Table 4

Gene expression trends of LongSAGE tags that consistently and significantly altered expression in CR prostate cancer*

13N

15N

13R


AS§

RADII

CR¶

AS

RAD

CR

AS

RAD

CR

Tag Sequence

S1885

S1886

S1887

S1888

S1889

S1890

S1891

S1892

S1893

Trend‡

Gene**

Accession§§


TCTAGAGAACACTGTGC

12†

79

382

7

67

136

7

52

200

A

ACPP‡‡

NM_001099

TAATTTTTCTAAGGTGT

101

311

648

119

397

895

120

546

918

A

C1ORF80

ENSG00000186063

TGAGAGAGGCCAGAACA

8

39

150

4

39

144

7

33

95

A

N/A

Genomic

CTCATAAGGAAAGGTTA

637

952

1680

653

1170

1540

688

1620

1930

A

RNF208

BC090061

GATTTCTATTTGTTTTT

89

169

446

116

208

339

86

311

555

A

SERINC5

ENSG00000164300

GTTGGGAAGACGTCACC

426

571

742

273

417

741

262

363

495

A

STEAP1

NM_012449

GAGGATCACTTGAGGCC

191

299

449

134

189

589

187

203

314

B

AMACR‡‡

BC009471

TTGTTGATTGAAAATTT

219

197

528

273

197

479

232

391

586

B

AMD1‡‡

NM_001634

TTTGCTTTTGTTTTGTT

53

16

169

34

51

129

7

28

72

B

AQP3

NM_004925

GTTCGACTGCCCACCAG

45

28

101

52

47

122

34

42

106

B

ASAH1††

NM_177924

TAATAAACAGGTTTTTA

426

232

648

332

315

700

138

250

491

B

ASAH1‡‡

NM_177924

TCACAGCTGTGAAGATC

85

110

277

161

71

258

310

438

945

B

BTG1

NM_001731

AAAAGAGAAAGCACTTT

24

75

199

19

35

85

15

90

552

B

CAMK2N1

NM_018584

CAAAACAGGCAGCTGGT

4

71

169

15

83

162

37

75

268

B

CAMK2N1††

NM_018584

AGGAGGAAGAATGGACT

33

59

187

49

67

247

26

42

223

B

CCNH

NM_001239

TTTTAAAAATATAAAAT

89

83

243

97

130

269

64

170

382

B

COMT

NM_000754

GAATGAAATAAAAAATA

134

252

626

209

240

357

116

160

272

B

DHRS7

NM_016029

AAAGTGCATCCTTTCCC

118

146

318

153

220

394

288

231

646

B

FGFRL1

NM_001004356

AAACTGAATAAGGAGAA

24

51

236

19

51

438

19

146

283

B

GALNT3

NM_004482

TTTAAGGAAACATTTGA

4

4

75

4

4

81

0

0

57

B

GALNT3††

NM_004482

CCAACCGTGCTTGTACT

191

327

521

202

279

534

172

363

510

B

GLO1

NM_006708

GAGGGCCGGTGACATCT

300

378

1170

321

476

1230

254

447

1030

B

H2AFJ

NM_177925

TATCATTATTTTTACAA

57

63

161

67

63

181

75

94

181

B

HSD17B4

NM_000414

AATGCACTTATGTTTGC

16

8

64

22

16

77

19

28

98

B

N/A

No map

ACCTTCGCAGGGGAGAG

0

0

19

0

4

41

0

5

34

B

N/A

Genomic

ATAACCTGAAAGGAAAG

0

16

56

7

4

74

0

28

87

B

N/A

No map

GTGATGTGCACCTGTTG

0

0

38

4

0

30

0

5

45

B

N/A

No map

GTTTGGAGGTACTAAAG

20

43

94

34

87

169

34

90

234

B

N/A

Genomic

TTTTCAAAAATTGGAAA

0

35

180

7

4

59

0

19

61

B

N/A

No map

GAAAAATTTAAAGCTAA

394

397

569

433

598

788

853

862

1060

B

NGFRAP1

NM_206917

CAAATTCAGGGAGCACA

0

4

139

4

16

228

0

14

136

B

OPRK1

NM_000912

CTATTGTCTGAACTTGA

0

8

109

0

12

70

0

9

227

B

OR51E2

BC020768

ATGCTAATTATGGCAAT

4

12

75

4

8

74

0

5

57

B

PCGEM1

NR_002769

CAGAAAGCATCCCTCAC

4

43

195

0

16

111

7

33

264

B

PLA2G2A‡‡

NM_000300

TAATTTTAGTGCTTTGA

16

75

154

37

59

162

4

57

132

B

PTGFR

NM_000959

TTGTTTGTAAATAGAAT

0

12

94

0

4

162

0

14

72

B

QKI

NM_206853

TAAACACTGTAAAATCC

0

4

75

0

4

66

0

0

42

B

QKI††

NM_206853

AGCAGATCAGGACACTT

20

35

112

15

16

140

15

42

98

B

S100A10

NM_002966

CTGCCATAACTTAGATT

37

55

161

93

63

192

56

99

264

B

SBDS

NM_016038

TGGCTGAGTTTATTTTT

20

24

79

41

8

96

4

42

147

B

SFRS2B

NM_032102

GAAGATTAATGAGGGAA

126

142

277

108

130

402

101

188

325

B

SNX3

NM_003795

ATGGTACTAAATGTTTT

16

47

124

37

28

88

11

19

76

B

SPIRE1

NM_020148

TATATATTAAGTAGCCG

45

39

101

45

75

133

41

75

178

B

STEAP2‡‡

NM_152999

CAACAATATATGCTTTA

24

32

82

75

32

136

26

99

212

B

STEAP2††

NM_152999

TTTCATTGCCTGAATAA

24

43

150

34

59

114

22

61

178

B

TACC1‡‡

NM_006283

TTGGCCAGTCTGCTTTC

8

16

67

4

4

77

0

5

38

B

TMEM30A

ENSG00000112697

ATATCACTTCTTCTAGA

12

4

26

7

4

26

0

52

140

C

ADAM2‡‡

NM_001464

ATGTGTGTTGTATTTTA

812

338

768

1010

315

1020

269

702

865

C

BNIP3

NM_004052

CCACGTTCCACAGTTGC

601

291

599

530

346

700

381

339

559

C

ENO2

NM_001975

CTGATCTGTGTTTCCTC

16

0

26

0

4

41

19

0

34

C

HLA-B

BC013187

AGCCCTACAAACAACTA

382

441

596

508

456

619

400

631

1010

C

MT-ND3

ENSG00000198840

ATATTTTCTTTGTGGAA

20

12

90

7

0

48

4

0

23

C

N/A

No map

CAAGCATCCCCGTTCCA

2400

2130

2440

2730

1720

2250

1020

2010

2340

C

N/A

ENSG00000211459

GTTGTAAAATAAACTTT

118

83

172

228

87

247

112

203

378

C

N/A

Genoic

TTGGATTTCCAAAGCAG

12

0

19

0

0

33

0

0

26

C

N/A

Genomic

TCTTTTAGCCAATTCAG

138

181

420

381

326

468

389

334

457

C

NKX3-1††

NM_006167

TGATTGCCCTTTCATAT

73

39

86

86

39

107

108

99

181

C

P4HA1

NM_000917

GTAACAAGCTCTGGTAT

28

16

56

49

24

66

11

19

72

C

PJA2

NM_014819

ACAGTGCTTGCATCCTA

85

75

139

108

98

203

101

118

196

C

PPP2CB

NM_004156

AGGCGAGATCAATCCCT

57

39

101

37

24

122

131

66

268

C

PSMA7

NM_002792

TATTTTGTATTTATTTT

73

59

180

93

51

111

22

94

253

C

SLC25A4

NM_001151

TTATGGATCTCTCTGCG

1050

1260

1820

1140

1300

2260

1990

1010

1530

C

SPON2

NM_012445

CAGTTCTCTGTGAAATC

767

515

1060

855

503

914

467

608

1200

C

TMEM66

NM_016127

AAATAAATAATGGAGGA

138

59

255

82

118

284

165

90

159

C

TRPM8

NM_024080

ATGTTTAATTTTGCACA

61

87

154

157

59

195

217

85

344

C

WDR45L

NM_019613

GGGCCCCAAAGCACTGC

861

543

1180

1020

657

1590

1240

739

937

E

C19orf48

NM_199249

TCCCCGTGGCTGTGGGG

1670

1390

2290

1740

1410

1720

3370

970

1180

E

DHCR24‡‡

BC004375

GCATCTGTTTACATTTA

487

201

345

444

208

468

684

226

423

E

ELOVL5

NM_021814

GAAATTAGGGAAGCCTT

317

153

311

310

181

542

359

193

298

E

ENDOD1

XM_290546

GGATGGGGATGAAGTAA

2780

1160

4780

2950

1350

3620

2930

1230

1890

E

KLK3‡‡

NM_001648

TGAAAAGCTTAATAAAT

313

142

322

474

181

332

273

179

314

E

TPD52

NM_001025252

GTTGTGGTTAATCTGGT

1770

634

1270

1800

806

1190

2480

659

960

F

B2M

NM_004048

GAAACAAGATGAAATTC

4380

1170

2260

5300

1110

2720

3750

2220

2830

F

PGK1

NM_000291

AGCACCTCCAGCTGTAC

2150

1130

648

2060

1560

939

1560

1200

722

G

EEF2

NM_001961

GCACAAGAAGATTAAAA

536

228

124

762

425

195

838

278

174

G

GAS5

NR_002578

CCGCTGCGTGAGGGCAG

451

169

56

429

197

44

516

94

0

G

HES6

NM_018645

GCCCAGGTCACCCACCC

585

55

4

519

79

7

456

66

0

G

LOC644844

XM_927939

ATGCAGCCATATGGAAG

2650

386

82

2470

216

129

1210

259

98

G

ODC1

NM_002539

CGCTGGTTCCAGCAGAA

1420

811

479

1250

959

553

800

589

374

G

RPL11

NM_000975

AAGACAGTGGCTGGCGG

2650

1730

1220

2460

1860

1350

2120

1630

1270

G

RPL37A‡‡

NM_000998

TTCTTGTGGCGCTTCTC

925

543

217

1030

708

273

1130

419

306

G

RPS11††

NM_001015

GGTGAGACACTCCAGTA

463

252

165

485

346

192

363

245

159

G

SLC25A6

NM_001636

AGGTTTTGCCTCATTCC

982

515

281

1200

491

243

688

782

166

H

ABHD2

NM_007011

TGAAGGAGCCGTCTCCA

317

272

187

392

295

199

366

259

140

H

ATP5G2

NM_001002031

CTCAGCAGATCCAAGAG

191

185

67

254

232

66

142

231

79

H

C17orf45

NM_152350

CTGTGACACAGCTTGCC

308

397

172

209

307

125

295

226

110

H

CCT2

NM_006431

TCTGCACCTCCGCTTGC

495

606

277

426

570

276

366

471

204

H

EEF1A2

NM_001958

GCCCAAGGACCCCCTGC

114

114

38

138

98

41

101

42

4

H

FLNA‡‡

NM_001456

TTATGGGATCTCAACGA

564

425

180

642

452

317

430

490

253

H

GNB2L1

NM_006098

TCTGCAAAGGAGAAGTC

81

102

38

105

87

26

165

80

30

H

HMGB2

NM_002129

CTTGTGAACTGCACAAC

268

228

124

231

177

103

273

160

57

H

HN1

NM_016185

TCTGAAGTTTGCCCCAG

313

291

150

254

299

155

187

226

72

H

MAOA

NM_000240

TTAATTGATAGAATAAA

483

350

199

422

287

103

273

235

83

H

MAOA

NM_000240

GGCAGCCAGAGCTCCAA

1200

1260

420

1050

672

350

681

819

23

H

MARCKSL1

NM_023009

CCCTGCCTTGTCCCTCT

353

240

112

310

263

107

176

193

102

H

MDK

NM_001012334

CTGTGGATGTGTCCCCC

649

476

169

459

389

214

430

297

117

H

N/A

No map

CTCCTCACCTGTATTTT

1120

771

262

1220

979

313

666

730

261

H

RPL13A‡‡

NM_012423

GCAGCCATCCGCAGGGC

1980

1770

809

2300

1730

928

2150

1570

1020

H

RPL28

NM_000991

GGATTTGGCCTTTTTGA

3470

2070

1370

4170

2910

1540

2800

2870

2500

H

RPLP2‡‡

NM_001004

TCTGTACACCTGTCCCC

2320

1670

850

1930

1880

825

2130

1490

1120

H

RPS11

NM_001015

GCTTTTAAGGATACCGG

1510

1050

626

1860

1120

593

1550

1550

960

H

RPS20‡‡

NM_001023

CCCCAGCCAGTCCCCAC

921

519

281

788

664

357

1100

438

291

H

RPS3

NM_001005

CCCCCAATGCTGAGGCC

89

138

26

90

94

30

90

80

30

H

SF3A2

NM_007165

GCCGCCATCTCCGAGAG

195

102

30

168

118

55

172

108

30

H

TKT

NM_001064

GGCCATCTCTTCCTCAG

349

307

202

317

346

173

277

254

121

H

YWHAQ

NM_006826

AGGCTGTGTTCCTCCGT

16

39

11

34

67

22

26

38

8

I

ACY1

NM_000666

TGCCTCTGCGGGGCAGG

446

649

427

399

664

424

501

462

317

I

CD151

NM_004357

GGCACAGTAAAGGTGGC

175

216

142

332

350

173

456

316

204

I

CUEDC2

NM_024040

TCACACAGTGCCTGTCG

49

71

7

30

47

15

34

66

4

I

CXCR7

NM_001047841

TGTGAGGGAAGCTGCTT

53

87

15

67

102

52

52

90

42

I

FKBP10

BC016467

TGCTTTGCTTCATTCTG

28

63

26

22

79

26

49

118

61

I

GRB10

NM_005311

GTACTGTATGCTTGCCA

170

212

82

134

153

88

123

188

113

I

KPNB1‡‡

NM_002265

GTGGCAGTGGCCAGTTG

106

193

97

123

173

96

94

137

76

I

N/A

ENSG00000138744

GGGGAGCCCCGGGCCCG

61

63

26

30

51

18

34

57

0

I

NAT14

NM_020378

TGTTCAGGACCCTCCCT

28

67

26

60

63

26

60

28

0

I

NELF

NM_015537

TTTTCCTGGGGATCCTC

41

130

15

37

87

33

56

104

45

I

PCOTH

NM_001014442

GAAACCCGGTAGTCTAG

41

75

4

37

75

26

52

151

30

I

PLCB4

NM_000933

GTCTGACCCCAGGCCCC

126

205

82

119

193

103

157

179

38

I

PPP2R1A

NM_014225

GGCCCGAGTTACTTTTC

231

150

75

161

232

136

142

160

45

I

RPL35A††

NM_000996

GTTCGTGCCAAATTCCG

881

696

390

1100

712

523

497

782

461

I

RPL35A‡‡

NM_000996

TTACCATATCAAGCTGA

877

535

311

1130

598

405

636

791

578

I

RPL39‡‡

NM_001000

GCTGCAGCACAAGCGGC

268

244

127

45

216

125

157

71

11

I

RPS18††

NM_022551

AGCTCTTGGAGGCACCA

203

319

206

142

421

243

269

259

162

I

SELENBP1

NM_003944

TGCTGGTGTGTAAGGGG

69

102

45

82

87

37

105

75

30

I

SH3BP5L

NM_030645

GAGAGTAACAGGCCTGC

191

150

71

112

181

111

108

165

64

I

SYNC1

NM_030786

CTGAAAACCACTCAAAC

394

508

225

306

547

236

310

381

200

I

TFPI

NM_006287

TAAAAAAGGTTTCATCC

183

248

127

86

130

66

142

268

87

I

TFPI

NM_006287

CTCCCTCCTCTCCTACC

28

32

4

30

39

7

71

24

0

I

TK1

NM_003258

CATTTTCTAATTTTGTG

544

744

236

407

771

181

288

664

185

J

N/A

No map

TGATTTCACTTCCACTC

3480

5260

3910

3700

6110

3590

3040

5960

2600

K

MT-CO3

ENSG00000198938

TTTCTGTCTGGGGAAGG

130

236

82

123

201

111

101

188

113

K

PIK3CD

NM_005026

GCCGCTACTTCAGGAGC

256

370

199

224

330

169

142

316

38

K

RAMP1

NM_005855

ATGGTTACACTTTTGGT

93

161

94

75

208

118

60

226

95

K

UTX

NM_021140

CACTACTCACCAGACGC

2820

3900

3020

2740

4290

2440

2620

3120

1260

K

VPS13B††

ENSG00000132549

CTAAGACTTCACCAGTC

7120

11000

9730

6390

10900

8330

3610

8870

7850

L

N/A

ENSG00000210082


* Statistics according to the Audic and Claverie test statistic (p ≤ 0.05)

† Tag count per 1 million = (observed tag count/total tags in the library) × 1,000,000

‡ Trends are visually represented from A to P in Additional file 1, Figure S3. In addition to p-value considerations, significantly different trends were also required to display uniform directions of change in each biological replicate.

§ AS, Androgen-sensitive

II RAD, Responsive to androgen-deprivation

¶ CR, Castration-recurrent

** Human Genome Nomenclature Committee (HGNC)-approved gene names were used when possible. Non-HGNC-approved gene names were not italicized.

†† Tag maps antisense to gene

‡‡ Gene is known to display this expression trend in castration-recurrence

§§ Accession numbers were displayed following the priority (where available): RefSeq > Mammalian Gene Collection > Ensembl Gene. If the tag mapped to more than one transcript variant of the same gene, the accession number of the lowest numerical transcript variant was displayed.

Romanuik et al. BMC Medical Genomics 2010 3:43   doi:10.1186/1755-8794-3-43

Open Data