:: DESCRIPTION
GeneNetStudio is a software package developed for visual reconstruction and analysis of network models of molecular-genetic systems.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GNTInfer aims to combine computational analysis of multiple microarray datasets and biological experiment results together for inferring gene regulatory network and further identifying compound targets of perturbation experiments.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen.
Recovering gene regulation and identifying compound targets by integrating multiple time course expression datasets and prior information.
Manuscript, 2007.
:: DESCRIPTION
TINGe (Tool for Inferring Networks of GEnes) is a parallel and multi-platform framework for reconstructing gene regulatory networks from large gene expression data. It uses parallel processing, information theoretic criteria and statistical testing to derive networks with thousands of genes from microarray sets with thousands of observations. TINGe has been used to reconstruct a whole-genome network of Arabidopsis thaliana from 3,546 microarray measurements, which comprises of 15,495 genes.
GeNA (GEne Networks Analyzer) is a tool that for a given set of “seed” genes uses gene ranking mechanism to extract subnetworks of genes with similar biological function. GeNA uses algorithm akin to the topic-sensitive PageRank and it has been implemented as a stand-alone tool and as a plugin for Cytoscape.
::DEVELOPER
Prof. Srinivas Aluru Research group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Jaroslaw Zola, et al.
Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks
IEEE Transactions on Parallel and Distributed Systems. December 2010 (vol. 21 no. 12) pp. 1721-1733
:: DESCRIPTION
SiGN-SSM is open source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by the statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles.
SiGN-L1 is network estimation software using sparse learning. It uses L1-regularization for simultaneous parameter estimation and model selection of statistical graphical models such as graphical Gaussian models and vector autoregressive models.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tamada, Y., Yamaguchi, R., Imoto, S., Hirose, O., Yoshida, R., Nagasaki, M., and Miyano, S. (2011).
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinformatics. 2011 Apr 15;27(8):1172-3. doi: 10.1093/bioinformatics/btr078.
Genome Inform. 2011;25(1):40-52.
Sign: large-scale gene network estimation environment for high performance computing.
Tamada Y, Shimamura T, Yamaguchi R, Imoto S, Nagasaki M, Miyano S.
:: DESCRIPTION
BUS can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).
::DEVELOPER
Group of Clinical Genomic Networks
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GFD-Net is a Cytoscape app designed to visualize and analyze the functional dissimilarity of gene networks. GFD-Net can analyze a gene network based on Gene Ontology (GO) and calculate a quantitative measure of its functional dissimilarity, i.e. a quantitative value of the degree of dissimilarity between the connected genes in it.
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:: MORE INFORMATION
Citation
F1000Res. 2014 Jul 1;3:142. doi: 10.12688/f1000research.4573.1. eCollection 2014.
Development and use of the Cytoscape app GFD-Net for measuring semantic dissimilarity of gene networks.
Diaz-Montana JJ, Diaz-Diaz N
:: DESCRIPTION
GeneNetVal is a Java application for network analysis. The application uses the metabolic pathways stored in kegg to rate the validity of an input network.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
ScientificWorldJournal. 2014;2014:540679. doi: 10.1155/2014/540679. Epub 2014 Sep 8.
Gene network biological validity based on gene-gene interaction relevance.
Gómez-Vela F, Díaz-Díaz N.
:: DESCRIPTION
GNC is a Java-based software tool for analyzing gene networks coherence using direct and indirect relationships.
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N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Gene network coherence based on prior knowledge using direct and indirect relationships.
Gómez-Vela F, Lagares JA, Díaz-Díaz N.
Comput Biol Chem. 2015 Jun;56:142-51. doi: 10.1016/j.compbiolchem.2015.03.002.
:: DESCRIPTION
FuseNet is a Markov network formulation that infers networks from a collection of nonidentically distributed datasets.
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N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gene network inference by fusing data from diverse distributions.
Žitnik M, Zupan B.
Bioinformatics. 2015 Jun 15;31(12):i230-i239. doi: 10.1093/bioinformatics/btv258.
:: DESCRIPTION
Red is a conceptually new probabilistic approach to gene network inference from quantitative interaction data
::DEVELOPER
BioLab , University of Ljubljana
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Jun 15;30(12):i246-i254. doi: 10.1093/bioinformatics/btu287.
Gene network inference by probabilistic scoring of relationships from a factorized model of interactions.
Zitnik M1, Župan B2.
