An expert system to identify transcription factor binding target genes by phylogenetic footprinting

  • Authors:

  • Yi-Ming Sun;Jorng-Tzong Horng;Jyh-Huang Torng;Li-Ching Wu

  • Affiliations:

  • Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan;Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan and Institute of System Biology and Bioinformatics, National Central University, Chung ...;Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan;Institute of System Biology and Bioinformatics, National Central University, Chung-Li 320, Taiwan

  • Venue:
  • Expert Systems with Applications: An International Journal
  • Year:
  • 2009

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Abstract

The analysis of gene expression is able to identify many possible transcription factor regulated gene groups. It has been proven that the phylogenetic footprinting method can help to identify transcription factor binding sites. Our work develops an expert system that combines motif searching and phylogenetic footprinting. After a motif and a gene group are submitted, the expert system is able to evaluate the statistics of the motif's appearance across all genes in genome and in gene upstream conserved regions by comparing human and mouse. A transcription factor-target gene group was used to test the proposed system. The results show that the system is able to distinguish transcription factor-target gene groups from random gene groups. By comparing motif distribution between all genes and a gene group, the proposed system is able to help biologists identify possible transcription factor regulated gene groups that have co-regulated gene expression