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 MaizeGGM program (Click here to download)

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’ tissues-specific expression patterns.

Some examples.

  • Detailed information for every module within the network

For each module, a web-page was created to show the module’s detailed information, including the list of gene within the module, Gene Ontology enrichment analysis results, developmental heatmap, and a gene sub-network extracted for the module, etc.

Here are some example of the modules (click the links to reach their web-pages).

For examples, Module #16,
Module #XX, for …
Module #XX, for …
Or the Module # 1 – 100,

To reach other modules, use the buttons and links below:

101 – 200, 201 – 300, 301 – 400, 401 – 500, 501 – 600, 601 – 700, 701 – 800, 801 – 900, 901 – 964

  • Bulk files containing the networks’ 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

 

Note:

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.

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