Abstract
Identification of multifactor gene-gene (GxG) and gene-environment (GxE) interactions underlying complex traits poses one of the great challenges to today’s genetic study. Development of the generalized multifactor dimensionality reduction (GMDR) method provides a practicable solution to problems in detection of interactions. To exploit the opportunities brought by the availability of diverse data, it is in high demand to develop the corresponding GMDR software that can handle a breadth of phenotypes, such as continuous, count, dichotomous, polytomous nominal, ordinal, survival and multivariate, and various kinds of study designs, such as unrelated case-control, family-based and pooled unrelated and family samples, and also allows adjustment for covariates. We developed a versatile GMDR package to implement this serial of GMDR analyses for various scenarios (e.g., unified analysis of unrelated and family samples) and large-scale (e.g., genome-wide) data. This package includes other desirable features such as data management and preprocessing. Permutation testing strategies are also built in to evaluate the threshold or empirical p values. In addition, its performance is scalable to the computational resources. The software is available at http:// www.soph.uab.edu/ssg/software or http://ibi.zju.edu.cn/software.
Keywords: Generalized multifactor dimensionality reduction, Gene-gene interactions, Gene-environment interactions, Complex traits, Unrelated sample, Family sample, Computer software.
Graphical Abstract
Current Genomics
Title:GMDR: Versatile Software for Detecting Gene-Gene and Gene-Environment Interactions Underlying Complex Traits
Volume: 17 Issue: 5
Author(s): Hai-Ming Xu, Li-Feng Xu, Ting-Ting Hou, Lin-Feng Luo, Guo-Bo Chen, Xi-Wei Sun and Xiang-Yang Lou
Affiliation:
Keywords: Generalized multifactor dimensionality reduction, Gene-gene interactions, Gene-environment interactions, Complex traits, Unrelated sample, Family sample, Computer software.
Abstract: Identification of multifactor gene-gene (GxG) and gene-environment (GxE) interactions underlying complex traits poses one of the great challenges to today’s genetic study. Development of the generalized multifactor dimensionality reduction (GMDR) method provides a practicable solution to problems in detection of interactions. To exploit the opportunities brought by the availability of diverse data, it is in high demand to develop the corresponding GMDR software that can handle a breadth of phenotypes, such as continuous, count, dichotomous, polytomous nominal, ordinal, survival and multivariate, and various kinds of study designs, such as unrelated case-control, family-based and pooled unrelated and family samples, and also allows adjustment for covariates. We developed a versatile GMDR package to implement this serial of GMDR analyses for various scenarios (e.g., unified analysis of unrelated and family samples) and large-scale (e.g., genome-wide) data. This package includes other desirable features such as data management and preprocessing. Permutation testing strategies are also built in to evaluate the threshold or empirical p values. In addition, its performance is scalable to the computational resources. The software is available at http:// www.soph.uab.edu/ssg/software or http://ibi.zju.edu.cn/software.
Export Options
About this article
Cite this article as:
Xu Hai-Ming, Xu Li-Feng, Hou Ting-Ting, Luo Lin-Feng, Chen Guo-Bo, Sun Xi-Wei and Lou Xiang-Yang, GMDR: Versatile Software for Detecting Gene-Gene and Gene-Environment Interactions Underlying Complex Traits, Current Genomics 2016; 17 (5) . https://dx.doi.org/10.2174/1389202917666160513102612
DOI https://dx.doi.org/10.2174/1389202917666160513102612 |
Print ISSN 1389-2029 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5488 |
Call for Papers in Thematic Issues
Current Genomics in Cardiovascular Research
Cardiovascular diseases are the main cause of death in the world, in recent years we have had important advances in the interaction between cardiovascular disease and genomics. In this Research Topic, we intend for researchers to present their results with a focus on basic, translational and clinical investigations associated with ...read more
Deep learning in Single Cell Analysis
The field of biology is undergoing a revolution in our ability to study individual cells at the molecular level, and to integrate data from multiple sources and modalities. This has been made possible by advances in technologies for single-cell sequencing, multi-omics profiling, spatial transcriptomics, and high-throughput imaging, as well as ...read more
New insights on Pediatric Tumors and Associated Cancer Predisposition Syndromes
Because of the broad spectrum of children cancer susceptibility, the diagnosis of cancer risk syndromes in children is rarely used in direct cancer treatment. The field of pediatric cancer genetics and genomics will only continue to expand as a result of increasing use of genetic testing tools. It's possible that ...read more
Related Journals
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
- Announcements
Related Articles
-
In Vitro and In Vivo Evaluation of DMSO and Azone as Penetration Enhancers for Cutaneous Application of Celecoxib
Current Drug Delivery A Study on Leukemic and Non-small Cell Lung Cancer Efficacy of Novel Isoxazoles Synthesized by Microwave Irradiation
Letters in Drug Design & Discovery Diethyldithiocarbamate complex with copper: the mechanism of action in cancer cells
Mini-Reviews in Medicinal Chemistry Polypharmacological Properties and Therapeutic Potential of β-Caryophyllene: A Dietary Phytocannabinoid of Pharmaceutical Promise
Current Pharmaceutical Design Taste Sensing in the Colon
Current Pharmaceutical Design Anti-inflammatory and Antioxidant Agents from Salvia Genus (Lamiaceae): An Assessment of the Current State of Knowledge
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry TGF Beta Inhibition for Cancer Therapy
Current Cancer Drug Targets Recent Advances in Azo Dye Degrading Enzyme Research
Current Protein & Peptide Science Deep Inspiration Breath-hold (DIBH) Technique to Reduce Cardiac Radiation Dose in the Management of Breast Cancer
Current Cancer Therapy Reviews Natural Sirtuin Modulators in Drug Discovery: A Review (2010 -2020)
Current Medicinal Chemistry Binding of Tris to Bacillus licheniformis α-Amylase Can Affect Its Starch Hydrolysis Activity
Protein & Peptide Letters MicroRNAs and the Warburg Effect: New Players in an Old Arena
Current Gene Therapy Biomarkers Determining Cardiovascular Risk in Patients with Kidney Disease
Current Medicinal Chemistry Changes in the Apoptotic and Survival Signaling in Cancer Cells and Their Potential Therapeutic Implications
Current Cancer Drug Targets Curcumin: A Boon to Colonic Diseases
Current Drug Targets Targeting CSC-Related miRNAs for Cancer Therapy by Natural Agents
Current Drug Targets Scope of Nanotechnology-based Radiation Therapy and Thermotherapy Methods in Cancer Treatment
Current Cancer Drug Targets Advancement of Targeted Ultrasound Contrast Agents and their Applications in Molecular Imaging and Targeted Therapy
Current Pharmaceutical Design The Heme Oxygenase System: Its Role in Liver Inflammation
Current Drug Targets - Cardiovascular & Hematological Disorders Muscarinic Acetylcholine Receptors: New Potential Therapeutic Targets in Antinociception and in Cancer Therapy
Recent Patents on CNS Drug Discovery (Discontinued)