Construction the first gene co-expression-based interactome in cattle

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

doi:10.7287/peerj.preprints.3178v1

Construction the first gene co-expression-based interactome in cattle

Yan Chen¹, Yining Liu², Min Du³, Wengang Zhang¹, Xue Gao¹, Lupei Zhang¹, Huijiang Gao¹, Lingyang Xu¹, Junya Li ¹, Min Zhao ⁴

1 Innovation Team of Cattle Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China

2 The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China

3 Department of Animal Science, Washington State University, Pullman, USA

4 School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia

DOI: 10.7287/peerj.preprints.3178v1

Published: 2017-08-22
Accepted: 2017-08-22

Subject Areas: Agricultural Science, Genetics, Genomics
Keywords: Co-expression, WGCNA, network, systems biology, functional enrichment, cattle

Copyright: © 2017 Chen et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.

Cite this article: Chen Y, Liu Y, Du M, Zhang W, Gao X, Zhang L, Gao H, Xu L, Li J, Zhao M. 2017. Construction the first gene co-expression-based interactome in cattle. PeerJ Preprints 5:e3178v1 https://doi.org/10.7287/peerj.preprints.3178v1

Abstract

Integrating genomic information into cattle breeding is an important approach to exploring the molecular mechanism 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 genotype-phenotype relationships. To this end we constructed a co-expression analysis of 92 tissues and this represents the first systematic exploration of gene-gene relationship in cattle. By using robust WGCNA (Weighted Gene Correlation Network Analysis), we described the gene co-expression network of 13,405 protein-coding genes from the cattle genome. Using the 5,000 genes with majority variations in expression across 92 tissues, we compiled a network with 72,306 co-associations and that provides functional insights into thousands of poorly characterized proteins. 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 cattle. 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 cattle genome.