| Summary: | <p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) regulate gene transcription and play pivotal roles in various biological processes such as development, cell cycle progression, cell differentiation and tumor suppression. Identifying <it>cis</it>-regulatory elements associated with TF-encoding genes is a crucial step in understanding gene regulatory networks. To this end, we have used a comparative genomics approach to identify putative <it>cis</it>-regulatory elements associated with TF-encoding genes in vertebrates.</p> <p>Description</p> <p>We have created a database named TFCONES (Transcription Factor Genes & Associated COnserved Noncoding ElementS) (<url>http://tfcones.fugu-sg.org</url>) which contains all human, mouse and fugu TF-encoding genes and conserved noncoding elements (CNEs) associated with them. The CNEs were identified by gene-by-gene alignments of orthologous TF-encoding gene loci using MLAGAN. We also predicted putative transcription factor binding sites within the CNEs. A significant proportion of human-fugu CNEs contain experimentally defined binding sites for transcriptional activators and repressors, indicating that a majority of the CNEs may function as transcriptional regulatory elements. The TF-encoding genes that are involved in nervous system development are generally enriched for human-fugu CNEs. Users can retrieve TF-encoding genes and their associated CNEs by conducting a keyword search or by selecting a family of DNA-binding proteins.</p> <p>Conclusion</p> <p>The conserved noncoding elements identified in TFCONES represent a catalog of highly prioritized putative <it>cis</it>-regulatory elements of TF-encoding genes and are candidates for functional assay.</p>
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