ArticleBMC genomics2007
TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
- Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective.Frontiers in genetics · 2021Review
- Multiple Isolated Transcription Factors Act as Switches and Contribute to Species Uniqueness.Genes · 2020Article
- BicPAMS: software for biological data analysis with pattern-based biclustering.BMC bioinformatics · 2017Article
- TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions.Nucleic acids research · 2017Article
- ChIP-Seq analysis identifies p27(Kip1)-target genes involved in cell adhesion and cell signalling in mouse embryonic fibroblasts.PloS one · 2017Article
- Transcription Factor Repertoire of Necrotrophic Fungal PhytopathogenFrontiers in plant science · 2017Article
- AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors.Nucleic acids research · 2015Article
- The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates.The Plant cell · 2014Article
- UCbase 2.0: ultraconserved sequences database (2014 update).Database : the journal of biological databases and curation · 2014Article
- BicPAM: Pattern-based biclustering for biomedical data analysis.Algorithms for molecular biology : AMB · 2014Article
- UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks.Nucleic acids research · 2013Article
- An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example.PloS one · 2013Article
- Identification of molecular compartments and genetic circuitry in the developing mammalian kidney.Development (Cambridge, England) · 2012Article
- A genome-wide screen to identify transcription factors expressed in pelvic Ganglia of the lower urinary tract.Frontiers in neuroscience · 2012Article
- AnimalTFDB: a comprehensive animal transcription factor database.Nucleic acids research · 2012Article
- Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus.PloS one · 2011Article
- TFCat: the curated catalog of mouse and human transcription factors.Genome biology · 2009Article
- Evolution of conserved secondary structures and their function in transcriptional regulation networks.BMC genomics · 2008Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscription 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.
conclusionThe 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.