RT Journal Article
SR Electronic
T1 SANe: The Seed Active Network For Mining Transcriptional Regulatory Programs of Seed Development
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 165894
DO 10.1101/165894
A1 Chirag Gupta
A1 Arjun Krishnan
A1 Eva Collakova
A1 Pawel Wolinski
A1 Andy Pereira
YR 2017
UL http://biorxiv.org/content/early/2017/07/20/165894.abstract
AB Seed development is an evolutionarily important phase of the plant life cycle that governs the fate of next progeny. Distinct sub-regions within seeds have diverse roles in protecting and nourishing the embryo as it enlarges, and for the synthesis of storage reserves that serve as an important source of nutrients and energy for germination. Several studies have revealed that transcription factors (TFs) act in fine coordination to regulate target genes that ensure proper maintenance, metabolism, and development of the embryo. Here, we present genome-wide predictions of seed-specific regulatory interactions between TFs and their target genes in the model plant Arabidopsis thaliana. The network is based on a panel of high-resolution seed-specific gene expression datasets and takes the form of a module-regulatory network. TFs that are well studied in the literature were often found at the top of the predicted ranks for the module that corresponds to their validated function role. Furthermore, we brought together a dedicated web resource for the systematic analysis of transcriptional-level regulatory programs underlying the development of seeds (https://plantstress-pereira.uark.edu/SANe/). The platform will enable biologists to query a subset of modules, TFs of interest, as well as analyze new transcriptomes to find modules significantly perturbed in their experiment.