Supplemental Table 1. Gene categories overrepresented in genes differentially expressed between D2 and B6 mice.

Gene Category / Biological System / Chip% (n) / List% (n) / p-value
All Clusters (n = 788)
SwissProt keyword / Acetylation / 2.0 (75) / 6.0 (18) / 6.4E-05
Biological Process / carboxylic acid metabolism / 2.9 (199) / 6.0 (32) / 1.9E-04
Cellular Component / cytosol / 3.8 (258) / 6.6 (35) / 1.6E-03
Biological Process / response to heat / 0.2 (19) / 1.3 (7) / 2.7E-03
KEGG pathway / Metabolism of Other Amino / 6.4 (46) / 15.6 (13) / 3.5E-03
Cellular Component / virion / 0.6 (43) / 1.9 (10) / 5.1E-03
Cellular Component / plastid / 0.3 (23) / 1.3 (7) / 7.0E-03
KEGG pathway / Glutamate metabolism / 1.6 (12) / 7.2 (6) / 7.3E-03
Biological Process / DNA packaging / 1.2 (85) / 2.6 (14) / 1.6E-02
Biological Process / antigen presentation / 0.2 (20) / 1.1 (6) / 1.8E-02
Chromosome / Mus musculus 4 / 6 (518) / 8.1 (55) / 1.9E-02
Molecular Function / ligase activity / 2.2 (158) / 3.8 (21) / 2.3E-02
Molecular Function / transferase activity, alkyl or aryl groups / 0.5 (38) / 1.4 (8) / 2.7E-02
Molecular Function / motor activity / 0.9 (64) / 2.0 (11) / 2.7E-02
Biological Process / small GTPase mediated signal transduction / 1.9 (131) / 3.3 (18) / 2.9E-02
SwissProt keyword / Hydroxylation / 0.6 (23) / 2.0 (6) / 3.3E-02
Biological Process / lipoprotein metabolism / 0.2 (17) / 0.9 (5) / 4.1E-02
Biological Process / sulfur metabolism / 0.4 (33) / 1.3 (7) / 4.3E-02
Molecular Function / cysteine-type endopeptidase activity / 1.1 (79) / 2.2 (12) / 4.4E-02
Molecular Function / lipid transporter activity / 0.4 (34) / 1.2 (7) / 4.7E-02
KEGG pathway / Translation - Mus musculus / 9.9 (71) / 16.8 (14) / 5.0E-02
Cluster 1 (n = 60)
Molecular Function / ligase activity\, forming carbon-nitrogen bonds / 1.1 (75) / 9.1 (4) / 1.1E-02
Biological Process / nucleosome assembly / 0.4 (27) / 6.7 (3) / 1.3E-02
Molecular Function / small GTPase regulatory/interacting protein / 1.6 (107) / 9.1 (4) / 2.9E-02
Cluster 2 (n=103)
Molecular Function / lyase activity / 1.3 (90) / 9.9 (7) / 2.8E-04
Biological Process / antigen presentation / 0.3 (20) / 4.2 (3) / 1.9E-02
Biological Process / DNA metabolism / 4.4 (294) / 11.1 (8) / 3.5E-02
Chromosome / Mus musculus 17 / 5.4 (456) / 11.5 (10) / 4.0E-02
Chromosome / Mus musculus 7 / 8.0 (681) / 14.9 (13) / 4.1E-02
Cluster 3 (n=128)
Biological Process / response to heat / 0.3 (18) / 3.4 (3) / 2.2E-02
Cellular Component / cytosol / 3.8 (256) / 10.0 (8) / 3.1E-02
Chromosome / Mus musculus 9 / 5.3 (453) / 10.7 (12) / 3.4E-02
Molecular Function / oxidoreductase activity / 0.3 (23) / 3.4 (3) / 3.4E-02
Cellular Component / small ribosomal subunit / 0.4 (29) / 3.8 (3) / 4.5E-02
Cluster 4 (n = 30)
Molecular Function / structural constituent of ribosome / 2.2 (153) / 25.0 (5) / 7.0E-04
Molecular Function / hydrogen ion transporter activity / 1.2 (80) / 15.0 (3) / 2.0E-02
Cluster 5 (n=216)
Molecular Function / cysteine-type endopeptidase activity / 1.7 (80) / 5.12 (8) / 2.0E-03
SwissProt keyword / NADP / 1.2 (46) / 6.9 (6) / 3.9E-03
Biological Process / amine metabolism / 2.2 (147) / 6.7 (10) / 5.2E-03
Molecular Function / transferase activity\, transferring alkyl or aryl / 0.6 (38) / 3.2 (5) / 1.0E-02
Biological Process / carboxylic acid metabolism / 3.0 (199) / 7.3 (11) / 1.3E-02
SwissProt keyword / Oxidoreductase / 5.2 (193) / 12.6 (11) / 1.3E-02
Cellular Component / virion / 0.6 (43) / 3.4 (5) / 1.5E-02
Biological Process / amino acid metabolism / 1.5 (100) / 4.7 (7) / 2.3E-02
Chromosome / Mus musculus 4 / 6.1 (518) / 10.3 (20) / 2.6E-02
SwissProt keyword / Acetylation / 2.0 (76) / 6.9 (6) / 3.0E-02
Biological Process / pyrimidine nucleotide biosynthesis / 0.2 (14) / 2.0 (3) / 3.7E-02
Biological Process / protein lipidation / 0.2 (14) / 2.0 (3) / 3.7E-02
Molecular Function / prenyltransferase activity / 0.2 (15) / 1.9 (3) / 4.4E-02
Cellular Component / viral capsid / 0.6 (37) / 2.7 (4) / 4.8E-02
Molecular Function / enzyme regulator activity / 3.5 (244) / 7.1 (11) / 4.8E-02
Cluster 6 (n=68)
Biological Process / ubiquitin cycle / 0.7 (49) / 8.3 (4) / 4.7E-03
Cellular Component / endoplasmic reticulum / 4.3 (286) / 15.2 (7) / 1.2E-02
Cellular Component / viral nucleocapsid / 0.5 (33) / 6.5 (3) / 2.0E-02
Biological Process / glycolysis / 0.6 (40) / 6.3 (3) / 3.2E-02
SwissProt keyword / Selenocysteine / 0.2 (6) / 8.7 (2) / 3.5E-02
Cluster 7 (n=46)
Biological Process / G-protein coupled receptor protein signaling / 5.1 (343) / 18.2 (6) / 2.2E-02
Cluster 8 (n=137)
Biological Process / cell-cell signaling / 3.1 (207) / 9.7 (10) / 4.0E-03
SwissProt keyword / Voltage-gated channel / 1.2 (46) / 7.8 (5) / 7.2E-03
Biological Process / lipid transport / 0.5 (35) / 3.9 (4) / 1.6E-02
Biological Process / Rho protein signal transduction / 0.3 (21) / 2.9 (3) / 4.0E-02

All differentially expressed genes and individual k-means clusters in Figure 1were compared to 12,422 Affymetrix MG-U74Av2 probesets for over-representation of gene categories provided by the EASE program (Hosack et al., 2003). n = number of genes in gene list or cluster. Chip% : percentage of U74Av2 probesets in biological system also in gene category. List%: percentage of differentially expressed genes (probesets) in biological system also in gene category. (n): number of probesets on chip or list in gene category.