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TFdb specifications

Information


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

Maintainers


  • person_outline Yoshihide Hayashizaki
  • person_outline Harukazu Suzuki

Publication for The Mouse transcription factor database

TFdb citations

 (16)
library_books

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

2018
Sci Rep
PMCID: 5834537
PMID: 29500448
DOI: 10.1038/s41598-018-22275-z

[…] ort.org). TMHHM server v2.0 (http://www.cbs.dtu.dk/services/TMHMM/) was used to predict the membrane-bound CsGRAS members. The GRAS family TF databases of other species were downloaded from the plant TFDB database (http://planttfdb.cbi.edu.cn/). […]

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

[…] 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 (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 gu […]

library_books

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

2017
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 (http://planttfdb.cbi.pku.edu.cn/). 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 […]

library_books

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

2017
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 […]

library_books

Transcriptome of neonatal preBötzinger complex neurones in Dbx1 reporter mice

2017
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 (http://genome.gsc.riken.jp/TFdb/tf_list.html) and the TF-checkpoint database (http://www.tfcheckpoint.org/data/TFCheckpoint_download_180515.txt) from the Norwegian University of Science and Technology (Trondheim, Norway). We ev […]

call_split

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

2017
Int J Mol Sci
PMCID: 5372634
PMID: 28287502
DOI: 10.3390/ijms18030619
call_split See protocol

[…] //www.megasoftware.net) [] 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: planttfdb.cbi.edu.cn/). […]

Citations

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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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