AnimalTFDB Edit

Citations: 190

z-index: 31.67

Basic information
Short name AnimalTFDB
Full name Animal Transcription Factors Database
Description AnimalTFDB is a comprehensive database including classification and annotation of genome-wide transcription factors (TFs),transcription co-factors and chromatin remodeling factors in 65 animal genomes.
URL http://bioinfo.life.hust.edu.cn/AnimalTFDB/
Year founded 2011
Last update & version 2018-01-01 v2.0
Availability Free to all users
Contact information
University/Institution hosted Huazhong University of Science and Technology
Address Wuhan, Hubei 430074, PR China
City Wuhan
Province/State Hubei
Country/Region China
Contact name An-Yuan Guo
Contact email guoay@hust.edu.cn
Data information
Object(s)
  • Animal
Data type(s)
  • Protein
Data Category/Categories
  • Gene genome and annotation
Major organism(s)
  • Homo sapiens
  • Caenorhabditis elegans
Keyword(s)
  • chromatin remodeling factor
  • DNA-binding domain
  • transcription co-factor
  • transcription factor
Publications
  • AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors.[PMID: 25262351]
    Hong-Mei Zhang, Teng Liu, Chun-Jie Liu, Shuangyang Song, Xiantong Zhang, Wei Liu, Haibo Jia, Yu Xue, An-Yuan Guo

    Transcription factors (TFs) are key regulators for gene expression. Here we updated the animal TF database AnimalTFDB to version 2.0 (http://bioinfo.life.hust.edu.cn/AnimalTFDB/). Using the improved prediction pipeline, we identified 72 336 TF genes, 21 053 transcription co-factor genes and 6502 chromatin remodeling factor genes from 65 species covering main animal lineages. Besides the abundant annotations (basic information, gene model, protein functional domain, gene ontology, pathway, protein interaction, ortholog and paralog, etc.) in the previous version, we made several new features and functions in the updated version. These new features are: (i) gene expression from RNA-Seq for nine model species, (ii) gene phenotype information, (iii) multiple sequence alignment of TF DNA-binding domains, and the weblogo and phylogenetic tree based on the alignment, (iv) a TF prediction server to identify new TFs from input sequences and (v) a BLAST server to search against TFs in AnimalTFDB. A new nice web interface was designed for AnimalTFDB 2.0 allowing users to browse and search all data in the database. We aim to maintain the AnimalTFDB as a solid resource for TF identification and studies of transcription regulation and comparative genomics. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

    Nucleic acids research 2015:43(Database issue)

    62 Citations (from Europe PMC, 2018-10-19)

  • AnimalTFDB: a comprehensive animal transcription factor database.[PMID: 22080564]
    Hong-Mei Zhang, Hu Chen, Wei Liu, Hui Liu, Jing Gong, Huili Wang, An-Yuan Guo

    Transcription factors (TFs) are proteins that bind to specific DNA sequences, thereby playing crucial roles in gene-expression regulation through controlling the transcription of genetic information from DNA to RNA. Transcription cofactors and chromatin remodeling factors are also essential in the gene transcriptional regulation. Identifying and annotating all the TFs are primary and crucial steps for illustrating their functions and understanding the transcriptional regulation. In this study, based on manual literature reviews, we collected and curated 72 TF families for animals, which is currently the most complete list of TF families in animals. Then, we systematically characterized all the TFs in 50 animal species and constructed a comprehensive animal TF database, AnimalTFDB. To better serve the community, we provided detailed annotations for each TF, including basic information, gene structure, functional domain, 3D structure hit, Gene Ontology, pathway, protein-protein interaction, paralogs, orthologs, potential TF-binding sites and targets. In addition, we collected and annotated transcription cofactors and chromatin remodeling factors. AnimalTFDB has a user-friendly web interface with multiple browse and search functions, as well as data downloading. It is freely available at http://www.bioguo.org/AnimalTFDB/.

    Nucleic acids research 2012:40(Database issue)

    128 Citations (from Europe PMC, 2018-10-19)

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Record metadata

  • Created on: 2015-06-21
    • Ma Lina [2018-06-01]
    • Zou Dong [2018-03-05]
    • Ma Lina [2016-09-26]
    • Ma Lina [2016-09-23]
    • Li Mengwei [2016-03-31]
    • Li Mengwei [2016-03-28]
    • Li Mengwei [2015-11-24]
    • Li Mengwei [2015-06-28]
    • Li Mengwei [2015-06-26]

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