An Expression Database for Node Coloring on GRNsight: a web application for visualizing models of gene regulatory networks
Date of Completion
5-8-2020
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 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, a MATLAB program that performs parameter estimation and forward simulation of a differential equations model of a GRN, can mathematically model GRNs. Using a GRNmap output workbook, GRNsight automatically visualizes the network as a graph. GRNsight uses the model output to color-code the edges based on the activation and repression relationships between the transcription factors and colors the nodes based on time course gene expression data. We have added a feature to store expression data in a database, so that users of GRNsight can view and interact with already-existing expression data pulled from the Dahlquist lab and other publicly available datasets. The database is hosted by Amazon Web Services (AWS) Relational Database Service (RDS) and uses a PostgreSQL engine, from which GRNsight performs dynamic queries in response to user requests. GRNsight is available at https://dondi.github.io/GRNsight/, and its code can be viewed at https://github.com/dondi/GRNsight.
Recommended Citation
Filler, Alexia; Dionisio, John David N.; and Dahlquist, Kam D., "An Expression Database for Node Coloring on GRNsight: a web application for visualizing models of gene regulatory networks" (2020). Honors Thesis. 403.
https://digitalcommons.lmu.edu/honors-thesis/403
