topological features using cytoscape 3.2.1

#TOPOLOGICAL FEATURES USING CYTOSCAPE 3.2.1 HOW TO#

Maglott D, Ostell J, Pruitt KD, Tatusova T (2006) Entrez Gene: gene-centered information at NCBI. Mol Syst Biol 5:290īader GD, Cary MP, Sander C (2006) Pathguide: a pathway resource list. Key wordsīauer-Mehren A, Furlong LI, Sanz F (2009) Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Each part is illustrated by step-by-step instructions on an example use case and visualized by many screenshots and figures. Finally, we briefly outline how the integrated data can help in building mathematical network models for analyzing the effect of the sequence variation onto the dynamics of the biological system. The chapter is divided into five parts: (1) obtaining information about the functional effect of sequence variation in a Cytoscape readable format, (2) loading and displaying different types of biological networks in Cytoscape, (3) integrating the genomic information (SNPs and mutations) with the biological networks, and (4) analyzing the effect of the genomic perturbation onto the network structure using Cytoscape built-in functions.

#TOPOLOGICAL FEATURES USING CYTOSCAPE 3.2.1 HOW TO#

This chapter explains how to use Cytoscape to analyze the functional effect of sequence variations in the context of biological networks such as protein–protein interaction networks and signaling pathways. Cytoscape is an open-source software for visualizing, analyzing, and modeling biological networks.

Topological features using cytoscape 3.2.1