We also tested for enrichment within each of these subsets. Many of the module enrichment scores are highly significant indicating that correlated groups of vari able genes are enriched for specific biological functions. Most modules in a given tissue share similar features with at least one module in another tissue. Several sets of modules shared similar patterns of between mouse variation and had significant gene overlap and functional enrichment. Other sets of modules shared similar patterns of within mouse variation, but with distinct between mouse varia tion. Several pairs of modules had significant gene over lap but did not have correlated patterns of variation. Examples of each are described below.

Inhibitors,Modulators,Libraries Between mouse patterns of variation are shared across tissues Modules from different tissues that are enriched for similar functional categories typically have high intraclass correlation and similar patterns of between mouse variation. To quantify this similarity, we com puted a between mouse correlation, rb, for Inhibitors,Modulators,Libraries all pairs of module eigengenes by averaging the two within mouse samples before computing the Pearson correlation. Each of the four tissues has at least one module that is enriched for immune response. The heart brown, kidney gold, and liver pink modules are enriched for the GO category exogenous antigen presentation. The between mouse cor relations, rb, range from 0. 53 to 0. 80, and the genes in these modules overlap significantly based on a hypergeo metric test. Pairwise overlaps range from 16 to 19 genes and seven genes are found in all 3 modules.

The kidney blue and liver brown modules are enriched for GO category extracellular matrix, each containing more than 12 genes of that category. Their between mouse profiles are correlated and they share 20 genes in common including Entinostat Adamts2, Col5a1, Col6a1, Col14a1, Ecm1, Igfbp3, Tgfbi and Timp2. The adipose red, heart blue, kid ney brown Inhibitors,Modulators,Libraries Inhibitors,Modulators,Libraries and liver black modules are enriched for the GO category apoptosis and have between mouse correlations, rb, ranging from 0. 52 to 0. 93. These modules overlap with 16 genes present in at least 3 of the 4 modules including Ccrn4l, Gadd45g, and Map3k6. The liver blue module also has a high between mouse correlation and signifi cant gene overlap with these adipose, heart and kidney modules including Fkbp5 and Per1.

The kidney pink and liver magenta modules have correlated between mouse profiles, and each contains 18 or more genes of the GO category DNA dependent regulation of transcription. Their gene overlap includes Bcl6, Cish, Rgs3, and Socs2. The between mouse profiles of the kidney green and liver red modules are correlated and each module contains 12 or more genes of the GO category cellular lipid metabolic process. They have 12 genes in common including Acaa2, Acadm, Agxt2l1, Cyp26b1, Cyp4a10, Cyp4a14 and Slc2a2.