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Analysis of Multiple DNA Microarray Datasets

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Springer Handbook of Bio-/Neuroinformatics

Part of the book series: Springer Handbooks ((SHB))

Abstract

In contrast to conventional clustering algorithms, where a single dataset is used to produce a clustering solution, we introduce herein a MapReduce approach for clustering of datasets generated in multiple-experiment settings. It is inspired by the map-reduce functions commonly used in functional programming and consists of two distinctive phases. Initially, the selected clustering algorithm is applied (mapped) to each experiment separately. This produces a list of different clustering solutions, one per experiment. These are further transformed (reduced) by portioning the cluster centers into a single clustering solution. The obtained partition is not disjoint in terms of the different participating genes, and it is further analyzed and refined by applying formal concept analysis.

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Abbreviations

BiNGO:

biological networks gene ontology

DNA:

deoxyribonucleic acid

DTW:

dynamic time warping

EM:

expectation-maximization

FCA:

formal concept analysis

GO-id:

GO category identification

GO:

gene ontology

SI:

silhouette index

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Author information

Authors and Affiliations

  1. Department of Computer Systems and Technologies, Technical University of Sofia, Branch Plovdiv, Str. Tsanko Dyustabanov 25, 4000, Plovdiv, Bulgaria

    Veselka Boeva

  2. Department of ICT & Software Engineering, Sirris, The Collective Center for the Belgian Technological Industry, A. Reyerslaan 80, 1030, Brussels, Belgium

    Elena Tsiporkova

  3. Department of Computer Systems and Technologies, Technical University of Sofia, Plovdiv Branch, Str. Tsanko Dyustabanov 25, 4000, Plovdiv, Bulgaria

    Elena Kostadinova

Authors
  1. Veselka Boeva
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  2. Elena Tsiporkova
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  3. Elena Kostadinova
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Corresponding authors

Correspondence to Veselka Boeva , Elena Tsiporkova or Elena Kostadinova .

Editor information

Editors and Affiliations

  1. KEDRI – Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, 120 Mayoral Drive, 1010, Auckland, New Zealand

    Nikola Kasabov

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Boeva, V., Tsiporkova, E., Kostadinova, E. (2014). Analysis of Multiple DNA Microarray Datasets. In: Kasabov, N. (eds) Springer Handbook of Bio-/Neuroinformatics. Springer Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30574-0_14

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  • DOI: https://doi.org/10.1007/978-3-642-30574-0_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-30573-3

  • Online ISBN: 978-3-642-30574-0

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