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 (Transcription Factor 
Genes & Associated COnserved Noncoding ElementS) (http://tfcones.fugu-sg.org) 
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.