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Efficient mining of multilevel gene association rules from microarray and gene ontology

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Abstract

Some recent studies have shown that association rules can reveal the interactions between genes that might not have been revealed using traditional analysis methods like clustering. However, the existing studies consider only the association rules among individual genes. In this paper, we propose a new data mining method named MAGO for discovering the multilevel gene association rules from the gene microarray data and the concept hierarchy of Gene Ontology (GO). The proposed method can efficiently find out the relations between GO terms by analyzing the gene expressions with the hierarchy of GO. For example, with the biological process in GO, some rules like Process A (up) → Process B (up) cab be discovered, which indicates that the genes involved in Process B of GO are likely to be up-regulated whenever those involved in Process A are up-regulated. Moreover, we also propose a constrained mining method named CMAGO for discovering the multilevel gene expression rules with user-specified constraints. Through empirical evaluation, the proposed methods are shown to have excellent performance in discovering the hidden multilevel gene association rules.

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Acknowledgement

This research was supported by the Landmark Project of National Cheng Kung University, Taiwan and National Science Council, Taiwan, R.O.C. under grant no. NSC 96-2221-E-006-143-MY3.

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Authors and Affiliations

  1. Department Computer Science and Information Engineering, National Cheng Kung University, Taiwan, ROC

    Vincent S. Tseng, Hsieh-Hui Yu & Shih-Chiang Yang

  2. Institute of Medical Informatics, National Cheng Kung University, Taiwan, ROC

    Vincent S. Tseng

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  1. Vincent S. Tseng
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  2. Hsieh-Hui Yu
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Correspondence to Vincent S. Tseng.

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Tseng, V.S., Yu, HH. & Yang, SC. Efficient mining of multilevel gene association rules from microarray and gene ontology. Inf Syst Front 11, 433–447 (2009). https://doi.org/10.1007/s10796-009-9156-1

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