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

Yan Chen,Lupei Zhang,Lingyang Xu,Yining Liu,Huijiang Gao,Xue Gao,Min Zhao,Ling Xu,Min Du,Junya Li,Wengang Zhang

doi:10.7717/peerj.4107

Abstract

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.

Highlights

As the importance in dairy and beef production, the genome of the domestic cattle, Bos taurus, was sequenced in 2009 using hierarchical and whole-genome shotgun sequencing strategy (Zimin et al, 2009)
To demonstrate our reconstructed interactome could provide a new approach for network-based data mining of cattle genetics data, we focused on the DNA-binding genes in Bos taurus and extracted a DNA-binding regulatory network
To characterized the gene expression in multiple tissues, we chose the gene expression dataset based on the criteria: (i) it covered the most comprehensive tissue types for Bos taurus; (ii) it was based on next-generation sequencing, which is more accurate than array-based quantification; (iii) it was generated in consistent and high-quality way

Summary

Introduction

As the importance in dairy and beef production, the genome of the domestic cattle, Bos taurus, was sequenced in 2009 using hierarchical and whole-genome shotgun sequencing strategy (Zimin et al, 2009). How to cite this article Chen et al (2017), Constructing a comprehensive gene co-expression based interactome in Bos taurus. Most of production traits are complex traits involving multiple genes. The recent development of systems biology-based approach was promising to explore the genome and gene-gene interactions in a global view to understand molecular mechanisms underlying complex traits (Zhao, Kong & Qu, 2014)

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