Maize Interactome

Overview

Networks offer a reasonable means of describing complex life systems. Here, we generate a first-generation interactome of maize , a first-generation functional genome, which contains over 6 million edges for more than 4000 functional modules, covering the whole genetic transmission from genome, to transcriptome, to translatome, and to proteome. The first-generation interactome integrates genomic interactions by ChIA-PET, transcriptomic co-expression networks by mRNA-seq, lncRNA-seq, circRNA-seq, and small RNA-seq across root, leaf, tassel, SAM and other tissues or developmental stages (totally 26 different tissues/stages), translatomic co-expression networks by Ribo-seq across 20 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 interactome can trace the functional divergence of functional elements originated from different evolutionary time-points and classify distinct functional coherent sets of molecular interactions and pathway modules, indicative of evolutionary and biological senses. It can help to dig out the key genes from a subset of differentially expressed genes, assist mutant/QTL cloning, and systematically dissect the molecular mechanisms conferring the agronomic important traits. Importantly, this database presented here integrates state-of-the-art technologies such as machine-learning, network comparison for the network Big-Data mining. This interactome resource database paves the way for the complete era of functional genomics and offers an unprecedented chance for rapid gene cloning and network analyses.

Maize EMS induced Mutant Database (MEMD) is strongly recommended for the functional validation of genes, which are functionally predicted and systematically dissected for the molecular networks by the interactome big data.

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Differential Gene Network

QTG Interaction Score

Trait Decoder

Pathway Mapping

Interactome Network Summary Information

Network
Node numbers
Edge numbers
Average distance
Modules(>=5 genes)
PPI Network High confidence 18,305 87,775 3.953 1,285
PPI Network Middle confidence 24,106 301,210 3.018 815
PPI Network Low confidence 25,155 367,868 2.906 680
Translatome Network High confidence 23,646 68,972 7.77 1,485
Translatome Network Middle confidence 24,313 187,649 5.218 1,341
Translatome Network Low confidence 24,341 309,758 4.51 1,090
Transcriptome Network High confidence 178,025 2,944,080 6.316 5,998
Transcriptome Network Middle confidence 179,157 6,097,526 5.1 2,985
Transcriptome Network Low confidence 179,255 9,328,238 4.566 1,733
Slim-Transcriptome Network High confidence 23,542 121,761 5.59 1,263
Slim-Transcriptome Network Middle confidence 24,293 271,520 4.299 971
Slim-Transcriptome Network Low confidence 24,375 430,303 3.846 645
Transcriptome without siRNAs Network High confidence 33,107 150,873 5.786 1,816
Transcriptome without siRNAs Network Middle confidence 34,994 341,966 4.398 1,335
Transcriptome without siRNAs Network Low confidence 35,207 545,956 3.896 912
3D Network 13,142 14,788 27.09 689
Integrative Omics Network High confidence 182,995 3,111,490 6.105 11,490
Integrative Omics Network Middle confidence 185,401 6,585,263 4.937 7,351
Integrative Omics Network Low confidence 185,868 9,989,038 4.451 5,203
Slim-Integrative Omics Network High confidence 28,878 290,539 3.812 7,299
Slim-Integrative Omics Network Middle confidence 30,580 764,689 3.002 8,650
Slim-Integrative Omics Network Low confidence 30,988 101,613 2.855 8,965
Integrative Omics without siRNAs Network High confidence 38,556 320,015 4.226 2,829
Integrative Omics without siRNAs Network Middle confidence 41,316 836,470 3.329 2,452
Integrative Omics without siRNAs Network Low confidence 41,834 1,220,001 3.107 2,139