site detection methods such as known site matching, over-presented oligonucleotide detection and DNA motif discovery programs. User profiles and history pages enable users to trace the sequence analyses of these transcriptional regulatory sites. Two groups of co-regulated genes were used to test the proposed system. The results predicted by the proposed system consist of known site homologs and putative regulatory sites. By comparing these sites with previously published results, the proposed system is able to help biologists identify possible candidates for the regulatory sites from groups of co-regulated genes. The integrated system is now available at http://rgsminer. csie.ncu.edu.tw/.


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