Unveiling crucial genes for maize seed development via highly-interwoven communities of gene regulatory network
Wenwei Xiong, Chunguang Du*
Department of Biology, Montclair State University, Montclair, NJ 07043
Topological properties of genes in the regulatory network often reflect the importance of their roles and contributions. Identifying the most important players in maize seed development can have profound implications in our understanding of the genetic control as well as agriculture. We carried out a data mining approach to tackle this challenge issue by integrating spatial-temporal RNA-Seq profiles, microdissected compartments data of maize seed, and manually curate KEGG pathways. First, based on information theory, we calculated the marginal entropy and joint entropy of every gene and every pair of genes respectively. A mutual information value (MIV) between any two genes were calculated to measure their mutual dependence or causal relationship in terms of gene expression. Z-scores of MIV considering gene context were used to eliminate indirect relationships. Then we studied collective gene interaction patterns and uncovered highly-interwoven network communities as the building blocks of the regulatory network. These communities were created by joining fully connected sub-networks or cliques so that genes within a community interact with almost every other gene in the same community. Well-known genes affecting seed phenotypes like opaque2, shruken1, and zein genes all fall into one community. Another community consisting of unknown genes has a surprisingly high percentage of genes localized in the basal endosperm transfer layer. Our findings not only coincide with reported genes and TF-gene regulations, but also shed lights on mechanisms to the cascade of genetic information flow in maize seed development. We further carried out yeast one-hybrid (Y1H) assay and verified some of our predicted interactions between TFs and genes in our network. In conclusion, this study uncovers genes and functional units as communities dynamically and collaboratively that are crucial to maize seed development.
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