Links on transcription regulation databases in plants

Transcription factor regulation in plants

General databases:

Plant Transcriptional Regulatory Map.URL:

PlantRegMap includes multiple types of regulatory elements derived from high-throughput assays for six species(cis-map) and genome-wide regulatory interacttions for 132 species (network) currently (2017).
Jin JP, He K, Tang X, Li Z, Lv L, Zhao Y, Luo JC, Gao G. (2015). An Arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors. Molecular Biology and Evolution, 32(7):1767-1773.

PlnTFDB (3.0)URL:

PlnTFDB (3.0) is a catalogue all Plant genes involved in transcriptional control. PlnTFDB currently contains 28193 protein models, 26184 distinct* protein sequences, arranged in 84 gene families.
Paulino Perez-Rodriguez; Diego Mauricio Riano-Pachon; Luiz Gustavo Guedes Correa; Stefan A. Rensing; Birgit Kersten; Bernd Mueller-Roeber. PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research 2009; doi: 10.1093/nar/gkp805

PlantTFDB (4.0)URL:

PlantTFDB 4.0 includes 165 species, with 89 newly sequenced species added, covering the main lineages across the green plants. Multiple types of regulatory elements (e.g., DNase I hypersensitive site, genomic TF footprints, TF binding peaks, histone modifications and nucleosome position) derived from high-throughput assays.
Jin JP, Tian F, Yang DC, Meng YQ, Kong L, Luo JC and Gao G. (2017). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research, 45(D1):D1040-D1045.

database of gene networks, including plant species.

Arabidopsis thaliana model databases:

Plant DNase I hypersenitive Sites (DHSs) Database. URL:

3 model plants: Arabidopsis, Rice, Brachypodium. Zhang, T., Marand, A., Jiang, J.M. (2015) PlantDHS: a database for DNase I hypersensitive sites in plants. Nucleic Acids Res. 44: D1148-D1153 (2016)


AthaMap provides a genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana. The MicroRNA Targets function permits the identifcation of target genes for miRNAs. Additional tools: 190 screening sequences corresponding to the 243 miRNA genes and the number of genomic hits. The Small RNA Targets function enables identification of small RNA targets from different small RNA libraries. (Last update – 2018)

Espresso URL:

Espresso is an online web server for exploring the interaction of transcription factors and their target genes in plants using ChIP-Seq data. Expresso now contains 20 Arabidopsis ChIP-Seq datasets form NCBI GEO database.