title: Gene expression biomarkers in the brain of a mouse model for Alzheimer's disease: mining of microarray data by logic classification and feature selection.
abstract: The identification of early and stage-specific biomarkers for Alzheimer's disease (AD) is critical, as the development of disease-modification therapies may depend on the discovery and validation of such markers. The identification of early reliable biomarkers depends on the development of new diagnostic algorithms to computationally exploit the information in large biological datasets. To identify potential biomarkers from mRNA expression profile data, we used the Logic Mining method for the unbiased analysis of a large microarray expression dataset from the anti-NGF AD11 transgenic mouse model. The gene expression profile of AD11 brain regions was investigated at different neurodegeneration stages by whole genome microarrays. A new implementation of the Logic Mining method was applied both to early (1-3 months) and late stage (6-15 months) expression data, coupled to standard statistical methods. A small number of "fingerprinting" formulas was isolated, encompassing mRNAs whose expression levels were able to discriminate between diseased and control mice. We selected three differential "signature" genes specific for the early stage (Nudt19, Arl16, Aph1b), five common to both groups (Slc15a2, Agpat5, Sox2ot, 2210015, D19Rik, Wdfy1), and seven specific for late stage (D14Ertd449, Tia1, Txnl4, 1810014B01Rik, Snhg3, Actl6a, Rnf25). We suggest these genes as potential biomarkers for the early and late stage of AD-like neurodegeneration in this model and conclude that Logic Mining is a powerful and reliable approach for large scale expression data analysis. Its application to large expression datasets from brain or peripheral human samples may facilitate the discovery of early and stage-specific AD biomarkers.
authors.affiliation: European Brain Research Institute (EBRI) "Rita Levi-Montalcini", Italian Institute of Technology Neurogenomics Unit, Roma, Italy.
authors.forename: Ivan
authors.initials: I
authors.lastname: Arisi
authors.forename: Mara
authors.initials: M
authors.lastname: D'Onofrio
authors.forename: Rossella
authors.initials: R
authors.lastname: Brandi
authors.forename: Armando
authors.initials: A
authors.lastname: Felsani
authors.forename: Simona
authors.initials: S
authors.lastname: Capsoni
authors.forename: Guido
authors.initials: G
authors.lastname: Drovandi
authors.forename: Giovanni
authors.initials: G
authors.lastname: Felici
authors.forename: Emanuel
authors.initials: E
authors.lastname: Weitschek
authors.forename: Paola
authors.initials: P
authors.lastname: Bertolazzi
authors.forename: Antonino
authors.initials: A
authors.lastname: Cattaneo
mesh_terms: D000544:Alzheimer Disease / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D000818:Animals; D001923:Brain Chemistry / Q000235:genetics*; D057225:Data Mining / Q000379:methods*; D004195:Disease Models, Animal; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D005819:Genetic Markers / Q000235:genetics; D051379:Mice; D008810:Mice, Inbred C57BL; D008822:Mice, Transgenic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D005819:Genetic Markers