2023 Undergraduate Research Symposium Abstract, Ahmad R. Mersaghian, Sarron A. Tadesse, and Ngan N. Tran

Improved Functionality of GRNsight 6.0: a Web Application for Visualizing Gene Regulatory Network Models

Ahmad R. Mersaghian, Sarron A. Tadesse, Ngan N. Tran, 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. GRNsight reads Microsoft Excel input and output workbooks from GRNmap and automatically displays the model data as a graph. Graph edges are color-coded based on the activation and repression relationships between the transcription factors, and nodes are color-coded with time course gene expression data. The addition of backend gene expression and gene regulatory network databases allows users with no data of their own to generate a network, color the notes with expression data, and export an Excel workbook for modeling in GRNmap. Network data was obtained from the Saccharomyces Genome Database via the Yeastmine search and retrieval interface. A new gene expression dataset from Apweiler et al. (2012) was integrated into the GRNsight database and user interface. Developer documentation for the databases was improved, and the Application Programming Interface (API) and Data Access Layer (DAL) modules were refactored and expanded to improve separation of concerns. In parallel, the ongoing development of GRNsight is focused on fixing bugs and adding enhancements to the user interface and graph layout. GRNsight is freely available at http://dondi.github.io/GRNsight/.

(240 words)