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

Date of Completion

5-2-2018

Degree Type

Honors Thesis

Discipline

Computer Science (CMSI)

First Advisor

John David N. Dionisio

Second Advisor

Kam Dahlquist

Abstract

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 control 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 is designed to accept Excel workbooks from GRNmap, a MATLAB GRN modeling program, and lay out the network graph specified by an adjacency matrix contained within one of the worksheets. However, the GRNmap output contains additional worksheets which store data about the GRN and results of the GRNmap simulations that have not been displayed or visualized by GRNsight. To address this, in GRNsight v3, the Excel spreadsheet importer has been redesigned to parse and store data from the entire GRNmap output workbook in a standardized JavaScript Object Notation (JSON) data structure. The complete data extraction from the GRNsight output includes experimental and simulated temporal expression data for each gene in the network. A coloring framework has been developed to visualize this expression data in the form of a stacked heat map overlay of the nodes which compares the experimental and simulated gene expression levels. Node coloring allows 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.

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