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Table 5 Most significant BAC clones that differentiate patients in the Recurrence group from those in the Non-recurrence group by SAM analysis

From: Genomic alterations identified by array comparative genomic hybridization as prognostic markers in tamoxifen-treated estrogen receptor-positive breast cancer

BAC Clone

Chromosome Location

Representative genes

d

Fold Change

q value (%)

BAC165_D01

11p15.5

RIC8A, SIRT3, PSMD13, NALP6, MRPS24P1, IFITM2

-4.537

0.817

0.339

BAC121_J14

11p15.5

TOLLIP, STK29

-4.015

0.795

0.339

BAC60_J23

11p15.4

KCNQ1, CDKN1C, KCNQ1DN, SLC22A1LS, SLC22A18

-3.943

0.774

0.339

BAC101_I16

1p36.33

SLC35E2

-3.872

0.799

0.339

BAC144_G04

7q22.1

PDAP1, G10, CPSF4, PTCD1, ATP5J2

-3.804

0.860

0.339

BAC193_P15

11p15.4

NUP98, FRAG1, RHOG, STIM1

-3.676

0.811

0.339

BAC252_K02

11p15.4

CDKN1C, KCNQ1DN, SLC22A1LS, SLC22A18, PHLDA2, NAP1L4

-3.566

0.800

0.339

BAC176_F17

1p36.33

PRKCZ, SKI

-3.561

0.799

0.339

BAC121_J11

11p15.4

SMPD1, APBB1, HPX

-3.531

0.844

0.339

BAC228_L09

11q13.1

ESRRA, HSPC152, PRDX5, RPS6KA4

-3.513

0.828

0.339

BAC33_L13

19p13.3

NFIC, FZR1, C19orf28

-3.486

0.804

0.339

BAC75_B14

19p13.3

EDG6, BRUNOL5

-3.335

0.817

0.339

BAC146_F01

19q13.2

MAP3K10, AKT2

-3.327

0.847

0.339

BAC249_F13

19q13.2

CYP2S1, AXL, HNRPUL1

-3.288

0.869

0.339

BAC176_M06

9q34.3

TRAF2, FBXW5, C8G, LCN12

-3.286

0.862

0.339

BAC82_M18

3q21.2

SLC12A8

-3.271

0.913

0.339

BAC162_J04

19q13.2

SNRPA, MIA, RAB4B, EGLN2, CYP2T2P, CYP2F1P

-3.266

0.862

0.339

BAC91_J13

11p15.4

TRIM3, ARFIP2, FXC1

-3.224

0.853

0.339

BAC96_L08

19p13.3

PPAP2C, THEG

-3.195

0.860

0.339

BAC185_L04

11q13.1

SF1, MAP4K2, MEN1, HSMDPKIN, EHD1, KIAA0404, PPP2R5B

-3.182

0.833

0.339

BAC168_E17

19q13.42

ZNF579, ZNF524

-3.182

0.872

0.339

BAC65_N13

19p13.3

TJP3, APBA3, MRPL54, MATK

-3.175

0.825

0.339

BAC224_C15

9q34.3

MAN1B1, DPP7, GRIN1

-3.128

0.857

0.339

BAC42_H14

10q26.2-26.3

 

-3.127

0.863

0.339

BAC122_I18

11q13.1

NAALADL1, CDCA5, ZFPL1, C11orf2, TM7SF2, ZNHIT2, FAU, MRPL49, HRD1

-3.126

0.846

0.339

BAC37_C21

19p13.3

ANKRD24, EBI3, SHD, FSD1, STAP2, SH3GL1

-3.116

0.840

0.339

BAC167_H05

11p11.2

KAI1

-3.112

0.883

0.339

BAC29_C11

2p25.1

HPCAL1, ODC1

-3.084

0.867

0.339

BAC195_K21

11q12.3

EEF1G, RBM21

-3.060

0.868

0.339

BAC80_E04

21q22.3

UBE2G2, SUMO3, PTTG1IP

-3.053

0.854

0.339

BAC192_C22

11q13.1

TIGD3, FKSG44

-3.051

0.875

0.339

BAC57_D10

19p13.3

PRSS15, FUT6, NRTN

-3.044

0.858

0.339

BAC76_D18

2p25.1

HPCAL1, ODC1

-3.024

0.907

0.339

BAC30_K23

19q13.32

 

-3.022

0.890

0.339

BAC128_J04

11q13.1

BANF1, CST6, CATSPER1, GAL3ST3, SF3B2, PACS1

-2.997

0.879

0.339

BAC76_C20

5q35.3

RASGEF1C

-2.994

0.884

0.339

BAC215_J18

1p34.2

MYCL1

-2.976

0.896

0.339

BAC63_I09

1p35.3

 

-2.959

0.886

0.339

BAC78_D10

19q13.31

PLAUR

-2.950

0.875

0.339

BAC132_L20

17p11.2

FBXW10, FAM18B

-2.948

0.877

0.339

BAC104_F07

6p21.32

CREBL1, FKBPL, C6orf31, PPT2, EGFL8, AGPAT1, RNF5, AGER, PBX2, GPSM3, NOTCH4

-2.947

0.850

0.339

BAC38_N15

1p36.33

SKI

-2.939

0.875

0.339

BAC209_K24

21q22.3

PTTG1IP, ITGB2, C21orf69, C21orf67, C21orf70

-2.931

0.853

0.339

BAC136_D13

21q22.3

UBE2G2, SUMO3, PTTG1IP

-2.894

0.869

0.339

BAC252_I22

16p13.3

TSC2, PKD1, TRAF7, RAB26

-2.881

0.820

0.339

BAC30_F19

7q32.2

UBE2H

-2.873

0.901

0.339

BAC197_D09

11q12.2

PGA5

-2.872

0.874

0.339

BAC183_D06

19q13.31

RIC-8, SIRT3, PSMD13, NALP6, MRPS24P1, IFITM2

-2.839

0.891

0.339

BAC239_N12

19q13.31

TOLLIP, STK29

-2.835

0.889

0.339

BAC120_F15

1p35.3

KCNQ1, CDKN1C, SLC22A1LS, SLC22A18

-2.833

0.908

0.339

BAC219_C01

6p21.33

SLC35E2

-2.824

0.857

0.339

BAC91_A07

1p36.21

PDAP1, G10, CPSF4, PTCD1, ATP5J2

-2.822

0.888

0.339

BAC59_B08

16p13.3

NUP98, FRAG1, RHOG, STIM1

-2.809

0.854

0.339

BAC1_C02

21q22.3

CDKN1C, KCNQ1DN, SLC22A1LS, SLC22A18, PHLDA2, NAP1L4

-2.804

0.878

0.339

BAC142_E13

9q34.2

PRKCZ, SKI

-2.803

0.888

0.339

BAC100_L06

7q11.22

SMPD1, APBB1, HPX

-2.803

0.927

0.339

BAC149_E07

11q13.2

ESRRA, HSPC152, PRDX5, RPS6KA4

-2.801

0.886

0.339

BAC10_E08

15q25.1

NFIC, FZR1, C19orf28

-2.797

0.895

0.339

BAC232_G07

13q34

EDG6, BRUNOL5

-2.780

0.895

0.339

BAC155_O07

21q22.3

MAP3K10, AKT2

-2.773

0.875

0.339

BAC219_N21

2q14.3

CYP2S1, AXL, HNRPUL1

-2.762

0.912

0.339

BAC24_E16

10q22.2

TRAF2, FBXW5, C8G, LCN12

-2.751

0.867

0.339

BAC142_B18

9q34.11

SLC12A8

-2.747

0.873

0.339

BAC168_H24

19q13.33

SNRPA, MIA, RAB4B, EGLN2, CYP2T2P, CYP2F1P

-2.745

0.912

0.339

BAC233_C05

19q13.32

TRIM3, ARFIP2, FXC1

-2.744

0.905

0.339

BAC70_M18

10p15.3

PPAP2C, THEG

-2.718

0.880

0.339

BAC32_K13

11p15.4

SF1, MAP4K2, MEN1, HSMDPKIN, EHD1, KIAA0404, PPP2R5B

-2.712

0.907

0.339

BAC127_P09

12q13.13

ZNF579, ZNF524

-2.696

0.929

0.339

BAC104_G21

5p15.33

TJP3, APBA3, MRPL54, MATK

-2.690

0.917

0.339

BAC110_G12

19p13.3

MAN1B1, DPP7, GRIN1

-2.676

0.879

0.339

BAC125_M06

9q34.13

 

-2.668

0.880

0.339

BAC4_J24

9q34.3

NAALADL1, CDCA5, ZFPL1, C11orf2, TM7SF2, ZNHIT2, FAU, MRPL49, HRD1

-2.663

0.890

0.339

BAC142_G12

16p13.3

ANKRD24, EBI3, SHD, FSD1, STAP2, SH3GL1

-2.657

0.826

0.339

BAC100_M24

6p21.32

KAI1

-2.656

0.896

0.339

BAC195_F16

7q32.1

HPCAL1, ODC1

-2.655

0.913

0.339

BAC109_M06

7q22.1

EEF1G, RBM21

-2.653

0.916

0.339

BAC247_C06

3q21.3

UBE2G2, SUMO3, PTTG1IP

-2.645

0.935

0.339

BAC140_C04

5q12.3

TIGD3, FKSG44

3.601

1.104

0.686

BAC86_O11

20p12.1

PRSS15, FUT6, NRTN

3.435

1.160

0.686

BAC125_H18

2p11.2

HPCAL1, ODC1

3.308

1.119

0.686

BAC122_F23

7p14.1

 

3.295

1.131

0.686

BAC89_K07

7p14.2

BANF1, CST6, CATSPER1, GAL3ST3, SF3B2, PACS1

3.286

1.146

0.686

BAC69_J21

2p12

RASGEF1C

3.244

1.097

0.686

BAC24_A20

7p14.2

MYCL1

3.236

1.135

0.686

BAC165_M10

20p12.1

 

3.601

1.104

0.686

BAC140_C04

5q12.3

PLAUR

3.435

1.160

0.686

BAC86_O11

20p12.1

FBXW10, FAM18B

3.308

1.119

0.686

BAC125_H18

2p11.2

CREBL1, FKBPL, C6orf31, PPT2, EGFL8, AGPAT1, RNF5, AGER, PBX2, GPSM3, NOTCH4

3.295

1.131

0.686

BAC122_F23

7p14.1

SKI

3.286

1.146

0.686

BAC89_K07

7p14.2

PTTG1IP, ITGB2, C21orf69, C21orf67, C21orf70

3.244

1.097

0.686

BAC69_J21

2p12

UBE2G2, SUMO3, PTTG1IP

3.236

1.135

0.686

BAC24_A20

7p14.2

TSC2, PKD1, TRAF7, RAB26

3.601

1.104

0.686

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