Bao Weier, Greenwold Matthew J, Sawyer Roger H
Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
Funct Integr Genomics. 2017 Nov;17(6):641-651. doi: 10.1007/s10142-017-0561-0. Epub 2017 May 5.
Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis. Significant enrichment annotations were discovered from customized enrichment tools such as Modular Single-Set Enrichment Test (MSET) and Medical Subject Headings (MeSH). Hub genes in both trait-correlated modules showed strong specific functional enrichment toward epidermal development. Also, regulatory elements, such as transcription factors and miRNAs, were targeted in the significant enrichment result. This work highlights the advantage of this methodology for functional prediction of genes not previously associated with scale- and feather trait-related modules.
基因共表达网络分析是一种广泛用于系统探索基因功能和相互作用的研究方法。利用加权基因共表达网络分析（WGCNA）方法，通过鸡胚胎表皮定制44K微阵列转录组数据构建基因共表达网络，我们鉴定出两个与鳞片或羽毛发育性状高度相关的不同模块。在传统的KEGG通路分析中，与羽毛发育相关的信号通路得到富集，在基因本体分析中，与胚胎表皮发育特异性相关的功能术语也得到富集。从定制的富集工具如模块化单集富集测试（MSET）和医学主题词表（MeSH）中发现了显著的富集注释。两个与性状相关模块中的枢纽基因对表皮发育表现出强烈的特定功能富集。此外，转录因子和miRNA等调控元件也在显著富集结果中被靶向。这项工作突出了该方法在预测先前与鳞片和羽毛性状相关模块无关的基因功能方面的优势。
