1. SHC2416.58319p13.3 SHC (Src homology 2 domain containing) transforming protein 2 CDC34531.73319p13.3cell division cycle 34 GZMM544.03419p13.3granzyme M (lymphocyte met-ase 1) BSG572.45419p13.3basigin (Ok blood group) FGF22639.92619p13.3fibroblast growth factor 22 RNF126647.52619p13.3ring finger protein 126 FSTL3676.38919p13follistatin-like 3 (secreted glycoprotein) PTBP1797.39219p13.3polypyrimidine tract binding protein 1 AZU1827.83119p13.3azurocidin 1 PRTN3840.98519p13.3proteinase 3 ELANE852.29119p13.3elastase, neutrophil expressed KISS1R917.34219p13.3KISS1 receptor ARID3A926.03719p13.3AT rich interactive domain 3A (BRIGHT-like) TMEM2 59 1009.65019p13.3transmembrane protein 259 HMHA11065.92219p13.3histocompatibility (minor) HA-1 POLR2E1086.57819p13.3 polymerase (RNA) II (DNA directed) polypeptide E, 25kDa GPX41103.93619p13.3glutathione peroxidase 4 STK111205.79819p13.3serine/threonine kinase 11 CIRBP1269.26719p13.3cold inducible RNA binding protein EFNA21286.15319p13ephrin-A2 MUM11354.97619p13.3melanoma associated antigen (mutated) 1 DAZAP11407.58419p13.3DAZ associated protein 1 RPS151438.36319p13.3ribosomal protein S15 APC21450.14819p13.3adenomatosis polyposis coli 2 PCSK41481.42719p13.3proprotein convertase subtilisin/kexin type 4 REEP61491.16519p13.3receptor accessory protein 6 PLK51524.07319p13.3polo-like kinase 5 MEX3D1554.66819p13.3mex-3 homolog D (C. elegans) MBD31576.67819p13methyl-CpG binding domain protein 3 TCF31609.28919p13.3transcription factor 3 ATP8B31782.07419p13.3 ATPase, aminophospholipid transporter, class I, type 8B, member 3 CSNK1G 2 1941.16119p13.3casein kinase 1, gamma 2 BTBD21985.447 19p13.3 -p12 BTB (POZ) domain containing 2 MKNK22037.47019p13.3MAP kinase interacting serine/threonine kinase 2 AP3D12100.98719p13.3adaptor-related protein complex 3, delta 1 subunit DOT1L2164.14819p13.3DOT1-like histone H3K79 methyltransferase AMH2249.11319p13.3anti-Mullerian hormone OAZ12269.52019p13.3ornithine decarboxylase antizyme 1 SPPL2B2328.62919p13.3signal peptide peptidase like 2B TIMM132425.62219p13.3 translocase of inner mitochondrial membrane 13 homolog (yeast) GADD45B2476.12319p13.3growth arrest and DNA-damage-inducible, beta GNG72511.21819p13.3 guanine nucleotide binding protein (G protein), gamma 7 DIRAS12714.56519p13.3DIRAS family, GTP-binding RAS-like 1 SLC39A32732.52319p13.3 solute carrier family 39 (zinc transporter), member 3 SGTA2754.71219p13 small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha TLE62977.53619p13.3 transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila) AES3052.90819p13.3amino-terminal enhancer of split GNA113094.40819p13.3 guanine nucleotide binding protein (G protein), alpha 11 (Gq class) GNA153136.19119p13.3 guanine nucleotide binding protein (G protein), alpha 15 (Gq class) S1PR43178.73619p13.3sphingosine-1-phosphate receptor 4 NFIC3366.56519p13.3 nuclear factor I/C (CCAAT-binding transcription factor) DOHH3490.81919p13.3deoxyhypusine hydroxylase/monooxygenase FZR13522.95419p13.3fizzy/cell division cycle 20 related 1 (Drosophila) HMG20B3572.94319p13.3high mobility group 20B TBXA2R3594.50419p13.3thromboxane A2 receptor CACTIN3610.62719p13.3cactin, spliceosome C complex subunit PIP5K1C3630.17919p13.3 phosphatidylinositol-4-phosphate 5-kinase, type I, gamma MATK3777.96719p13.3megakaryocyte-associated tyrosine kinase NMRK23933.10119p13.3nicotinamide riboside kinase 2 DAPK33958.45219p13.3death-associated protein kinase 3 MIR6373961.41219p13.3microRNA 637 EEF23976.05419p13.3eukaryotic translation elongation factor 2 PIAS44007.74919p13.3protein inhibitor of activated STAT, 4 ZBTB7A4045.21619p13.3zinc finger and BTB domain containing 7A MAP2K24090.32019p13.3mitogen-activated protein kinase kinase 2 SIRT64174.10619p13.3sirtuin 6 EBI34229.54019p13Epstein-Barr virus induced 3 List of genes in human melanoma 19p13.3 focal deletion Liu et al. Supplementary Figure S1

2. Rank 19p13.3 Gene Name Gene DescriptionProbe Fold Chan ge P Value 1CFD complement factor D (adipsin)205382_s_at 0.083 0661 1.90E -10 2 GNA1 5 guanine nucleotide binding protein (G protein), alpha 15 (Gq class)205349_at 0.248 9184 5.50E -06 3 STAP 2 signal transducing adaptor family member 2221610_s_at 0.329 7773 4.30E -09 4INSRinsulin receptor213792_s_at 0.396 3676 6.30E -06 5 SH2D 3A SH2 domain containing 3A219513_s_at 0.406 7233 5.50E -08 6 MKN K2 MAP kinase interacting serine/threonine kinase 2218205_s_at 0.415 1389 0.000 76 7 ZBTB 7A zinc finger and BTB domain containing 7A219186_at 0.424 1946 4.90E -07 Rank 19p13. 3 Gene Name Gene DescriptionProbe Fold Chang e P Value 1C3 complement component 3217767_at 0.0113 25 1.80E- 19 2CFD complement factor D (adipsin)205382_s_at 0.0120 048 7.30E- 13 3 GADD 45B growth arrest and DNA- damage- inducible, beta207574_s_at 0.1937 9840.0004 4ELANE elastase, neutrophil expressed206871_at 0.2427 1840.008 5 GADD 45B growth arrest and DNA- damage- inducible, beta209304_x_at 0.2785 5150.001 6 ZBTB7 A zinc finger and BTB domain containing 7A213303_x_at 0.2881 844 0.0000 28 7 ANGP TL4 angiopoietin- like 4221009_s_at 0.3003 0030.0025 A B Talantov dataset Kabbarah dataset Liu et al. Supplementary Figure S2

3. Ran kProbe set Gene Symbolfold changeP value 11456137_atNRXN34.920.222497 21416357_a_atMCAM3.430.014862 31424067_atICAM13.060.10178 41438193_atNRXN32.970.11258 51458652_atCD8B2.50.601338 61417597_atCD282.330.021032 71445388_atCD2262.30.439999 81416072_atCD341.980.016671 91436482_a_atSDC31.890.267842 101421966_atNCAM11.870.699974 111455143_atNLGN21.850.082354 121436568_atJAM21.820.044304 131420841_atPTPRF1.760.158278 141433788_atNRXN31.750.126968 151450295_s_atPVR1.740.17447 161449408_atJAM21.720.01615 171423903_atPVR1.70.08544 181449906_atSELP1.690.286053 191439629_atNRXN31.650.429062 A B * * * * * RankNAMESIZENESFDR q-val 1KEGG_GALACTOSE_METABOLISM452.2740740 2 KEGG_CELL_ADHESION_MOLECULES_CA MS2631.9802790.004938 3 KEGG_FRUCTOSE_AND_MANNOSE_MET ABOLISM681.979290.003679 4KEGG_ALLOGRAFT_REJECTION301.9760240.003327 5 KEGG_STARCH_AND_SUCROSE_METAB OLISM521.9505930.00447 6KEGG_LYSOSOME2451.9245180.005045 7 KEGG_EPITHELIAL_CELL_SIGNALING_IN_ HELICOBACTER_PYLORI_INFECTION1601.8811290.006712 8KEGG_GRAFT_VERSUS_HOST_DISEASE231.8626130.006288 9KEGG_OTHER_GLYCAN_DEGRADATION261.8458610.006572 10KEGG_BLADDER_CANCER991.8358970.007127 11 KEGG_SYSTEMIC_LUPUS_ERYTHEMATO SUS961.8259390.007579 12KEGG_AUTOIMMUNE_THYROID_DISEASE371.8222130.007031 13 KEGG_ARACHIDONIC_ACID_METABOLIS M621.8180770.006583 14 KEGG_AMINO_SUGAR_AND_NUCLEOTID E_SUGAR_METABOLISM841.7906790.008669 15 KEGG_DORSO_VENTRAL_AXIS_FORMATI ON591.7881250.008309 16 KEGG_HYPERTROPHIC_CARDIOMYOPAT HY_HCM2061.7723180.008852 17KEGG_DILATED_CARDIOMYOPATHY2301.7495630.010844 18KEGG_VIBRIO_CHOLERAE_INFECTION1251.7447380.010825 19KEGG_INSULIN_SIGNALING_PATHWAY3321.7143270.014388 Liu et al. Supplementary Figure S3

4. Con Zbtb7a Δ/Δ Mcam Mcam Zbtb7a Mcam Hsp90 Zbtb7a Primary MEF Transformed MEF Microarray data Rt-PCR Con Zbtb7a Δ/Δ A B P=1x10 -6 P=1x10 -5 P=0.01 Relative mRNA expression Liu et al. Supplementary Figure S4

5. MCAM Prognosis A B Primary melanoma Metastasis melanoma MCAM CNV 1.0 0.8 0.6 0.4 0.2 0.0 0 1000 2000 3000 4000 Survival probability Time (Days) High MCAM expression Low MCAM expression n. s. P=0.005 Relative CNV value Liu et al. Supplementary Figure S5

6. (Human) (Mouse) Sequence alignment between human and mouse MCAM promoter A E D FLAG-ZBTB7A ZBTB7A  -actin B FLAG-ZBTB7A Con Con ZBTB7A P=0.002P=0.0004 % input MCAM promoter primer 2# MCAM promoter primer 3# Liu et al. Supplementary Figure S6 Conserved ZBTB7A binding sites in human MCAM promoter Luciferase/Renilla pGL3 (basic) pGL3-MCAM ZBTB7A -- Luciferase/Renilla ZBTB7A -- C P=0.0005 P=0.00002 P=0.0001