Discovering phenotype specific gene module using a novel biclustering algorithm in colorectal cancer

Jungrim Kim, Youngmi Yoon, Sang Hyun Park, Jeagyoon Ahn, Yunku Yeu

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

Abstract

Gene clustering is a method for finding gene sets which are related to the same biological processes or molecular function. In order to find these gene sets, previous studies have clustered genes which showed similar mRNA expression or a specific expression pattern in a (sub) sample set. However, for two contrasting groups of samples, it is not easy to identify gene sets which show significant expression pattern in only one group using current gene clustering methods. Existing biclustering methods use only one group (disease) of samples. It is hard to identify disease specific biclusters which are differentially expressed in the disease although those methods can find biclusters which have specific expression pattern. Here, we proposed a novel method using a genetic algorithm in gene expression data, in order to find gene sets which can represent specific subtype of cancer. Proposed method finds gene sets which have statistically differential mRNA expression on two contrasting samples and fraction of cancer samples. The resulting gene modules share higher number of GO (Gene Ontology) terms related to a specific disease than gene modules identified by current algorithms. We also identify that when we integrate protein-protein interaction data with gene expression data of colorectal cancer samples, proposed method can find more functionally related gene sets.

Original languageEnglish
Title of host publicationProceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
EditorsHuiru Zheng, Xiaohua Tony Hu, Yadong Wang, Jin-Kao Hao, David Gilbert, Daniel Berrar, Kwang-Hyun Cho, Werner Dubitzky
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages201-204
Number of pages4
ISBN (Electronic)9781479956692
DOIs
Publication statusPublished - 2014 Jan 1
Event2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 - Belfast, United Kingdom
Duration: 2014 Nov 22014 Nov 5

Publication series

NameProceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014

Other

Other2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014
CountryUnited Kingdom
CityBelfast
Period14/11/214/11/5

Fingerprint

Gene Regulatory Networks
Colorectal Neoplasms
Genes
Phenotype
Cluster Analysis
Gene expression
Biological Phenomena
Gene Expression
Messenger RNA
Gene Ontology
Proteins
Neoplasms
Ontology
Genetic algorithms

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics

Cite this

Kim, J., Yoon, Y., Park, S. H., Ahn, J., & Yeu, Y. (2014). Discovering phenotype specific gene module using a novel biclustering algorithm in colorectal cancer. In H. Zheng, X. T. Hu, Y. Wang, J-K. Hao, D. Gilbert, D. Berrar, K-H. Cho, ... W. Dubitzky (Eds.), Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014 (pp. 201-204). [6999154] (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2014.6999154
Kim, Jungrim ; Yoon, Youngmi ; Park, Sang Hyun ; Ahn, Jeagyoon ; Yeu, Yunku. / Discovering phenotype specific gene module using a novel biclustering algorithm in colorectal cancer. Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. editor / Huiru Zheng ; Xiaohua Tony Hu ; Yadong Wang ; Jin-Kao Hao ; David Gilbert ; Daniel Berrar ; Kwang-Hyun Cho ; Werner Dubitzky. Institute of Electrical and Electronics Engineers Inc., 2014. pp. 201-204 (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014).
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Kim, J, Yoon, Y, Park, SH, Ahn, J & Yeu, Y 2014, Discovering phenotype specific gene module using a novel biclustering algorithm in colorectal cancer. in H Zheng, XT Hu, Y Wang, J-K Hao, D Gilbert, D Berrar, K-H Cho & W Dubitzky (eds), Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014., 6999154, Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014, Institute of Electrical and Electronics Engineers Inc., pp. 201-204, 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014, Belfast, United Kingdom, 14/11/2. https://doi.org/10.1109/BIBM.2014.6999154

Discovering phenotype specific gene module using a novel biclustering algorithm in colorectal cancer. / Kim, Jungrim; Yoon, Youngmi; Park, Sang Hyun; Ahn, Jeagyoon; Yeu, Yunku.

Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. ed. / Huiru Zheng; Xiaohua Tony Hu; Yadong Wang; Jin-Kao Hao; David Gilbert; Daniel Berrar; Kwang-Hyun Cho; Werner Dubitzky. Institute of Electrical and Electronics Engineers Inc., 2014. p. 201-204 6999154 (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014).

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

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Kim J, Yoon Y, Park SH, Ahn J, Yeu Y. Discovering phenotype specific gene module using a novel biclustering algorithm in colorectal cancer. In Zheng H, Hu XT, Wang Y, Hao J-K, Gilbert D, Berrar D, Cho K-H, Dubitzky W, editors, Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. Institute of Electrical and Electronics Engineers Inc. 2014. p. 201-204. 6999154. (Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014). https://doi.org/10.1109/BIBM.2014.6999154