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Protocols

PlantTFcat specifications

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Unique identifier OMICS_00559
Name PlantTFcat
Restrictions to use None
Maintained Yes

Publication for PlantTFcat

PlantTFcat citations

 (6)
library_books

A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.)

2017
BMC Genomics
PMCID: 5700742
PMID: 29166879
DOI: 10.1186/s12864-017-4306-1

[…] Transcription factors (TFs) and transcriptionally active proteins (TAPs) were identified by using three approaches: the PlantTFcat pipeline [], the iTAK pipeline [], and a TavernaPBS [] workflow (see Additional file ) that uses HMMER 3 [] for Hidden Markov models and PFAM [] for finding protein domains. TF and TAP clas […]

library_books

Diurnal Cycling Transcription Factors of Pineapple Revealed by Genome Wide Annotation and Global Transcriptomic Analysis

2017
Genome Biol Evol
PMCID: 5737478
PMID: 28922793
DOI: 10.1093/gbe/evx161

[…] r no homolog or had a homolog with a different classification in public TF and TC databases. We therefore compared our annotations of these 86 TFs and TCs to those predicted independently by iTAK and PlantTFcat webservers (, Supplementary Material online). Our classification matched iTAK and/or PlantTFcat predictions for 55 TF and TC proteins but differed for five proteins due to the presence of a […]

call_split

Transcriptomic profiling of hemp bast fibres at different developmental stages

2017
Sci Rep
PMCID: 5504027
PMID: 28694530
DOI: 10.1038/s41598-017-05200-8
call_split See protocol

[…] The annotation of the putative transcription factors (TFs) in the de novo assembly was carried out with PlantTFcat (http://plantgrn.noble.org/PlantTFcat/), which gave a total of 2484 TFs (Suppl. Dataset File). The ICA was performed with the on-line program MetaGeneAlyse v1.7.1 (http://metagenealyse.mpim […]

library_books

Comparative transcriptome analysis of shoot and root tissue of Bacopa monnieri identifies potential genes related to triterpenoid saponin biosynthesis

2017
BMC Genomics
PMCID: 5490213
PMID: 28659188
DOI: 10.1186/s12864-017-3865-5

[…] Transcripts coding for transcription factors in the transcriptome of Bacopa monnieri shoot and root tissues were anticipated by searching against all transcription factor protein sequences present in PlantTFcat (http://plantgrn.noble.org/PlantTFcat/about.gy) using BLASTX with an E-value cutoff 1e−6 and domain analysis within transcription factor was performed by using InterPro. […]

library_books

Suppression Substractive Hybridization and NGS Reveal Differential Transcriptome Expression Profiles in Wayfaring Tree (Viburnum lantana L.) Treated with Ozone

2016
Front Plant Sci
PMCID: 4887494
PMID: 27313581
DOI: 10.3389/fpls.2016.00713

[…] he plant GO slim (available from http://www.geneontology.org) and classified according to biological and molecular functions and cellular localization. Transcription factors were identified using the PlantTFcat (Dai et al., ). […]

library_books

Dataset of UV induced changes in nuclear proteome obtained by GeLC Orbitrap/MS in Pinus radiata needles

2016
PMCID: 4857224
PMID: 27182543
DOI: 10.1016/j.dib.2016.03.074

[…] s employing a 5% false discovery rate (FDR), two peptides per protein, medium confidence, and an XCorr score above 1.8 as identification threshold. Unknown and unannotated proteins were analysed with PlantTFcat tool and blasted against PlnTFDB transcription factors database in order to identify transcription factors and nuclear regulators. Contaminant proteins not belonging to the nuclei or endo […]


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PlantTFcat institution(s)
Plant Biology Division, The Samuel Roberts Noble Foundation,Ardmore, OK, USA

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