CyNetworkBMA: A Cytoscape App for Inferring Gene Regulatory Networks

Inference of gene networks from expression data is an important problem in computational biology. Many algorithms have been proposed for solving the problem efficiently. However, many of the available implementations are programming libraries that require users to write code, which limits their accessibility

Additinal file 3

Generated edge list. The CyNetworkBMA output consisting of a list of edges and their probabilities that represent a gene network generated from the example DREAM4 input data set (available as Additional file 2). This output file corresponding to Additional file 3 is a text file consisting of three columns: parent, child, posterior probabilities. Each line represents a directed edge from parent node to child node with the posterior probability in the third column. We provide this file so that the user can verify the examples shown in this manuscript. (CSV 345 kb

Additinal file 1

User Manual. This document provides screen shots and step-by-step guide for installing and using CyNetworkBMA. (PDF 157 kb

CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks

BACKGROUND: Inference of gene networks from expression data is an important problem in computational biology. Many algorithms have been proposed for solving the problem efficiently. However, many of the available implementations are programming libraries that require users to write code, which limits their accessibility. RESULTS: We have developed a tool called CyNetworkBMA for inferring gene networks from expression data that integrates with Cytoscape. Our application offers a graphical user interface for networkBMA, an efficient implementation of Bayesian Model Averaging methods for network construction. The client-server architecture of CyNetworkBMA makes it possible to distribute or centralize computation depending on user needs. CONCLUSIONS: CyNetworkBMA is an easy-to-use tool that makes network inference accessible to non-programmers through seamless integration with Cytoscape. CyNetworkBMA is available on the Cytoscape App Store at http://apps.cytoscape.org/apps/cynetworkbma. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13029-015-0043-5) contains supplementary material, which is available to authorized users