NDLI: Building transcriptional association networks in cytoscape with $\textit{RegNetC}$

Content Provider	ACM Digital Library
Author	Nepomuceno-chamorro, Isabel A. Aguilar-ruiz, Jesus S. Marquez-chamorro, Alfonso
Copyright Year	2015
Description	Author Affiliation: Universidad de Sevilla, Spain(Aguilar-ruiz, Jesus S.; Pablo de olavide university, Seville, Spain (Marquez-Chamorro, Alfonso; Nepomuceno-chamorro, Isabel A.))
Abstract	The Regression Network plugin for Cytoscape $(\textit{RegNetC})$ 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 $\textit{RegNetC},$ as a Cytoscape plugin that can operate on its own as well. $\textit{RegNetC}$ 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 $\textit{RegNetC}$ 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.
Starting Page	823
Ending Page	824
Page Count	2
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2014.2385702
Volume Number	12
Issue Number	4
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2015-07-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Gene expression profiles Linear regression Model tree Systems biology Transcriptional association networks
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Building Transcriptional Association Networks in Cytoscape with RegNetC

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Identification of Gene Networks with Time Delayed Regulation Based on Temporal Expression Profiles

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Building transcriptional association networks in cytoscape with $\textit{RegNetC}$

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