PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

AnArabidopsisTranscriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors

(2015) Jinpu Jin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

DNA-binding specificities of plant transcription factors and their potential to define target genes

(2014) José M. Franco-Zorrilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

TreeTFDB: An Integrative Database of the Transcription Factors from Six Economically Important Tree Crops for Functional Predictions and Comparative and Functional Genomics

(2013) K. Mochida et al.   DNA RESEARCH

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

(2013) Jizeng Jia et al.   NATURE

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

(2013) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Prediction of Regulatory Interactions from Genome Sequences Using a Biophysical Model for theArabidopsisLEAFY Transcription Factor

(2011) Edwige Moyroud et al.   PLANT CELL

wDBTF: an integrated database resource for studying wheat transcription factor families

(2010) Isabelle Romeuf et al.   BMC GENOMICS

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database

(2010) He Zhang et al.   NUCLEIC ACIDS RESEARCH

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

(2010) A. Yilmaz et al.   NUCLEIC ACIDS RESEARCH

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors

(2009) Keiichi Mochida et al.   BIOINFORMATICS

PlnTFDB: updated content and new features of the plant transcription factor database

(2009) Paulino Pérez-Rodríguez et al.   NUCLEIC ACIDS RESEARCH

TOBFAC: the database of tobacco transcription factors

(2008) Paul J Rushton et al.   BMC BIOINFORMATICS

DATFAP: A Database of Primers and Homology Alignments for Transcription Factors from 13 Plant Species

(2008) Jakob Fredslund   BMC GENOMICS

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

(2008) A. Yilmaz et al.   PLANT PHYSIOLOGY