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Table S1. Genes Contributing to the Enrichment Scores of GSEA for Gene-Sets Down-Regulated in Adipose Tissue from Diabetic Compared with Non-Diabetic Co-Twins

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Table S1. Genes Contributing to the Enrichment Scores of GSEA for Gene-Sets Down-Regulated in Adipose Tissue from Diabetic Compared with Non-Diabetic Co-Twins Table S1. Genes contributing to the enrichment scores of GSEA for gene-sets down-regulated in adipose tissue from diabetic compared with non-diabetic co-twins. Gene-set name Genes contributing to the enrichment score ALDH9A1, ECHS1, HADHA, AUH, ABAT, HSD17B4, HADHB, HMGCS1, DBT, PCCB, HSA00280 Valine, leucine and isoleucine degradation HIBADH, OXCT1, ALDH7A1, MCCC2, BCKDHB, ACADM, MCCC1, MCEE, PCCA, MUT, ALDH2, ACAT1, DLD, ALDH6A1, HADH, HIBCH ALDH9A1, ECHS1, HADHA, ABAT, SUCLG2, SUCLA2, PCCB, ALDH7A1, SUCLG1, ACACB, HSA00640 Propanoate metabolism ACADM, LDHB, MCEE, ACACA, PCCA, ACSS2, MUT, ALDH2, ACAT1, ALDH6A1, HIBCH ACO2, IDH2, SDHA, IDH3B, PCK1, MDH1, CS, CLYBL, SDHB, ACLY, IDH1, SDHD, FH, ACO1, HSA00020 Citrate cycle SUCLG2, SUCLA2, IDH3A, DLST, SUCLG1, PC, DLD HADHA, ELOVL6, SCD, ACOX1, HSD17B12, HSA01040 Polyunsaturated fatty acid biosynthesis FADS2, ELOVL5, FADS1, PECR, FASN ALDH9A1, ECHS1, HADHA, L2HGDH, ABAT, PDHB, HSD17B4, ALDH5A1, HMGCS1, BDH1, HSA00650 Butanoate metabolism OXCT1, ALDH7A1, PDHA1, AACS, PRDX6, ALDH2, ACAT1, HADH ATP5J, NDUFA1, UQCRQ, ATP12A, ATP6V1E2, NDUFA4, SDHA, NDUFB6, NDUFV3, ATP6V1G1, NDUFC1, ATP5E, COX7A2, ATP5F1, ATP6V1H, ATP6V1G3, NDUFB4, NDUFA12, COX6A1, COX6C, ATP6V1D, UQCRFS1, NDUFB8, SDHB, NDUFS3, HSA00190 Oxidative phosphorylation COX7C, ATP5H, NDUFA6, NDUFS2, ATP5L, SDHD NDUFA8, NDUFB3, ATP6V1C1, NDUFS5, NDUFA9, ATP5A1, ATP5B, COX4I2, COX10, NDUFA5, ATP6V1E1, UQCRH, NDUFV2, PPA2, NDUFA10, NDUFS1, NDUFB5, UQCRB, UQCRC2, ATP5C1, NDUFAB1 ALDH9A1, ECHS1, HADHA, ADH1B, ACSL4, HSA00071 Fatty acid metabolism ACSL3, HSD17B4, HADHB, ACOX1, ADHFE1, ACSL1, GCDH, ALDH7A1, ACADSB, ACADL, ACADM, ALDH2, ACAT1, HADH ACYP2, PCK1, MDH1, ALDH9A1, DLAT, GLO1, HSA00620 Pyruvate metabolism PDHB, LDHD, ME1, ALDH7A1, ACACB, PDHA1, PC, LDHB, ACACA, ACSS2, ALDH2, ACAT1, DLD TAF1, TAF13, GTF2E2, GTF2H2, TBPL1, TAF12, HSA03022 Basal transcription factors GTF2IRD1, TAF2, TAF7, GTF2A1, GTF2H1, GTF2B, TAF9B, GTF2I, GTF2A2, GTF2H3, TAF9 HSA00072 Synthesis and degradation of keton bodies HMGCS1, BDH1, OXCT1, ACAT1 ACO2, IDH2, MDH1, ACLY, IDH1, FH, ACO1, HSA00720 Reductive carboxylate cycle SUCLA2, ACSS2 SUV39H1, RDH14, ALDH9A1, ECHS1, HADHA, TMLHE, HSD17B4, NSD1, DLST, GCDH, HSA00310 Lysine degradation AASDHPPT, ALDH7A1, SHMT1, PLOD2, AASS, ALDH2, ACAT1, HADH NARS2, DLAT, ADSSL1, ABAT, PDHB, DDO, GPT, HSA00252 Alanine and aspartate metabolism DARS, PDHA1, PC, ASPA, GPT2, DLD HSA00061 Fatty acid biosynthesis OXSM, ACACB, ACACA, FASN Table S2. Genes contributing to the enrichment scores of GSEA for gene- sets up-regulated in adipose tissue from diabetic compared with non-diabetic co-twins. Gene-set name Genes contributing to the enrichment score HSA01032 Glycan structures MAN2B2, HEXB, GBA, IDS, GLB1, NEU3, FUCA1, HEXA, degradation MAN2B1, NEU1, NAGLU, GUSB, ARSB, GALNS, FUCA2, NEU4 HSA00603 Glycosphingolipid A4GALT, HEXB, NAGA, HEXA, ST8SIA1, GBGT1, GLA biosynthesis globoseries PLAUR, SERPINA5, F5, C2, SERPINE1, SERPING1, C1S, MASP1, HSA04610 Complement and C1QC, C1R, C3, C3AR1, C7, F10, C1QB, F13A1, C1QA, C5AR1, coagulation cascades PROS1, CFH, CFD, PLAU, F2R, BDKRB2, C4BPB, C6, BDKRB1, FGB, CFB, CR1, CD55, VWF MAN2B2, HEXB, GLB1, NEU3, FUCA1, HEXA, MAN2B1, NEU1, HSA00511 N-glycan degradation FUCA2, NEU4 CD44, CSF1, ANPEP, CD9, CD14, CSF1R, ITGA3, CD38, IL7, IL6R, CD33, CD4, HLA-DRB4, IL11RA, ITGA5, IL4R, FCER2, HSA04640 Hematopoietic cell lineage ITGAM, TNF, HLA-DRB5, HLA-DRA, TFRC, CSF2RA, FLT3LG, CD1C, CD37, HLA-DRB3, CD5, CD3E, CD2, EPO, CD8A, CR1, CD1A, CD55, CD1B, IL1B, ITGA4, CD1E, IL3, CD19, IL1R1, CD22 CTSB, TAPBP, CD74, LGMN, IFI30, HLA-DMB, CALR, RFXANK, CD4, HLA-DRB4, HLA-DMA, CTSL1, HLA-DQA2, HLA-DPB1, HSA04612 Antigen processing and CIITA, HSPA5, HLA-DRB5, HLA-DRA, IFNA1, IFNA6, HLA-DRB3, presentation CD8A, CTSS, HLA-DQA1, HLA-DQB1, HLA-DPA1, KIR2DS5, IFNA14 HSA00604 Glycosphingolipid HEXB, GLB1, B3GALT4, HEXA, ST8SIA1 biosynthesis ganglioseries HSA00532 Glycosaminoglycan XYLT1, UST, CHPF, B3GAT3, CHST14, CHST7, CHST13, biosynthesis B3GALT6 HSA00531 Glycosaminoglycan HEXB, IDS, GLB1, HEXA, NAGLU, GUSB, ARSB, GALNS degradation CD276, ALCAM, ICAM1, ITGB2, CLDN11, GLG1, ITGAV, NLGN2, CLDN20, HLA-DMB, CADM3, CD99, CD28, SIGLEC1, NEGR1, CD4, HLA-DRB4, HLA-DMA, CD86, CNTNAP1, PDCD1LG2, HLA- HSA04514 Cell adhesion molecules DQA2, ITGAM, HLA-DPB1, VCAN, VCAM1, HLA-DRB5, CLDN8, ICOSLG, HLA-DRA, SDC1, CTLA4, PVRL2, MADCAM1, NRXN3, CLDN15, HLA-DRB3, SPN, CD2, ITGB7, CD8A, MPZ, HLA-DQA1, HLA-DQB1, CNTN2, SELPLG, HLA-DPA1, ITGA4, SDC3, MPZL1, SDC4, CD22, PTPRC, CD80, CLDN14, CLDN23, CLDN22, CLDN18 HS3ST2, DDOST, XYLT1, ALG12, UST, GALNT6, CHPF, MAN1B1, B4GALT2, GALNT12, B3GNT1, CHST14, GCNT1, B3GNT7, HSA01030 Glycan structures GALNT10, MAN1C1, ALG3, RPN1, CHST7, EXT2, DPAGT1, biosynthesis 1 B3GNT2, CHST13, MAN1A1, GALNTL1, FUT11, GALNT9, ALG1, MGAT4B, CHST2, RPN2, B3GALT6, CHST11, ST3GAL4, MGAT5, MGAT5B, GALNT4, HS6ST1, GALNT2, MGAT1, NDST2, HS3ST1 RPS16, RPL18, RPS5, RPL10L, RPS27, RPS2, RPL18A, RPS9, RPSA, RPL28, RPS3, RPS4Y1, RPL13A, RPL13, RPS11, RPL8, HSA03010 Ribosome RPL31, RPL19, RPS26, RPL3, RPL12, RPS10, RPS8, RPS28, RPL38, RPL39, RPS24 TNFRSF11A, TNFRSF14, CSF1, CCL22, XCR1, LTBR, PDGFRA, TNFRSF1A, PDGFRB, CXCL16, CCL13, CCL18, IL18, CSF1R, CCL26, TNFRSF10D, IL7, IL6R, PLEKHO2, CCR1, IL10RA, IL12RB2, CCL19, TNFRSF11B, CCL2, TGFB1, IL11RA, PDGFB, IL10RB, VEGFB, IL4R, TGFB2, TNF, TGFB3, CCL8, CCL3, CXCR3, TNFSF8, TNFRSF12A, IL10, EDA2R, IL17RB, CSF2RA, HSA04060 Cytokine cytokine receptor TNFSF15, XCL1, TNFRSF9, IL2RG, IL12RB1, IL21R, IFNA1, interaction FLT3LG, IFNA6, TGFBR2, IL28RA, IL26, ACVR2B, IL15RA, LEP, IL2RB, GH2, EPO, OSMR, CTF1, HGF, CCR2, IL22RA2, CRLF2, TNFRSF1B, CSF2RB, IL17RA, TNFSF9, EDA, CCR4, IL1B, CLCF1, IL3, IL1R1, CCL21, CXCR4, IL29, IFNA14, IL23A, AMH, OSM, INHBB, IL5RA, CXCL12, CXCL6, CCL7, IL28A, CXCL9, GH1, FAS, IL1A HLA-DMB, CD28, HLA-DRB4, HLA-DMA, CD86, HLA-DQA2, TNF, PTPRN, HLA-DPB1, HLA-DRB5, HLA-DRA, HLA-DRB3, HSA04940 Type 1 diabetes mellitus PRF1, HLA-DQA1, HLA-DQB1, HLA-DPA1, IL1B, CD80, FAS, IL1A, LTA, GZMB GBA, SMPD1, GLB1, NEU3, SGMS2, SGPP2, GLA, GALC, NEU1, HSA00600 Sphingolipid metabolism SMPD4, SGPP1, ARSD, NEU4 COL6A2, LAMB2, CD44, TNXB, COL6A1, ITGB5, THBS2, SPP1, VTN, ITGA3, COL1A2, ITGAV, FNDC4, COL6A3, THBS3, FN1, ITGA5, THBS1, HSPG2, LAMB3, FNDC1, SDC1, TNC, COL5A1, HSA04512 ECM receptor interaction SV2A, LAMA2, COL3A1, COL1A1, COL4A4, COL4A6, ITGB7, DAG1, IBSP, ITGB4, LAMC2, VWF, FNDC5, ITGA4, SDC3, RELN, SDC4 IKBKE, CD14, MAPK13, SPP1, IRAK1, IRF5, MAP3K8, MAPK3, HSA04620 Toll like receptor signaling FADD, IKBKB, PIK3R2, LY96, IRF3, MAP2K2, CD86, MYD88, pathway TLR7, PIK3CG, IKBKG, PIK3R5, TRAF3, TNF, TICAM1, CCL3, LBP, MAP2K3, FOS, IFNA1, RELA, IFNA6, TLR5 Table S3. Genes differently expressed in adipose tissue from T2D discordant twin pairs (q<0.15). Non-T2D T2D Difference Gene Symbol Probe ID p value q value mean ± SD mean ± SD (%) ACAT1 7943605 743.5 ± 137.3 604.7 ± 91.1 -18.7 0.0005 0.135 ACVR1C 8055992 2010.2 ± 442.2 1576.0 ± 273.4 -21.6 0.0005 0.135 ADAM20 7979927 168.3 ± 24.9 146.3 ± 15.5 -13.1 0.0005 0.135 ALCAM 8081431 201.2 ± 80.8 316.8 ± 88.5 36.5 0.00098 0.144 ALDH3B1 7941961 182.2 ± 23.6 214.0 ± 18.7 14.8 0.0005 0.135 ALDH6A1 7980098 898.8 ± 170.7 729.5 ± 117.5 -18.8 0.00098 0.144 ANAPC16 7928300 449.9 ± 31.7 402.2 ± 48.7 -10.6 0.00098 0.144 ANKRD18DP 8093272 12.0 ± 1.5 13.8 ± 2.4 13.4 0.00098 0.144 APOC1 8029536 120.0 ± 22.0 162.9 ± 28.7 26.3 0.00098 0.144 ARHGAP1 7947681 1577.3 ± 109.7 1671.6 ± 106.1 5.6 0.00098 0.144 ASB1 8049657 191.2 ± 18.2 211.6 ± 21.2 9.6 0.0005 0.135 ASF1B 8034772 51.1 ± 4.4 59.6 ± 7.8 14.2 0.0005 0.135 ATPAF1 7915870 168.8 ± 16.9 151.2 ± 15.8 -10.5 0.0005 0.135 AVPR1A 7964660 239.9 ± 33.4 214.2 ± 39.3 -10.7 0.0005 0.135 AZGP1 8141374 563.2 ± 302.7 323.5 ± 155.9 -42.6 0.00098 0.144 BAD 7949067 207.6 ± 15.7 226.6 ± 11.3 8.4 0.00098 0.144 BCCIP 7931268 180.2 ± 18.6 158.5 ± 13.8 -12.1 0.0005 0.135 BRAF 8143417 844.8 ± 75.7 779.4 ± 63.4 -7.7 0.00098 0.144 C11orf68 7949540 235.0 ± 15.6 247.5 ± 10.1 5.1 0.0005 0.135 C13orf33 7968351 772.9 ± 305.7 1007.5 ± 378.8 23.3 0.00098 0.144 C14orf39 7979483 23.6 ± 7.2 17.9 ± 5.4 -24.3 0.0005 0.135 C18orf21 8020919 184.4 ± 9.4 167.0 ± 9.0 -9.4 0.00098 0.144 C1S 7953603 1692.1 ± 277.8 2024.4 ± 287.6 16.4 0.00098 0.144 C9orf95 8161839 125.5 ± 22.6 107.0 ± 18.1 -14.8 0.0005 0.135 CAPG 8053417 190.0 ± 43.6 234.6 ± 45.9 19.0 0.00098 0.144 CCDC80 8089544 2739.3 ± 553.6 3205.1 ± 500.4 14.5 0.00098 0.144 CD14 8114612 948.3 ± 484.1 1500.7 ± 622.2 36.8 0.00098 0.144 CD276 7984743 237.4 ± 33.1 288.1 ± 37.0 17.6 0.00098 0.144 CD44 7939341 1888.7 ± 357.0 2272.0 ± 318.5 16.9 0.00098 0.144 CD68 8004510 1931.7 ± 637.0 2879.1 ± 660.8 32.9 0.00098 0.144 CDC20 7900699 89.1 ± 13.2 98.4 ± 11.6 9.4 0.0005 0.135 CHPT1 7958000 1205.7 ± 124.6 1102.7 ± 74.3 -8.5 0.00098 0.144 CLEC3B 8079305 555.9 ± 111.9 675.9 ± 112.9 17.8 0.0005 0.135 CLN3 8000543 262.1 ± 22.9 297.8 ± 26.2 12.0 0.0005 0.135 COMMD5 8153911 144.5 ± 13.5 161.1 ± 8.1 10.3 0.00098 0.144 COPS2 7988605 1343.5 ± 97.9 1182.2 ± 123.9 -12.0 0.0005 0.135 CRB1 7908508 40.9 ± 3.6 36.8 ± 2.5 -9.9 0.00098 0.144 CRBN 8085081 738.9 ± 56.7 677.9 ± 61.2 -8.3 0.00098 0.144 CRELD2 8073949 130.8 ± 9.5 144.0 ± 5.4 9.1 0.0005 0.135 CSE1L 8063283 626.8 ± 46.2 585.3 ± 33.0 -6.6 0.0005 0.135 CTBP2 7936904 182.7 ± 8.3 193.3 ± 11.0 5.5 0.0005 0.135 CTDSPL2 7983335 603.0 ± 55.9 550.3 ± 31.5 -8.7 0.00098 0.144 CTSB 8149330 2508.5 ± 557.8 3148.2 ± 544.4 20.3 0.0005 0.135 CTSD 7945666 2485.5 ± 390.8 3070.1 ± 470.5 19.0 0.00098 0.144 CTSZ 8067279 718.1 ± 129.3 849.7 ± 110.7
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