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With the rapid accumulation of gene expression data, gene functional module identification has become a widely used approach in functional analysis. However, tools to identify organelle functional modules and analyze their relationships are still missing. We present a soft thresholding approach to construct networks of functional modules using gene expression datasets, in which nodes are strongly co-expressed genes that encode proteins residing in the same subcellular localization, and links represent strong inter-module connections. Our algorithm has three steps. First, we identify functional modules by analyzing gene expression data. Next, we use a self-adaptive approach to construct a mixed network of functional modules and genes. Finally, we link functional modules that are tightly connected in the mixed network. Analysis of experimental data from Arabidopsis demonstrates that our approach is effective in improving the interpretability of high-throughput transcriptomic data and inferring function of unknown genes.

Constructing Networks of Organelle Functional Modules in Arabidopsis