HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis
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 pat...
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| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2020-03-01
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| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gi-2020-18-1-e11.pdf |
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| Summary: | 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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| ISSN: | 2234-0742 |