CytoCave: An Interactive Visualization Tool for Exploring Protein and Drug Interaction Networks

Abstract

CytoCave is an immersive interactive online visualization platform based on the NeuroCave connectome visualization application, but modified and optimized for general -omics network visual- ization. CytoCave leverages existing features of NeuroCave, in- cluding the side-by-side viewports designed for freeform explo- ration of node-link diagrams under various transformations or co- ordinate system embeddings, as well its immersive capabili- ties. However, CytoCave introduces a range of new features that facilitate the exploration of multi-omics networks using di- mensionality reduction projections of high-dimensional biological data with cluster membership highlighting, and includes scalabil- ity upgrades to support visualizing and interacting with large scale proteomics and multi-omics datasets. The CytoCave project source code, which includes the web application JavaScript and the data processing pipeline Jupyter notebook, is available on GitHub at https://github.com/iMammal/CytoCave. In this paper, we describe how to use CytoCave to facilitate the following proteomics and drug discovery tasks. CytoCave enables users: (Task 1) to select a protein and analyze drugs that target them, or, similarly, (Task 2) to select a drug and visualize the proteins that are strongly associated with the drug response. Additionally, CytoCave re-designs the traditional 2D force-directed layout visu- alization of protein interaction networks, providing an interactive interface that allows users to pan, rotate, and zoom in and out of the network, and to switch layouts and color coding templates from a variety of pre-calculated options, with optional pop-up annotations on mouse hovers and edge display / edge hiding on mouse clicks.