Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis

  • Jiang, Nan (Interdisciplinary Program in Bioinformatics, Seoul National University) ;
  • Lee, Sungyoung (Center for Precision Medicine, Seoul National University Hospital) ;
  • Park, Taesung (Interdisciplinary Program in Bioinformatics, Seoul National University)
  • Received : 2020.02.28
  • Accepted : 2020.03.11
  • Published : 2020.03.31
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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.

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References

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