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Open Access Highly Accessed Database

TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements

Alison P Lee, Yuchen Yang, Sydney Brenner and Byrappa Venkatesh*

Author Affiliations

Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore

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BMC Genomics 2007, 8:441  doi:10.1186/1471-2164-8-441

Published: 29 November 2007

Abstract

Background

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 cis-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 cis-regulatory elements associated with TF-encoding genes in vertebrates.

Description

We have created a database named TFCONES (

    T
ranscription
    F
actor Genes & Associated
    CO
nserved
    N
oncoding
    E
lement
    S
) (http://tfcones.fugu-sg.org webcite) 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.

Conclusion

The conserved noncoding elements identified in TFCONES represent a catalog of highly prioritized putative cis-regulatory elements of TF-encoding genes and are candidates for functional assay.