Pathway to Functional Studies: Pipeline Linking Phylogenetic Footprinting and Transcription-Factor Binding Analysis

Chakka, N. and Gready, J.E.

Identification of transcription-factor binding sites is a critical first step in studying transcriptional regulation of genes. The comparative genomics method of phylogenetic footprinting is based on identifying sequence elements that are conserved across multiple genomes, and, thus, likely to be functional. We have developed a systematic high throughput screening pipeline to first search for conserved motifs using two different phylogenetic footprinting methods (motifdiscovery and alignment-based) , and then rapid evaluate the motifs as potential transcription-factor binding sites. The results are displayed in an interactive graphical user interface, FactorScan, which integrates three separate complementary databases (conservedsequence motifs, transcription-factor binding site motifs, TRANSFAC). We applied this pipeline for transcription-factor binding site analysis to the orthologous gene regions of prion-protein family genes from vertebrate lineages, taking account of the gene annotations

Cite as: Chakka, N. and Gready, J.E. (2006). Pathway to Functional Studies: Pipeline Linking Phylogenetic Footprinting and Transcription-Factor Binding Analysis. In Proc. 2006 Workshop on Intelligent Systems for Bioinformatics (WISB 2006), Hobart, Australia. CRPIT, 73. Boden, M. and Bailey, T. L., Eds. ACS. 15-21.

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