Computational protocol: The effects of globin on microarray-based gene expression analysis of mouse blood

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Protocol publication

[…] Probe sets that were present in all 18 samples were assigned to two categories (whole-blood RNA or globin-reduced RNA) (Supplementary Tables 1 and 2) and imported into MetaCore (http://www.genego.com) for enrichment analysis in GeneGo Pathway Maps, GeneGo Diseases by Biomarkers (GeneGo, St. Joseph, MI), GO Processes, and GO Molecular Functions. GeneGo Pathway Maps represent a set of genes participating in a consecutive set of metabolic signals, or metabolic transformations, confirmed as a whole by experimental data or by inferred relationships. GeneGo Diseases by Biomarkers are groups of genes implicated in certain diseases based on classifications in Medical Subject Headings (http://www.nlm.nih.gov/mesh/). The list of genes represented on the Affymetrix Mouse 430 2.0 array was used as a base gene list when calculating P values in the MetaCore enrichment procedures. MetaCore (GeneGo) uses a hypergeometric model to determine the significance of enrichment (Falcon and Gentleman ). [...] For mouse and human whole-blood gene expression comparisons, raw human whole-blood gene expression data were downloaded from the Gene Expression Omnibus (GSE2888, GSE 16728). MAS5 calls were obtained as outlined above and filtered for orthologous probe sets present in 80% or more of globin-reduced samples for each study individually. Orthologous genes and their associated Affymetrix probe sets were identified using Ensembl Biomart (http://www.www.ensembl.org/biomart). Filtered probe set lists (Supplementary Table 3) were imported into MetaCore and tested for enrichment in GeneGo Pathway Maps. The list of genes represented on the Affymetrix HG U133A array was used as a base gene list when calculating P values in the MetaCore enrichment procedures for GSE2888 and GSE16728. […]

Pipeline specifications

Software tools MetaCore, Meshes, BioMart
Databases GEO
Application Genome annotation
Organisms Mus musculus