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Table 2 OncoCis annotations of mutations from 17 whole breast cancer genomes sorted by differential gene expression P -value of the sample where there is an associated mutation and the samples without any associated mutation for a particular gene

From: OncoCis: annotation of cis-regulatory mutations in cancer

    

Distance

Gene expression

    

Conservation

Motifs

Fantom5

RegulomeDB

Funseq

Chromosome

Position

Sample ID

Gene

to TSS

Fold change

P-value

DHS

H3K4me1

H3K4me3

H3K27ac

Mutated base

Created

Removed

Promoter

Enhancer

Category

Sensitive?

Chr6

71,108,774

PD4006a

COL9A1

-95,988

100.12

1.39E-23

1

1

1

1

1

Hand1::Tcfe2a

Klf1

1

0

4

No

Chr1

160,094,923

PD4116a

ATP1A2

-9,404

71.15

2.99E-19

1

1

0

1

0.981

ELF1;Hltf

SP1;ZEB1

1

0

4

No

Chr7

92,347,495

PD4107a

CDK6

118,446

5.06

7.75E-07

1

1

1

1

1

-

NFIC;THAP1

1

0

4

No

Chr9

109,651,512

PD4006a

ZNF462

-26,135

4.79

2.27E-06

1

1

0

1

0.993

-

EHF;Erg;FLI1;PPARG::RXRA;.

0

0

5

No

Chr1

208,412,585

PD4116a

PLXNA2

5,080

1.63

4.17E-06

1

1

0

1

0.993

Nobox;Hltf

-

0

1

4

No

Chr4

7,5560,994

PD4103a

BTC

158,888

2.38

7.39E-05

1

1

0

0

0.938

-

CREB1;Mafb

0

0

4

No

Chr5

97,643,723

PD4109a

RGMB

461,275

2.50

2.47E-04

1

1

0

1

0.801

-

ARID3A

0

1

3a

No

Chr17

2,080,270

PD4005a

HIC1

-120,667

1.29

4.02E-04

1

1

0

1

1

NFIC

-

0

0

5

No

Chr16

57,334,425

PD4115a

PLLP

-15,841

2.09

8.51E-04

1

1

1

1

1

-

TFAP2C

1

0

4

Yes

Chr2

219,147,431

PD4198a

TMBIM1

9,849

1.65

2.23E-03

1

1

0

1

0.973

Foxd3

NFATC2;Erg

1

0

5

No

Chr8

100,811,550

PD4116a

COX6C

94,692

2.46

2.63E-03

1

1

0

0

1

-

NFKB1;Stat4;Spi1;Bcl6

0

0

2b

No

Chr14

37,612,228

PD4115a

SLC25A21

29,637

1.54

3.15E-03

1

1

0

0

1

Hand1::Tcfe2a

RUNX1;RUNX2;FOXI1

0

0

2b

No

Chr1

185,688,035

PD4005a

HMCN1

15,647

0.61

4.98E-03

1

1

0

1

0.997

FOXP1;FOXL1

-

0

0

5

No

Chr2

208,890,286

PD3904a

PLEKHM3

-2

1.48

1.09E-02

1

1

1

1

0.998

-

ELF5;GABPA;FLI1;ELK4;ELK1

1

0

2b

No

Chr10

93,058,182

PD4005a

PCGF5

-77,814

0.65

2.28E-02

1

1

0

0

0.935

-

Zfx

1

0

2a

No

Chr7

22,617,382

PD4107a

IL6

-149,383

2.29

2.62E-02

1

1

0

1

1

Hltf;CEBPA;CEBPB

AR

1

1

2a

Yes

Chr6

26,533,145

PD4192a

HMGN4

5,426

0.49

2.62E-02

1

1

0

0

0.979

-

Zfx

0

1

2b

Yes

Chr22

31,644,327

PD4103a

LIMK2

-36,078

0.79

3.43E-02

1

1

1

1

0.989

-

Klf4;SP2;SP1;KLF5;Klf1;ELK1

1

0

3a

No

  1. All mutations in the list are selected based on having a DHS, either a H3K4me1 or H3K4me3 histone mark, conservation (phastCons) >0.8 and the creation or removal of at least one transcription factor binding motif. The category and whether the mutation falls within a `sensitive’ region as defined by RegulomeDB and Funseq, respectively, are also shown.