Gene Expressio Array Exploration Using K-Formal Concept Analysis

Abstract

Proceeding of: 9th International Conference, ICFCA 2011, Nicosia, Cyprus, May 2-6, 2011.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 [1,2,3] a generalisation of Formal Concept Analysis was developed with data mining applications in mind, 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 (Rmin+)- and (Rmax+) 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.Spanish Government-Comision Interministerial de Ciencia y Tecnología projects 2008-06382/TEC and 2008-02473/TEC and the regional projects S-505/TIC/0223 (DGUI-CM) and CCG08-UC3M/TIC- 4457 (Comunidad Aut onoma de Madrid - UC3M)