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AnimalTFDB specifications

Information


Unique identifier OMICS_01856
Name AnimalTFDB
Alternative name Animal Transcription Factor DataBase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 3.0
Maintained Yes

Maintainer


  • person_outline An-Yuan Guo

Publications for Animal Transcription Factor DataBase

AnimalTFDB citations

 (21)
call_split

Estrogen receptors orchestrate cell growth and differentiation to facilitate liver regeneration

2018
Theranostics
PMCID: 5957001
PMID: 29774067
DOI: 10.7150/thno.23624
call_split See protocol

[…] indirectly interact or are functionally associated with ERα or ERβ. Several bioinformatics databases were used including TFcheckpoint (http://www.tfcheckpoint.org/) to identify transcription factors; AnimalTFDB (http://www.bioguo.org/AnimalTFDB/) to identify cofactors; TRANSFAC (http://www.biobase-international.com/product/transcription-factor-binding-sites) to identify eukaryotic transcription fa […]

library_books

An integrated approach to infer cross talks between intracellular protein transport and signaling pathways

2018
BMC Bioinformatics
PMCID: 5850946
PMID: 29536825
DOI: 10.1186/s12859-018-2036-2

[…] dmark transcripts plus imputed genes (Fig. b). Finally, to map transcription factors and gene interactions information on the 591 perturbation experiments, we use the human transcription factors from AnimalTFDB 2.0 [] and manually curated human signaling network data from Edwin Wang and associated group (http://www.cancer-systemsbiology.org/data-software). This signaling network dataset contains m […]

library_books

Coordination of olfactory receptor choice with guidance receptor expression and function in olfactory sensory neurons

2018
PLoS Genet
PMCID: 5809090
PMID: 29385124
DOI: 10.1371/journal.pgen.1007164

[…] ty of Denmark http://www.cbs.dtu.dk/services/TargetP/) []. Genes with reliability class (RC) score = 1 were selected as containing a signal peptide and included in a list of candidate guidance genes. AnimalTFDB2.0 (Guo Lab, College of Life Science and Technology, HUST, China http://bioinfo.life.hust.edu.cn/AnimalTFDB/) [] was used to download a list of zebrafish genes with known or putative transc […]

library_books

A Unique TGFB1 Driven Genomic Program Links Astrocytosis, Low Grade Inflammation and Partial Demyelination in Spinal Cord Periplaques from Progressive Multiple Sclerosis Patients

2017
Int J Mol Sci
PMCID: 5666779
PMID: 28981455
DOI: 10.3390/ijms18102097

[…] (ECM); or (iii) transcription factors (TF). Identification of functionally-relevant genes was performed by a survey of the literature, on the basis of GO terms annotation, and using the TF database “AnimalTFDB” []. Finally, the 200 genes forming the Cx43/GJA1 co-expression network were also analyzed with regard to their enrichment in: (i) genes involved in specific pathways; (ii) genes identified […]

library_books

Transcriptomes and neurotransmitter profiles of classes of gustatory and somatosensory neurons in the geniculate ganglion

2017
Nat Commun
PMCID: 5624912
PMID: 28970527
DOI: 10.1038/s41467-017-01095-1

[…] ption factors and co-factors and chromatin remodeling factors (collectively, TF). We merged lists from the Riken TF (http://genome.gsc.riken.jp/TFdb/tf_list.html) and Bioguo TF (http://www.bioguo.org/AnimalTFDB/species.php?spe=Mus_musculus) databases and then filtered the combined list for those TFs expressed at average FPKM ≥ 1 across all gustatory neurons. As described above, this criterion simp […]

library_books

Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity

2017
PLoS One
PMCID: 5612723
PMID: 28945800
DOI: 10.1371/journal.pone.0185409

[…] r Molecular Function, Biological Process and Cellular Component and, in addition, for genes enriched for the Reactome pathways term, in each case comparing to the reference set of 2087 genes from the AnimalTFDB 2.0 database []. Sets were selected that demonstrated more than a 2.5 fold enrichment with a significant probability of p<0.05. Whilst individual genes may contribute to organismal complexi […]

Citations

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AnimalTFDB institution(s)
Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou, China
AnimalTFDB funding source(s)
Supported by the National Key Research and Development Program of China [2017YFA0700403] and National Natural Science Foundation of China (NSFC) [31822030, 31771458, 31801154, 31801113].

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