Table 3

Selected list of allele-specific expression genes detected in the HCC1954 cell line

Gene

Number of reads ratio major/minor

Chr.

Gene product

Non-ASE P-value

Known SNV ID


CTBP2

404/0

10

C-terminal binding protein 2

0.000

3 novel SNVs

415/1

395/0

HLA-A

267/4

6

Major histocompatibility complex, class I, A

0.000

rs2231114

546/0

0.000

rs1059517

TAOK1

223/16

17

TAO kinase 1

0.000

rs508706

PLAU

140/0

10

Plasminogen activator, urokinase

0.000

rs2227568

PODXL2

124/1

3

Podocalyxin-like 2

0.000

rs920232

ITGB2

53/2

21

Integrin, beta 2

0.000

rs11088969

LXN

45/1

3

Latexin

0.000

rs8455

SNUPN

48/2

15

Snurportin 1

0.000

rs11547316

RAB3A

50/5

19

RAB3A, member RAS oncogene family

0.000

rs1046565

KIN

31/0

10

KIN, antigenic determinant of recA protein homolog (mouse)

0.000

rs61752337

GLB1L2

26/0

11

Galactosidase, beta 1-like 2

0.000

rs3741097

MGMT

21/0

10

O-6-methylguanine-DNA methyltransferase

0.001

rs2308327

PLEKHA6

340/1

1

Pleckstrin homology domain containing, family A member 6

0.000

rs33911350

THNSL2

36/0

2

Threonine synthase-like 2 (S. cerevisiae)

0.000

rs35051888

LBP

220/10

20

Lipopolysaccharide binding protein

0.000

rs5744204

123/6

rs2232582

238/10

rs2232596

FGFR4

267/27

5

Fibroblast growth factor receptor 4

0.000

rs1966265

SLC44A5

57/0

1

Solute carrier family 44, member 5

0.000

rs17096508

40/0

rs10493565

31/0

rs588098

41/0

Novel SNV

FGFR2

44/0

10

Fibroblast growth factor receptor 2

0.000

rs1047100

SYTL5

48/2

X

Synaptotagmin-like 5

0.000

rs5918476

30/3

rs4827330


Genes under ASE regulation in HCC1954 but expressed from both alleles in HCC1954BL are shown in bold; genes under ASE regulation in HCC1954 but barely expressed in HCC1954BL are shown in regular font. ASE, allele-specific expression; SNV, single nucleotide variant.

Zhao et al. Genome Biology 2010 11:R114   doi:10.1186/gb-2010-11-11-r114

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