Files and links (2)
Preprint VersionCC BY V4.0, Open Access
Preprint
Construction the first gene co-expression-based interactome in cattle
PeerJ Preprints, Vol.5, e3178v1
PeerJ, Ltd.
2017
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.
Details
- Title
- Construction the first gene co-expression-based interactome in cattle
- Authors
- Yan Chen (Author) - Chinese Academy of Agricultural Science, ChinaYining Liu (Author) - Guangzhou Medical University, ChinaMin Du (Author) - Washington State University, United StatesWengang Zhang (Author) - Chinese Academy of Agricultural Science, ChinaXue Gao (Author) - Chinese Academy of Agricultural Science, ChinaLupei Zhang (Author) - Chinese Academy of Agricultural Science, ChinaHuijang Gao (Author) - Chinese Academy of Agricultural Science, ChinaLingyang Xu (Author) - Chinese Academy of Agricultural Science, ChinaJunya Li (Author) - Chinese Academy of Agricultural Science, ChinaMin Zhao (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
- Publication details
- PeerJ Preprints, Vol.5, e3178v1
- Publisher
- PeerJ, Ltd.
- Date published
- 2017
- DOI
- 10.7287/peerj.preprints.3178v1
- ISSN
- 2167-9843
- Copyright note
- Copyright © 2017 Chen et al. 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.
- Organisation Unit
- School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; GeneCology Research Centre - Legacy; School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99451135002621
- Output Type
- Preprint
Metrics
115 File views/ downloads
978 Record Views