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AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors.

Zhang HM, Liu T, Liu CJ, Song S, Zhang X, Liu W, Jia H, Xue Y, Guo AY - Nucleic Acids Res. (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.

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The new annotations and tools in AnimalTFDB 2.0. (A) The multiple sequence alignment of TF DBDs, the weblogo and phylogenetic tree based on the alignment in each TF family. (B) The TF prediction server and examples of prediction result. (C) The BLAST search server. (D) One example of gene expression information. (E) The gene phenotype information.
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Figure 1: The new annotations and tools in AnimalTFDB 2.0. (A) The multiple sequence alignment of TF DBDs, the weblogo and phylogenetic tree based on the alignment in each TF family. (B) The TF prediction server and examples of prediction result. (C) The BLAST search server. (D) One example of gene expression information. (E) The gene phenotype information.

Mentions: In an attempt to construct a comprehensive knowledgebase for animal TFs, we provided rich information for them. Besides, the abundant annotations provided in version 1.0, we collected gene function description, gene expression at mRNA and protein levels, and phenotype data from various public resources and performed annotation for these factors (Figure 1). Through checking the transcription regulation-related GO annotation with experimental evidence codes, we marked the regulators as experimentally validated or putative in seven model species. As a result, we found 426 TFs, 236 co-factors and 37 CRFs with experimental evidence in human. In addition, using the DBD sequences, we made multiple sequence alignment by ClustalW2 (36) and constructed phylogenetic trees for TFs in each family of each species by applying neighbor-joining method in PHYLIP package (37) with bootstrap 100. The multiple sequence alignment result and phylogenetic tree were displayed by Weblogo (38) and Phylogeny.fr (39), respectively (Figure 1A). The phylogenetic tree will be helpful for users to infer the functions of poorly studied TFs.


AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors.

Zhang HM, Liu T, Liu CJ, Song S, Zhang X, Liu W, Jia H, Xue Y, Guo AY - Nucleic Acids Res. (2014)

The new annotations and tools in AnimalTFDB 2.0. (A) The multiple sequence alignment of TF DBDs, the weblogo and phylogenetic tree based on the alignment in each TF family. (B) The TF prediction server and examples of prediction result. (C) The BLAST search server. (D) One example of gene expression information. (E) The gene phenotype information.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384004&req=5

Figure 1: The new annotations and tools in AnimalTFDB 2.0. (A) The multiple sequence alignment of TF DBDs, the weblogo and phylogenetic tree based on the alignment in each TF family. (B) The TF prediction server and examples of prediction result. (C) The BLAST search server. (D) One example of gene expression information. (E) The gene phenotype information.
Mentions: In an attempt to construct a comprehensive knowledgebase for animal TFs, we provided rich information for them. Besides, the abundant annotations provided in version 1.0, we collected gene function description, gene expression at mRNA and protein levels, and phenotype data from various public resources and performed annotation for these factors (Figure 1). Through checking the transcription regulation-related GO annotation with experimental evidence codes, we marked the regulators as experimentally validated or putative in seven model species. As a result, we found 426 TFs, 236 co-factors and 37 CRFs with experimental evidence in human. In addition, using the DBD sequences, we made multiple sequence alignment by ClustalW2 (36) and constructed phylogenetic trees for TFs in each family of each species by applying neighbor-joining method in PHYLIP package (37) with bootstrap 100. The multiple sequence alignment result and phylogenetic tree were displayed by Weblogo (38) and Phylogeny.fr (39), respectively (Figure 1A). The phylogenetic tree will be helpful for users to infer the functions of poorly studied TFs.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.

Show MeSH