Presentation Title

GRNsight v2: a web application for visualizing models of gene regulatory networks

Faculty Mentor

John David N. Dionisio, Kam D. Dahlquist

Start Date

18-11-2017 9:30 AM

End Date

18-11-2017 9:45 AM

Location

9-247

Session

Engineering/CS 3

Type of Presentation

Oral Talk

Subject Area

engineering_computer_science

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 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. After GRNsight v1’s release, feedback from users motivated improvements and new features. In GRNsight v2, the graph bounding box is separated from the viewport and expands as far as required for the graph to converge to a steady state, allowing the force graph parameters to be fully applied. The ability to zoom and scroll the graph within the viewport was also added. New analysis features include options for showing edge weight values, customizing the edge thickness normalization factor, and setting the threshold for coloring the edges gray. The addition of features in GRNsight v2 increased the number of possible combinations of functions a user can perform on GRNsight. Thus, we developed an automatic client-side test generator which produces a systematic testing manual. On the server side, syntactic tests for malformed Simple Interaction Format (.sif) files were written, which report end user-targeted errors if an incorrectly formatted SIF file is imported into GRNsight. Future work includes developing a framework to visualize the gene expression over time through coloring the nodes in the network graph. The node coloring feature coupled with the visual and analysis features in GRNsight v2 will provide a more complete visual representation of the GRN, allowing GRNsight users to better derive insights from them. 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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Nov 18th, 9:30 AM Nov 18th, 9:45 AM

GRNsight v2: a web application for visualizing models of gene regulatory networks

9-247

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. After GRNsight v1’s release, feedback from users motivated improvements and new features. In GRNsight v2, the graph bounding box is separated from the viewport and expands as far as required for the graph to converge to a steady state, allowing the force graph parameters to be fully applied. The ability to zoom and scroll the graph within the viewport was also added. New analysis features include options for showing edge weight values, customizing the edge thickness normalization factor, and setting the threshold for coloring the edges gray. The addition of features in GRNsight v2 increased the number of possible combinations of functions a user can perform on GRNsight. Thus, we developed an automatic client-side test generator which produces a systematic testing manual. On the server side, syntactic tests for malformed Simple Interaction Format (.sif) files were written, which report end user-targeted errors if an incorrectly formatted SIF file is imported into GRNsight. Future work includes developing a framework to visualize the gene expression over time through coloring the nodes in the network graph. The node coloring feature coupled with the visual and analysis features in GRNsight v2 will provide a more complete visual representation of the GRN, allowing GRNsight users to better derive insights from them. The GRNsight application http://dondi.github.io/GRNsight/ and code https://github.com/dondi/GRNsight are available under the open source BSD license.