Dr. Nita Parekh and her students Sanchari Sircar and Mayank Musaddi published their research work on NetREx – Network-based Rice Expression Analysis Server for Abiotic Stress Conditions, and Nita Parekh in Database – The Journal of Biological Databases and Curation.
Research work as explained by the authors:
Recent focus on transcriptomic studies in food crops like rice, wheat and maize provide new opportunities to address issues related to agriculture and climate change. Re-analysis of such data available in public domain supplemented with annotations across molecular hierarchy can be of immense help to the plant research community, particularly co-expression networks representing transcriptionally coordinated genes that are often part of the same biological process. With this objective, we have developed NetREx, a Network-based Rice Expression Analysis Server, that hosts ranked co-expression networks of Oryza sativa using publicly available messenger RNA sequencing data across uniform experimental conditions. It provides a range of interactable data viewers and modules for analysing user-queried genes across different stress conditions (drought, flood, cold and osmosis) and hormonal treatments (abscisic and jasmonic acid) and tissues (root and shoot). Subnetworks of user-defined genes can be queried in pre-constructed tissue-specific networks, allowing users to view the fold change, module memberships, gene annotations and analysis of their neighbourhood genes and associated pathways. The web server also allows querying of orthologous genes from Arabidopsis, wheat, maize, barley and sorghum. Here, we demonstrate that NetREx can be used to identify novel candidate genes and tissue-specific interactions under stress conditions and can aid in the analysis and understanding of complex phenotypes linked to stress response in rice.
About the journal: Database – The Journal of Biological Databases and Curation provides an open access platform for the presentation of novel ideas in database research surrounding biological information, and aims to help strengthen the bridge between database developers, curators, and users. In addition, the journal provides a platform for the description of novel advances in the field of biocuration and promotes the use of information from biological databases to assist in the planning and design of original research projects. Biocuration involves the translation of information relevant to biology and medicine, into an organised format, typically as a database, which enables the integration of scientific literature as well as large datasets such that information is accurately represented and readily accessible, as a source of information for scientists, and as a basis for computational analysis.
January 2023