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Shockley and Churchill, 2006 SUPPLEMENTAL MATERIAL Table

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Shockley and Churchill, 2006 SUPPLEMENTAL MATERIAL Table Shockley and Churchill, 2006 SUPPLEMENTAL MATERIAL Table S1. NetAffx Mapping of Probe Set IDs to Chromosomal Location CHR Number of Unique Probe IDs 1 2,667 2 3,396 3 2,132 4 2,445 5 2,559 6 2,304 7 2,711 8 2,032 9 2,234 10 1,927 11 3,152 12 1,547 13 1,580 14 1,478 15 1,619 16 1,415 17 1,692 18 1,197 19 1,398 X 1,255 Y 8 M 1 Un 152 Total Unique 40,901 Total Probe IDs 45,101 Non-Unique or 4,200 Missing Probe IDs Gene mapping was performed with the Affymetrix tool NetAffx (available at http://www.affymetrix.com/analysis/index.affx). “M” refers to mitochondria; “Un” is unknown location. Gene Expression in Mouse Chromosome Substitution Strains 1 Shockley and Churchill, 2006 Table S2. Over-representation of Canonical Pathways in Mouse Liver from Ingenuity Systems Database p-value NAME Description FC q B.A1 Arginine and Proline Metabolism 0.04 ODC1 ornithine decarboxylase 1 -2.1 0.01 P4HA2 procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II -2.2 0.01 B.A2 Sulfur Metabolism 0.00 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.8 0.00 SULT1B1 sulfotransferase family, cytosolic, 1B, member 1 1.8 0.00 Bile Acid Biosynthesis 0.01 ALDH4A1 aldehyde dehydrogenase -1.5 0.00 CYP7A1 cytochrome P450, family 7, subfamily A, polypeptide 1 2.3 0.00 LIPA lipase A -3.6 0.01 Histidine Metabolism 0.04 ALDH4A1 aldehyde dehydrogenase -1.5 0.00 FTCD formiminotransferase cyclodeaminase -2.5 0.01 B.A3 Sulfur Metabolism 0.03 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.5 0.00 JAK/Stat Signaling 0.04 CISH cytokine inducible SH2-containing protein -1.8 0.01 SOCS2 suppressor of cytokine signaling 2 -1.8 0.01 Death Receptor Signaling 0.04 APAF1 apoptotic protease activating factor -1.2 0.00 TNFSF10 tumor necrosis factor (ligand) superfamily, member 10 2.5 0.00 Taurine and Hypotaurine Metabolism -0.05 CSAD cysteine sulfinic acid decarboxylase -2.0 0.01 Purine Metabolism 0.00 ADCY1 adenylate cyclase 1 (brain) 1.3 0.00 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.5 0.00 POLR2A polymerase (RNA) II (DNA directed) polypeptide A, 220kDa -1.5 0.01 SPAST spastin -1.5 0.00 B.A4 Phenylalanine Metabolism 0.02 GOT1 glutamic-oxaloacetic transaminase 1, soluble 1.6 0.00 MAOA monoamine oxidase A -1.3 0.01 Tyrosine Metabolism 0.03 GOT1 glutamic-oxaloacetic transaminase 1, soluble 1.6 0.00 MAOA monoamine oxidase A -1.3 0.01 Nucleotide Excision Repair Pathway 0.04 RAD23B RAD23 homolog B (S. cerevisiae) -1.7 0.00 XPA xeroderma pigmentosum, complementation group A 1.3 0.00 B.A5 Selenoamino Acid Metabolism 0.00 GGT1 gamma-glutamyl transferase 1 -1.2 0.01 MAT1A methionine adenosyltransferase I, alpha 1.2 0.01 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 2.0 0.00 Fatty Acid Metabolism 0.01 ACAD10 Acyl-Coenzyme A dehydrogenase family 1.6 0.00 ACOX1 acyl-Coenzyme A oxidase 1, palmitoyl 1.8 0.01 ALDH1A1 aldehyde dehydrogenase 1 family, member A1 2.0 0.00 CYP2B6 cytochrome P450, family 2, subfamily B, polypeptide 6 1.8 0.00 CYP3A7 cytochrome P450 -3.6 0.00 Gluthionone Metabolism 0.02 GGT1 gamma-glutamyl transferase 1 -1.2 0.01 GSTM2 glutathione S-transferase M2 (muscle) 1.5 0.00 GSTT3 glutathione S-transferase theta-3 1.4 0.01 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, N-Glycan Biosynthesis 0.03 B4GALT1 polypeptide 1 -1.3 0.01 MAN1A2 mannosidase, alpha, class 1A, member 2 1.3 0.00 MGAT3 mannosyl (beta-1,4-)-glycoprotein beta-1,4-N- acetylglucosaminyltransferase -1.2 0.00 Arginine and Proline Metabolism 0.03 ALDH1A1 aldehyde dehydrogenase 1 family, member A1 2.0 0.00 P4HA2 procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II -1.6 0.01 procollagen-proline, 2-oxoglutarate 4-dioxygenase P4HB (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1) 1.8 0.01 Gene Expression in Mouse Chromosome Substitution Strains 2 Shockley and Churchill, 2006 B.A6 None B.A7 Aminosugars Metabolism 0.01 DIA1 diaphorase (NADH) (cytochrome b-5 reductase) 3.5 0.01 NANS N-acetylneuraminic acid synthase (sialic acid synthase) -1.5 0.00 PDGF Signaling 0.01 EIF2AK2 eukaryotic translation initiation factor 2-alpha kinase 2 1.5 0.00 PDGFRB platelet-derived growth factor receptor, beta polypeptide -1.7 0.00 STAT1 signal transducer and activator of transcription 1, 91kDa 1.4 0.01 Sulfur Metabolism 0.04 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 3.1 0.00 B.A8 Sulfur Metabolism 0.02 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 3.2 0.00 Methane Metabolism 0.05 PRDX2 peroxiredoxin 2 -4.0 0.00 B.A9 Alanine and Aspartate Metabolism 0.00 ASL argininosuccinate lyase 1.4 0.01 ASS argininosuccinate synthetase 1.2 0.01 GOT1 glutamic-oxaloacetic transaminase 1, soluble 1.5 0.01 GPT2 glutamic pyruvate transaminase (alanine aminotransferase) 2 1.6 0.01 PC pyruvate carboxylase 2.0 0.01 Sulfur Metabolism 0.00 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 3.0 0.00 SULT1B1 sulfotransferase family, cytosolic, 1B, member 1 1.3 0.01 SUOX sulfite oxidase 1.4 0.01 Integrin Signaling 0.00 ACTB actin, beta 1.8 0.01 AKT2 v-akt murine thymoma viral oncogene homolog 2 1.9 0.01 ARF3 ADP-ribosylation factor 3 1.5 0.01 CAPN1 calpain 1, (mu/I) large subunit 1.8 0.00 GRB7 growth factor receptor-bound protein 7 1.7 0.00 PARVA parvin, alpha 1.7 0.00 PXN paxillin 2.0 0.00 RAP2B RAP2B, member of RAS oncogene family 1.3 0.00 RAPGEF1 Rap guanine nucleotide exchange factor (GEF) 1 1.5 0.01 SHC1 SHC (Src homology 2 domain containing) transforming protein 1 2.0 0.01 Gluthionone Metabolism 0.00 GSTM2 glutathione S-transferase M2 (muscle) 1.7 0.01 GSTM3 glutathione S-transferase M3 (brain) 1.7 0.00 GSTM6 glutathione S-transferase, mu 6 1.6 0.00 GSTT3 glutathione S-transferase, theta 3 2.0 0.00 Urea Cycle and Metabolism of Amino Groups 0.00 ACY1 aminoacylase 1 1.9 0.00 ASL argininosuccinate lyase 1.4 0.01 ASS argininosuccinate synthetase 1.2 0.01 Arginine and Proline Metabolism 0.00 ALDH4A1 aldehyde dehydrogenase 4 family, member A1 1.4 0.00 ASL argininosuccinate lyase 1.4 0.01 ASS argininosuccinate synthetase 1.2 0.01 GOT1 glutamic-oxaloacetic transaminase 1, soluble 1.5 0.01 One Carbon Pool by Folate 0.00 FTCD formiminotransferase cyclodeaminase -2.1 0.01 SHMT1 serine hydroxymethyltransferase 1 (soluble) 1.4 0 SHMT2 serine hydroxymethyltransferase 2 (mitochondrial) 1.9 0.01 Lysine Degradation 0.01 ALDH4A1 aldehyde dehydrogenase 4 family, member A1 1.4 0.00 BAT8 euchromatic histone-lysine N-methyltransferase 2 1.6 0.01 SHMT1 serine hydroxymethyltransferase 1 (soluble) 1.4 0 SHMT2 serine hydroxymethyltransferase 2 (mitochondrial) 1.9 0.01 VEGF Signaling 0.01 ACTB actin, beta 1.8 0.01 AKT2 v-akt murine thymoma viral oncogene homolog 2 1.9 0.01 BCLDL1 BCL2-like 1 1.8 0.01 PXN paxillin 2.0 0.00 SHC1 SHC (Src homology 2 domain containing) transforming protein 1 2.0 0.01 Glutamate Metabolism 0.02 ALDH4A1 aldehyde dehydrogenase 4 family, member A1 1.4 0.00 Gene Expression in Mouse Chromosome Substitution Strains 3 Shockley and Churchill, 2006 GOT1 glutamic-oxaloacetic transaminase 1, soluble 1.5 0.01 GPT2 glutamic pyruvate transaminase (alanine aminotransferase) 2 1.6 0.01 Methane Metabolism 0.02 SHMT1 serine hydroxymethyltransferase 1 (soluble) 1.4 0 SHMT2 serine hydroxymethyltransferase 2 (mitochondrial) 1.9 0.01 Pyruvate Metabolism 0.02 ALDH4A1 aldehyde dehydrogenase 4 family, member A1 1.4 0.00 ME1 malic enzyme 1, NADP(+)-dependent, cytosolic -1.5 0.01 PC pyruvate carboxylase 2.0 0.01 PKLR pyruvate kinase, liver and RBC 2.2 0.00 Insulin Receptor Signaling 0.03 AKT2 v-akt murine thymoma viral oncogene homolog 2 1.1 0.01 PDPK1 3-phosphoinositide dependent protein kinase-1 -1.5 0.01 RAPGEF1 Rap guanine nucleotide exchange factor (GEF) 1 1.5 0.01 SHC1 SHC (Src homology 2 domain containing) transforming protein 1 2.0 0.01 TSC2 tuberous sclerosis 2 1.7 0.01 P13K/AKT Signaling 0.03 AKT2 v-akt murine thymoma viral oncogene homolog 2 1.1 0.01 BCL2L1 BCL2-like 1 1.8 0.01 PDPK1 3-phosphoinositide dependent protein kinase-1 -1.5 0.01 TP53 tumor protein p53 (Li-Fraumeni syndrome) 2.0 0.00 TSC2 tuberous sclerosis 2 1.7 0.01 IL-2 Signaling 0.04 AKT2 v-akt murine thymoma viral oncogene homolog 2 1.1 0.01 SHC1 SHC (Src homology 2 domain containing) transforming protein 1 2.0 0.01 STAT5A signal transducer and activator of transcription 5A 2.1 0.01 Hypoxia Signaling in the Cardiovascular System 0.05 TP53 tumor protein p53 (Li-Fraumeni syndrome) 2.0 0.00 ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, UBE2D1 yeast) 1.7 0.00 UBE2L6 ubiquitin-conjugating enzyme E2L 6 2.1 0.01 B.A10 Nicotinate and Nicotinamide Metabolism 0.00 ENPP1 ectonucleotide pyrophosphatase/phosphodiesterase 1 -1.6 0.00 ENPP3 ectonucleotide pyrophosphatase/phosphodiesterase 3 -1.5 0.01 NT5C3 5'-nucleotidase, cytosolic III -1.5 0.01 PBEF1 pre-B-cell colony enhancing factor 1 -1.4 0.00 B.A11 Pyruvate Metabolism 0.01 ALDH1B1 aldehyde dehydrogenase family 1 1.6 0.01 NKD1 naked cuticle homolog 1 (Drosophila) 1.3 0.00 PCK1 phosphoenolpyruvate carboxykinase 1 -1.7 0.00 Gluthionone Metabolism 0.02 ALDH1B1 aldehyde dehydrogenase family 1 1.6 0.01 NKD1 naked cuticle homolog 1 (Drosophila) 1.3 0.00 PCK1 phosphoenolpyruvate carboxykinase 1 -1.7 0.00 Lysine Degradation 0.03 ALDH1B1 aldehyde dehydrogenase family 1 1.6 0.01 SHMT1 serine hydroxymethyltransferase 1 (soluble) 1.9 0.00 Sulfur Metabolism 0.04 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 3.3 0.00 B.A12 Cell Cycle: G1/S Checkpoint Regulation 0.01 E2F6 E2F transcription factor -1.9 0.00 SKP1A S-phase kinase associated protein 1A -1.1 0.00 Phototransduction
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