Development and use of a cytoscape app for GRNCOP2

Abstract

Background and Objective: Gene regulatory networks (GRNs) are essential for understanding most molecular processes. In this context, the so-called model-free approaches have an advantage modeling the complex topologies behind these dynamic molecular networks, since most GRNs are difficult to map correctly by any other mathematical model. Abstract model-free approaches, also known as rule-based extraction methods, offer valuable benefits when performing data-driven analysis; such as requiring the least amount of data and simplifying the inference of large models at a faster analysis speed. In particular, GRNCOP2 is a combinatorial optimization method with an adaptive criterion for the discretization of gene expression data and high performance, in contrast to other rule-based extraction methods for discovering GRNs. However, the analysis of the large relational structures of the networks inferred by GRNCOP2 requires the support of effective tools for interactive network visualization and topological analysis of the extracted associations. This need motivated the possibility of integrating GRNCOP2 in the Cytoscape ecosystem in order to benefit from Cytoscapes core functionality, as well as all the other apps in its ecosystem. Methods: In this paper, we introduce the implementation of a GRNCOP2 Cytoscape app. This incorporation to Cytoscape platform includes new functionality for GRN visualizations, dynamic user-interaction and integration with other apps for topological analysis of the networks. Results: In order to demonstrate the usefulness of integrating GRNCOP2 in Cytoscape, the new app was used to tackle a novel use case for GRNCOP2: the analysis of crosstalk between pathways. In this regard, datasets associated with Alzheimer's disease (AD) were analyzed using GRNCOP2 app and other apps of the Cytoscape ecosystem by performing a topological analysis of the AD progression and its synchronization with the Ubiquitin Mediated Proteolysis pathway. Finally, the biological relevance of the findings achieved by this new app were evaluated by searching for evidence in the literature. Conclusions: The proposed crosstalk analysis with the new GRNCOP2 app focused on assessing the phase of the Alzheimer's disease progression where the coordination with the Ubiquitin Mediated Proteolysis pathway increase, and identifying the genes that explain the signalling between these cellular processes. Both questions were explored by topological contrastive analysis of the GRNs generated for the GRNCOP2 app, where several facilities of Cytoscape were exploited. The topological patterns inferred by this new App have been consistent with biological evidence reported in the scientic literature, illustrating the effectiveness of using this new GRNCOP2 App in pathway analysis.