Please use this identifier to cite or link to this item: http://bura.brunel.ac.uk/handle/2438/8530
Title: Paradigm of tunable clustering using binarization of consensus partition matrices (Bi-CoPaM) for gene discovery
Authors: Abu-Jamous, B
Fa, R
Roberts, DJ
Nandi, AK
Keywords: Genes;Gene clustering;Binarization of Consensus Partition Matrices (Bi-CoPaM);Cell cycles
Issue Date: 2013
Publisher: Public Library of Science
Citation: PLoS ONE, 8(2): Article no. e56432, 2013
Abstract: Clustering analysis has a growing role in the study of co-expressed genes for gene discovery. Conventional binary and fuzzy clustering do not embrace the biological reality that some genes may be irrelevant for a problem and not be assigned to a cluster, while other genes may participate in several biological functions and should simultaneously belong to multiple clusters. Also, these algorithms cannot generate tight clusters that focus on their cores or wide clusters that overlap and contain all possibly relevant genes. In this paper, a new clustering paradigm is proposed. In this paradigm, all three eventualities of a gene being exclusively assigned to a single cluster, being assigned to multiple clusters, and being not assigned to any cluster are possible. These possibilities are realised through the primary novelty of the introduction of tunable binarization techniques. Results from multiple clustering experiments are aggregated to generate one fuzzy consensus partition matrix (CoPaM), which is then binarized to obtain the final binary partitions. This is referred to as Binarization of Consensus Partition Matrices (Bi-CoPaM). The method has been tested with a set of synthetic datasets and a set of five real yeast cell-cycle datasets. The results demonstrate its validity in generating relevant tight, wide, and complementary clusters that can meet requirements of different gene discovery studies.
Description: Copyright @ 2013 Abu-Jamous et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
URI: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056432
http://bura.brunel.ac.uk/handle/2438/8530
DOI: http://dx.doi.org/10.1371/journal.pone.0056432
ISSN: 1932-6203
Appears in Collections:Electronic and Computer Engineering
Publications
Dept of Electronic and Computer Engineering Research Papers

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