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 coexpression analysis of 92 tissues and this represents the systematic exploration of genegene relationship in Bos taurus. By using robust WGCNA (Weighted Gene Correlation Network Analysis), we described the gene co-expression network of 5000 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 coexpression 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.PeerJ reviewing PDF | Manuscript to be reviewed 18 Abstract 19 Integrating genomic information into cattle breeding is an important approach to exploring 20 genotype-phenotype relationships for complex traits related to diary and meat production. To 21 assist with genomic-based selection, a reference map of interactome is needed to fully 22 understand and identify the functional relevant genes. To this end, we constructed a co-23 expression analysis of 92 tissues and this represents the systematic exploration of gene-gene 24 relationship in Bos taurus. By using robust WGCNA (Weighted Gene Correlation Network 25 Analysis), we described the gene co-expression network of 5000 protein-coding genes with 26 majority variations in expression across 92 tissues. The compiled network contained 72,306 co-27 expression gene pairs and provided functional insights into thousands of poorly characterized 28 proteins. Further module identifications found 55 highly organized functional clusters 29 representing diverse cellular activities. To demonstrate the re-use of our interaction for 30 functional genomics analysis, we extracted a sub-network associated with DNA binding genes in 31 Bos taurus. The subnetwork was enriched within regulation of transcription from RNA 32 polymerase II promoter representing central cellular functions. In addition, we identified 28 33 novel linker genes associated with more than 100 DNA binding genes. Our WGCNA-based co-34 expression network reconstruction will be a valuable resource for exploring the molecular 35 mechanisms of incompletely characterized proteins and for elucidating larger-s...