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Paradigm of tunable clustering using Binarization of Consensus Partition Matrices (Bi-CoPaM) for gene discovery.

Abu-Jamous B, Fa R, Roberts DJ, Nandi AK - PLoS ONE (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical Engineering and Electronics, The University of Liverpool, Brownlow Hill, Liverpool, United Kingdom.

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.

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Correctly assigned genes.The number of correctly assigned genes at the y-axis is plotted versus the 16 binarization configurations at the x-axis for three representative synthetic datasets out of 60. It should be noted that the binarization configurations are not entirely ordered according to their tightness.
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pone-0056432-g002: Correctly assigned genes.The number of correctly assigned genes at the y-axis is plotted versus the 16 binarization configurations at the x-axis for three representative synthetic datasets out of 60. It should be noted that the binarization configurations are not entirely ordered according to their tightness.

Mentions: We assessed the performance of different binarization techniques in forming clusters which maximised the number of correct assignments, while minimising the number of false-assignments. Three representative sets out of the 60 available ones were picked; the best (SNR = 7.31 dB), the worst (SNR = 2.96 dB), and the median (the 31st best one, SNR = 5.19 dB). The number of correctly assigned genes versus each of the 16 binarization configurations for these datasets is plotted in Figure 2.


Paradigm of tunable clustering using Binarization of Consensus Partition Matrices (Bi-CoPaM) for gene discovery.

Abu-Jamous B, Fa R, Roberts DJ, Nandi AK - PLoS ONE (2013)

Correctly assigned genes.The number of correctly assigned genes at the y-axis is plotted versus the 16 binarization configurations at the x-axis for three representative synthetic datasets out of 60. It should be noted that the binarization configurations are not entirely ordered according to their tightness.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3569426&req=5

pone-0056432-g002: Correctly assigned genes.The number of correctly assigned genes at the y-axis is plotted versus the 16 binarization configurations at the x-axis for three representative synthetic datasets out of 60. It should be noted that the binarization configurations are not entirely ordered according to their tightness.
Mentions: We assessed the performance of different binarization techniques in forming clusters which maximised the number of correct assignments, while minimising the number of false-assignments. Three representative sets out of the 60 available ones were picked; the best (SNR = 7.31 dB), the worst (SNR = 2.96 dB), and the median (the 31st best one, SNR = 5.19 dB). The number of correctly assigned genes versus each of the 16 binarization configurations for these datasets is plotted in Figure 2.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical Engineering and Electronics, The University of Liverpool, Brownlow Hill, Liverpool, United Kingdom.

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.

Show MeSH