Gene Co-Expression in Mouse Embryo Tissues

Gene Co-Expression in Mouse Embryo Tissues

Simon Andrews (Conceptual Structures Research Group, Sheffield Hallam University, Sheffield, UK) and Kenneth McLeod (Department of Computer Science, Heriot-Watt University, Edinburgh, UK)
Copyright: © 2013 |Pages: 14
DOI: 10.4018/ijiit.2013100104
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Abstract

This paper develops some existing ideas in Formal Concept Analysis (FCA) to provide an analysis of a large data set of gene expressions in mouse embryo tissues. It develops a new technique for managing complexity based on 'fault tolerance' and the identification of disjoint sets in data. Using this technique, distinct groups of co-expressed genes are identified. The work represents some early experiments with FCA, with many questions arising and much left as future research, although promising results are shown that are of interest to both FCA developers and geneticists. This work has been carried out as part the European CUBIST Project.
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2. The Mouse-Embryo Gene Expressions Data Set: Emage

A gene is a unit of instructions that provides directions for one essential task, i.e., the creation of a protein. Gene expression information describes whether or not a gene is expressed (active) in a location. Broadly speaking there are two types of gene expression information: those that focus on where the gene is expressed, and those whose primary concern is the strength of expression. This work concentrates on the former category, and in particular a technology called in situ hybridisation (ISH) gene expression.

Information on gene expression is often given in relation to a tissue in a particular model organism. Here the model organism is the mouse. This organism is studied from conception until adulthood. The time window is split into 28 Theiler Stages (TS). Each stage has its own anatomy, and corresponding anatomy ontology called EMAP (Baldock & Davidson, 2008). The first 26 stages cover the developmental mouse: the mouse from conception until birth. Stage 27 is the new born mouse, and 28 the adult.

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