ArticleBMC genomics2007
cTFbase: a database for comparative genomics of transcription factors in cyanobacteria.
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 9 papers.
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Who cites it
9 citing papers in PubMed, 31 citations in OpenAlex.
- Recent advances in synthetic biology of cyanobacteria for improved chemicals production.Bioengineered · 2020Review
- BioPS: System for screening and assessment of biofuel-production potential of cyanobacteria.PloS one · 2018Article
- Transcription factors in microalgae: genome-wide prediction and comparative analysis.BMC genomics · 2016Article
- Cyanobacterial KnowledgeBase (CKB), a Compendium of Cyanobacterial Genomes and Proteomes.PloS one · 2015Article
- Genomic repertoires of DNA-binding transcription factors across the tree of life.Nucleic acids research · 2010Review
- Genomic structure of an economically important cyanobacterium, Arthrospira (Spirulina) platensis NIES-39.DNA research : an international journal for rapid publication of reports on genes and genomes · 2010Article
- The repertoire and evolution of ATP-binding cassette systems in Synechococcus and Prochlorococcus.Journal of molecular evolution · 2009Article
- Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria.Journal of molecular evolution · 2008Article
- Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.Chemical reviews · 2007Review
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComprehensive identification and classification of the transcription factors (TFs) in a given genome is an important aspect in understanding transcriptional regulatory networks of a specific organism. Cyanobacteria are an ancient group of gram-negative bacteria with strong variation in genome size ranging from about 1.6 to 9.1 Mb and little is known about their TF repertoires. Therefore, we constructed the cTFbase database to classify and analyze all the putative TFs in cyanobacterial genomes, followed by genome-wide comparative analysis. DESCRIPTION: In the current release, cTFbase contains 1288 putative TFs identified from 21 fully sequenced cyanobacterial genomes. Through its user-friendly interactive interface, users can employ various criteria to retrieve all TF sequences and their detailed annotation information, including sequence features, domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase provides phylogenetic trees of individual TF family, multiple sequence alignments of the DNA-binding domains and ortholog identification from any selected genomes. Comparative analysis revealed great variability of the TF sequences in cyanobacterial genomes. The high variance on the gene number and domain organization would be related to their diverse biological functions and their adaptation to various environmental conditions.
conclusioncTFbase provides a centralized warehouse for comparative analysis of putative TFs in cyanobacterial genomes. The availability of such an extensive database would be of great interest for the community of researchers working on TFs or transcriptional regulatory networks in cyanobacteria. cTFbase can be freely accessible at http://cegwz.com/ and will be continuously updated when the newly sequenced cyanobacterial genomes are available.
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