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

Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.
BMC Genomics (Impact Factor: 3.99). 02/2007; 8(1):441. DOI: 10.1186/1471-2164-8-441
Source: PubMed


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.
We have created a database named TFCONES (Transcription Factor Genes & Associated COnserved Noncoding ElementS) ( 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.
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.

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    • "Several other resources are currently available for the analysis of UCRs, e.g. UCNEbase (19), cneViewer (20), CONDOR (21), VISTA Enhancer browser (22), Ancora (23), ECR browser (24), TFCONES (25), FANTOM 5 enhancer atlas (26) and FANTOM 5 promoter atlas (27). In detail: "
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    ABSTRACT: UCbase 2.0 ( is an update, extension and evolution of UCbase, a Web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase 2.0 is a platform-independent Web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for Single Nucleotide Polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase 2.0 now includes a graph visualization interface directly linked to UCSC genome browser.Database URL:
    Full-text · Article · Jan 2014 · Database The Journal of Biological Databases and Curation
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    • "In the human genome, there are about 2000 transcription factors (TFs) [1]–[3]. In these TFs, approximately more than 700 are DNA-binding TFs [3], [4]. These DNA-binding TFs can bind to various DNA binding sites (DBSs) in genome and regulate the transcription of their target genes. "
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    ABSTRACT: SELEX-Seq is now the optimal high-throughput technique for characterizing DNA-binding specificities of transcription factors. In this study, we introduced an improved EMSA-based SELEX-Seq strategy with several advantages. The improvements of this strategy included: (1) using a FAM-labeled probe to track protein-DNA complex in polyacrylamide gel for rapidly recovering the protein-bound dsDNA without relying on traditional radioactive labeling or ethidium bromide staining; (2) monitoring the specificity of SELEX selection by detecting a positive and negative sequence doped into the input DNAs used in each round with PCR amplification; (3) using nested PCR to ensure the specificity of PCR amplification of the selected DNAs after each round; (4) using the nucleotides added at the 5' end of the nested PCR primers as the split barcode to code DNAs from various rounds for multiplexing sequencing samples. The split barcode minimized selection times and thus greatly simplified the current SELEX-Seq procedure. The reliability of the strategy was demonstrated by performing a successful SELEX-Seq of a well-known transcription factor, NF-κB. Therefore, this study provided a useful SELEX-Seq strategy for characterizing DNA-binding specificities of transcription factors.
    Full-text · Article · Oct 2013 · PLoS ONE
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    • "There are several other resources on CNEs with partially overlapping objectives, in particular: CONDOR, CORG (23), cneViewer (24), Ancora, VISTA Enhancer browser, ECR browser and TFCONES (25). Despite a common theme, the scopes of these resources are quite different which makes a direct comparison difficult. "
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    ABSTRACT: UCNEbase ( is a free, web-accessible information resource on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs). It currently covers 4351 such elements in 18 different species. The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes. As most of them occur as clusters near potential target genes, the database is organized along two hierarchical levels: individual UCNEs and ultra-conserved genomic regulatory blocks (UGRBs). UCNEbase introduces a coherent nomenclature for UCNEs reflecting their respective associations with likely target genes. Orthologous and paralogous UCNEs share components of their names and are systematically cross-linked. Detailed synteny maps between the human and other genomes are provided for all UGRBs. UCNEbase is managed by a relational database system and can be accessed by a variety of web-based query pages. As it relies on the UCSC genome browser as visualization platform, a large part of its data content is also available as browser viewable custom track files. UCNEbase is potentially useful to any computational, experimental or evolutionary biologist interested in conserved non-coding DNA elements in vertebrates.
    Full-text · Article · Nov 2012 · Nucleic Acids Research
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