Database Commons

a catalog of biological databases

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

Database information

ATRM (Arabidopsis Transcriptional Regulatory Map)

General information

Description: Here, we used two data sources, PubMed Abstracts and ResNet Plant 3.0 to collect verified transcriptional regulatory interactions in A. thaliana. We retrieved transcription factor(TF)-associated interactions from ResNet Plant 3.0 as well as mined them from PubMed abstracts by MedScan. After manual curation each interaction by reviewing the original texts, we constructed an Arabidopsis transcriptional regulatory map (ATRM) that covers 388 TFs from 47 families, with directly supporting evidences from 974 references.
Year founded: 2015
Last update: 2015
Version: 1
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Country/Region: China
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Contact information

University/Institution: Peking University
Address: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing, P.R. China
City: Beijing
Province/State: Beijing
Country/Region: China
Contact name (PI/Team): Ge Gao
Contact email (PI/Helpdesk): gaog@mail.cbi.pku.edu.cn

Related Database

Record metadata

Created on: 2018-02-10
Curated by:
Dong Zou [2020-10-14]
Lina Ma [2018-12-04]
[2018-12-03]
Qi Wang [2018-02-16]

Ranking

All databases:
974/4694 (79.271%)
Interaction:
161/698 (77.077%)
974
Total Rank
38
Citations
7.6
z-index

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Publications

25750178
An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. [PMID: 25750178]
Jin J, He K, Tang X, Li Z, Lv L, Zhao Y, Luo J, Gao G.

Transcription factors (TFs) play key roles in both development and stress responses. By integrating into and rewiring original systems, novel TFs contribute significantly to the evolution of transcriptional regulatory networks. Here, we report a high-confidence transcriptional regulatory map covering 388 TFs from 47 families in Arabidopsis. Systematic analysis of this map revealed the architectural heterogeneity of developmental and stress response subnetworks and identified three types of novel network motifs that are absent from unicellular organisms and essential for multicellular development. Moreover, TFs of novel families that emerged during plant landing present higher binding specificities and are preferentially wired into developmental processes and these novel network motifs. Further unveiled connection between the binding specificity and wiring preference of TFs explains the wiring preferences of novel-family TFs. These results reveal distinct functional and evolutionary features of novel TFs, suggesting a plausible mechanism for their contribution to the evolution of multicellular organisms.

Mol Biol Evol. 2015:32(7) | 38 Citations (from Europe PMC, 2020-10-24)