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AtTFDB specifications

Information


Unique identifier OMICS_26228
Name AtTFDB
Alternative name Arabidopsis transcription factor database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


  • person_outline Alper Yilmaz

Publications for Arabidopsis transcription factor database

AtTFDB citations

 (11)
library_books

eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice

2017
Front Plant Sci
PMCID: 5645499
PMID: 29081784
DOI: 10.3389/fpls.2017.01753

[…] es 1, 4, and 12 using the Bioconductor package “BiomaRt” (, ). We employed 100 curated motifs (filename: element_name_and_motif_IUPACsupp.txt) that are based on the Gene Regulatory Information Server AtTFDB database (). The abundance of motif elements in promoters of genes with trans-eQTLs was compared with that of all considered genes using Fisher’s exact test and the Biostrings package (). […]

library_books

Transcript profiling of genes expressed during fibre development in diploid cotton (Gossypium arboreum L.)

2017
BMC Genomics
PMCID: 5580217
PMID: 28859611
DOI: 10.1186/s12864-017-4066-y

[…] Conserved sequences of all probe sets presented in cotton GeneChip were searched for putative transcription factors related to phytohormone biosynthesis and signal transduction pathways, against the Arabidopsis transcription factor database (http://plntfdb.bio.uni-potsdam.de, version 3.0) and Arabidopsis hormone database (http://ahd.cbi.pku.edu.cn, version 2.0) respectively, by BLASTX with E valu […]

library_books

RNA Seq and Gene Network Analysis Uncover Activation of an ABA Dependent Signalosome During the Cork Oak Root Response to Drought

2016
Front Plant Sci
PMCID: 4707443
PMID: 26793200
DOI: 10.3389/fpls.2015.01195

[…] Transcription factors were identified from Arabidopsis DEG orthologs using the AGRIS Arabidopsis TF database (AtTFDB; ), MapMan (transcripton pathway bin; ), and manual curation. Cis-element enrichment analysis was carried using AtCOECis () and Athena (), with default parameters. Gene networks were predicted […]

library_books

De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines

2015
PLoS One
PMCID: 4457790
PMID: 26047102
DOI: 10.1371/journal.pone.0128331

[…] TBLASTN (Search translated nucleotide database using a protein query) was used for sequence alignment against Transcriptome Shotgun Assembly (TSA) of Momordica charantia (taxid: 3673) organism. The Arabidopsis transcription factor database sequences were used as model sequence for search against Transcriptome Shotgun Assembly (TSA) of M. charantia. Dof Transcription Factor associated genes were […]

library_books

Microarray analysis of Arabidopsis under gold exposure to identify putative genes involved in the synthesis of gold nanoparticles (AuNPs)

2014
Genom Data
PMCID: 4536028
PMID: 26484157
DOI: 10.1016/j.gdata.2014.12.001

[…] h ANOVA p-value of < 0.05 (Condition unpaired) and corrected p-value (FDR) of ≤ 0.16 in the analysis.To filter out the known transcription factors from DEGs, we submitted TAIR IDs of DEGs to a public Arabidopsis transcription factor database (AtTFDB) using a web based tool available on this link, http://arabidopsis.med.ohio-state.edu/AtTFDB/ . In order to obtain a view of significantly changed bio […]

library_books

Transcriptome Analysis of Yellow Horn (Xanthoceras sorbifolia Bunge): A Potential Oil Rich Seed Tree for Biodiesel in China

2013
PLoS One
PMCID: 3770547
PMID: 24040247
DOI: 10.1371/journal.pone.0074441

[…] etions of two or more bases, the coverage depth of the isotigs and the InDel allele frequency were set at 10 and 10%, respectively.To identify TFs, a BLAST search for all unigenes was conducted using AtTFDB (Arabidopsis transcription factor database) with shared identities >77%, as described previously . […]

Citations

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AtTFDB institution(s)
Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, Columbus, OH, USA; School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, USA
AtTFDB funding source(s)
Supported by National Science Foundation (MCB-0418891); and National Institutes of Health (5 T32 CA106196-05).

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