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Genomics Inform > Volume 16(4); 2018 > Article
DOI: https://doi.org/10.5808/GI.2018.16.4.e38    Published online December 28, 2018.
HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions
Sungkyoung Choi1, Sungyoung Lee2, Taesung Park3,4
1Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Korea
2Center for Precision Medicine, Seoul National University Hospital, Seoul 03080, Korea
3Department of Statistics, Seoul National University, Seoul 08826, Korea
4Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
Corresponding author:  Taesung Park
Email: tspark@stats.snu.ac.kr
Received: December 11, 2018   Accepted: December 18, 2018
Abstract
Gene-gene interaction (GGI) analysis is known to play an important role in explain missing heritability issue. Many previous studies have already proposed software to analyze GGI, but most methods focus on a binary phenotype in case-control design. In this study, we developed ‘Hierarchical structural CoMponent analysis of Gene-Gene Interactions’ (HisCoM-GGI) software for gene-gene interaction analysis with a continuous phenotype. The HisCoM-GGI method considers hierarchical structural relationships between genes and SNPs, that enables both gene-level and SNP-level interaction analysis in a single model. Furthermore, this software accepts various type of genomic data, and supports a data management and multithreading to improve the efficiency of GWAS data analysis. We expect that the HisCoM-GGI software provides advanced accessibility to the researchers on the genetic interaction studies and a more effective way to understand biological mechanisms of complex diseases.
Keywords: Gene-Gene interactions, Generalized Structured Component Analysis, Ridge regression, Genome-wide association study
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