NAR Molecular Biology Database Collection entry number 1460
Guo, An-Yuan; Zhang, Hong-Mei.; Liu, Teng; Liu, Chun-Jie; Song, Shuangyang; Zhang, Xiantong; Liu, Wei.; Jia, Haibo; Xue, Yu
Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, PR China
Transcription factor are key regulators in gene expression. AnimalTFDB is a comprehensive database including classification and annotation of genome-wide transcription factors (TFs), transcription co-factors and chromatin remodeling factors in animal genomes. The TFs are further classified into 70 families based on their conserved DBDs. The AnimalTFDB 1.0 predicted TFs in 50 animal genomes and it was online in 2011. In 2014, we updated the database to version 2.0 as many more annotation data and new genome sequences available. In AnimalTFDB 2.0, we identified 72336 TF genes, 21053 transcription co-factor genes, and 6502 chromatin remodeling factor genes from 65 species covering main animal lineages. Abundant annotations, such as gene basic information, protein functional domain, gene ontology, pathway, protein-protein interaction, ortholog, paralog and gene model are provided. Besides that, we also made several new features and functions. These includes (1) gene expression from RNA-Seq for 9 model species, (2) gene phenotype information, (3) multiple sequence alignment of TF DNA-binding domains, and the weblogo and phylogenetic tree based on the alignment, (4) a TF prediction server to identify new TFs from input sequences, and (5) a BLAST server to search against TFs in AnimalTFDB. We aim to maintain the AnimalTFDB as a solid resource for TF identification and studies of transcription regulation and comparative genomics.
This work has been supported by grants from NSFC and NCET.
1. Zhang, H.M., Chen, H., Liu, W., Liu, H., Gong, J., Wang, H. and Guo, A.Y. (2012) AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res, 40,
Category: Nucleotide Sequence Databases
Go to the abstract in the NAR 2015 Database Issue.
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