THE PROJECT:

SRGPs: An online resource for comparative analysis of ‘Stress Responsive Genes in Plants’

MYCHAL W. IVANCICH, RAFI SHAIK AND WUSIRIKA RAMAKRISHNA

Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA

Plants face a number of different kinds of stresses during their lifetime which negatively affect their survival and productivity. Many of the recent studies suggest that each stress response has a distinct molecular profile yet extensive cross-talk occurs between different stress responses via hormones and signal transduction pathways. Thus, it is critical to comprehensively understand the stress responses and their interactions to design strategies which enhance stress response. Towards this end, we performed meta-analysis of drought, salinity, bacterial and fungal stress microarray studies in rice and Arabidopsis to identify the differentially expressed genes (DEGs) in each of the stresses. The lists of DEGs referred as stress responsive genes (SRGs) are available online through a user friendly interface built using HTML5, PHP and JavaScript with MySQL backend. The expression levels (fold change), direction of differential expression (up or down) of SRGs in different stresses are displayed along with other references reporting the gene as a DEG. The users can also query for gene ontology terms, transcription factor genes, microRNA targets, DAVID annotations, protein domains and metabolic pathways that are enriched in any or all of the stresses. Network graphs based on co-expression and protein-protein interactions are provided using a CytoScape plugin. Further links to orthologs between rice and Arabidopsis are provided that present expression level of orthologous SRGs in different stress conditions. The above capabilities make SRGPs a valuable resource for plant biology community to study stress responsive genes and their characteristics.

   

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