Pathway to functional studies

摘要

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 (motif-discovery 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 (conserved-sequence 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.