Genomics Inform.  2020 Mar;18(1):e11. 10.5808/GI.2020.18.1.e11.

HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis

• Jiang N
• Lee S
• Park T

• KMID: 2501331
• DOI: http://doi.org/10.5808/GI.2020.18.1.e11

Abstract

In genome-wide association studies, pathway-based analysis has been widely performed to enhance interpretation of single-nucleotide polymorphism association results. We proposed a novel method of hierarchical structural component model (HisCoM) for pathway analysis of common variants (HisCoM for pathway analysis of common variants [HisCoM-PCA]) which was used to identify pathways associated with traits. HisCoM-PCA is based on principal component analysis (PCA) for dimensional reduction of single nucleotide polymorphisms in each gene, and the HisCoM for pathway analysis. In this study, we developed a HisCoM-PCA software for the hierarchical pathway analysis of common variants. HisCoM-PCA software has several features. Various principle component scores selection criteria in PCA step can be specified by users who want to summarize common variants at each gene-level by different threshold values. In addition, multiple public pathway databases and customized pathway information can be used to perform pathway analysis. We expect that HisCoM-PCA software will be useful for users to perform powerful pathway analysis.

Keyword

genome-wide association study; hierarchical structural component model; pathway analysis; principal component analysis