shc2416.58319p13.3 shc (src homology 2 domain containing) transforming protein 2...
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SHC2 416.583 19p13.3 SHC (Src homology 2 domain containing) transforming protein 2
CDC34 531.733 19p13.3 cell division cycle 34
GZMM 544.034 19p13.3 granzyme M (lymphocyte met-ase 1)
BSG 572.454 19p13.3 basigin (Ok blood group)FGF22 639.926 19p13.3 fibroblast growth factor 22RNF126 647.526 19p13.3 ring finger protein 126
FSTL3 676.389 19p13 follistatin-like 3 (secreted glycoprotein)
PTBP1 797.392 19p13.3 polypyrimidine tract binding protein 1
AZU1 827.831 19p13.3 azurocidin 1PRTN3 840.985 19p13.3 proteinase 3
ELANE 852.291 19p13.3 elastase, neutrophil expressed
KISS1R 917.342 19p13.3 KISS1 receptor
ARID3A 926.037 19p13.3 AT rich interactive domain 3A (BRIGHT-like)
TMEM259
1009.650 19p13.3 transmembrane protein 259
HMHA1 1065.922 19p13.3 histocompatibility (minor) HA-1
POLR2E 1086.578 19p13.3 polymerase (RNA) II (DNA directed) polypeptide E, 25kDa
GPX4 1103.936 19p13.3 glutathione peroxidase 4STK11 1205.798 19p13.3 serine/threonine kinase 11
CIRBP 1269.267 19p13.3 cold inducible RNA binding protein
EFNA2 1286.153 19p13 ephrin-A2
MUM1 1354.976 19p13.3 melanoma associated antigen (mutated) 1
DAZAP1 1407.584 19p13.3 DAZ associated protein 1RPS15 1438.363 19p13.3 ribosomal protein S15
APC2 1450.148 19p13.3 adenomatosis polyposis coli 2
PCSK4 1481.427 19p13.3 proprotein convertase subtilisin/kexin type 4
REEP6 1491.165 19p13.3 receptor accessory protein 6PLK5 1524.073 19p13.3 polo-like kinase 5
MEX3D 1554.668 19p13.3 mex-3 homolog D (C. elegans)
MBD3 1576.678 19p13 methyl-CpG binding domain protein 3
TCF3 1609.289 19p13.3 transcription factor 3
ATP8B3 1782.074 19p13.3 ATPase, aminophospholipid transporter, class I, type 8B, member 3
CSNK1G2
1941.161 19p13.3 casein kinase 1, gamma 2
BTBD2 1985.447 19p13.3-p12 BTB (POZ) domain containing 2
MKNK2 2037.470 19p13.3 MAP kinase interacting serine/threonine kinase 2
AP3D1 2100.987 19p13.3 adaptor-related protein complex 3, delta 1 subunit
DOT1L 2164.148 19p13.3 DOT1-like histone H3K79 methyltransferase
AMH 2249.113 19p13.3 anti-Mullerian hormone
OAZ1 2269.520 19p13.3 ornithine decarboxylase antizyme 1
SPPL2B 2328.629 19p13.3 signal peptide peptidase like 2B
TIMM13 2425.622 19p13.3 translocase of inner mitochondrial membrane 13 homolog (yeast)
GADD45B 2476.123 19p13.3 growth arrest and DNA-damage-inducible, beta
GNG7 2511.218 19p13.3 guanine nucleotide binding protein (G protein), gamma 7
DIRAS1 2714.565 19p13.3 DIRAS family, GTP-binding RAS-like 1
SLC39A3 2732.523 19p13.3 solute carrier family 39 (zinc transporter), member 3
SGTA 2754.712 19p13 small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha
TLE6 2977.536 19p13.3 transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)
AES 3052.908 19p13.3 amino-terminal enhancer of split
GNA11 3094.408 19p13.3 guanine nucleotide binding protein (G protein), alpha 11 (Gq class)
GNA15 3136.191 19p13.3 guanine nucleotide binding protein (G protein), alpha 15 (Gq class)
S1PR4 3178.736 19p13.3 sphingosine-1-phosphate receptor 4
NFIC 3366.565 19p13.3 nuclear factor I/C (CCAAT-binding transcription factor)
DOHH 3490.819 19p13.3 deoxyhypusine hydroxylase/monooxygenase
FZR1 3522.954 19p13.3 fizzy/cell division cycle 20 related 1 (Drosophila)
HMG20B 3572.943 19p13.3 high mobility group 20BTBXA2R 3594.504 19p13.3 thromboxane A2 receptor
CACTIN 3610.627 19p13.3 cactin, spliceosome C complex subunit
PIP5K1C 3630.179 19p13.3 phosphatidylinositol-4-phosphate 5-kinase, type I, gamma
MATK 3777.967 19p13.3 megakaryocyte-associated tyrosine kinase
NMRK2 3933.101 19p13.3 nicotinamide riboside kinase 2
DAPK3 3958.452 19p13.3 death-associated protein kinase 3
MIR637 3961.412 19p13.3 microRNA 637
EEF2 3976.054 19p13.3 eukaryotic translation elongation factor 2
PIAS4 4007.749 19p13.3 protein inhibitor of activated STAT, 4
ZBTB7A 4045.216 19p13.3 zinc finger and BTB domain containing 7A
MAP2K2 4090.320 19p13.3 mitogen-activated protein kinase kinase 2
SIRT6 4174.106 19p13.3 sirtuin 6EBI3 4229.540 19p13 Epstein-Barr virus induced 3
List of genes in human melanoma 19p13.3 focal deletion
Liu et al. Supplementary Figure S1
Rank
19p13.3 Gene Name
Gene Description Probe
Fold Change
P Value
1 CFD
complement factor D (adipsin) 205382_s_at
0.0830661
1.90E-10
2GNA15
guanine nucleotide binding protein (G protein), alpha 15 (Gq class) 205349_at
0.2489184
5.50E-06
3STAP2
signal transducing adaptor family member 2 221610_s_at
0.3297773
4.30E-09
4 INSR insulin receptor 213792_s_at0.3963676
6.30E-06
5SH2D3A
SH2 domain containing 3A 219513_s_at
0.4067233
5.50E-08
6MKNK2
MAP kinase interacting serine/threonine kinase 2 218205_s_at
0.4151389
0.00076
7ZBTB7A
zinc finger and BTB domain containing 7A 219186_at
0.4241946
4.90E-07
Rank
19p13.3 Gene Name
Gene Description Probe
Fold Change
P Value
1 C3complement component 3 217767_at
0.011325
1.80E-19
2 CFD
complement factor D (adipsin) 205382_s_at
0.0120048
7.30E-13
3GADD45B
growth arrest and DNA-damage-inducible, beta 207574_s_at
0.1937984 0.0004
4 ELANE
elastase, neutrophil expressed 206871_at
0.2427184 0.008
5GADD45B
growth arrest and DNA-damage-inducible, beta 209304_x_at
0.2785515 0.001
6ZBTB7A
zinc finger and BTB domain containing 7A 213303_x_at
0.2881844
0.000028
7ANGPTL4
angiopoietin-like 4 221009_s_at
0.3003003 0.0025
A BTalantov datasetKabbarah dataset
Liu et al. Supplementary Figure S2
Rank Probe set
Gene Symbol fold change P value
1 1456137_at NRXN3 4.92 0.222497
2 1416357_a_at MCAM 3.43 0.014862
3 1424067_at ICAM1 3.06 0.10178
4 1438193_at NRXN3 2.97 0.11258
5 1458652_at CD8B 2.5 0.601338
6 1417597_at CD28 2.33 0.021032
7 1445388_at CD226 2.3 0.439999
8 1416072_at CD34 1.98 0.016671
9 1436482_a_at SDC3 1.89 0.267842
10 1421966_at NCAM1 1.87 0.699974
11 1455143_at NLGN2 1.85 0.082354
12 1436568_at JAM2 1.82 0.044304
13 1420841_at PTPRF 1.76 0.158278
14 1433788_at NRXN3 1.75 0.126968
15 1450295_s_at PVR 1.74 0.17447
16 1449408_at JAM2 1.72 0.01615
17 1423903_at PVR 1.7 0.08544
18 1449906_at SELP 1.69 0.286053
19 1439629_at NRXN3 1.65 0.429062
A B
*
*
*
*
*
Rank NAME SIZE NES FDR q-val
1 KEGG_GALACTOSE_METABOLISM 45 2.274074 0
2KEGG_CELL_ADHESION_MOLECULES_CAMS 263 1.980279 0.004938
3KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 68 1.97929 0.003679
4 KEGG_ALLOGRAFT_REJECTION 30 1.976024 0.003327
5KEGG_STARCH_AND_SUCROSE_METABOLISM 52 1.950593 0.00447
6 KEGG_LYSOSOME 245 1.924518 0.005045
7KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION 160 1.881129 0.006712
8 KEGG_GRAFT_VERSUS_HOST_DISEASE 23 1.862613 0.006288
9 KEGG_OTHER_GLYCAN_DEGRADATION 26 1.845861 0.006572
10 KEGG_BLADDER_CANCER 99 1.835897 0.007127
11KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS 96 1.825939 0.007579
12 KEGG_AUTOIMMUNE_THYROID_DISEASE 37 1.822213 0.007031
13 KEGG_ARACHIDONIC_ACID_METABOLISM 62 1.818077 0.006583
14KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM 84 1.790679 0.008669
15KEGG_DORSO_VENTRAL_AXIS_FORMATION 59 1.788125 0.008309
16KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM 206 1.772318 0.008852
17 KEGG_DILATED_CARDIOMYOPATHY 230 1.749563 0.010844
18 KEGG_VIBRIO_CHOLERAE_INFECTION 125 1.744738 0.010825
19 KEGG_INSULIN_SIGNALING_PATHWAY 332 1.714327 0.014388
Liu et al. Supplementary Figure S3
Con Zbtb7aΔ/Δ0
100200300400500600700800900
1000
0
1
2
3
4
5
6
7
0
0.2
0.4
0.6
0.8
1
1.2
Mcam Mcam Zbtb7a
Mcam
Hsp90
Zbtb7a
Primary MEF Transformed MEF
Microarray data Rt-PCR
Con Zbtb7aΔ/Δ Con Zbtb7aΔ/Δ
A
B
Con Zbtb7aΔ/Δ Con Zbtb7aΔ/Δ
P=1x10-6P=1x10-5
P=0.01
Re
lativ
e m
RN
A e
xpre
ssio
n
Re
lativ
e m
RN
A e
xpre
ssio
n
Re
lativ
e m
RN
A e
xpre
ssio
n
Liu et al. Supplementary Figure S4
MCAM Prognosis A
B
-0.3
-0.295
-0.29
-0.285
-0.28
-0.275
-0.27
-0.265
-0.26
Primar
y m
elan
oma
Met
asta
sis m
elan
oma
MCAM CNV
1.0
0.8
0.6
0.4
0.2
0.0
0 1000 2000 3000 4000
Su
rviv
al p
rob
ab
ility
Time (Days)
High MCAM expression
Low MCAM expression
n. s.
P=0.005
Re
lativ
e C
NV
va
lue
Liu et al. Supplementary Figure S5
(Human)(Mouse)
Sequence alignment between human and mouse MCAM promoter
A
E
D
FLAG-ZBTB7A
ZBTB7AZBTB7A
b-actin
B
FLAG-ZBTB7A
Con
Con ZBTB7A Con ZBTB7A
P=0.002 P=0.0004
% in
put
% in
put
MCAM promoter primer 2#
MCAM promoter primer 3#
0
0.2
0.4
0.6
0.8
1
1.2
1.4
0
0.2
0.4
0.6
0.8
1
1.2
1.4
Liu et al. Supplementary Figure S6
Conserved ZBTB7A binding sites in human MCAM promoter
0.65
0.7
0.75
0.8
0.85
0.9
0
5
10
15
20
25
Luci
fera
se/R
enill
a pGL3 (basic)
pGL3-MCAM
ZBTB7A --
Luci
fera
se/R
enill
a
ZBTB7A --
C
P=0.0005P=0.00002
P=0.0001