Networks offer reasonable means of describing complex life systems. Here, we generate a first-generation multi-omics integrative network map of maize, which contains over 15 million edges for more than 1000 functional modules, covering the whole genetic transmission from genome, to transcriptome, to translatome, and to proteome. The first-generation multi-omics integrative network map integrates genomic interactions by ChIA-PET, transcriptomic co-expression networks by mRNA-seq, circRNA-seq, and small RNA-seq across root, leaf, tassel, SAM and other 31 tissues or developmental stages , translatomic co-expression networks by Ribo-seq across 21 different tissues/stages, and protein-protein interactions by high-throughput Yeast-2-hybridyzation across 8 distinct tissues for the maize reference inbred line B73. The first-generation multi-omics network map can trace the functional divergence of functional elements originated from different evolutionary time-points and classify distinct functional coherent sets of molecular interactions and potential pathway modules, indicative of evolutionary and biological senses. It can help to assist mutant/QTL cloning, and systematically dissect possible molecular mechanisms conferring agronomic important traits. Totally, it paves the way for rapid gene cloning and network analyses efficiently.

Feng JW, Han L, Liu H, et al. MaizeNetome: A multi-omics network database for functional genomics in maize. Mol Plant. 2023;16(8):1229-1231. doi:10.1016/j.molp.2023.08.002
Han, L., Zhong, W., Qian, J. et al. A multi-omics integrative network map of maize. Nat Genet 55, 144–153 (2023). doi:10.1038/s41588-022-01262-1

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QTG Interaction Score

Pathway Mapping

Interactome Network Summary Information

Node numbers
Edge numbers
Average distance
Modules(>=5 genes)
Interactome High confidence 15,476 56,243 4.110 1,147
Interactome Low confidence 18,304 367,868 2.906 680
Co-translation Network 17,835 1,355,426 2.906 680
Slim Co-expression Network 18,607 1,862,532 5.232 603
Co-expression Network 33,389 14,248,262 3.724 985
3D Network 13,142 14,788 27.09 689
Slim Integrative Omics High confidence 27,875 2,849,794 3.411 1,412
Slim Integrative Omics Low confidence 30,966 3,157,473 2.915 780
Integrative Omics High confidence 35,338 14,793,658 3.009 1,082
Integrative Omics Low confidence 37,116 15,088,758 2.773 933