GENIE3 – Inference of Gene Regulatory Networks from Expression data

GENIE3

:: DESCRIPTION

GENIE3 is an algorithm for the inference of gene regulatory networks from expression data. It decomposes the prediction of a regulatory network between p genes into p different regression problems. In each of the regression problems, the expression pattern of one of the genes (target gene) is predicted from the expression patterns of all the other genes (input genes), using tree-based ensemble methods Random Forests or Extra-Trees. The importance of an input gene in the prediction of the target gene expression pattern is taken as an indication of a putative regulatory link.

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dynGENIE3 : Extension of GENIE3 for time series data

::DEVELOPER

vân anh huynh-thu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • MatLab / R Package

:: DOWNLOAD

 GENIE3 / dynGENIE3

:: MORE INFORMATION

Citation

Huynh-Thu VA, Geurts P.
dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data.
Sci Rep. 2018 Feb 21;8(1):3384. doi: 10.1038/s41598-018-21715-0. PMID: 29467401; PMCID: PMC5821733.

Inferring regulatory networks from expression data using tree-based methods
Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., and Geurts, P.
PLoS ONE, 5(9):e12776, 2010.