IADIS International Journal on Computer Science and Information Systems

Published by IADIS (International Association for Development of the Information Society) • ISSN (Online): 1646-3692 • ISSN (Print): 1646-3692
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Evolutionary Algorithms for Finding Interpretable Patterns in Gene Expression Data

Carlos Cano *
Armando Blanco *
Fernando García *
* IADIS - International Association for Development of the Information Society (Portugal)
* IADIS - International Association for Development of the Information Society (Portugal)
* IADIS - International Association for Development of the Information Society (Portugal)

Abstract

Microarray Technology allows us to measure the expression of thousa nds of genes simultaneously, and under specific conditions. Clustering is the main tool used to analyze gene expression data obtained from microarray experiments. By grouping together genes with the same be havior across samples, resultant clusters suggest new functions for some of the gene s. Non-exclusive clustering algorithms are required, as a gene may have more th an one biological function. Gene Shaving (Hastie et al. 2000) is a clustering algorithm which looks for coherent clusters with high variance acro ss samples, allowing clusters to overlap. In this paper we present two Evolutionary Algorithm approaches, based on Genetics Algorithms (GA) and Estimation of Distributi on Algorithms (EDA), whose aim is to find clusters of similar genes with large between-sample vari ance. We apply our methods GA-Shaving and EDA-Shaving to S. cerevisiae cell cycle dataset outperforming Gene-Shaving results in terms of quality and size of obtained clusters. Furthermore, we use GO Term Finder (Boyle et al. 2004) to evaluate the biological interpretation of the results. It computes the most st atistically significant biological processes associated to every cluster by means of the annotations of the Gene Ontology (Gene Ontology Consortium 2004).

Keywords

Microarrays Cluster Estimation of Distribution Algorithms.
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Funding: This research received academic dissemination support through ESCAP / JournalsHub publishing programs.
Conflicts of Interest: The authors declare no competing financial or institutional interests.
Peer Review: Double-blind peer reviewed by international subject specialists.
License: Creative Commons Attribution 4.0 International (CC BY 4.0).
How to Cite This Article
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Cano, et al. (2006). Evolutionary Algorithms for Finding Interpretable Patterns in Gene Expression Data. IADIS International Journal on Computer Science and Information Systems, 1(2). https://doi.org/10.33965/ijcsis_2006_v1i2_08
Cano, et al. "Evolutionary Algorithms for Finding Interpretable Patterns in Gene Expression Data." IADIS International Journal on Computer Science and Information Systems, vol. 1, no. 2, 2006. https://doi.org/10.33965/ijcsis_2006_v1i2_08
Cano, et al. "Evolutionary Algorithms for Finding Interpretable Patterns in Gene Expression Data." IADIS International Journal on Computer Science and Information Systems 1, no. 2 (2006). https://doi.org/10.33965/ijcsis_2006_v1i2_08