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Gene expression array exploration using \(\mathcal{K}\)-formal concept analysis. (English) Zbl 1328.92048

Valtchev, Petko (ed.) et al., Formal concept analysis. 9th international conference, ICFCA 2011, Nicosia, Cyprus, May 2–6, 2011. Proceedings. Berlin: Springer (ISBN 978-3-642-20513-2/pbk). Lecture Notes in Computer Science 6628. Lecture Notes in Artificial Intelligence, 119-134 (2011).
Summary: DNA micro-arrays are a mechanism for eliciting gene expression values, the concentration of the transcription products of a set of genes, under different chemical conditions. The phenomena of interest-up-regulation, down-regulation and co-regulation-are hypothesized to stem from the functional relationships among transcription products.
In [Zbl 1132.68062; Zbl 1216.68285] the second and the third author developed a generalisation of formal concept analysis with data mining applications in mind, \(\mathcal{K}\)-formal concept analysis, where incidences take values in certain kinds of semirings, instead of the usual Boolean carrier set. In this paper, we use (\(\overline{\mathbb{R}}_{\min, +}\))- and (\(\overline{\mathbb{R}}_{\max, +}\))-formal concept analysis to analyse gene expression data for Arabidopsis thaliana. We introduce the mechanism to render the data in the appropriate algebra and profit by the wealth of different Galois connections available in generalized formal concept analysis to carry different analysis for up- and down-regulated genes.
For the entire collection see [Zbl 1214.68022].

MSC:

92D10 Genetics and epigenetics
68T05 Learning and adaptive systems in artificial intelligence
68T30 Knowledge representation
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References:

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