Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

Description: a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them, advancing the understanding of plant transcriptional regulatory system.
Year founded: 2019
Last update: 2019-10-11
Version:
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: China
Data type:
DNA
Data object:
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: Peking University
Address:
City: Beijing
Province/State: Beijing
Country/Region: China
Contact name (PI/Team): Ge Gao
Contact email (PI/Helpdesk): gaog@mail.cbi.pku.edu.cn

Publications

31701126
PlantRegMap: charting functional regulatory maps in plants. [PMID: 31701126]
Tian F, Yang DC, Meng YQ, Jin J, Gao G.

With the goal of charting plant transcriptional regulatory maps (i.e. transcription factors (TFs), cis-elements and interactions between them), we have upgraded the TF-centred database PlantTFDB (http://planttfdb.cbi.pku.edu.cn/) to a plant regulatory data and analysis platform PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) over the past three years. In this version, we updated the annotations for the previously collected TFs and set up a new section, 'extended TF repertoires' (TFext), to allow users prompt access to the TF repertoires of newly sequenced species. In addition to our regular TF updates, we are dedicated to updating the data on cis-elements and functional interactions between TFs and cis-elements. We established genome-wide conservation landscapes for 63 representative plants and then developed an algorithm, FunTFBS, to screen for functional regulatory elements and interactions by coupling the base-varied binding affinities of TFs with the evolutionary footprints on their binding sites. Using the FunTFBS algorithm and the conservation landscapes, we further identified over 20 million functional TF binding sites (TFBSs) and two million functional interactions for 21 346 TFs, charting the functional regulatory maps of these 63 plants. These resources are publicly available at PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) and a cloud-based mirror (http://plantregmap.gao-lab.org/), providing the plant research community with valuable resources for decoding plant transcriptional regulatory systems.

Nucleic Acids Res. 2020:48(D1) | 11 Citations (from Europe PMC, 2020-10-31)

Ranking

All databases:
720/4695 (84.686%)
Modification:
29/202 (86.139%)
720
Total Rank
11
Citations
11
z-index

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Record metadata

Created on: 2020-10-14
Curated by:
Dong Zou [2020-10-14]