Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model

Wei Cheng, Xiang Zhang, Yubao Wu, Xiaolin Yin, Jing Li, David Heckerman, Wei Wang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Citations (Scopus)

Abstract

Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression traits. A major drawback of this approach is that it cannot model the joint effect of a set of SNPs on a set of genes, which may corresponds to biological pathways. In this paper, we propose a sparse (ℓ1-regularized) graphical model, SET-eQTL, to identify novel associations between sets of SNPs and sets of genes. Such associations are captured by hidden variables connecting SNPs and genes. These hidden variables also naturally model the potential effect of unknown confounding factors. We compare three different methods on a yeast segregant dataset. Extensive experimental results demonstrate that the proposed graphical model SET-eQTL achieves better performance than the other two alternatives.

Original languageEnglish (US)
Title of host publication2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012
Pages466-473
Number of pages8
DOIs
StatePublished - Nov 26 2012
Event2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012 - Orlando, FL, United States
Duration: Oct 7 2012Oct 10 2012

Publication series

Name2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012

Other

Other2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012
CountryUnited States
CityOrlando, FL
Period10/7/1210/10/12

Fingerprint

Quantitative Trait Loci
Nucleotides
Polymorphism
Single Nucleotide Polymorphism
Genes
Gene expression
Gene Expression
Yeast
Yeasts
Genome
Testing

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Information Management

Cite this

Cheng, W., Zhang, X., Wu, Y., Yin, X., Li, J., Heckerman, D., & Wang, W. (2012). Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model. In 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012 (pp. 466-473). (2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012). https://doi.org/10.1145/2382936.2382996
Cheng, Wei ; Zhang, Xiang ; Wu, Yubao ; Yin, Xiaolin ; Li, Jing ; Heckerman, David ; Wang, Wei. / Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model. 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012. 2012. pp. 466-473 (2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012).
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abstract = "Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression traits. A major drawback of this approach is that it cannot model the joint effect of a set of SNPs on a set of genes, which may corresponds to biological pathways. In this paper, we propose a sparse (ℓ1-regularized) graphical model, SET-eQTL, to identify novel associations between sets of SNPs and sets of genes. Such associations are captured by hidden variables connecting SNPs and genes. These hidden variables also naturally model the potential effect of unknown confounding factors. We compare three different methods on a yeast segregant dataset. Extensive experimental results demonstrate that the proposed graphical model SET-eQTL achieves better performance than the other two alternatives.",
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Cheng, W, Zhang, X, Wu, Y, Yin, X, Li, J, Heckerman, D & Wang, W 2012, Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model. in 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012. 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012, pp. 466-473, 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012, Orlando, FL, United States, 10/7/12. https://doi.org/10.1145/2382936.2382996

Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model. / Cheng, Wei; Zhang, Xiang; Wu, Yubao; Yin, Xiaolin; Li, Jing; Heckerman, David; Wang, Wei.

2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012. 2012. p. 466-473 (2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Cheng W, Zhang X, Wu Y, Yin X, Li J, Heckerman D et al. Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model. In 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012. 2012. p. 466-473. (2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012). https://doi.org/10.1145/2382936.2382996