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Table 1 Clones with significant difference in frequency of copy number changes between cell lines and tumor tissue specimens

From: Breast cancer cell lines carry cell line-specific genomic alterations that are distinct from aberrations in breast cancer tissues: Comparison of the CGH profiles between cancer cell lines and primary cancer tissues

A: Clones with significant difference in frequency of copy number gain between cell lines and tumor tissue specimens

Chromosomal region

Candidate genes

Frequency (%)

P-value

  

Cell lines

Tissue

 

20q13.33

ZGPAT, BTBD4,

18/24

1/35

5.68551E-09

20q13.13

COX6CP2

18/24

1/33

1.26370E-08

2q22.3

 

16/24

0/34

2.20899E-08

20q13.31

TFAP2C, PTMAP6

20/24

6/35

4.89015E-07

7p22.3

FLJ20397, UNC84A,

14/24

1/35

1.52990E-06

20q13.12

MYBL2

14/24

1/35

1.52990E-06

20q13.12

ADA, WISP2

14/24

2/35

7.97121E-06

20q11.21

DNMT3B, MAPRE1

11/24

0/35

8.97575E-06

20q11.21-20q11.22

SNTA1

11/24

0/35

8.97575E-06

8q24.3

HSF1, DGAT1, SCRT1

17/24

5/35

1.02265E-05

20q13.33

TPD52L2, DNAJC5

17/24

5/35

1.02265E-05

3q29

LRCH3, IQCG,

12/24

1/35

1.77298E-05

20p13

DEFB32, TRIB3

12/24

1/35

1.77298E-05

20q13.33

ARFGAP1, CHRNA4

19/24

8/35

2.00152E-05

5p14.1

 

13/24

2/35

2.68521E-05

11q13.3-11q13.4

PPFIA1, CTTN, SHANK2

13/24

2/35

2.68521E-05

20q11.21

BCL2L1, TPX2, MYLK2

13/24

2/35

2.68521E-05

20q13.33

KCNQ2, EEF1A2, PTK6,

17/24

6/35

3.26970E-05

5p15.31

 

15/24

4/35

3.72069E-05

5p15.2

MARCH6

15/24

4/35

3.72069E-05

5p15.1

BASP1, FTHL10

15/24

4/35

3.72069E-05

6q22.31

 

16/24

4/31

3.94622E-05

8q24.21

MYC, PVT1,

22/24

14/35

6.40836E-05

7q11.23

POR, TMPIT, DUSP24

9/24

0/35

8.30527E-05

14q22.2-14q22.3

GALIG, LGALS3 DLG7

9/24

0/35

8.30527E-05

19q13.43

ZNF544, ZNF8, HKR2

9/24

0/35

8.30527E-05

20p11.23

ZNF339, RPL15P1

9/24

0/35

8.30527E-05

3q29

TMEM44, FLJ11301

12/24

2/35

8.56953E-05

10p15.3

GTPBP4, IDI2, IDI1

12/24

2/35

8.56953E-05

20p13

CSNK2A1

12/24

2/35

8.56953E-05

20q13.2

ZNF217

17/24

7/35

9.43882E-05

B: Clones with siginificant difference in frequecy of copy number loss between cell lines and tumor tissue specimens

Chromosomal region

Candidate genes

Frrequency (%)

P-value

  

Cell lines

Tissue

 

Xp11.3

UTX

21/24

1/35

3.98705E-11

Xq27.1

-

16/24

0/35

1.52947E-08

Xq21.1

-

18/24

2/35

3.33574E-08

4p15.1

-

16/24

1/35

1.05951E-07

4p13

-

14/24

0/34

3.16890E-07

18q12.3

RIT2

16/23

2/34

3.88478E-07

Xq26.2

OR2AF1

15/24

1/35

4.14685E-07

Xq27.3

HCP44

15/24

1/35

4.14685E-07

18q21.1

MAPK4

18/24

4/35

7.03535E-07

Xq28

F8, VBP1, RAB39B, CLIC2 PHF10P1

13/24

0/35

8.17519E-07

18q21.1

KIAA0427

17/24

3/34

9.90978E-07

8p12

WRN

18/24

4/34

1.01721E-06

2q34

SPAG16

13/24

0/34

1.10437E-06

Xq26.2

GPC3

14/24

1/35

1.52990E-06

4p16.3

FLJ35816

15/24

2/35

2.23384E-06

4p15.1

-

15/24

2/35

2.23384E-06

18q12.2

-

15/24

2/35

2.23384E-06

Xq28

SLC14A2, SLC14A1

15/24

2/35

2.23384E-06

18q21.1

KIAA0427

17/24

3/34

9.90978E-07

8p12

WRN

18/24

4/34

1.01721E-06

2q34

SPAG16

13/24

0/34

1.10437E-06

Xq26.2

GPC3

14/24

1/35

1.52990E-06

4p16.3

FLJ35816

15/24

2/35

2.23384E-06

4p15.1

-

15/24

2/35

2.23384E-06

18q12.2

-

15/24

2/35

2.23384E-06

18q12.3

SLC14A2, SLC14A1

15/24

2/35

2.23384E-06

4p15.1

-

17/24

4/34

4.02576E-06

18q21.32

-

17/24

4/34

4.02576E-06

Xq28

CSAG2, MAGEA2B MAGEA12, CSAG1

14/23

2/35

4.27750E-06

4q13.1

EPHA5

8/16

0/35

5.21729E-06

3p22.1

NKTR, ZNF651, KBTBD5

13/24

1/35

5.34274E-06

4p16.3

HD,

13/24

1/35

5.34274E-06

4p13

-

13/24

1/35

5.34274E-06

4q22.1

-

13/24

1/35

5.34274E-06

5q14.3

-

13/24

1/35

5.34274E-06

18q12.1

-

13/24

1/35

5.34274E-06