HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions
Gene-gene interaction (GGI) analysis is known to play an important role in explaining missing heritability. Many previous studies have already proposed software to analyze GGI, but most methods focus on a binary phenotype in a case-control design. In this study, we developed “Hierarchical structural...
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| Format: | Article |
| Language: | English |
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BioMed Central
2018-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e38.pdf |
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| author | Sungkyoung Choi Sungyoung Lee Taesung Park |
| author_facet | Sungkyoung Choi Sungyoung Lee Taesung Park |
| author_sort | Sungkyoung Choi |
| collection | DOAJ |
| description | Gene-gene interaction (GGI) analysis is known to play an important role in explaining missing heritability. Many previous studies have already proposed software to analyze GGI, but most methods focus on a binary phenotype in a case-control design. In this study, we developed “Hierarchical structural CoMponent analysis of Gene-Gene Interactions” (HisCoM-GGI) software for GGI analysis with a continuous phenotype. The HisCoM-GGI method considers hierarchical structural relationships between genes and single nucleotide polymorphisms (SNPs), enabling both gene-level and SNP-level interaction analysis in a single model. Furthermore, this software accepts various types of genomic data and supports data management and multithreading to improve the efficiency of genome-wide association study data analysis. We expect that HisCoM-GGI software will provide advanced accessibility to researchers in genetic interaction studies and a more effective way to understand biological mechanisms of complex diseases. |
| format | Article |
| id | doaj-art-09e4fb652b2a469a90171a3f80eff5a6 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-09e4fb652b2a469a90171a3f80eff5a62025-02-02T11:11:23ZengBioMed CentralGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e38540HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene InteractionsSungkyoung Choi0Sungyoung Lee1Taesung Park2 Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Korea Center for Precision Medicine, Seoul National University Hospital, Seoul 03080, Korea Department of Statistics, Seoul National University, Seoul 08826, KoreaGene-gene interaction (GGI) analysis is known to play an important role in explaining missing heritability. Many previous studies have already proposed software to analyze GGI, but most methods focus on a binary phenotype in a case-control design. In this study, we developed “Hierarchical structural CoMponent analysis of Gene-Gene Interactions” (HisCoM-GGI) software for GGI analysis with a continuous phenotype. The HisCoM-GGI method considers hierarchical structural relationships between genes and single nucleotide polymorphisms (SNPs), enabling both gene-level and SNP-level interaction analysis in a single model. Furthermore, this software accepts various types of genomic data and supports data management and multithreading to improve the efficiency of genome-wide association study data analysis. We expect that HisCoM-GGI software will provide advanced accessibility to researchers in genetic interaction studies and a more effective way to understand biological mechanisms of complex diseases.http://genominfo.org/upload/pdf/gi-2018-16-4-e38.pdfgene-gene interactionsgeneralized structured component analysisgenome-wide association studyridge regression |
| spellingShingle | Sungkyoung Choi Sungyoung Lee Taesung Park HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions Genomics & Informatics gene-gene interactions generalized structured component analysis genome-wide association study ridge regression |
| title | HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions |
| title_full | HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions |
| title_fullStr | HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions |
| title_full_unstemmed | HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions |
| title_short | HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions |
| title_sort | hiscom ggi software for hierarchical structural component analysis of gene gene interactions |
| topic | gene-gene interactions generalized structured component analysis genome-wide association study ridge regression |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e38.pdf |
| work_keys_str_mv | AT sungkyoungchoi hiscomggisoftwareforhierarchicalstructuralcomponentanalysisofgenegeneinteractions AT sungyounglee hiscomggisoftwareforhierarchicalstructuralcomponentanalysisofgenegeneinteractions AT taesungpark hiscomggisoftwareforhierarchicalstructuralcomponentanalysisofgenegeneinteractions |