Daphne EzerSamuel J.K. ShepherdAnna BrestovitskyPatrick DickinsonSandra CortijoVarodom CharoensawanMathew S. BoxSurojit BiswasKatja E. JaegerPhilip A. WiggeUniversity of CambridgeMahidol UniversityHarvard Medical School2018-12-212019-03-142018-12-212019-03-142017-10-01Plant Physiology. Vol.175, No.2 (2017), 628-64015322548003208892-s2.0-85030835199https://repository.li.mahidol.ac.th/handle/20.500.14594/41330© 2017 American Society of Plant Biologists. All Rights Reserved. Plants have significantly more transcription factor (TF) families than animals and fungi, and plant TF families tend to contain more genes; these expansions are linked to adaptation to environmental stressors. Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG), so it is difficult to predict regulatory relationships. We determined that the flanking sequences near G-boxes help determine in vitro specificity but that this is insufficient to predict the transcription pattern of genes near G-boxes. Therefore, we constructed a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of the expression of genes downstream of perfect G-boxes. This network accurately predicts transcriptional patterns and reconstructs known regulatory subnetworks. Finally, we present Ara-BOX-cis (araboxcis.org), a Web site that provides interactive visualizations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations.Mahidol UniversityAgricultural and Biological SciencesBiochemistry, Genetics and Molecular BiologyArticleSCOPUS10.1104/pp.17.01086