PlantTFDB statistics

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Protocols

PlantTFDB specifications

Information


Unique identifier OMICS_00560
Name PlantTFDB
Alternative name Plant Transcription Factor Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 4.0
Maintained Yes

Documentation


Maintainer


  • person_outline PlantRegMap Team

Publication for Plant Transcription Factor Database

PlantTFDB citations

 (98)
library_books

Transcriptome and Co Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.

2018
Sci Rep
PMCID: 5945678
PMID: 29748645
DOI: 10.1038/s41598-018-25826-6

[…] assembled transcripts with an E-value threshold of 10āˆ’1 (http://www.nematodes.org/bioinformatics/annot8r). To derive transcription factor family related information PlnTFDB database was used (http://planttfdb.cbi.pku.edu.cn). All the unigenes were searched against this database using BLASTX with an E-value threshold of 10āˆ’5. […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] ., ).To identify TFs in A. ipaensis, the PlantTFDB database was used to search TFs in other plant species (http://planttfdb.cbi.pku.edu.cn/). The predicted genes were used to BLAST search against the PlantTFDB (E-value: 1e-10). The FAR1 motif was predicted using the Multiple Expectation Maximization for Motif Elicitation (MEME)/Motif Alignment and Search Tool (MAST) system (http://meme-suite.org/) […]

call_split

An APETALA2 Homolog, RcAP2, Regulates the Number of Rose Petals Derived From Stamens and Response to Temperature Fluctuations

2018
Front Plant Sci
PMCID: 5906699
PMID: 29706982
DOI: 10.3389/fpls.2018.00481
call_split See protocol

[…] ogenetic analyses were conducted with MEGA7 using the Neighbor-Joining method and the bootstrap consensus tree was inferred from 1000 replicates. The function prediction of transcription factor using PlantTFDB online tool, the RegRNA 2.0 online tool () was used to identifying the functional motifs and sites of RcAP2. The cis-acting element analyses were completed using online software PlantCARE () […]

library_books

Genome wide comparative and evolutionary analysis of Calmodulin binding Transcription Activator (CAMTA) family in Gossypium species

2018
Sci Rep
PMCID: 5882909
PMID: 29615731
DOI: 10.1038/s41598-018-23846-w

[…] s/index.jsp) and of G. raimondii from Phytozome (http://www.phytozome.net/). A total of 465 CAMTA domain sequences from 75 plant species were obtained from Plant Transcription Factor Database (http://planttfdb.cbi.pku.edu.cn/) and utilized to construct Hidden Markov Model (HMM) profile. Further, HMM profile of the CAMTA domains (CG-1, TIG domain, Ankyrin repeats, IQ) was employed as a query to ide […]

library_books

Transcriptomic analysis of Perilla frutescens seed to insight into the biosynthesis and metabolic of unsaturated fatty acids

2018
BMC Genomics
PMCID: 5863459
PMID: 29562889
DOI: 10.1186/s12864-018-4595-z

[…] To identify the transcription factors (TFs) represented in Perilla seed transcriptome, all assembled unigenes were searched against plant transcription factor database PlantTFDB (http://planttfdb.cbi.pku.edu.cn/) by BLAST with a cut-off of 1eāˆ’ā€‰5. Beased on the average of RPKM of genes across RNA-seq library replicates for a condition. Hierarchical clustering was per […]

call_split

Transcript Profiling Identifies NAC Domain Genes Involved in Regulating Wall Ingrowth Deposition in Phloem Parenchyma Transfer Cells of Arabidopsis thaliana

2018
Front Plant Sci
PMCID: 5862824
PMID: 29599795
DOI: 10.3389/fpls.2018.00341
call_split See protocol

[…] Full-length amino acid sequences of selected transcription factors from Arabidopsis were obtained from PlantTFDB under the latest modified (July 21, 2017) version 4.0 (http://planttfdb.cbi.pku.edu.cn/index.php?sp=Ath; Jin et al., , ). These sequences were aligned using webservers of Clustal Omega (http […]

Citations

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PlantTFDB institution(s)
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
PlantTFDB funding source(s)
This work was supported by National Natural Science Foundation of China [1470330]; International Collaboration Program for Proteome Biological Big Data and Standard System [2014DFB30030]; State Key Laboratory of Protein and Plant Gene Research; China Postdoctoral Science Foundation Grant [2014M560017, 2015T80015]; Postdoctoral Fellowship at Peking Tsinghua Center for Life Sciences; National Program for Support of Top-notch Young Professionals.

PlantTFDB reviews

 (6)
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Emmanuel John Tabilin

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Dataset
I can't reach your site, http://planttfdb.cbi.pku.edu.cn/ as of 11:46 pm (PH time) today. When will it be available?

Emmanuel Quevillon

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Dataset
Hi Mariette,

Service is now back in business!
Regards
Emmanuel