HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Hormone Signaling and Regulatory Networks

Background. Plant hormone (also known as phytohormone) signaling and regulatory networks play critical roles in almost all aspects of plant growth, development, senescence, and its responses to different environmental challenges. Systematic knowledge of global hormone signaling and regulatory networks is therefore fundamentally important to understanding plant biology. Significant progress in hormone research has been made during the past decade. Yet to date, little is known about the hormonal cross-talks, regulation mechanisms between different plant hormones, and interactions between downstream regulatory genes. And, key components are yet-to-be discovered to fill the pathway holes.

Results We constructed comprehensive global hormonal signaling and regulatory networks, which comprehensively integrate hormone biosynthesis, metabolism cascades, signaling transductions and gene co-expression networks, for the model plant Arabidopsis thaliana. Currently, the HRGRN hosts protein-protein interactions, none-coding RNAs (ncRNAs) and their regulatory targets, transcription factors and their target genes, and gene-gene interactions from co-expression-based network analysis, which were manually curated and integrated. Furthermore, we developed powerful “Graph Search”-based pathway and sub-network analysis and visualization tools for global hormonal signaling and network analysis, novel and essential gene relationship discovery. In addition, we developed interactive and visualized graph based network analysis tools, by which researchers can investigate genes, pathways, and subnetworks, including hormonal cross-talks.  

Conclusions. We developed HRGRN: a graph search-empowered integrative database of Arabidopsis hormone signaling and gene regulation, which is publically and freely available at http://plantgrn.noble.org/hrgrn/.