Publication Date:
2015-08-07
Description:
The Regression Network plugin for Cytoscape ( RegNetC ) implements the RegNet algorithm for the inference of transcriptional association network from gene expression profiles. This algorithm is a model tree-based method to detect the relationship between each gene and the remaining genes simultaneously instead of analyzing individually each pair of genes as correlation-based methods do. Model trees are a very useful technique to estimate the gene expression value by regression models and favours localized similarities over more global similarity, which is one of the major drawbacks of correlation-based methods. Here, we present an integrated software suite, named RegNetC , as a Cytoscape plugin that can operate on its own as well. RegNetC facilitates, according to user-defined parameters, the resulted transcriptional gene association network in .sif format for visualization, analysis and interoperates with other Cytoscape plugins, which can be exported for publication figures. In addition to the network, the RegNetC plugin also provides the quantitative relationships between genes expression values of those genes involved in the inferred network, i.e., those defined by the regression models.
Print ISSN:
1545-5963
Electronic ISSN:
1557-9964
Topics:
Biology
,
Computer Science
Published by
Institute of Electrical and Electronics Engineers (IEEE)
on behalf of
The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
