List of Supplementary Tables

Supplementary Table 1. Candidate chosen for analysis.

Supplementary Table 2. Candidate sets chosen for analysis from the Molecular

Signatures Database

Supplementary Table 3. Changes in serum biomarker levels from baseline to 6-months.

Supplementary Table 4. Changes in adipose-tissue (unsupervised) by weight- change category.

Supplementary Table 1. Candidate genes chosen for analysis.

Gene Location Description ADIPOQ 3q27.3a Homo sapiens adiponectin, C1Q and collagen domain containing (ADIPOQ), mRNA. ALOX5 10q11.21d Homo sapiens arachidonate 5-lipoxygenase (ALOX5), mRNA. ALOX5AP 13q12.3c Homo sapiens arachidonate 5-lipoxygenase-activating (ALOX5AP), mRNA. CCL2 17q12a Homo sapiens chemokine (C-C motif) ligand 2 (CCL2), mRNA. CD14 5q31.3b Homo sapiens CD14 molecule (CD14), transcript variant 1, mRNA. CD3D 11q23.3d Homo sapiens CD3D antigen, delta polypeptide (TiT3 complex) (CD3D), mRNA. CD4 12p13.31d Homo sapiens CD4 molecule (CD4), mRNA. CD68 17p13.1d Homo sapiens CD68 molecule (CD68), transcript variant 1, mRNA. CD8B 2p11.2e Homo sapiens CD8b molecule (CD8B), transcript variant 1, mRNA. CRP 1q23.2b Homo sapiens C-reactive protein, pentraxin-related (CRP), mRNA. Homo sapiens colony stimulating factor 1 (macrophage) (CSF1), transcript variant 1, CSF1 1p13.3b mRNA. CSF2 5q31.1b Homo sapiens colony stimulating factor 2 (granulocyte-macrophage) (CSF2), mRNA. Homo sapiens cytochrome P450, family 19, subfamily A, polypeptide 1 (CYP19A1), CYP19A1 15q21.2b transcript variant 1, mRNA. ESR1 6q25.1c Homo sapiens estrogen receptor 1 (ESR1), mRNA. ESR2 14q23.2b Homo sapiens estrogen receptor 2 (ER beta) (ESR2), transcript variant b, mRNA. FABP1 2p11.2d Homo sapiens fatty acid binding protein 1, liver (FABP1), mRNA. FABP2 4q26f Homo sapiens fatty acid binding protein 2, intestinal (FABP2), mRNA. Homo sapiens fatty acid binding protein 3, muscle and heart (mammary-derived FABP3 1p35.2a growth inhibitor) (FABP3), mRNA. FABP4 8q21.13b Homo sapiens fatty acid binding protein 4, adipocyte (FABP4), mRNA. FASLG 1q24.3d Homo sapiens Fas ligand (TNF superfamily, member 6) (FASLG), mRNA. FLT3LG 19q13.33b Homo sapiens fms-related tyrosine kinase 3 ligand (FLT3LG), mRNA. FOXP3 Xp11.23b Homo sapiens forkhead box P3 (FOXP3), mRNA. HMOX1 22q12.3c Homo sapiens heme oxygenase (decycling) 1 (HMOX1), mRNA. Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1 (HSD11B1), transcript HSD11B1 1q32.2b variant 2, mRNA. Homo sapiens hydroxysteroid (11-beta) dehydrogenase 1-like (HSD11B1L), transcript HSD11B1L 19p13.3b variant c, mRNA. HSD11B2 16q22.1b Homo sapiens hydroxysteroid (11-beta) dehydrogenase 2 (HSD11B2), mRNA. HSD17B1 17q21.31a Homo sapiens hydroxysteroid (17-beta) dehydrogenase 1 (HSD17B1), mRNA. Homo sapiens hydroxysteroid (17-beta) dehydrogenase 10 (HSD17B10), nuclear HSD17B10 Xp11.22a gene encoding mitochondrial protein, transcript variant 1, mRNA. HSD17B11 4q22.1a Homo sapiens hydroxysteroid (17-beta) dehydrogenase 11 (HSD17B11), mRNA. HSD17B12 11p11.2e Homo sapiens hydroxysteroid (17-beta) dehydrogenase 12 (HSD17B12), mRNA. HSD17B4 5q23.1c Homo sapiens hydroxysteroid (17-beta) dehydrogenase 4 (HSD17B4), mRNA. HSD17B7 1q23.3c Homo sapiens hydroxysteroid (17-beta) dehydrogenase 7 (HSD17B7), mRNA. HSD17B8 6p21.32a Homo sapiens hydroxysteroid (17-beta) dehydrogenase 8 (HSD17B8), mRNA. Homo sapiens intercellular adhesion molecule 1 (CD54), human rhinovirus receptor ICAM1 19p13.2c (ICAM1), mRNA. Homo sapiens intercellular adhesion molecule 4 (Landsteiner-Wiener blood group) ICAM4 19p13.2c (ICAM4), transcript variant 2, mRNA. IFNG 12q15a Homo sapiens interferon, gamma (IFNG), mRNA. IGF1 12q23.2a Homo sapiens insulin-like growth factor 1 (somatomedin C) (IGF1), mRNA. Gene Location Description IGFBP1 7p13b Homo sapiens insulin-like growth factor binding protein 1 (IGFBP1), mRNA. Homo sapiens insulin-like growth factor binding protein 3 (IGFBP3), transcript variant IGFBP3 7p13b 2, mRNA. IL10 1q32.1h Homo sapiens interleukin 10 (IL10), mRNA. IL1B 2q13d Homo sapiens interleukin 1, beta (IL1B), mRNA. IL6 7p15.3c Homo sapiens interleukin 6 (interferon, beta 2) (IL6), mRNA. IL8 4q13.3d Homo sapiens interleukin 8 (IL8), mRNA. INSR 19p13.2e Homo sapiens insulin receptor (INSR), transcript variant 1, mRNA. Homo sapiens integrin, alpha L (antigen CD11A (p180), lymphocyte function- ITGAL 16p11.2c associated antigen 1; alpha polypeptide) (ITGAL), mRNA. Homo sapiens integrin, alpha M (complement component 3 receptor 3 subunit) ITGAM 16p11.2c (ITGAM), mRNA. Homo sapiens integrin, alpha X (complement component 3 receptor 4 subunit) ITGAX 16p11.2c (ITGAX), mRNA. Homo sapiens integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated ITGB2 21q22.3e antigen 1; macrophage antigen 1 (mac-1) beta subunit) (ITGB2), mRNA. LEP 7q32.1a Homo sapiens leptin (obesity homolog, mouse) (LEP), mRNA. LIPE 19q13.2c Homo sapiens lipase, hormone-sensitive (LIPE), mRNA. LPL 8p21.3c Homo sapiens lipoprotein lipase (LPL), mRNA. Homo sapiens myeloperoxidase (MPO), nuclear gene encoding mitochondrial protein, MPO 17q22d mRNA. 10p12.33c- MRC1 Homo sapiens mannose receptor, C type 1 (MRC1), mRNA. p12.33b MYD88 3p22.2a Homo sapiens myeloid differentiation primary response gene (88) (MYD88), mRNA. Homo sapiens nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 NFKB1 4q24b (p105) (NFKB1), mRNA. Homo sapiens POT1 protection of telomeres 1 homolog (S. pombe) (POT1), POT1 7q31.33a transcript variant 3, transcribed RNA. 3p25.2a- Homo sapiens proliferator-activated receptor gamma (PPARG), transcript PPARG p25.1d variant 2, mRNA. Homo sapiens prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase PTGS1 9q33.2b and cyclooxygenase) (PTGS1), transcript variant 1, mRNA. Homo sapiens prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase PTGS2 1q31.1a and cyclooxygenase) (PTGS2), mRNA. RBP4 10q23.33b Homo sapiens retinol binding protein 4, plasma (RBP4), mRNA. RETN 19p13.2e Homo sapiens resistin (RETN), mRNA. SAA1 11p15.1d Homo sapiens serum amyloid A1 (SAA1), transcript variant 1, mRNA. SHBG 17p13.1d Homo sapiens sex hormone-binding globulin (SHBG), mRNA. Homo sapiens solute carrier family 2 (facilitated glucose transporter), member 4 SLC2A4 17p13.1d (SLC2A4), mRNA. Xp22.31e- STS Homo sapiens sulfatase (microsomal), isozyme S (STS), mRNA. p22.31d Homo sapiens sulfotransferase family 1E, estrogen-preferring, member 1 (SULT1E1), SULT1E1 4q13.3a mRNA. TEP1 14q11.2b Homo sapiens telomerase-associated protein 1 (TEP1), mRNA. TERC 3q26.2b Homo sapiens telomerase RNA component (TERC), non-coding RNA. Homo sapiens telomeric repeat binding factor (NIMA-interacting) 1 (TERF1), TERF1 8q21.11a transcript variant 1, mRNA. TERF2 16q22.1d Homo sapiens telomeric repeat binding factor 2 (TERF2), mRNA. Homo sapiens telomeric repeat binding factor 2, interacting protein (TERF2IP), TERF2IP 16q23.1a mRNA. Gene Location Description TERT 5p15.33d Homo sapiens telomerase reverse transcriptase (TERT), transcript variant 1, mRNA. TGFB1 19q13.2c Homo sapiens transforming growth factor, beta 1 (TGFB1), mRNA. TINF2 14q12a Homo sapiens TERF1 (TRF1)-interacting nuclear factor 2 (TINF2), mRNA. TLR2 4q31.3d Homo sapiens toll-like receptor 2 (TLR2), mRNA. TLR4 9q33.1c Homo sapiens toll-like receptor 4 (TLR4), mRNA. TNF 6p21.33a Homo sapiens tumor necrosis factor (TNF superfamily, member 2) (TNF), mRNA. Homo sapiens tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase TNKS 8p23.1c (TNKS), mRNA. 10q23.32a- Homo sapiens tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2 TNKS2 q23.32b (TNKS2), mRNA. TPP1 11p15.4c Homo sapiens tripeptidyl peptidase I (TPP1), mRNA. Homo sapiens vascular cell adhesion molecule 1 (VCAM1), transcript variant 2, VCAM1 1p21.2a mRNA. Homo sapiens vascular endothelial growth factor A (VEGFA), transcript variant 3, VEGFA 6p21.1c mRNA.

Supplementary Table 2. Candidate gene sets chosen for analysis from the Molecular Signatures Database Diet Exercise Diet + Exercise % Weight Change # of p Adj. p p Adj. p p Adj. p p Adj. p Gene Set Name Source genes value value value value value value value value† dcpathway Biocarta 22 0.63 0.93 0.61 0.90 0.30 0.68 0.88 0.95 hsa00010_glycolysis_and_gluconeogenesis KEGG 64 0.90 0.96 0.07 0.53 0.68 0.82 0.25 0.77 hsa00071_fatty_acid_metabolism KEGG 47 0.82 0.95 0.84 0.90 0.80 0.83 0.58 0.95 hsa00140_c21_steroid_hormone_metabolism KEGG 11 0.62 0.93 0.11 0.53 0.61 0.82 0.005 0.07 hsa03320_ppar_signaling_pathway KEGG 70 0.98 0.98 0.80 0.90 0.11 0.45 0.82 0.95 hsa04630_jak_stat_signaling_pathway KEGG 153 0.004 0.06 0.48 0.90 0.64 0.82 0.042 0.30 hsa04660_t_cell_receptor_signaling_pathway KEGG 93 0.16 0.91 0.20 0.65 0.63 0.82 0.43 0.85 hsa04910_insulin_signaling_pathway KEGG 135 0.53 0.93 0.83 0.90 0.83 0.83 0.26 0.77 hsa04920_adipocytokine_signaling_pathway KEGG 72 0.75 0.93 0.43 0.90 0.12 0.45 0.76 0.95 hypoxia_review Wash U 81 0.36 0.93 0.22 0.65 0.71 0.82 0.99 0.99 il1rpathway Biocarta 33 0.70 0.93 0.69 0.90 0.32 0.68 0.45 0.85 il6pathway Biocarta 21 0.46 0.93 0.06 0.53 0.0002 0.003 0.06 0.30 nkcellspathway Biocarta 20 0.18 0.91 1.00 1.00 0.19 0.58 0.42 0.85 tnfr1pathway Biocarta 29 0.45 0.93 0.76 0.90 0.61 0.82 0.89 0.95 Tollpathway Biocarta 37 0.73 0.93 0.44 0.90 0.03 0.20 0.80 0.95

† adjusted to account for 82 simultaneous comparisons, using the Benjamini and Hochberg method [42]

Supplementary Table 3. Changes in serum biomarker levels from baseline to 6- months. Intervention Group Diet+ Control Diet Exercise Exercise (n=7) (n=8) (n=14) (n=16) Mean† Mean† Mean† Serum values Mean† (95% CI) (95% CI) (95% CI) (95% CI) (pg/mL) Baseline 35.2 32.2 40.6 35.4 (22.4-55.2) (22.6-45.8) (33.5-49.3) (29.5-42.5) 6 month 41.3 34.5 40.3 39.1 (28.4-60.1) (27.6-43.0) (32.7-49.8) (32.3-47.2) Δ% 17.5 7.2 -0.7 10.4 p* 0.48 0.13 0.55 Estradiol (pg/mL) Baseline 11.5 8.7 12.2 10.8 (7.2-18.3) (6.2-12.2) (9.7-15.3) (8.4-13.9) 6 month 17.9 9.6 13.1 12.2 (11.1-28.9) (7.1-12.9) (10.2-16.7) (10.0-14.9) Δ% 55.9 9.8 7.4 12.7 p* 0.18 0.13 0.20 Total Testosterone (ng/dL) Baseline 24.5 25.9 29.5 29.7 (14.3-42.1) (16.9-39.6) (23.2-37.5) (23.5-37.5) 6 month 30.2 27.2 28.5 29.0 (19.8-46.1) (19.6-37.8) (22.0-36.9) (22.2-37.7) Δ% 23.2 5.2 -3.3 -2.5 p* 0.15 0.02 <0.01 Androstenedione (ng/dL) Baseline 47.2 52.9 53.7 55.1 (33.6-66.4) (40.2-69.6) (42.1-68.6) (47.0-64.7) 6 month 69.7 58.1 57.3 53.3 (47.6-102.2) (46.5-72.8) (45.3-72.5) (45.2-62.8) Δ% 22.5 10.0 6.7 -3.3 p* 0.01 0.01 <0.001 SHBG (nmol/L) Baseline 31.4 36.0 40.7 34.3 (23.4-42.1) (26.3-49.3) (32.2-51.6) (30.1-39.1) 6 month 31.1 44.4 41.3 40.9 (31.1-23.2) (34.4-57.3) (33.1-51.7) (36.0-46.4) Δ% -1.1 23.4 1.5 19.1 p* <0.01 0.68 0.01 CRP (mg/L) Baseline 2.60 1.68 3.13 2.40 (1.71-3.95) (0.69-4.08) (2.01-4.86) (1.46-3.97) 6 month 2.57 1.22 2.55 1.46 (1.65-4.01) (0.46-3.22) (1.63-3.99) (0.85-2.51) Δ% -0.9 -27.5 -18.4 -39.3 p* 0.29 0.34 0.05 SAA (mg/L) Baseline 6.37 4.40 5.35 6.52 (3.90-10.4) (2.62-7.41) (4.15-6.88) (4.75-8.95) 6 month 5.46 3.09 5.47 4.46 (3.63-8.19) (1.88-5.08) (4.13-7.25) (3.34-5.95) Δ% -14.3 -29.9 2.4 -31.7 Intervention Group Diet+ Control Diet Exercise Exercise (n=7) (n=8) (n=14) (n=16) Mean† Mean† Mean† Serum values Mean† (95% CI) (95% CI) (95% CI) (95% CI) p* 0.56 0.22 0.21 IL-6 (pg/mL) Baseline 1.62 2.09 1.33 1.53 (1.07-2.44) (0.95-4.57) (1.05-1.67) (1.25-1.88) 6 month 1.21 1.24 1.22 1.10 (0.81-1.80) (0.94-1.64) (0.98-1.53) (0.94-1.30) Δ% -25.3 -40.6 -7.9 -27.9 p* 0.53 0.24 0.79 Adiponectin (µg/mL) Baseline 12.4 11.5 12.6 13.3 (8.8-17.4) (9.1-14.6) (9.8-16.3) (10.5-16.8) 6 month 11.1 13.0 12.5 13.8 (7.3-16.9) (9.6-17.5) (9.5-16.4) (10.7-17.7) Δ% -10.4 12.3 -1.1 3.5 p* 0.14 0.52 0.28 Leptin (ng/mL) Baseline 31.4 22.0 24.7 28.6 (25.1-39.2) (15.5-31.1) (19.0-32.0) (23.1-35.3) 6 month 33.7 11.3 28.4 16.1 (25.8-44.0) (8.0-16.0) (18.2-44.3) (11.4-22.8) Δ% 7.5 -48.5 15.1 -43.5 p* <0.001 0.40 <0.0001 Insulin (µIU/mL) Baseline 13.0 8.5 12.3 9.8 (7.8-21.5) (5.5-13.0) (10.1-15.0) (7.8-12.2) 6 month 11.0 5.9 12.0 6.5 (8.1-15.0) (4.0-8.8) (9.6-14.9) (4.8-8.9) Δ% -15.3 -30.5 -2.9 -33.5 p* 0.42 0.48 0.24 Glucose (mg/dL) Baseline 92.6 92.7 97.2 96.7 (88.7-96.6) (89.9-95.5) (91.9-102.8) (92.9-100.7) 6 month 94.9 93.3 100.7 98.0 (90.8-99.1) (88.8-98.0) (95.9-105.8) (93.3-102.9) Δ% 2.5 0.7 3.7 1.3 p* 0.44 0.45 0.54

Supplementary Table 4. Changes in adipose-tissue gene expression (unsupervised) by weight-change category (all women combined).* Weight-Change Group Gene All groups Gained <= 5% loss 5-10% loss >10% loss >10% loss

(n=45) (n=10) (n=10) (n=11) (n=14) vs. <=10% Adj. 6 % 6 % 6 % 6 % 6 % loss P

Baseline month change Baseline month change Baseline month change Baseline month change Baseline month change Adj. P trend ZNF10 93 91 -3% 101 76 -24% 101 88 -13% 92 94 3% 85 103 21% 0.012 0.004 BCYRN1 1024 827 -19% 928 1648 78% 723 863 19% 1379 910 -34% 1115 455 -59% 0.014 0.009 ZFP2 111 111 1% 133 105 -21% 115 103 -10% 99 111 12% 102 122 20% 0.016 0.009 HSZFP36 218 222 2% 239 198 -17% 238 217 -9% 206 207 0% 200 260 30% 0.012 0.009 EIF4A2 6380 6370 0% 7065 5487 -22% 6962 6772 -3% 5938 5859 -1% 5897 7244 23% 0.010 0.010 CHAF1A 38 38 -1% 35 43 23% 34 38 11% 39 39 2% 43 33 -24% 0.014 0.013 KBTBD2 634 606 -4% 669 520 -22% 728 632 -13% 585 611 4% 590 654 11% 0.016 0.013 RSBN1 531 525 -1% 563 451 -20% 565 528 -7% 497 491 -1% 512 614 20% 0.012 0.013 ABCC6 88 77 -13% 92 96 4% 80 81 1% 87 83 -4% 92 59 -35% 0.014 0.013 PELI2 233 228 -2% 238 179 -25% 252 234 -7% 227 214 -6% 223 280 26% 0.012 0.013 ZNF33B 226 236 4% 238 202 -15% 237 223 -6% 230 245 7% 209 266 27% 0.026 0.013 HIST1H4H 129 101 -22% 143 154 8% 90 99 9% 147 123 -16% 140 65 -53% 0.014 0.014 CEBPZ 727 753 4% 790 666 -16% 761 746 -2% 694 706 2% 687 871 27% 0.014 0.014 C6 320 476 49% 315 269 -15% 379 403 6% 292 326 12% 307 1083 253% 0.012 0.014 MRAP 3366 2785 -17% 3364 3673 9% 3120 2863 -8% 3429 3292 -4% 3502 1966 -44% 0.012 0.017 TMEM189 291 251 -14% 293 301 3% 279 272 -2% 300 277 -8% 292 192 -34% 0.016 0.017 MGC13057 92 82 -11% 82 106 29% 81 79 -3% 104 90 -13% 99 66 -34% 0.016 0.017 MAST4 228 222 -3% 200 281 41% 214 225 6% 248 240 -4% 247 174 -30% 0.016 0.017 RCOR3 830 824 -1% 906 674 -26% 899 872 -3% 767 792 3% 782 942 20% 0.014 0.017 SFRS7 597 581 -3% 642 515 -20% 676 573 -15% 524 505 -3% 576 714 24% 0.016 0.017 LOC643496 20 20 0% 22 17 -24% 21 18 -11% 19 20 2% 17 23 32% 0.030 0.017 PTK2 1106 1082 -2% 1197 987 -18% 1188 1102 -7% 1036 1066 3% 1045 1154 10% 0.036 0.023 ZNF627 215 215 0% 233 195 -16% 229 214 -6% 202 208 3% 203 239 17% 0.034 0.023 HS.333084 1966 1371 -30% 2109 3001 42% 1280 1474 15% 2601 2067 -21% 2038 539 -74% 0.026 0.024 HIST1H1C 333 316 -5% 267 350 31% 288 356 23% 379 364 -4% 392 243 -38% 0.047 0.024 ANKRD12 489 461 -6% 538 406 -25% 511 463 -9% 454 437 -4% 468 526 12% 0.026 0.024 ZNF225 62 60 -3% 67 54 -19% 64 60 -6% 61 60 -1% 59 66 13% 0.030 0.024 ZNF615 324 314 -3% 353 274 -22% 350 322 -8% 295 296 0% 309 354 15% 0.026 0.024 ZNF529 205 203 -1% 224 191 -15% 223 196 -12% 191 189 -1% 191 228 20% 0.046 0.024 Weight-Change Group Gene All groups Gained <= 5% loss 5-10% loss >10% loss >10% loss

(n=45) (n=10) (n=10) (n=11) (n=14) vs. <=10% Adj. 6 % 6 % 6 % 6 % 6 % loss P

Baseline month change Baseline month change Baseline month change Baseline month change Baseline month change Adj. P trend EIF4B 4691 4899 4% 4991 4174 -16% 5040 4898 -3% 4348 4882 12% 4527 5508 22% 0.042 0.024 ZNF816A 169 164 -2% 187 156 -16% 180 157 -13% 157 154 -2% 158 185 17% 0.048 0.026 ABCA1 3274 3364 3% 3553 2840 -20% 3415 3240 -5% 3028 3315 9% 3188 3945 24% 0.045 0.026 BNC2 204 203 -1% 225 171 -24% 209 198 -5% 182 190 4% 204 244 20% 0.026 0.027 GPLD1 73 61 -16% 72 73 2% 65 66 2% 77 67 -13% 78 48 -39% 0.052 0.030 RAB3B 31 31 -3% 31 37 19% 28 31 9% 33 32 -3% 33 26 -22% 0.046 0.030 GRB10 92 88 -4% 103 81 -21% 99 89 -10% 83 88 7% 87 93 7% 0.049 0.030 LOC728564 444 431 -3% 440 376 -14% 475 418 -12% 443 428 -3% 426 486 14% 0.055 0.030 RNF38 352 348 -1% 378 296 -22% 390 369 -5% 324 338 4% 332 383 16% 0.033 0.030 TP53INP1 206 201 -3% 210 165 -22% 231 211 -8% 196 199 1% 195 224 15% 0.036 0.030 LEP 8768 7081 -19% 9473 9513 0% 7837 7881 1% 9170 8015 -13% 8678 4820 -44% 0.047 0.031 BOAT 98 94 -4% 81 107 32% 90 92 2% 110 107 -3% 110 81 -26% 0.030 0.031 HIST2H2AA 325 325 0% 259 381 47% 300 334 11% 352 332 -6% 379 279 -26% 0.047 0.031 3 LOC402560 481 468 -3% 433 518 19% 436 506 16% 492 482 -2% 545 403 -26% 0.065 0.031 NUP133 548 528 -4% 580 455 -22% 593 554 -6% 534 535 0% 507 559 10% 0.036 0.031 ZFP82 124 117 -6% 143 112 -22% 136 111 -18% 115 114 0% 112 128 14% 0.069 0.031 HS.375537 22 21 -5% 20 24 22% 22 22 -1% 25 22 -12% 23 19 -19% 0.045 0.031 MB 28 26 -6% 27 31 13% 27 26 -3% 28 26 -7% 30 24 -18% 0.042 0.031 POGK 818 801 -2% 893 752 -16% 841 777 -8% 812 791 -3% 759 866 14% 0.048 0.031 ZNF187 92 94 2% 96 86 -11% 98 94 -4% 91 90 -1% 86 104 21% 0.046 0.031 JAG1 393 388 -1% 423 343 -19% 436 372 -15% 368 372 1% 365 449 23% 0.067 0.034 SNRK 1079 1027 -5% 1169 928 -21% 1201 1079 -10% 991 961 -3% 1009 1123 11% 0.042 0.035 DCP2 407 393 -3% 446 346 -22% 396 371 -6% 406 393 -3% 388 450 16% 0.042 0.035 FLJ10213 80 83 4% 89 75 -15% 84 81 -3% 78 83 6% 72 91 25% 0.055 0.035 ATP6V0E2 1894 1760 -7% 1875 2137 14% 1825 1752 -4% 1907 1897 -1% 1949 1450 -26% 0.026 0.035 ACYP2 349 346 -1% 337 407 21% 323 351 9% 355 358 1% 373 298 -20% 0.051 0.035 ZNF818 21 22 2% 26 20 -23% 23 22 -7% 20 21 8% 18 23 26% 0.058 0.035 POP5 255 251 -2% 247 298 21% 236 257 9% 262 250 -4% 272 218 -20% 0.065 0.036 ZNF71 35 36 4% 30 39 29% 33 39 17% 38 37 -4% 38 33 -14% 0.070 0.036 ACVR1 681 694 2% 674 583 -14% 812 696 -14% 623 630 1% 649 845 30% 0.058 0.036 CSTA 61 58 -5% 57 76 34% 52 55 5% 72 66 -7% 65 45 -30% 0.043 0.038 Weight-Change Group Gene All groups Gained <= 5% loss 5-10% loss >10% loss >10% loss

(n=45) (n=10) (n=10) (n=11) (n=14) vs. <=10% Adj. 6 % 6 % 6 % 6 % 6 % loss P

Baseline month change Baseline month change Baseline month change Baseline month change Baseline month change Adj. P trend LOC390349 21 19 -7% 19 20 4% 17 22 28% 21 19 -12% 24 17 -29% 0.121 0.038 HS.542955 23 23 -1% 20 26 30% 25 24 -2% 23 24 8% 24 19 -22% 0.016 0.038 PCDH18 999 1009 1% 1102 785 -29% 1244 1117 -10% 782 774 -1% 964 1381 43% 0.019 0.038 LOC654113 21 21 -2% 25 17 -32% 22 21 -6% 19 23 22% 20 23 12% 0.055 0.038 C6ORF52 85 89 5% 74 107 46% 70 86 23% 106 93 -12% 89 76 -15% 0.067 0.039 PHIP 278 275 -1% 283 215 -24% 303 287 -6% 257 264 3% 273 327 20% 0.045 0.040 DPYSL2 5827 5699 -2% 6381 5362 -16% 6049 5584 -8% 5712 5492 -4% 5400 6217 15% 0.055 0.041 C16ORF61 1301 1252 -4% 1202 1495 24% 1249 1255 1% 1416 1275 -10% 1326 1086 -18% 0.055 0.046 ZNF26 118 113 -4% 129 102 -21% 126 111 -11% 107 108 0% 115 128 12% 0.065 0.046 RPS6KA5 61 65 5% 61 55 -9% 67 64 -3% 60 65 8% 59 73 22% 0.070 0.046 C20ORF24 3376 3004 -11% 3551 3860 9% 3020 2972 -2% 3574 3176 -11% 3373 2422 -28% 0.058 0.048 DBI 4255 4080 -4% 3976 4911 24% 3880 4176 8% 4463 4141 -7% 4594 3475 -24% 0.069 0.048 NIPBL 172 165 -4% 184 149 -19% 183 168 -8% 163 166 2% 163 175 7% 0.067 0.048 ZNF200 63 62 -2% 68 57 -16% 69 60 -12% 59 60 2% 59 68 15% 0.082 0.048 RIOK2 382 382 0% 424 345 -19% 373 381 2% 357 339 -5% 380 451 19% 0.014 0.048 ZNF823 125 131 5% 132 119 -10% 128 125 -2% 125 126 1% 118 148 25% 0.060 0.048 ZNF22 840 860 2% 864 768 -11% 898 859 -4% 793 792 0% 821 995 21% 0.049 0.048 C9ORF116 64 62 -3% 59 75 26% 62 64 3% 61 64 5% 70 51 -27% 0.048 0.049 GLT8D3 173 164 -5% 196 155 -21% 176 158 -10% 165 164 0% 161 175 9% 0.069 0.049 CLK2 106 116 9% 110 108 -1% 109 113 3% 100 113 13% 106 127 20% 0.077 0.049 ZNF226 52 53 2% 48 58 21% 49 57 16% 56 57 2% 57 46 -19% 0.077 0.049 LOC401115 1411 1348 -4% 1243 1882 51% 1324 1316 -1% 1689 1462 -13% 1403 1012 -28% 0.048 0.049 ADNP 87 86 -1% 91 73 -19% 94 87 -8% 79 83 5% 87 100 16% 0.067 0.049 * Only transcripts with adjusted P trend <0.05 † adjusted to account for 82 simultaneous comparisons, using the Benjamini and Hochberg method [42]