Jen Shin :: LMU Undergraduate Research Symposium Abstract 2018

New Graph Layouts for 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 imports data from an adjacency matrix in either an Excel workbook, SIF, or GraphML file, then 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. Visual issues regarding edge thickness and end markers have been adjusted and test files created. The new GRNsight graph now displays self-regulatory arrows with consistent positions regardless of the node size, edge thickness, or whether it is weighted. The GRNsight layout depends on the force graph engine from D3. We updated GRNsight from D3 version 3 to version 4, allowing the developers to utilize new D3 functionalities. We have implemented block layout where the nodes align into a grid alphabetically by node label. This graph layout feature will allow the users to organize and align the nodes with a simple button interface instead of manually dragging them as before. This will facilitate easier side-by-side comparison of the data from different GRN models. Alternatively, we plan to explore a hierarchical layout option as well. GRNsight is freely available at http://dondi.github.io/GRNsight/; the code is available under the open source BSD license at https://github.com/dondi/GRNsight.

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