Chr
c
|
Gene
|
Description
|
Samples with LOH sites
e
|
6
|
AKAP12
d
|
A kinase (PRKA) anchor protein 12
|
Gastric1, Gastric3, Liver1
|
6
|
PARK2
|
Parkin RBR E3 ubiquitin protein ligase
|
Glioma3, Glioma5, Lung5
|
7
|
FBXL13
|
F-box and leucine-rich repeat protein 13
|
Glioma3, Liver1, Lung5
|
7
|
CUX1
d
|
Cut-like homeobox 1
|
Glioma5, Liver4, Lung5, Lung-Brain3
|
8
|
CSMD1
d
|
CUB and Sushi multiple domains 1
|
Gastric1, Glioma2 (2), Glioma3 (2), Liver1, Liver3, Liver5, Lung1, Lung5, Lung-Brain2 (1 + 1)
|
8
|
MFHAS1
|
Malignant fibrous histiocytoma amplified sequence 1
|
Gastric1, Liver4, Liver5
|
9
|
PPP2R4
|
Protein phosphatase 2A activator, regulatory subunit 4
|
Glioma1, Lung3, Lung5
|
9
|
PTPRD
d
|
Protein tyrosine phosphatase, receptor type, D
|
Glioma1, Glioma3, Leukemia5, Liver1, Lung5 (3), Lung-Brain2
|
9
|
ROR2
|
Receptor tyrosine kinase-like orphan receptor 2
|
Gastric1 (3), Glioma3, Lung2
|
11
|
NUP98
d
|
Nucleoporin 98 kDa
|
Gastric3, Glioma3, Liver2, Lung-Brain1 (3)
|
12
|
CHFR
|
Checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase
|
Glioma3, Liver2, Lung-Brain4
|
14
|
EGLN3
|
Egl-9 family hypoxia-inducible factor 3
|
Lung5 (1 + 1), Lung-Brain4, Lung-Brain5
|
16
|
DNAJA3
|
DnaJ (Hsp40) homolog, subfamily A, member 3
|
Liver4, Lung1, Lung5
|
16
|
AXIN1
d
|
Axin 1
|
Glioma2, Liver1, Lung5
|
19
|
GLTSCR1
d
|
Glioma tumor suppressor candidate region gene 1
|
Glioma5, Lung5, Lung-Brain4
|
22
|
PRR5
|
Proline rich 5 (renal)
|
Glioma3, Liver3, Lung5
|
B. Additional genes present in NCG4.0 database with LOH occurrence in three or more cancer samples
b
|
Chr
c
|
Gene
|
Description
|
Samples with LOH sites
e
|
1
|
SMG5
|
SMG5 Nonsense Mediated MRNA Decay Factor
|
Liver2, Lung1, Lung5 (3), Lung-Brain2, Lung-Brain4
|
1
|
KAZN
|
Kazrin, Periplakin Interacting Protein
|
Gastric3, Liver1, Lung5, Lung-Brain2
|
2
|
CTNNA2
|
Catenin (Cadherin-Associated Protein), Alpha 2
|
Lung1, Lung3, Lung5 (2 + 2)
|
2
|
DPP10
|
Dipeptidyl-Peptidase 10 (Non-Functional)
|
Gastric1, Glioma3, Glioma5
|
3
|
ERC2
|
ELKS/RAB6-Interacting/CAST Family Member 2
|
Gastric3, Glioma3, Lung2
|
4
|
ELOVL6
|
ELOVL Fatty Acid Elongase 6
|
Glioma3, Glioma4, Lung-Brain2
|
4
|
FSTL5
|
Follistatin-Like 5
|
Glioma2, Lung5, Lung-Brain2
|
5
|
AFF4
|
AF4/FMR2 Family, Member 4
|
Gastric1, Glioma3, Lung5 (2)
|
5
|
DMGDH
|
Dimethylglycine Dehydrogenase
|
Gastric1, Liver5 (2), Lung2, Lung-Brain4
|
7
|
HIP1
|
Huntingtin Interacting Protein 1
|
Gastric1, Glioma5, Liver1, Liver4, Lung2, Lung5, Lung-Brain2
|
7
|
CARD11
|
Caspase Recruitment Domain Family, Member 11
|
Glioma2, Glioma5, Lung-Brain5
|
8
|
RIMS2
|
regulating synaptic membrane exocytosis 2
|
Glioma3 (1 + 1), Lung5, Liver5
|
9
|
FNBP1
|
Formin Binding Protein 1
|
Gastric5, Glioma5, Liver2 (2)
|
10
|
SORCS1
|
Sortilin-Related VPS10 Domain Containing Receptor 1
|
Gastric1, Glioma3, Liver4
|
10
|
CTNNA3
|
Catenin (Cadherin-Associated Protein), Alpha 3
|
Gastric1 (2), Glioma2, Lung-Brain1, Lung-Brain2
|
10
|
PFKP
|
Phosphofructokinase, Platelet
|
Glioma3, Lung5, Lung-Brain4
|
10
|
TACC2
|
Transforming, acidic coiled-coil containing protein 2
|
Gastric1, Lung2, Leukemia3, Liver4
|
10
|
DLG5
|
Discs, Large Homolog 5 (Drosophila)
|
Glioma5, Liver1, Lung5 (2)
|
10
|
TET1
|
Tet Methylcytosine Dioxygenase 1
|
Glioma3, Lung5 (4), Lung-Brain2 (1 + 1)
|
11
|
NUMA1
|
Nuclear Mitotic Apparatus Protein 1
|
Glioma2, Glioma4, Lung2
|
11
|
PGAP2
|
Post-GPI attachment to proteins 2
|
Lung4, Lung5, Liver2
|
13
|
FREM2
|
FRAS1 Related Extracellular Matrix Protein 2
|
Liver1, Lung2, Lung-Brain2
|
13
|
ZMYM2
|
Zinc Finger, MYM-Type 2
|
Gastric1, Liver1, Lung2
|
16
|
SLC38A8
|
Solute Carrier Family 38, Member 8
|
Glioma3, Glioma5, Lung-Brain2
|
16
|
RBFOX1
|
RNA Binding Protein, Fox-1 Homolog (C. Elegans) 1
|
Glioma3, Liver4, Lung5 (6)
|
17
|
SEPT9
|
Septin 9
|
Glioma1, Liver1, Lung5 (2)
|
17
|
CDK12
|
Cyclin-Dependent Kinase 12
|
Glioma5, Liver3, Lung5 (1 + 2)
|
17
|
DNAH9
|
Dynein, axonemal, heavy chain 9
|
Glioma3, Lung5 (2), Lung-Brain1, Lung-Brain4
|
17
|
GAS7
|
Growth Arrest-Specific 7
|
Gastric3 (2), Glioma2, Glioma3, Glioma4, Liver2, Lung-Brain4
|
17
|
RPS6KB1
|
Ribosomal Protein S6 Kinase, 70 kDa, Polypeptide 1
|
Gastric1, Liver2 (3), Liver4, Lung5
|
17
|
WIPF2
|
WAS/WASL Interacting Protein Family, Member 2
|
Liver2, Lung4, Lung-Brain2
|
18
|
MBP
|
Myelin Basic Protein
|
Gastric1, Glioma4, Lung5
|
18
|
LAMA1
|
Laminin, Alpha 1
|
Glioma3, Liver4, Lung5
|
18
|
LDLRAD4
|
Low Density Lipoprotein Receptor Class A Domain Containing 4
|
Gastric4, Glioma2, Glioma5, Lung5 (2), Lung-Brain4
|
18
|
GREB1L
|
Growth Regulation By Estrogen In Breast Cancer-Like
|
Liver4, Lung5, Lung-Brain2
|
19
|
GLTSCR1
|
Glioma Tumor Suppressor Candidate Region Gene 1
|
Glioma5, Lung-Brain4, Lung5
|
20
|
ZSWIM3
|
Zinc Finger, SWIM-Type Containing 3
|
Gastric1, Glioma3, Glioma5, Liver1
|
22
|
TRIOBP
|
TRIO And F-Actin Binding Protein
|
Glioma5, Lung5 (3), Lung-Brain2
|
C. Genes present in TSGene database with GOH occurrence in three or more cancer samples
b
|
Chr
c
|
Gene
|
Description
|
Samples with GOH sites
|
8
|
CSMD1
f
|
CUB and Sushi multiple domains 1
|
Gastric3 (2), Gastric4, Glioma3 (2), Lung5 (2)
|
9
|
PTPRD
f
|
Protein Tyrosine Phosphatase, Receptor Type, D
|
Glioma1, Liver1, Lung5, Lung-Brain5
|
9
|
DAPK1
|
Death-Associated Protein Kinase 1
|
Glioma4, Liver1, Lung1
|
9
|
ROR2
|
Receptor Tyrosine Kinase-Like Orphan Receptor
|
Gastric5, Glioma5, Lung5 (2)
|
11
|
ST5
|
Suppression of Tumorigenicity 5
|
Glioma3, Glioma4, Glioma5
|
12
|
CHFR
|
Checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase
|
Gastric1, Glioma5, Lung5 (3), Lung-Brain3
|
16
|
CDH1
f
|
Cadherin 1, Type 1, E-Cadherin (Epithelial)
|
Gastric2 (3), Lung5 (3), Lung-Brain4
|
22
|
CHEK2
f
|
Checkpoint kinase 2
|
Glioma3, Lung2, Lung5
|
D. Additional genes present in NCG4.0 database with GOH occurrence in three or more cancer samples
b
|
Chr
c
|
Gene
|
Description
|
Samples with GOH sites
|
1
|
KAZN
|
Kazrin, Periplakin Interacting Protein
|
Gastric4, Glioma4, Lung5 (4)
|
1
|
FMN2
|
Formin 2
|
Lung5, Liver1, Lung-Brain1
|
1
|
NLRP3
|
NLR Family, Pyrin Domain Containing 3
|
Glioma3 (3), Liver1 (2), Lung5
|
4
|
FSTL5
|
Follistatin-Like 5
|
Liver4, Lung2, Lung5 (2)
|
5
|
PCDHGC5
|
Protocadherin Gamma Subfamily C, 5
|
Liver2, Lung2, Lung5 (2)
|
7
|
KMT2C
|
Lysine (K)-Specific Methyltransferase 2C
|
Gastric2, Gastric5 (2), Leukemia4, Liver2, Liver4
|
9
|
FNBP1
|
Formin Binding Protein 1
|
Glioma5, Lung5, Lung-Brain1
|
9
|
TRPM6
|
Transient Receptor Potential Cation Channel, Subfamily M, Member 6
|
Glioma3, Liver4, Lung5
|
10
|
CTNNA3
|
Catenin (Cadherin-Associated Protein), Alpha 3
|
Glioma3, Liver1, Lung2, Lung5
|
10
|
PFKP
|
Phosphofructokinase, Platelet
|
Gastric1, Glioma1, Lung5
|
12
|
SP1
|
Sp1 Transcription Factor
|
Glioma3, Glioma4, Lung4 (2)
|
12
|
KDM2B
|
Lysine (K)-specific demethylase 2B
|
Glioma5, Lung5, Lung-Brain4
|
12
|
ERC1
|
ELKS/RAB6-Interacting/CAST Family Member 1
|
Gastric1, Lung2, Lung5, Liver5
|
13
|
ATP11A
|
ATPase, class VI, type 11A
|
Glioma3, Liver1, Liver2
|
16
|
CNOT1
|
CCR4-NOT Transcription Complex, Subunit 1
|
Glioma2, Glioma3, Lung5
|
16
|
SNX29
|
Sorting nexin 29
|
Gastric5, Lung5 (3), Liver1, Lung-Brain2
|
16
|
RBFOX1
|
RNA Binding Protein, Fox-1 Homolog (C. Elegans) 1
|
Gastric2, Glioma3 (4), Liver1 (2), Liver2, Lung4, Lung5 (3)
|
17
|
SEPT9
|
Septin 9
|
Liver1, Lung3, Lung5
|
17
|
RPS6KB1
|
Ribosomal Protein S6 Kinase, 70 kDa, Polypeptide 1
|
Gastric3, Glioma4, Lung-Brain3
|
17
|
TRIM37
|
Tripartite Motif Containing 37
|
Glioma1 (2), Glioma3, Glioma4
|
17
|
ITGAE
|
Integrin, Alpha E (Antigen CD103, Human Mucosal Lymphocyte Antigen 1; Alpha Polypeptide)
|
Glioma3, Glioma4 (2), Glioma5, Lung5 (2)
|
18
|
GREB1L
|
Growth Regulation By Estrogen In Breast Cancer-Like
|
Lung2, Lung4, Lung-Brain2 (2)
|
19
|
PTPRS
|
Protein tyrosine phosphatase, receptor type, S
|
Gastric1, Glioma5, Lung4
|
22
|
TUBA8
|
Tubulin, alpha 8
|
Gastric5, Glioma3, Lung5
|
E. Additional genes present in Ensemble database with extensive LOH occurrences
g
|
|
Gene
|
Description
|
Samples with LOH sites
e
|
2
|
MTA3
|
Metastasis associated 1 family, member 3 [Source:HGNC Symbol;Acc:23784]
|
Gastric1, Lung-Brain2, Lung3 (2), Liver2, Lung-Brain3
|
3
|
EIF2B5
|
Eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82 kDa [Source:HGNC Symbol;Acc:3261]
|
Glioma3, Lung5 (8), Liver5, Leukemia1
|
4
|
SMIM14
|
Small integral membrane protein 14 [Source:HGNC Symbol;Acc:27,321]
|
Liver2, Lung-Brain5, Glioma3, Leukemia5, Lung1 (2)
|
6
|
ATXN1
|
Ataxin 1 [Source:HGNC Symbol;Acc:10548]
|
Glioma5, Lung4, Lung5, Liver1, Lung-Brain5
|
6
|
RP11-146I2.1
|
Not Applicable
|
Glioma3, Lung3, Lung5, Liver2, Lung-Brain4
|
7
|
COL26A1
|
Collagen, type XXVI, alpha 1 [Source:HGNC Symbol;Acc:18038]
|
Gastric1, Lung1, Lung2, Liver1, Lung-Brain1
|
7
|
TYW1B
|
tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:33908]
|
Gastric1, Glioma3, Glioma5, Lung1, Lung5
|
8
|
LOXL2
|
Lysyl oxidase-like 2 [Source:HGNC Symbol;Acc:6666]
|
Liver2 (2), Glioma3, Glioma4, Liver1, Liver3
|
8
|
RP11-124B13.1
|
Not Applicable
|
Gastric1, Glioma1, Glioma3, Lung2, Liver2
|
9
|
DMRT1
|
Doublesex and mab-3 related transcription factor 1 [Source:HGNC Symbol;Acc:2934]
|
Glioma5, Gastric3, Lung5, Glioma1, Gastric1, Lung-Brain2
|
9
|
ODF2
|
Outer dense fiber of sperm tails 2 [Source:HGNC Symbol;Acc:8114]
|
Lung-Brain2, Lung5 (2), Glioma5, Lung4, Lung-Brain4, Liver4
|
10
|
CAMK1D
|
Calcium/calmodulin-dependent protein kinase ID [Source:HGNC Symbol;Acc:19341]
|
Lung5 (4), Liver5, Glioma5 (2), Leukemia4, Lung-Brain4, Liver1 (1 + 1), Glioma3
|
10
|
FRMD4A
|
FERM domain containing 4A [Source:HGNC Symbol;Acc:25491]
|
Lung5 (2 + 8), Glioma5, Glioma3, Gastric1, Liver5
|
11
|
TMEM135
|
Transmembrane protein 135 [Source:HGNC Symbol;Acc:26167]
|
Gastric1, Glioma3, Glioma4, Glioma5, Lung3
|
14
|
KLC1
|
Kinesin light chain 1 [Source:HGNC Symbol;Acc:6387]
|
Liver5, Lung-Brain2, Gastric1, Glioma3, Liver2, Lung5
|
16
|
ABCC1
|
ATP-binding cassette, sub-family C (CFTR/MRP), member 1 [Source:HGNC Symbol;Acc:51]
|
Lung5 (2 + 2), Lung1, Liver2, Lung-Brain2, Lung-Brain1
|
16
|
C16orf45
|
Chromosome 16 open reading frame 45 [Source:HGNC Symbol;Acc:19213]
|
Gastric1, Glioma3, Lung2, Lung5, Lung-Brain5
|
17
|
NMT1
|
N-myristoyltransferase 1 [Source:HGNC Symbol;Acc:7857]
|
Glioma5, Liver4, Lung5 (2), Gastric1 (2), Glioma3,
|
17
|
PITPNC1
|
Phosphatidylinositol transfer protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:21045]
|
Gastric1, Gastric4, Glioma3, Glioma5, Lung2
|
17
|
RAP1GAP2
|
RAP1 GTPase activating protein 2 [Source:HGNC Symbol;Acc:29176]
|
Liver2 (2), Glioma5 (2), Lung-Brain2 (2 + 1), Gastric5, Gastric1, Lung4, Lung5
|
17
|
RBFOX3
|
RNA binding protein, fox-1 homolog (C. elegans) 3 [Source:HGNC Symbol;Acc:27097]
|
Glioma3, Glioma5, Liver3, Lung-Brain4 (1 + 3), Lung-Brain5
|
18
|
DLGAP1
|
Discs, large (Drosophila) homolog-associated protein 1 [Source:HGNC Symbol;Acc:2905]
|
Lung-Brain2, Lung5 (2 + 1), Gastric4, Gastric1, Lung-Brain2, Glioma3
|
19
|
INSR
|
Insulin receptor [Source:HGNC Symbol;Acc:6091]
|
Liver3, Liver4, Lung2, Lung5 (1 + 1), Gastric1 (2)
|
19
|
SIPA1L3
|
Signal-induced proliferation-associated 1 like 3 [Source:HGNC Symbol;Acc:23801]
|
Glioma3, Lung-Brain2, Liver2, Lung5, Glioma3, Lung5
|
19
|
TDRD12
|
Tudor domain containing 12 [Source:HGNC Symbol;Acc:25044]
|
Lung-Brain1, Glioma5, Lung1, Glioma5, Glioma2, Liver2
|
19
|
GNG7
|
Guanine nucleotide binding protein (G protein), gamma 7 [Source:HGNC Symbol;Acc:4410]
|
Lung5 (1 + 7), Lung-Brain4 (3)
|
22
|
SYN3
|
Synapsin III [Source:HGNC Symbol;Acc:11496]
|
Lung3, Lung5, Lung-Brain4, Glioma3 (1 + 2), Glioma5
|
F. Additional genes present in Ensemble database with extensive GOH occurrences
g
|
Chr
c
|
Gene
|
Description
|
Samples with GOH sites
e
|
1
|
RPRD2
|
Regulation of nuclear pre-mRNA domain containing 2 [Source:HGNC Symbol;Acc:29039]
|
Gastric2, Glioma3, Glioma4, Glioma5 (2), Liver1, Lung4, Lung5
|
1
|
CLSTN1
|
Calsyntenin 1 [Source:HGNC Symbol;Acc:17447]
|
Gastric5, Lung2, Lung5, Lung-Brain2, Lung-Brain4
|
1
|
KIF26B
|
Kinesin family member 26B [Source:HGNC Symbol;Acc:25484]
|
Liver3, Glioma3, Glioma5 (2), Lung5 (3), Gastric1
|
1
|
GON4L
|
Gon-4-like (C. elegans) [Source:HGNC Symbol;Acc:25973]
|
Lung2 (2), Lung5 (2), Glioma4 (2), Lung-Brain1, Gastric4
|
1
|
NMNAT2
|
Calsyntenin 1 [Source:HGNC Symbol;Acc:17447]
|
Glioma5, Lung1, Lung5, Liver1, Lung-Brain1
|
2
|
FAM178B
|
Family with sequence similarity 178, member B [Source:HGNC Symbol;Acc:28036]
|
Gastric5, Glioma3, Liver3, Liver5, Lung3
|
2
|
MTA3
|
Metastasis associated 1 family, member 3 [Source:HGNC Symbol;Acc:23784]
|
Glioma1, Glioma2, Glioma4, Liver1, Lung-Brain3
|
3
|
EIF2B5
|
Eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82 kDa [Source:HGNC Symbol;Acc:3261]
|
Gastric3, Glioma5 (3), Lung5, Lung-Brain2, Lung-Brain4
|
4
|
AFAP1
|
Actin filament associated protein 1 [Source:HGNC Symbol;Acc:24017]
|
Glioma3 (2), Liver1, Lung5 (6), Leukemia4, Liver4, Glioma5
|
5
|
PDZD2
|
PDZ domain containing 2 [Source:HGNC Symbol;Acc:18486]
|
Lung2, Lung5 (4), Glioma1, Gastric2, Glioma3 (2)
|
5
|
PCDHGA1
|
Protocadherin gamma subfamily A, 1 [Source:HGNC Symbol;Acc:8696]
|
Glioma3, Glioma5, Liver2, Lung2, Lung5 (2)
|
7
|
CALN1
|
Calneuron 1 [Source:HGNC Symbol;Acc:13248]
|
Glioma3, Glioma3, Lung2 (5), Lung4, Lung5 (2)
|
7
|
KMT2C
|
Protocadherin gamma subfamily A, 1 [Source:HGNC Symbol;Acc:8696]
|
Gastric2, Gastric5 (2), Liver2, Liver4, Leukemia4
|
7
|
TYW1
|
tRNA-yW synthesizing protein 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25598]
|
Glioma3, Glioma5 (3), Liver1, Lung-Brain1 (5)
|
8
|
PSD3
|
Pleckstrin and Sec7 domain containing 3 [Source:HGNC Symbol;Acc:19093]
|
Lung3, Lung5 (9)
|
10
|
CAMK1D
|
Calcium/calmodulin-dependent protein kinase ID [Source:HGNC Symbol;Acc:19341]
|
Glioma3, Liver1, Lung3, Lung4 (5), Lung5 (5), Glioma4
|
11
|
SHANK2
|
SH3 and multiple ankyrin repeat domains 2 [Source:HGNC Symbol;Acc:14295]
|
Glioma3, Lung3, Lung5, Liver1, Liver5
|
12
|
MPHOSPH9
|
M-phase phosphoprotein 9 [Source:HGNC Symbol;Acc:7215]
|
Leukemia3, Lung-Brain5, Lung2, Lung4 (2), Lung5, Glioma4
|
17
|
STX8
|
Syntaxin 8 [Source:HGNC Symbol;Acc:11443]
|
Glioma3, Glioma4 (2), Lung2, Lung4 (2), Leukemia2
|
17
|
USP43
|
SH3 and multiple ankyrin repeat domains 2 [Source:HGNC Symbol;Acc:14295]
|
Liver1, Lung2, Lung5, Glioma5, Lung-Brain4
|
19
|
INSR
|
Insulin receptor [Source:HGNC Symbol;Acc:6091]
|
Liver4, Glioma3 (2), Glioma4 (2), Lung-Brain3, Lung5 (3)
|
19
|
CTC-490E21.12
|
Not Applicable
|
Gastric2, Gastric3, Glioma4, Glioma5, Lung1
|
19
|
CTC-525D6.1
|
Not Applicable
|
Gastric2 (4), Lung5 (8)
|
19
|
SAE1
|
SUMO1 activating enzyme subunit 1 [Source:HGNC Symbol;Acc:30660]
|
Glioma3, Lung2, Lung4, Lung5, Liver1
|
20
|
ATP9A
|
ATPase, class II, type 9A [Source:HGNC Symbol;Acc:13540]
|
Liver1 (3), Glioma4, Gastric3, Lung4, Lung5 (2)
|
22
|
LARGE
|
Like-glycosyltransferase [Source:HGNC Symbol;Acc:6511]
|
Liver1 (2), Lung1, Lung2, Leukemia5 (2), Glioma5 (3), Gastric5 (2)
|
22
|
SGSM1
|
Lysine (K)-specific methyltransferase 2C [Source:HGNC Symbol;Acc:13726]
|
Gastric2, Glioma3, Leukemia5, Lung-Brain2 (2), Lung-Brain3
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