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GMDR specifications

Information


Unique identifier OMICS_24673
Name GMDR
Alternative name Generalized Multifactor Dimensionality Reduction
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.9
Stability Beta
Requirements
Java SE Runtime Environment
Maintained Yes

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Documentation


Maintainers


  • person_outline Xiang-Yang Lou
  • person_outline Guo-Bo Chen

Publications for Generalized Multifactor Dimensionality Reduction

GMDR citations

 (94)
library_books

Fuzzy set based generalized multifactor dimensionality reduction analysis of gene gene interactions

2018
BMC Med Genomics
PMCID: 5918459
PMID: 29697366
DOI: 10.1186/s12920-018-0343-0

[…] In this study, we proposed a FGMDR, a fuzzy extension of GMDR to detect GGIs. FGMDR can handle both binary and quantitative traits, and allows adjustment for covariates. Thus, FGMDR is a method to overcome shortcomings due to the […]

library_books

Association and cis mQTL analysis of variants in CHRNA3 A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population

2018
PMCID: 5904126
PMID: 29666375
DOI: 10.1038/s41398-018-0130-x

[…] ogical roles in both the peripheral and the central nervous systems. To determine whether there exists any epistatic effect among these nAChR subunits, we performed interaction analysis using our own GMDR-GPU program, which revealed two significant interaction models for FTND. The first model consists of SNPs rs16969968 in CHRNA5 and rs7178270 in CHRNB4, with a CVC 7 of 10, prediction accuracy of […]

library_books

Interactions among variants in TXA2R, P2Y12 and GPIIIa are associated with carotid plaque vulnerability in Chinese population

2018
Oncotarget
PMCID: 5915141
PMID: 29707133
DOI: 10.18632/oncotarget.24801

[…] testamong patients with VP, SP and non-plaque. Difference of genotype frequencies among patients with VP, SP and non-plaque was also compared by χ2-test. Gene-gene interaction was assessed using the GMDR method, as described in our previous studies [, ]. The GMDR v 0.7 program was used in this study (www.healthsystem. virginia.edu/internet/addiction-genomics/Software) []. This model was then conf […]

library_books

Childhood trauma interacted with BDNF Val66Met influence schizophrenic symptoms

2018
PMCID: 5895403
PMID: 29595641
DOI: 10.1097/MD.0000000000010160

[…] ed that BDNF played a pivotal role effecting by methylation, and glucocorticoid receptor.[]Our case-only study found models of BDNF Val66Met interacted with some ChT types on the excitement factor by GMDR. The case-only test has been proposed as a more powerful approach to detect G × E interactions. In this study, the excitement factors include items of excitement, hostility, noncooperation, and i […]

call_split

GxGrare: gene gene interaction analysis method for rare variants from high throughput sequencing data

2018
BMC Syst Biol
PMCID: 5861485
PMID: 29560826
DOI: 10.1186/s12918-018-0543-4
call_split See protocol

[…] In the methods section, we introduce a novel collapsing idea. Then, we briefly review the GMDR method and evaluation measures. Last, we explain our proposed analysis steps. […]

call_split

UCP2 and UCP3 variants and gene environment interaction associated with prediabetes and T2DM in a rural population: a case control study in China

2018
BMC Med Genet
PMCID: 5848510
PMID: 29529994
DOI: 10.1186/s12881-018-0554-4
call_split See protocol

[…] included additive, recessive and dominant models. Frequencies of haplotypes were calculated and compared among the three groups. Finally, we employed the general multifactor dimensionality reduction (GMDR) method [] and logistic regression to estimate the interaction between gene and environmental risk factors.Multinomial logistic regression, χ2 test and one-way analyses of variance were performed […]

Citations

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GMDR institution(s)
Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China; Institute of Computer Application Technology, College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China; Queensland Brain Institute, University of Queensland, St Lucia, QLD, Australia; Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China; Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, USA
GMDR funding source(s)
Supported in part by National Institute of Health Grant R01 DA025095 and National Science Foundation DMS1462990, the National Basic Research Programs of China (973 Programs) 2011CB109306, and the National Natural Science Foundation 31271608 and 31470083.

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