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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BioMed Central
2020-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2020-18-1-e11.pdf |
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| author | Nan Jiang Sungyoung Lee Taesung Park |
| author_facet | Nan Jiang Sungyoung Lee Taesung Park |
| author_sort | Nan Jiang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-c835baefd39a4a1bb3de7549a8eb9bec |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2020-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-c835baefd39a4a1bb3de7549a8eb9bec2025-02-02T08:13:27ZengBioMed CentralGenomics & Informatics2234-07422020-03-0118110.5808/GI.2020.18.1.e11600HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysisNan Jiang0Sungyoung Lee1Taesung Park2 Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea Center for Precision Medicine, Seoul National University Hospital, Seoul 08826, Korea Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, KoreaIn 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.http://genominfo.org/upload/pdf/gi-2020-18-1-e11.pdfgenome-wide association studyhierarchical structural component modelpathway analysisprincipal component analysis |
| spellingShingle | Nan Jiang Sungyoung Lee Taesung Park HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis Genomics & Informatics genome-wide association study hierarchical structural component model pathway analysis principal component analysis |
| title | HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis |
| title_full | HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis |
| title_fullStr | HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis |
| title_full_unstemmed | HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis |
| title_short | HisCoM-PCA: software for hierarchical structural component analysis for pathway analysis based using principal component analysis |
| title_sort | hiscom pca software for hierarchical structural component analysis for pathway analysis based using principal component analysis |
| topic | genome-wide association study hierarchical structural component model pathway analysis principal component analysis |
| url | http://genominfo.org/upload/pdf/gi-2020-18-1-e11.pdf |
| work_keys_str_mv | AT nanjiang hiscompcasoftwareforhierarchicalstructuralcomponentanalysisforpathwayanalysisbasedusingprincipalcomponentanalysis AT sungyounglee hiscompcasoftwareforhierarchicalstructuralcomponentanalysisforpathwayanalysisbasedusingprincipalcomponentanalysis AT taesungpark hiscompcasoftwareforhierarchicalstructuralcomponentanalysisforpathwayanalysisbasedusingprincipalcomponentanalysis |