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TFdb specifications


Unique identifier OMICS_22217
Name TFdb
Alternative name The Mouse transcription factor database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • person_outline Yoshihide Hayashizaki
  • person_outline Harukazu Suzuki

Publication for The Mouse transcription factor database

TFdb citations


Genome wide identification and expression analysis of GRAS family transcription factors in tea plant (Camellia sinensis)

Sci Rep
PMCID: 5834537
PMID: 29500448
DOI: 10.1038/s41598-018-22275-z

[…] TMHHM server v2.0 ( was used to predict the membrane-bound CsGRAS members. The GRAS family TF databases of other species were downloaded from the plant TFDB database ( […]


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

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

[…] ustatory neurons using a list of genes encoding transcription factors and co-factors and chromatin remodeling factors (collectively, TF). We merged lists from the Riken TF ( and Bioguo TF ( databases and then filtered the combined list for those TFs expressed at average FPKM ≥ 1 across all gu […]


Identification and expression of GRAS family genes in maize (Zea mays L.)

PLoS One
PMCID: 5619761
PMID: 28957440
DOI: 10.1371/journal.pone.0185418

[…] All GRAS protein sequences of Arabidopsis, rice, Medicago truncatula, and Sorghum bicolor were downloaded from plant TFDB ( Then, together with the 86 maize GRAS proteins, the multiple sequence alignment was performed using Clustal X, (Version 2.0) []. The aligned sequences were the […]


Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH

Genome Biol Evol
PMCID: 5737581
PMID: 28961970
DOI: 10.1093/gbe/evx185

[…] and BLASTX (, online). Previously studied genetic fragments from strain MH (; ) were downloaded from NCBI: tnpA-sdpA [AJ628860.1], rdpA [AF516752.2], tfdK-ORFB-dccAII-dccDII-tnp A[AJ628863.1], cadR-tfdB [AJ628861.1], chloromuconate cycloisomerase [DQ146618.1], dccE-dccAI-dccDI [AJ628862.1], and tnpA-rdpA [AJ628859.1]. These nucleotide sequences were mapped to the MH genome using BLASTN (all matc […]


Transcriptome of neonatal preBötzinger complex neurones in Dbx1 reporter mice

Sci Rep
PMCID: 5561182
PMID: 28819234
DOI: 10.1038/s41598-017-09418-4

[…] th for each gene. We analysed transcription factors by cross-referencing our transcriptome data to the Riken Institute (Wako, Saitama, Japan) list of transcription factors ( and the TF-checkpoint database ( from the Norwegian University of Science and Technology (Trondheim, Norway). We ev […]


CmMYB19 Over Expression Improves Aphid Tolerance in Chrysanthemum by Promoting Lignin Synthesis

Int J Mol Sci
PMCID: 5372634
PMID: 28287502
DOI: 10.3390/ijms18030619
call_split See protocol

[…] // [] based on the neighbor-joining method and 1,000 bootstrap replicates following previous descriptions [,]. A. thaliana MYB polypeptides sequences were obtained from the Plant TFDB website (available on: […]


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TFdb institution(s)
Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama, Japan; Genome Science Laboratory, RIKEN, Wako, Japan
TFdb funding source(s)
Supported by a Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government, a Research Grant for Advanced and Innovational Research Program in Life Science, a Research Grant for Advanced and Innovational Research Program in Life Science, and CREST (Core Research for Evolutional Science and Technology) of the Japan Science and Technology Corporation (JST).

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