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Table 1 Hybridization signals detected in sample channel and reference channel

From: Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray

 

Detected N signals

Masked IMAGE ID

Putative antisense signals

C signals

 

total*

reported**

repeats***

double hits****

self-complementarity+

repeats, double, or self++

reported+++

total++++

reported$

new$$

total$$$

% paired N signal$$$$

UACC812 (A)

281

59

148

61

7

151

31

130

28 (21,5%)

102

353

27

ZR7530 (B)

316

67

149

57

8

153

33

163

34 (20,9%)

129

353

35

BT474 (C)

610

134

252

74

11

257

50

353

84 (23,8%)

269

478

64

MDA361 (D)

603

132

241

71

0

246

49

357

83 (23,2%)

274

465

66

MCF10A (E)

556

114

241

72

11

246

46

310

68 (21,9%)

242

473

57

SKBR3 (F)

449

94

192

65

8

196

41

253

53 (20,9%)

200

431

48

UACC893 (G)

516

110

216

67

8

220

43

296

67 (22,6%)

229

442

56

MDA453 (H)

562

115

233

72

9

238

47

324

68 (21,0%)

256

460

60

CAMA1 (I)

695

151

276

76

11

282

53

413

98 (23,7%)

315

501

74

Mean

509,78

108,44

216,44

68,33

9,22

221

43,67

288,8

64,78 (22,2%)

224

439,56

54,14

SD

137,63

30,55

44,89

6,32

1,56

45,7

7,53

92,37

23,10 (1,2%)

69,52

53,03

15,18

Nmbr(union)

776

169

300

78

11

306

60

470

109 (23,2%)

361

511

 

Nmbr(intersection)

244

52

125

55

7

128

27

116

25 (21,6%)

91

315

 

Reference (A)

753

169

296

78

11

303

62

450

107 (23,8%)

343

510

81

Reference (B)

751

169

288

79

11

295

59

456

110 (24,1%)

346

505

82

Reference (C)

813

185

303

77

11

309

65

504

120 (23,8%)

384

513

90

Reference (D)

808

179

301

79

11

308

62

500

117 (23,4%)

383

514

89

Reference (E)

806

178

301

80

11

307

62

499

116 (23,2%)

383

513

89

Reference (F)

826

186

307

79

11

314

65

512

121 (23,6%)

391

519

91

Reference (G)

745

169

288

78

11

294

62

451

107 (23,7%)

344

502

80

Reference (H)

822

182

311

78

11

317

66

505

116 (23,0%)

389

520

90

Reference (I)

874

196

316

79

11

323

64

551

132 (24,0%)

419

524

97

Mean

799,78

179,22

301,22

78,56

11

307,8

63

492

116,22 (23,6%)

375,8

513,33

87,79

SD

42,63

9,24

9,54

0,88

0

9,58

2,18

33,63

7,84 (0,4%)

26,02

7,07

5,65

Nmbr(union)

885

198

322

81

11

329

66

556

132 (23,7%)

424

525

 

Nmbr(intersection)

673

153

269

75

11

275

57

398

96 (24,1%)

302

489

 
  1. *Number of IMAGE clones where N probe SNR > 10
  2. **Number of IMAGE clones previously reported (ref 9) as transcribed from antisense (out of Detected N signals total*)
  3. ***Number of IMAGE clones with > = 40 continuous bases homologous to repeats (out of Detected N signals total*)
  4. ****Number of IMAGE clones with > = 30 continuous bases on both sense- and antisense strand that match RefSeq (out of Detected N signals total*)
  5. +Number of IMAGE clones with > = 30 continuous bases complementary between sense- and antisense transcript (out of Detected N signals total*)
  6. ++Number of IMAGE clones with either repeats***, double hits****, or self-complementarity+(out of Detected N signals total*)
  7. +++Number of IMAGE clones that overlap between masked++and clones priviously reported** (out of Detected N signals total*)
  8. ++++Number of IMAGE clones with putative antisense transcription, i.e. those clones that are not masked++(out of Detected N signals total*)
  9. $Number of IMAGE clones previously reported as transcribed from antisense out of, Putative antisense signals total++++(percentage within parenthesis)
  10. $$Number of IMAGE clones not masked++ and not privously reported** as transcribed from antisense (out of Detected N signals total*)
  11. $$$Number of IMAGE clones with putative sense transcription, i.e. where C probe SNR > 10, excluding clones that are masked++
  12. $$$$Percent of IMAGE clones displaying N signal out of those that display C signals excluding clones that are masked++
  13. Note: values are paired per clone, i.e. the number of IMAGE clones with C signal and N signal as percentage of the number of IMAGE clones with C signal
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BMC Genomics

ISSN: 1471-2164

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