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Protocols

PlnTFDB specifications

Information


Unique identifier OMICS_00561
Name PlnTFDB
Alternative name Plant Transcription Factor Database
Restrictions to use None
Database management system MySQL
Community driven No
User data submission Not allowed
Version 3.0
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Carica papaya
    • Oryza sativa
    • Populus trichocarpa
    • Vitis vinifera
    • Zea mays

Maintainers


  • person_outline Bernd Mueller-Roeber
  • person_outline Diego Riaño-Pachón
  • person_outline Slobodan Ruzicic

Publications for Plant Transcription Factor Database

PlnTFDB citations

 (72)
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

[…] was used to annotate the correctly assembled transcripts with an E-value threshold of 10−1 (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 10−5. […]

library_books

Ginseng Genome Database: an open access platform for genomics of Panax ginseng

2018
BMC Plant Biol
PMCID: 5898050
PMID: 29649979
DOI: 10.1186/s12870-018-1282-9

[…] Transcription factors (TFs) are the key regulators for development and stimulus responses. TFs were identified based on the criteria of PlnTFDB [] using iTAK (http://bioinfo.bti.cornell.edu/cgi-bin/itak/index.cgi). A total of 4439 TF and transcription regulator genes were identified and classified into 94 TF families (http://ginsengdb […]

library_books

De novo assembly and analysis of the Artemisia argyi transcriptome and identification of genes involved in terpenoid biosynthesis

2018
Sci Rep
PMCID: 5895812
PMID: 29643397
DOI: 10.1038/s41598-018-24201-9

[…] nt transcription factor database) using Hmmsearch with the default parameters. The abilities of the unigenes to encode proteins were evaluated based on the characteristics of TF families described in PlnTFDB. […]

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

[…] ject (http://cgp.genomics.org.cn/page/species/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 […]

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 1e− 5. Beased on the average of RPKM of genes across RNA-seq library replicates for a condit […]

library_books

Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death

2018
PLoS One
PMCID: 5834160
PMID: 29499063
DOI: 10.1371/journal.pone.0192945

[…] somerase activity (, ). Of these enzymes, seven fall into flavonoid biosynthesis pathway [] (), suggesting enhanced ROS scavenging activity maintained in the meristematic cells of the EM [].Using the Plant Transcription Factor Database [] we identified six MYB and MYB-like TFs up-regulated in the EM (). The function of most of these TFs in Arabidopsis was linked to the regulation of flavonoid bios […]


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PlnTFDB institution(s)
Department of Molecular Biology, Institute of Biochemistry and Biology, GoFORSYS, University of Potsdam, Potsdam-Golm, Germany; Colegio de Postgraduados, Mexico; GabiPD Team, Bioinformatics Group, Max Planck Institute of Molecular Plant Physiology, Golm, Germany; Cooperative Research Group, Max Planck Institute of Molecular Plant Physiology, Golm, Germany; FRISYS, Faculty of Biology, University of Freiburg, Freiburg, Germany
PlnTFDB funding source(s)
Supported by Bundesministerium fuer Bildung und Forschung, Germany (GABI-FUTURE grant 0315046, GoFORSYS grant 0313924 and FRISYS grant 0313921); Subdireccion de Investigacion: Lınea 15, Colegio de Postgraduados, Mexico; Deutscher Akademischer Austauschdienst (DAAD).

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