Prerequisites

• You will need Windows (98 or later version).
• Instllation of R is required for creating and visualizing the gaphical images of the outputs. It is not required if you perform only the numerical analysis (precompiled binary of TRANS-MNET).

Download

• TRANS-MNET (15-Mrach 2007)
• R (CRAN)

File Descriptions

• Make sure the following files are all right installed:
• • TRANS-MNET-EM.exe (Precompiled binary for the parameter estimation of the state space model)
  • TRANS-MNET-ModuleFinder.exe (Precompiled binary for module identification)
  • TRANS-MNET-GNET.exe (Precompiled binary for computing gene-gene interactions)
  • data.txt (Tab-delimed read data file)
  • TRANS-MNET.set (Input option parameters for excecution of TRANS-MNET)
  • Set of R scripts for graphical display
    • module_display.r (Heatmaps of gene expression patterns corresponding to the identified transcriptional modules)
    • gnet.r (Heatmap of the estimated temporal connectivities between the representative genes for the identified transcriptional modules)
    • gnet_graph.r (R function to visualize the gene networks of the user-specified genes)