Gene network inference via sparse structural equation modeling with genetic perturbations

Xiaodong Cai, Juan Andrés Bazerque, Georgios B. Giannakis

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

2 Citations (Scopus)

Abstract

Structural equation models (SEMs) have been recently proposed to infer gene regulatory network using gene expression data and genetic perturbations. However, lack of efficient inference method for SEMs prevents practical use of SEMs in the inference of relatively large gene networks. In this paper, relying on the sparsity of gene networks, we develop an efficient SEM-based method for inferring gene networks using both gene expression and expression quantitative trait locus (eQTL) data. Simulated tests demonstrate that the novel method significantly outperform state-of-the-art methods in the field.

Original languageEnglish
Title of host publicationProceedings - IEEE International Workshop on Genomic Signal Processing and Statistics
Pages66-69
Number of pages4
StatePublished - Dec 1 2011
Event2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11 - San Antonio, TX, United States
Duration: Dec 4 2011Dec 6 2011

Other

Other2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11
CountryUnited States
CitySan Antonio, TX
Period12/4/1112/6/11

Fingerprint

Gene Regulatory Networks
Structural Models
Genes
Gene expression
Gene Expression
Quantitative Trait Loci

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computational Theory and Mathematics
  • Signal Processing
  • Biomedical Engineering

Cite this

Cai, X., Bazerque, J. A., & Giannakis, G. B. (2011). Gene network inference via sparse structural equation modeling with genetic perturbations. In Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics (pp. 66-69). [6169445]

Gene network inference via sparse structural equation modeling with genetic perturbations. / Cai, Xiaodong; Bazerque, Juan Andrés; Giannakis, Georgios B.

Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics. 2011. p. 66-69 6169445.

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

Cai, X, Bazerque, JA & Giannakis, GB 2011, Gene network inference via sparse structural equation modeling with genetic perturbations. in Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics., 6169445, pp. 66-69, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11, San Antonio, TX, United States, 12/4/11.
Cai X, Bazerque JA, Giannakis GB. Gene network inference via sparse structural equation modeling with genetic perturbations. In Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics. 2011. p. 66-69. 6169445
Cai, Xiaodong ; Bazerque, Juan Andrés ; Giannakis, Georgios B. / Gene network inference via sparse structural equation modeling with genetic perturbations. Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics. 2011. pp. 66-69
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