DSS

A biclustering method to identify diverse and state specific gene modules in gene expression data

Jungrim Kim, Yunku Yeu, Jeongwoo Kim, Youngmi Yoon, Sang Hyun Park

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

1 Citation (Scopus)

Abstract

The biclustering method is a useful co-clustering technique to identify biologically relevant gene modules. In this paper, we propose a novel method to find not only functionally-related gene modules but also state specific gene modules by applying a genetic algorithm to gene expression data. To identify these gene modules, the proposed method finds biclusters in which genes are statistically overexpressed or under expressed, and are differentially-expressed in the samples in the bicluster compared to the samples not in the bicluster. In addition, we improve the genetic algorithm by adding a selection pool for preserving the diversity of the population. The resulting gene modules exhibit better performances than comparative methods in the GO (Gene Ontology) term enrichment test and an analysis connection between gene modules and disease. This is especially the case with gene modules that receive the highest score in the breast cancer dataset; they are closely linked to the ribosome pathway. Recent studies show that dysregulation of ribosome biogenesis is associated with breast tumor progression.

Original languageEnglish
Title of host publication2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages430-434
Number of pages5
ISBN (Electronic)9781509018970
DOIs
Publication statusPublished - 2017 Feb 6
Event2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Budapest, Hungary
Duration: 2016 Oct 92016 Oct 12

Publication series

Name2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings

Other

Other2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016
CountryHungary
CityBudapest
Period16/10/916/10/12

Fingerprint

Biclustering
Gene Expression Data
Gene expression
Genes
Gene
Module
Genetic Algorithm
Genetic algorithms
Gene Ontology
Breast Cancer
Progression
Tumor
Pathway
Ontology
Tumors
Clustering

All Science Journal Classification (ASJC) codes

  • Computer Vision and Pattern Recognition
  • Artificial Intelligence
  • Control and Optimization
  • Human-Computer Interaction

Cite this

Kim, J., Yeu, Y., Kim, J., Yoon, Y., & Park, S. H. (2017). DSS: A biclustering method to identify diverse and state specific gene modules in gene expression data. In 2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings (pp. 430-434). [7844279] (2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/SMC.2016.7844279
Kim, Jungrim ; Yeu, Yunku ; Kim, Jeongwoo ; Yoon, Youngmi ; Park, Sang Hyun. / DSS : A biclustering method to identify diverse and state specific gene modules in gene expression data. 2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 430-434 (2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings).
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Kim, J, Yeu, Y, Kim, J, Yoon, Y & Park, SH 2017, DSS: A biclustering method to identify diverse and state specific gene modules in gene expression data. in 2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings., 7844279, 2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings, Institute of Electrical and Electronics Engineers Inc., pp. 430-434, 2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016, Budapest, Hungary, 16/10/9. https://doi.org/10.1109/SMC.2016.7844279

DSS : A biclustering method to identify diverse and state specific gene modules in gene expression data. / Kim, Jungrim; Yeu, Yunku; Kim, Jeongwoo; Yoon, Youngmi; Park, Sang Hyun.

2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings. Institute of Electrical and Electronics Engineers Inc., 2017. p. 430-434 7844279 (2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings).

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

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Kim J, Yeu Y, Kim J, Yoon Y, Park SH. DSS: A biclustering method to identify diverse and state specific gene modules in gene expression data. In 2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings. Institute of Electrical and Electronics Engineers Inc. 2017. p. 430-434. 7844279. (2016 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2016 - Conference Proceedings). https://doi.org/10.1109/SMC.2016.7844279