Dragomir A, Mavroudi S, Bezerianos A. Som-based class discovery exploring the ICA-reduced features of microarray expression profiles.
Comp Funct Genomics 2008;
5:596-616. [PMID:
18629176 PMCID:
PMC2447468 DOI:
10.1002/cfg.444]
[Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2004] [Indexed: 11/24/2022] Open
Abstract
Gene expression datasets are large and complex, having many variables and unknown
internal structure. We apply independent component analysis (ICA) to derive a
less redundant representation of the expression data. The decomposition produces
components with minimal statistical dependence and reveals biologically relevant
information. Consequently, to the transformed data, we apply cluster analysis (an
important and popular analysis tool for obtaining an initial understanding of the
data, usually employed for class discovery). The proposed self-organizing map
(SOM)-based clustering algorithm automatically determines the number of ‘natural’
subgroups of the data, being aided at this task by the available prior knowledge of the
functional categories of genes. An entropy criterion allows each gene to be assigned
to multiple classes, which is closer to the biological representation. These features,
however, are not achieved at the cost of the simplicity of the algorithm, since the
map grows on a simple grid structure and the learning algorithm remains equal to
Kohonen’s one.
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