milar patterns of within mouse variation but different patterns of between mouse varia tion. To measure similarity of within mouse BAY 73-4506 variation, we centred the sample values on individual mouse means and then computed a Pearson correlation, rw. This measure is only meaningful for comparisons within the same tissue as there is no correspondence between the duplicate samples from different tissues. Adipose and heart each have multiple highly correlated modules. The adipose green, adipose red, adipose black, and adipose magenta modules have distinct pat terns of between mouse variation and different func tional enrichment, but they all share high within mouse correlation. A similar relationship was observed for the heart green, heart red, heart tur quoise, heart blue, heart brown, and heart gold modules.

Uncorrelated modules have gene overlap and similar functional enrichment Some modules share genes and functional enrichment categories but do not have correlated patterns of varia tion. The adipose gold, heart red, and kidney black modules have a high gene overlap. They are enriched for the GO category fatty acid metabolic pro cess. The adipose magenta and heart gold modules Inhibitors,Modulators,Libraries share 118 out of 120 genes including Cd8b1 and Lck and are enriched for the GO category immune system process. The adipose brown module shares 87 out of 182 genes with the heart green module and 31 out of 35 genes Inhibitors,Modulators,Libraries with the liver turquoise module. These modules are enriched for the GO actin cytoskeleton category and share 8 genes in common including Ckm and Myl1.

The adipose turquoise and kidney turquoise modules share Inhibitors,Modulators,Libraries 30 out of 40 genes including Apoal, Cyp8b1, and Ugt2b3 and are enriched for the KEGG pathway complementation and coagulation cascades. The adipose green and heart turquoise modules are overlapping in 12 out of 50 genes including Ccl9, Cxcl1, Egr1, Fos, and Hmox1 and are enriched for chemokine activity. The adipose black, heart black, kidney magenta, and liver green modules have pairwise over laps ranging from 33 to 146 genes. Twenty two genes are shared among all 4 of these modules and they are enriched for KEGG pathway oxidative phosphorylation and the GO category mitochondrial inner membrane. Comparison across platform Inhibitors,Modulators,Libraries We repeated the gene expression assays for only the liver samples on a different platform, the Affymetrix Whole Transcript Mouse Gene 1. 0 ST array.

Drug_discovery To facili tate comparison, we generated a cross platform probe map based on gene annotation. Using this map, we computed eigengenes of the previously defined clusters from the Affymetrix data. Correlation of the eigengenes across platforms was very high for 7 of the 9 modules. Two modules with lower correlation had less than 20% of variance selleck kinase inhibitor explained by the eigengene with Affymetrix data. How ever, for the liver gold module, low expression for mouse 6 was a consistent pattern across platforms. The profiles of all 19 genes that are highlighted in the Dis cussion are highly correlated across platform. Discu