Additional file 6.

List of Affymetrix probe sets associated with high variance in control rat liver and/or kidney. This list contains 373 genes with replicate evidence of high baseline variance among the six tissue-array sets. Baseline variance was calculated for each probe set (within each tissue-array set) based on the maximal model, in which each unique combination of factors was encoded as a distinct group. Using these variance measurements, probe sets that were ranked in the top 2% in baseline variance among expressed targets were intersected across tissue-array sets by probe identifier. The intersected list was then filtered for probe sets that were among the top 5% most variant on at least a second tissue-array set, or that were relevant to toxicogenomics (defined here as inclusion on the Affymetrix GeneChip Rat ToxFX 1.0 array). Column A: Probe set identifier on Affymetrix RAE230 and ToxFX arrays, Column B: Probe set identifier on Affymetrix RGU34 arrays, intersected by Affymetrix Best Match sequence mapping file or UniGene ID (grey background), Columns C-E: UniGene identifier, Gene Name, and Gene Symbol, Column F: Tissue where high variance observed; Liver (L), kidney (K), or both liver and kidney (B), Column G: Inclusion on the Affymetrix ToxFX 1.0 array: Yes (Y) or No (N), Column H: Functional annotation associated with the probe set, identified using the following sources of curation in DAVID [11], KEGG: Kyoto Encyclopedia of Genes and Genomes pathway; BP: Gene Ontology Biological Process; MF: Gene Ontology Molecular Function; CC: Gene Ontology Cellular Compartment; COG: Clusters of Orthologous Groups of Proteins; SP: Swiss Prot knowledgebase ; IP, Interpro database.

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Boedigheimer et al. BMC Genomics 2008 9:285   doi:10.1186/1471-2164-9-285