@article {Ezer128371, author = {Daphne Ezer and Samuel JK Shepherd and Anna Brestovitsky and Patrick Dickinson and Sandra Cortijo and Varodom Charoensawan and Mathew S. Box and Surojit Biswas and Philip Wigge}, title = {The G-box transcriptional regulatory code in Arabidopsis}, elocation-id = {128371}, year = {2017}, doi = {10.1101/128371}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Plants have significantly more transcription factor (TF) families than animals and fungi, and plant TF families tend to contain more genes{\textemdash}these expansions are linked to adaptation to environmental stressors (1, 2). 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 determine 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 construct a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of the gene 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 website that provides interactive visualisations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations.}, URL = {https://www.biorxiv.org/content/early/2017/04/18/128371}, eprint = {https://www.biorxiv.org/content/early/2017/04/18/128371.full.pdf}, journal = {bioRxiv} }