Literature DB >> 21918603

Identification of significant genes in genomics using Bayesian variable selection methods.

Eugene Lin1, Lung-Cheng Huang.   

Abstract

In the studies of genomics, it is essential to select a small number of genes that are more significant than the others for research ranging from candidate gene studies to genome-wide association studies. In this study, we proposed a Bayesian method for identifying the promising candidate genes that are significantly more influential than the others. We employed the framework of variable selection and a Gibbs sampling based technique to identify significant genes. The proposed approach was applied to a genomics study for persons with chronic fatigue syndrome. Our studies show that the proposed Bayesian methodology is effective for deriving models for genomic studies and for providing information on significant genes.

Entities:  

Keywords:  Bayesian variable selection; Gibbs sampling; genomics; variable selection

Year:  2008        PMID: 21918603      PMCID: PMC3169938          DOI: 10.2147/aabc.s3624

Source DB:  PubMed          Journal:  Adv Appl Bioinform Chem        ISSN: 1178-6949


  15 in total

1.  Stochastic search variable selection for identifying multiple quantitative trait loci.

Authors:  Nengjun Yi; Varghese George; David B Allison
Journal:  Genetics       Date:  2003-07       Impact factor: 4.562

2.  Gene selection: a Bayesian variable selection approach.

Authors:  Kyeong Eun Lee; Naijun Sha; Edward R Dougherty; Marina Vannucci; Bani K Mallick
Journal:  Bioinformatics       Date:  2003-01       Impact factor: 6.937

3.  Bayesian variable selection in multinomial probit models to identify molecular signatures of disease stage.

Authors:  Naijun Sha; Marina Vannucci; Mahlet G Tadesse; Philip J Brown; Ilaria Dragoni; Nick Davies; Tracy C Roberts; Andrea Contestabile; Mike Salmon; Chris Buckley; Francesco Falciani
Journal:  Biometrics       Date:  2004-09       Impact factor: 2.571

Review 4.  Pattern-recognition techniques with haplotype analysis in pharmacogenomics.

Authors:  Eugene Lin; Yuchi Hwang; Kung-Hao Liang; Ellson Y Chen
Journal:  Pharmacogenomics       Date:  2007-01       Impact factor: 2.533

Review 5.  A case study of the utility of the HapMap database for pharmacogenomic haplotype analysis in the Taiwanese population.

Authors:  Eugene Lin; Yuchi Hwang; Chi-Meng Tzeng
Journal:  Mol Diagn Ther       Date:  2006       Impact factor: 4.074

6.  Stochastic search gene suggestion: a Bayesian hierarchical model for gene mapping.

Authors:  Michael D Swartz; Marek Kimmel; Peter Mueller; Christopher I Amos
Journal:  Biometrics       Date:  2006-06       Impact factor: 2.571

7.  Gene-gene and gene-environment interactions in interferon therapy for chronic hepatitis C.

Authors:  Eugene Lin; Yuchi Hwang; Ellson Y Chen
Journal:  Pharmacogenomics       Date:  2007-10       Impact factor: 2.533

8.  Locating disease genes using Bayesian variable selection with the Haseman-Elston method.

Authors:  Cheongeun Oh; Kenny Q Ye; Qimei He; Nancy R Mendell
Journal:  BMC Genet       Date:  2003-12-31       Impact factor: 2.797

9.  A Bayesian genome-wide linkage analysis of quantitative traits for rheumatoid arthritis via perfect sampling.

Authors:  Cheongeun Oh
Journal:  BMC Proc       Date:  2007-12-18

10.  Application of an iterative Bayesian variable selection method in a genome-wide association study of rheumatoid arthritis.

Authors:  Soonil Kwon; Dai Wang; Xiuqing Guo
Journal:  BMC Proc       Date:  2007-12-18
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  7 in total

1.  A support vector machine approach to assess drug efficacy of interferon-alpha and ribavirin combination therapy.

Authors:  Eugene Lin; Yuchi Hwang
Journal:  Mol Diagn Ther       Date:  2008       Impact factor: 4.074

2.  Bayesian Variable Selection under the Proportional Hazards Mixed-effects Model.

Authors:  Kyeong Eun Lee; Yongku Kim; Ronghui Xu
Journal:  Comput Stat Data Anal       Date:  2014-07       Impact factor: 1.681

Review 3.  Machine learning and systems genomics approaches for multi-omics data.

Authors:  Eugene Lin; Hsien-Yuan Lane
Journal:  Biomark Res       Date:  2017-01-20

4.  A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.

Authors:  Lung-Cheng Huang; Sen-Yen Hsu; Eugene Lin
Journal:  J Transl Med       Date:  2009-09-22       Impact factor: 5.531

5.  Pilot study of an association between a common variant in the non-muscle myosin heavy chain 9 (MYH9) gene and type 2 diabetic nephropathy in a Taiwanese population.

Authors:  Chang-Hsun Hsieh; Yi-Jen Hung; Dee Pei; Shi-Wen Kuo; Eugene Lin
Journal:  Appl Clin Genet       Date:  2010-03-16

6.  Comparison of classification algorithms with wrapper-based feature selection for predicting osteoporosis outcome based on genetic factors in a taiwanese women population.

Authors:  Hsueh-Wei Chang; Yu-Hsien Chiu; Hao-Yun Kao; Cheng-Hong Yang; Wen-Hsien Ho
Journal:  Int J Endocrinol       Date:  2013-01-14       Impact factor: 3.257

7.  Association study of a brain-derived neurotrophic-factor polymorphism and short-term antidepressant response in major depressive disorders.

Authors:  Eugene Lin; Po See Chen; Lung-Cheng Huang; Sen-Yen Hsu
Journal:  Pharmgenomics Pers Med       Date:  2008-10-21
  7 in total

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