Application of Weighted Gene Co-expression Network Analysis for Data from Paired Design
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Date
2018
Author(s)
Li, Jianqiang
Zhou, Doudou
Shi, Yuliang
Yang, Ji-Jiang
Chen, Shi
Wang, Qing
Pan, Hui
Publisher
Nature Publishing Group UK
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Citation
Li, Jianqiang, Doudou Zhou, Weiliang Qiu, Yuliang Shi, Ji-Jiang Yang, Shi Chen, Qing Wang, and Hui Pan. 2018. “Application of Weighted Gene Co-expression Network Analysis for Data from Paired Design.” Scientific Reports 8 (1): 622. doi:10.1038/s41598-017-18705-z. http://dx.doi.org/10.1038/s41598-017-18705-z.
Abstract
Investigating how genes jointly affect complex human diseases is important, yet challenging. The network approach (e.g., weighted gene co-expression network analysis (WGCNA)) is a powerful tool. However, genomic data usually contain substantial batch effects, which could mask true genomic signals. Paired design is a powerful tool that can reduce batch effects. However, it is currently unclear how to appropriately apply WGCNA to genomic data from paired design. In this paper, we modified the current WGCNA pipeline to analyse high-throughput genomic data from paired design. We illustrated the modified WGCNA pipeline by analysing the miRNA dataset provided by Shiah et al. (2014), which contains forty oral squamous cell carcinoma (OSCC) specimens and their matched non-tumourous epithelial counterparts. OSCC is the sixth most common cancer worldwide. The modified WGCNA pipeline identified two sets of novel miRNAs associated with OSCC, in addition to the existing miRNAs reported by Shiah et al. (2014). Thus, this work will be of great interest to readers of various scientific disciplines, in particular, genetic and genomic scientists as well as medical scientists working on cancer.
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