Data Science Research Seminar

Schedule

12.00 - 12.30 hrs

Talk: DynOVis: a new tool to visualize dynamic perturbations of biological networks after toxic exposure
by T.J.M. Kuijpers, J.C.S. Kleinjans, and D.G.J. Jennen
Department of Toxicogenomics, Maastricht University

12.30 - 13.00 hrs

Discussion: Current approaches and challenges in the integration of mulitple omics data sets

Abstract Talk

Introduction

The development of high throughput sequencing techniques provides us with the possibilities to obtain large datasets, which capture the effect of toxic dose and time on cellular processes. However, because of the
dynamic nature of these cellular processes, the analysis of the results is challenging. Therefore there is a great need for new bioinformatics tools that address this problem.
Here, we present a new visualization tool that provides dynamic network visualization.

Method

DynOVis is an integrated work frame of R packages and JavaScript libraries, and is made freely available using the R shiny package. The tool is designed as a web based application and can be used locally or hosted on a remote server. This makes it easy for users to run the application on their laptop.
DynOVis offers a force-directed graph network style, involving multiple network analysis methods, but more importantly, it allows for node expression animations as well as a frame-by-frame view of the dynamic exposure.
Valuable biological information can be highlighted on the nodes in the network, by the integration of various databases within DynOVis. This information includes pathway-to-gene associations from ConsensusPathDB, disease-to-gene associations from the Comparative Toxicogenomics databases, as well as Entrez gene ID, gene symbol, gene synonyms and gene type from the NCBI database.

Results

DynOVis offers a tool for the visualization of dynamic changes that occur in biological networks which increases the understanding of the cellular response to perturbations. The animation and frame-by-frame view enable the user to investigate the effect of changes in the network across time and to identify important nodes. This is an important step forward for unravelling the effect of dynamic changes in biological systems.

Practicalities

Lunch will be provided during this event. That is why it is important for us to know the number of participants hence the request to register upfront.

To register, please fill in the form.