CMSI 402 Thesis Abstract (Eileen Choe)

Extending the Visualization Capabilties of GRNsight: a web application for visualizing models of gene regulatory networks

GRNsight is a web application and service for visualizing small- to medium-scale gene regulatory networks (GRNs). A GRN consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. GRNsight produces weighted or unweighted network graphs by representing genes as nodes and regulatory connections as edges, with colors, end markers, and thicknesses corresponding to the sign and magnitude of activation or repression. GRNsight was originally designed to accept Excel workbooks seamlessly from GRNmap, a MATLAB GRN modeling program, and lay out the network graph specified by an adjacency matrix contained within a worksheet named “network” or “network_optimized_weights.” However, the GRNmap output contains additional worksheets, which include temporal gene expression data and the results of the GRNmap forward simulation. In GRNsight v3, the Excel spreadsheet importer will be redesigned to read and store data from the entire GRNmap output workbook as a first step towards extending the visualization capabilities of GRNsight. Using the extended capabilities of the importer, a framework will be developed to visualize the gene expression over time, through coloring the nodes in the network graph. The node coloring feature provides a more complete visual representation of the GRN, allowing GRNsight users to better derive insights from the data that model these networks. The GRNsight application http://dondi.github.io/GRNsight/ and code https://github.com/dondi/GRNsight are available under the open source BSD license.

(231 words)