Table S2: Cancer associated genes that have a change in gene

Table S2: Cancer associated genes that have a change in gene copy number. Proteomic and genomic data
was compared to the cancer gene census” published by the welcome trust Sanger institute. Table indicates
deleted and amplified genes that positively correlate with the protein level.
HCC1143
HCC2218
Cell
Log 2
Ratio
proteome
Log2
Ratio
genome
CDH1
MAP2K4
TAF15
LASP1
HIP1
CBFB
HRPT2
TOP1
GOLGA5
PRKAR1A
COX6C
FH
TCEA1
ERBB2
LASP1
SDHB
ERCC4
LPP
SS18
TIF1
CEP1
SMARCB1
NF2
-3.0
-1.1
-0.6
-1.6
-1.0
-1.8
0.5
1.8
1.5
1.0
3.5
1.8
1.7
5.8
-1.1
-1.3
-0.5
0.7
0.9
1.5
2.0
1.6
-3.1
-1.0
-1.0
-0.9
-0.8
-0.7
0.6
0.6
0.7
1.0
1.1
1.1
1.1
2.3
-0.8
-0.8
-0.7
0.5
0.5
0.5
0.5
0.6
3.3
0.6
COX6C
TFG
D10S170
TAF15
0.9
0.8
0.5
0.6
0.6
0.6
0.9
0.6
CDK4
EP300
TPM3
ZNF278
MSN
FANCD2
SSH3BP1
FIP1L1
EWSR1
0.5
1.4
0.6
3.1
0.7
3.5
0.8
1.5
0.7
0.7
0.7
0.7
0.8
0.8
0.8
0.9
0.8
0.9
AKT1
CCND1
BRD4
1.1
2.2
1.5
2.4
2.1
2.5
Gene name
Cancer type
lobular breast, gastric
pancreatic, breast, colorectal
chondrosarcomas, ALL
AML
CMML
AML
parathyroid adenoma
AML
papillary thyroid
papillary thyroid
uterine leiomyoma
salivary adenoma
breast, ovarian
AML
lipoma, leukemia
synovial sarcoma
APL
MPD, NHL
malignant rhabdoid
meningioma, acoustic neuroma
uterine leiomyoma
papillary thyroid, ALCL
papillary thyroid, CML
extraskeletal myxoid chondrosarcomas,
ALL
colorectal, breast, pancreatic, AML
papillary thyroid, ALCL
Ewing sarcoma
ALCL
AML
idiopathic hypereosinophilic syndrome
Ewing sarcoma, desmoplastic small
round cell tumor , ALL
breast, colorectal, ovarian, NSCLC
CLL, B-ALL, breast
lethal midline carcinoma of young
people
Cancer
molecular
genetics
Rec
Rec
Dom
Dom
Dom
Dom
Rec
Dom
Dom
Dom, Rec
Dom
Rec
Dom
Dom
Dom
Rec
Rec
Dom
Dom
Dom
Dom
Rec
Rec
Mutation type
Dom
Dom
Dom
Dom
Mis, N, F, S
D, Mis, N
T
T
T
T
Mis, N, F
T
T
T, Mis, N, F, S
T
Mis, N, F
T
A, Mis, O
T
Mis, N, F
Mis, N, F
T
T
T
T
D, N, F, S
D, Mis, N, F, S,
O
T
T
T
T
Dom
Rec
Dom
Dom
Dom
Rec
Dom
Dom
Dom
Mis
T
T
T
T
D, Mis, N, F
T
T
T
Dom
Dom
Dom
Mis
T
T