Supplemental Table 1. Uniquely up- and down- regulated genes in the inguinal fat pads of wild-type ( MMP14 +/++/++/+ ) in response to nutritional change (HFD versus CD) Up-regulated genes HFD/CD (log2 Probe Symbol Description HFD 1 HFD 2 CD 1 CD 2 scale) 1434679_at Ncan neurocan 2.86 7.72 7.92 4.84 5.09 1422155_at Hist2h3c2 histone cluster 2, H3c2 2.08 8.53 8.53 6.41 6.50 1417688_at Fam20c family with sequence similarity 20, member C 2.02 9.45 9.37 7.39 7.39 1447520_at Lbp lipopolysaccharide binding protein 2.44 8.28 8.17 5.65 5.93 1452243_at Kcnj14 potassium inwardly-rectifying channel, subfamily J, member 14 1.87 7.48 7.56 5.61 5.69 1420674_at Pla2g2e phospholipase A2, group IIE 1.90 7.71 7.91 5.92 5.89 1417903_at Dfna5 deafness, autosomal dominant 5 (human) 1.73 6.90 7.01 5.23 5.22 1423294_at Mest mesoderm specific transcript 3.86 11.47 12.03 7.62 8.16 1424338_at Slc6a13 solute carrier family 6 (neurotransmitter transporter, GABA), member 13 1.67 8.97 9.03 7.29 7.36 1436829_at Trim67 tripartite motif-containing 67 2.07 7.95 8.27 6.01 6.07 1422561_at Adamts5 a disintegrin-like and metallopeptidase with thrombospondin type 1 motif, 5 (aggrecanase-2) 1.50 11.82 11.89 10.34 10.37 1422655_at Ptch2 patched homolog 2 1.55 7.91 8.09 6.45 6.45 1455099_at Mogat2 monoacylglycerol O-acyltransferase 2 1.53 6.75 6.54 5.12 5.10 1420553_x_at Serpina1a serine (or cysteine) peptidase inhibitor, clade A, member 1A 2.13 6.24 6.29 3.91 4.36 1455447_at D430019H16Rik RIKEN cDNA D430019H16 gene 1.88 9.74 9.73 7.68 8.04 1423516_a_at Nid2 nidogen 2 1.34 9.17 9.21 7.80 7.90 1423693_at Ela1 elastase 1, pancreatic 1.40 9.11 9.24 7.72 7.84 1435314_at Tph2 tryptophan hydroxylase 2 2.19 5.54 6.04 3.51 3.69 1425891_a_at Grtp1 GH regulated TBC protein 1 1.28 7.93 7.86 6.59 6.65 1428005_at Mosc1 MOCO sulphurase C-terminal domain containing 1 2.48 9.21 9.55 6.64 7.16 1452646_at Trp53inp2 transformation related protein 53 inducible nuclear protein 2 1.54 12.95 13.07 11.59 11.35 1434129_s_at Lhfpl2 lipoma HMGIC fusion partner-like 2 1.29 10.41 10.39 9.05 9.18 1435950_at Hr hairless 1.48 8.49 8.42 6.85 7.10 1416321_s_at Prelp proline arginine-rich end leucine-rich repeat 1.46 11.92 11.96 10.60 10.36 1449152_at Cdkn2b cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) 1.25 8.03 8.04 6.84 6.73 1434342_at S100b S100 protein, beta polypeptide, neural 1.70 8.50 8.38 6.92 6.57 1426562_a_at Olfm1 olfactomedin 1 1.80 8.37 8.31 6.34 6.75 1423136_at Fgf1 fibroblast growth factor 1 1.49 8.48 8.49 6.85 7.14 1445546_at AI844685 expressed sequence AI844685 1.42 9.70 9.93 8.35 8.45 1440649_at EG232599 predicted gene, EG232599 1.33 6.35 6.55 5.08 5.17 1425227_a_at Atp6v0a1 ATPase, H+ transporting, lysosomal V0 subunit A1 1.13 7.07 7.10 5.95 5.97 1434051_s_at Hspa12a heat shock protein 12A 1.36 9.31 9.38 7.86 8.11 1420655_at Pnpla3 patatin-like phospholipase domain containing 3 1.77 11.49 11.47 9.95 9.48 1429030_at C1qtnf7 C1q and tumor necrosis factor related protein 7 1.36 6.94 6.89 5.41 5.69 1416953_at Ctgf connective tissue growth factor 1.25 8.84 8.68 7.59 7.43 1425385_a_at Igh-6 immunoglobulin heavy chain 6 (heavy chain of IgM) 2.45 12.19 12.62 9.65 10.26 1426913_at Lss lanosterol synthase 1.61 7.13 7.12 5.30 5.72 1416121_at Lox lysyl oxidase 1.21 10.97 11.17 9.90 9.81 1416455_a_at Cryab crystallin, alpha B 1.13 10.55 10.71 9.52 9.48 1422558_at Gamt guanidinoacetate methyltransferase 1.15 8.71 8.68 7.45 7.64 1453592_at Lrrc39 leucine rich repeat containing 39 1.13 7.47 7.66 6.42 6.45 1416311_s_at Tuba3a tubulin, alpha 3A 1.10 7.83 7.69 6.62 6.71 1417673_at Grb14 growth factor receptor bound protein 14 2.27 10.51 10.38 7.81 8.53 1450344_a_at Ptger3 prostaglandin E receptor 3 (subtype EP3) 1.32 11.28 11.43 10.17 9.89 1422878_at Syt12 synaptotagmin XII 1.02 9.51 9.61 8.53 8.53 1422580_at Myl4 myosin, light polypeptide 4 1.45 8.72 8.58 7.01 7.39 1439849_at OTTMUSG00000008561 predicted gene, OTTMUSG00000008561 1.03 8.42 8.55 7.43 7.48 1433443_a_at LOC100040592 similar to Hmgcs1 protein 1.05 12.29 12.35 11.20 11.33 1434188_at Slc16a12 solute carrier family 16 (monocarboxylic acid transporters), member 12 1.50 9.01 9.18 7.39 7.78 1422582_at Lep leptin 2.38 12.60 12.58 9.81 10.61 1418884_x_at Tuba1a tubulin, alpha 1A 1.09 13.64 13.55 12.43 12.59 1450702_at Hfe hemochromatosis 1.03 9.09 9.12 8.00 8.15 1420944_at Zfp185 zinc finger protein 185 1.08 8.41 8.46 7.26 7.45 1423179_at Kcnb1 potassium voltage gated channel, Shab-related subfamily, member 1 1.22 7.11 7.19 6.07 5.79 1460583_at Golt1b golgi transport 1 homolog B (S. cerevisiae) 1.04 7.01 6.91 5.85 5.99 1450286_at Npr3 natriuretic peptide receptor 3 2.72 9.16 9.65 6.26 7.10 1455299_at Vgll3 vestigial like 3 (Drosophila) 1.70 8.35 8.69 6.61 7.03 1440888_at Oxtr oxytocin receptor 1.65 7.85 8.02 6.04 6.53 1423369_at Fmr1 fragile X mental retardation syndrome 1 homolog 1.33 11.45 11.52 9.98 10.33 1455025_at Paqr9 progestin and adipoQ receptor family member IX 1.26 10.20 10.22 9.11 8.78 1416529_at Emp1 epithelial membrane protein 1 1.70 12.48 12.45 10.49 11.04 1427247_at D3Bwg0562e DNA segment, Chr 3, Brigham & Women's Genetics 0562 expressed 1.33 6.77 6.83 5.29 5.66 1427123_s_at Copg2as2 coatomer protein complex, subunit gamma 2, antisense 2 1.06 7.44 7.31 6.23 6.39 1455720_at Adamts2 a disintegrin-like and metallopeptidase with thrombospondin type 1 motif, 2 1.44 6.89 7.17 5.75 5.41 1426513_at Rbm28 RNA binding motif protein 28 1.12 9.11 9.18 7.89 8.16 1427299_at Rps6ka3 ribosomal protein S6 kinase polypeptide 3 1.03 8.88 8.94 7.77 7.98 1434520_at Sc5d sterol-C5-desaturase (fungal ERG3, delta-5-desaturase) homolog (S. cerevisae) 1.21 9.93 10.12 8.95 8.67 1427352_at Krt79 keratin 79 1.02 8.00 7.97 7.07 6.86 1418123_at Unc119 unc-119 homolog (C. elegans) 1.01 9.61 9.74 8.57 8.74 1429135_at 1110059M19Rik RIKEN cDNA 1110059M19 gene 2.74 8.72 8.98 5.59 6.63 1438756_at Ankrd29 ankyrin repeat domain 29 1.54 7.54 7.71 5.82 6.34 1425039_at Itgbl1 integrin, beta-like 1 1.15 7.79 7.62 6.41 6.69 1436200_at Lonrf3 LON peptidase N-terminal domain and ring finger 3 1.18 6.39 6.35 5.36 5.02 1436359_at Ret ret proto-oncogene 1.54 7.50 7.74 5.82 6.32 1420427_a_at Dhx32 DEAH (Asp-Glu-Ala-His) box polypeptide 32 1.16 9.26 9.58 8.32 8.21 1429183_at Pkp2 plakophilin 2 1.39 8.56 8.84 7.11 7.51 1428738_a_at D14Ertd449e DNA segment, Chr 14, ERATO Doi 449, expressed 1.04 10.48 10.72 9.63 9.50 ©2010 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/cgi/content/full/db10-0073/DC1. 1423771_at Prkcdbp protein kinase C, delta binding protein 1.15 10.96 11.02 9.66 10.02 1436876_at Rgs7bp regulator of G-protein signalling 7 binding protein 1.13 8.59 8.44 7.55 7.22 1447851_x_at Atp10a ATPase, class V, type 10A 1.93 7.74 7.26 5.25 5.89 1415822_at Scd2 stearoyl-Coenzyme A desaturase 2 1.47 12.69 12.98 11.12 11.61 1448280_at Syp synaptophysin 1.10 7.35 7.31 6.05 6.41 1449249_at Pcdh7 protocadherin 7 1.22 8.31 8.70 7.19 7.38 1418713_at Pcbd1 pterin 4 alpha carbinolamine dehydratase 1 1.01 7.95 7.81 6.72 7.00 1427422_at EG624219 predicted gene, EG624219 1.29 8.10 8.59 7.08 7.04 1449901_a_at Map3k6 mitogen-activated protein kinase kinase kinase 6 1.03 8.37 8.24 7.42 7.11 1419149_at Serpine1 serine (or cysteine) peptidase inhibitor, clade E, member 1 1.15 8.51 8.38 7.10 7.49 1441206_at Synpo2 synaptopodin 2 1.21 9.27 9.21 7.81 8.26 1415993_at Sqle squalene epoxidase 1.13 8.78 9.03 7.62 7.94 1456563_at 4933429F08Rik RIKEN cDNA 4933429F08 gene 1.09 6.28 5.93 4.94 5.09 1417430_at Cdr2 cerebellar degeneration-related 2 1.19 9.23 9.34 7.88 8.32 1416434_at Bcl2l10 Bcl2-like 10 1.06 6.68 6.85 5.87 5.54 1429571_a_at Spaca1 sperm acrosome associated 1 1.10 6.93 7.34 6.10 5.98 1418497_at Fgf13 fibroblast growth factor 13 1.33 10.11 10.12 8.50 9.08 1434581_at 2410066E13Rik RIKEN cDNA 2410066E13 gene 1.10 9.47 9.62 8.24 8.65 1424631_a_at Ighg Immunoglobulin heavy chain (gamma polypeptide) 2.21 11.15 11.12 9.47 8.38 1422533_at Cyp51 cytochrome P450, family 51 1.29 7.32 7.54 5.88 6.41 1418879_at Fam110c family with sequence similarity 110, member C 1.50 7.90 7.97 6.79 6.08 1418547_at Tfpi2 tissue factor pathway inhibitor 2 1.13 7.35 7.45 6.52 6.03 1454623_at Cpa2 carboxypeptidase A2, pancreatic 1.12 6.00 6.27 4.80 5.23 1423596_at Nek6 NIMA (never in mitosis gene a)-related expressed kinase 6 1.02 8.82 8.82 7.59 8.02 1433696_at Hn1l hematological and neurological expressed 1-like 1.00 8.22 8.58 7.29 7.50 1442051_at Hist2h3c1 histone cluster 2, H3c1 1.54 8.82 8.87 7.70 6.91 1436590_at Ppp1r3b protein phosphatase 1, regulatory (inhibitor) subunit 3B 1.28 9.47 9.80 8.64 8.07 1435484_at Slc5a3 solute carrier family 5 (inositol transporters), member 3 1.05 11.58 11.59 10.29 10.79 1434695_at Dtl denticleless homolog (Drosophila) 1.12 6.37 6.31 4.94 5.50 1439885_at Hoxc5 homeo box C5 1.20 8.96 9.11 7.53 8.14 1444089_at Spnb2 spectrin beta 2 1.10 9.17 9.21 7.82 8.38 1450871_a_at Bcat1 branched chain aminotransferase 1, cytosolic 1.02 6.66 6.62 5.36 5.87 1425681_a_at Prnd prion protein dublet 1.46 6.18 6.93 4.89 5.31 1426858_at Inhbb inhibin beta-B 1.16 9.63 9.64 8.13 8.82 1434411_at Col12a1 collagen, type XII, alpha 1 1.02 6.46 6.74 5.30 5.86 1452295_at Pmepa1 prostate transmembrane protein, androgen induced 1 1.01 9.45 9.58 8.82 8.20 Down-regulated genes HFD/CD (log2 Probe Symbol Description HFD 1 HFD 2 CD 1 CD 2 scale) 1422217_a_at Cyp1a1 cytochrome P450, family 1, subfamily a, polypeptide 1 -3.01 4.72 4.75 7.88 7.62 1419669_at Prtn3 proteinase 3 -2.06 7.84 7.89 10.03 9.83 1438403_s_at Malat1 metastasis associated lung adenocarcinoma transcript