MaizeGGM Network

MaizeGGM gene network

MaizeGGM is a gene network for maize functional genomics studies. It was constructed using the graphical Gaussian modle (GGM), based on large scaled RNA-Seq data. The network contains 20,269 genes that assemble into 964 gene modules. These modules function in an array of maize development, nutrients uptake & utilization, metabolism, stress response, and cellular organization processes.The detailed information of this network are provided in this web-page, as listed below.

  • The MaizeGGM2016 program

  • (click here to download the program)
    This program, written in R, can be used to extract the gene modules' information from the MaizeGGM network. The program's major functions are: (A). Extracting sub-networks for genes of a specific module or for genes connected with a gene of interest. The extracted sub-networks can then be visualized to see how genes interact with each other. (B). Generating heatmaps for selected gene modules, showing their genes's tissues-specific expression patterns.

  • Bulk files containing the network's information for downloading

    • All the co-expressed gene pairs contained within the network

    • A table listing all the genes within the network, their module identities, and the GO analysis results for all the modules

    • The heatmaps for all the modules, showing their tissues-specific expression patterns

    • The SIF files for all the gene modules which can be opened in Cytoscape to generation graph visualization



The MaizeGGM gene network and the MaizeGGM program are free for academic usage. For commercial usage, please contact Dr. Shisong Ma.

Please cite this paper if you use the information the MaizeGGM program in your publication.

Ma S*, Ding Z, Li P*. 2017. Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. BMC Plant Biology 17:131. (*corresponding author)