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PeerJ. 2017 Dec 4;5:e4107. doi: 10.7717/peerj.4107. eCollection 2017.

Constructing a comprehensive gene co-expression based interactome in Bos taurus.

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Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China.
Department of Animal Science, Washington State University, Pullman, WA, United States of America.
School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia.


Integrating genomic information into cattle breeding is an important approach to exploring genotype-phenotype relationships for complex traits related to diary and meat production. To assist with genomic-based selection, a reference map of interactome is needed to fully understand and identify the functional relevant genes. To this end, we constructed a co-expression analysis of 92 tissues and this represents the systematic exploration of gene-gene relationship in Bos taurus. By using robust WGCNA (Weighted Gene Correlation Network Analysis), we described the gene co-expression network of 5,000 protein-coding genes with majority variations in expression across 92 tissues. Further module identifications found 55 highly organized functional clusters representing diverse cellular activities. To demonstrate the re-use of our interaction for functional genomics analysis, we extracted a sub-network associated with DNA binding genes in Bos taurus. The subnetwork was enriched within regulation of transcription from RNA polymerase II promoter representing central cellular functions. In addition, we identified 28 novel linker genes associated with more than 100 DNA binding genes. Our WGCNA-based co-expression network reconstruction will be a valuable resource for exploring the molecular mechanisms of incompletely characterized proteins and for elucidating larger-scale patterns of functional modulization in the Bos taurus genome.


Bos taurus; Co-expression; Functional enrichment; Network; Systems biology; WGCNA

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