Integrative Microarray Data Analysis

Normalized microarrays from seven studies (GSE84185, GSE43261, GSE56028, GSE118669, GSE54307, GSE6476, and GSE42940) were retrieved from GEO using GEOquery [160 (link)]. One last microarray was retrieved directly from the authors [50 (link)] and was normalized using RMA from the oligo R package [161 (link)]. The microarrays’ latest annotations were retrieved from Ensembl Biomart for Affymetrix GeneChip Mouse Genome 430 2.0, Affymetrix GeneChip Mouse 430A 2.0, Affymetrix Rat Gene 1.0 ST arrays, and Agilent SurePrint G3 Mouse Gene Expression 8 × 60 K microarrays. When unavailable, annotations from the original authors were completed using megablast queries (GSE42940). Probes with mapping to multiple genes were discarded. Differential gene expression analyses were produced with Limma [162 (link)].

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Ibrahim E.C., Gorgievski V., Ortiz-Teba P., Belzeaux R., Turecki G., Sibille E., Charbonnier G, & Tzavara E.T. (2022). Transcriptomic Studies of Antidepressant Action in Rodent Models of Depression: A First Meta-Analysis. International Journal of Molecular Sciences, 23(21), 13543.

Publication 2022

SurePrint G3 Mouse Gene Expression 8 × 60 K microarrays

Gene Gene expression Gene expression analyses Genechip Genome Microarrays Mouse Multiple genes Oligo

Corresponding Organization :

Other organizations : Institut de Neurosciences de la Timone, Fondation FondaMental, Hôpital Albert-Chenevier, Institut de Biologie Paris-Seine, Institut de Neurosciences Cognitives et Intégratives d’Aquitaine, Pompeu Fabra University, Centre Hospitalier Universitaire de Montpellier, Douglas Mental Health University Institute, Canada Research Chairs, University of Toronto, Theories and Approaches of Genomic Complexity, Hôpital Sainte-Marguerite

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Variable analysis

independent variables

Microarrays from seven studies (GSE84185, GSE43261, GSE56028, GSE118669, GSE54307, GSE6476, and GSE42940)
One last microarray retrieved directly from the authors

dependent variables

Differential gene expression

control variables

Normalized microarrays
Latest annotations retrieved from Ensembl Biomart
Probes with mapping to multiple genes were discarded

Annotations

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