Reconstruction of Gene Regulatory Networks using Seed Genes

By Selecting Reconstruction Method and Pressing Generate Button, the Corresponding Reconstruction Networks are Generated:
Please Select At Least One Reconstruction Method to Procede.

Mutual Information Reconstruction Methods:
CLR:Context Likelihood or Relatedness Network Reconstruction Algorithm.
Sales, G., Romualdi, C. (2011) Parmigene-a parallel R package for mutual information estimation and gene network reconstruction. Bioinformatics, 27 (13), art. no. btr274, pp. 1876-1877.

ARACNE.M:Reconstruction of Accurate Cellular Networks (Multiplicative Model).
Sales, G., Romualdi, C. (2011) Parmigene-a parallel R package for mutual information estimation and gene network reconstruction. Bioinformatics, 27 (13), art. no. btr274, pp. 1876-1877.

ARACNE.A:Reconstruction of Accurate Cellular Networks (Additive Model).
Sales, G., Romualdi, C. (2011) Parmigene-a parallel R package for mutual information estimation and gene network reconstruction. Bioinformatics, 27 (13), art. no. btr274, pp. 1876-1877.

MRNET.A:Reconstruction using the Maximum Relevance Minimum Redundancy Method.
Sales, G., Romualdi, C. (2011) Parmigene-a parallel R package for mutual information estimation and gene network reconstruction. Bioinformatics, 27 (13), art. no. btr274, pp. 1876-1877.

MRNET.B:Reconstruction using the Maximum Relevance Minimum Redundancy Method (Backward).
Meyer, P.E., Lafitte, F., Bontempi, G. (2008) Minet: A r/bioconductor package for inferring large transcriptional networks using mutual information. BMC Bioinformatics, 9, art. no. 461.

C3NET:Inferred Reconstruction Network using Mutual Information.
Altay, G., Emmert-Streib, F. (2011) Structural influence of gene networks on their inference: Analysis of C3NET. Biology Direct, 6, art. no. 31.

Correlation Based Reconstruction Methods:
WGCNA:Weighted Correlation Reconstruction Method.
Langfelder, P., Horvath, S. (2008) WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics, 9, art. no. 559.

Regression Reconstruction Methods:
GeneNet:Reconstruction Method using Gaussian Mixture Models.
A. Werhli, M. Grzegorczyk, and D. Husmeier (2006) Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical Gaussian models and Bayesian networks. Bioinformatics, 22, 2523�2531.
Zhong R, Allen JD, Xiao G, Xie Y (2014) Ensemble-based network aggregation improves the accuracy of gene network reconstruction. PLoS One, 9, e106319

Processing Data...
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Workspace
Generated Reconstructed Networks
Random Walk Simulated Networks