2022 Undergraduate Research Symposium Abstract, Onariaginosa Igbinedion

New Databases and Export Features for GRNsight: a Web Application for Visualizing Models of GRNs

Onariaginosa O. Igbinedion, John David N. Dionisio, Kam D. Dahlquist

Department of Computer Science, Department of Biology, Loyola Marymount University, 1 LMU Drive, Los Angeles, CA 90045 USA

GRNsight is an open source web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. GRNmap is a MATLAB program that performs parameter estimation and forward simulation of a differential equations model of a GRN based on user-provided expression data. A limitation for GRNmap is the manual creation of input Excel workbooks which is time-consuming and can be error-prone. GRNsight reads these input and output workbooks from GRNmap and automatically displays the model data as a graph with colored nodes and edges. We have updated the existing back-end GRNsight database to be compatible with other species in addition to Saccharomyces cerevisiae. We cleaned up the database schema and added appropriate types to the data so that proper sorting is achieved when retrieving expression data. We expanded the user interface for GRNsight’s export-to-Excel functionality and connected it to the database, so that users can select which particular expression data sheets to export. Furthermore, we are storing all of the interactions between regulatory genes in the database so that GRNsight users can specify which genes belong in their GRN of interest. In conjunction with the updated expression data export feature, this will allow users to fully automate and validate the creation of GRNmap input workbooks, speeding up the rate of research. GRNsight is available at http://dondi.github.io/GRNsight.