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Table 3 Summary of sequencing confirmation, random probes.

From: Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays

Probe_Set_ID

probe

Gene_Name

q-value

Rank (q < 0.05)

Rank (q < 0.05, |fold change| > 1)

SNP Code

SNP location

Ssc.19486.1.S1_at

3

CCNB1IP1

7.36E-23

28

28

none

 

Ssc.15621.1.A1_at

6

PCYOX1

4.32E-19

59

59

none

 

Ssc.24184.1.S1_at

4

GPD1L

1.32E-16

94

94

S

7

Ssc.7266.1.A1_at

2

POSTN

1.71E-15

114

114

none

 

Ssc.18458.1.S1_at

6

Q86V57

4.92E-15

126

126

Y

11

Ssc.1447.3.S1_at

4

NP_116255

1.51E-13

174

174

K

14

Ssc.16422.2.A1_at

2

PLAA

2E-13

175

175

S

10

Ssc.21553.1.S1_at

8

HDGF

2.76E-13

179

179

R

10

Ssc.16422.2.A1_at

1

PLAA

3.26E-13

185

185

S

17

Ssc.13948.1.S1_at

3

GET1_HUMAN

4.42E-13

188

188

W

9

Ssc.10435.1.A1_at

1

Q14156

1.47E-12

210

210

M, Y

8,17

Ssc.17315.1.S1_at

3

EIF3S2

4.64E-12

236

233

K

10

Ssc.19651.1.S1_at

10

WDR42A

8.3E-12

249

244

Y

11

Ssc.20060.1.A1_at

8

TRIP12

2.62E-11

269

262

Y

4

Ssc.13817.1.A1_at

6

VDAC3

5.89E-11

286

276

Y

13

Ssc.24025.1.A1_at

9

Q96E16

6.17E-11

287

277

S

19

Ssc.11787.2.A1_at

9

RASSF2

1.96E-10

326

312

M

9

Ssc.21613.1.S1_at

4

TIGD2

8.38E-10

357

339

R

12

Ssc.19447.1.A1_at

2

ARMCX3

1.37E-09

377

353

Y

9

Ssc.30685.1.A1_at

10

C5orf3

2.48E-09

402

372

Y

5

Ssc.16654.1.A2_at

3

HNRPK

3.15E-09

413

379

none

 

Ssc.6356.1.S1_at

5

ODC1

1.23E-08

470

419

R

10

Ssc.1442.1.S1_at

8

PHF3

1.98E-08

495

434

Y

7

Ssc.2042.1.S1_at

3

NP_079516

3.39E-08

522

448

none

 

Ssc.20974.1.A2_at

7

GNS

5.15E-08

549

467

R

16

Ssc.11173.1.A1_at

1

DEOC_HUMAN

7.88E-08

575

482

Y

17

Ssc.2042.1.S1_at

4

NP_079516

1.83E-07

632

512

none

 

Ssc.12013.1.A1_at

1

SYTL4

6.35E-07

726

554

R, Y

15,16

Ssc.10949.1.S1_at

6

GBAS

9.35E-07

757

566

none

 

Ssc.5052.1.S1_at

4

KIAA0674

9.74E-07

761

570

R

11

Ssc.25584.1.S1_at

8

CDW92

1.62E-06

797

589

W

6

Ssc.1031.1.S1_at

7

OAS1

3.2E-06

861

612

Y

25

Ssc.28305.1.A1_at

11

TACC1

3.22E-06

862

613

none

 

Ssc.17313.2.S1_at

7

CALD1

7.14E-06

938

638

Y

17

Ssc.17423.1.S1_at

4

YWHAZ

1.18E-05

990

661

R

8

Ssc.12029.1.S1_at

6

LAMA2

1.37E-05

1018

670

R

10

Ssc.2466.1.S1_at

5

LRP10

4.59E-05

1177

698

Y

5

Ssc.2466.1.S1_at

5

LRP10

4.59E-05

1177

698

R

5

Ssc.12365.1.A1_at

11

ADAMTS1

0.000135

1345

718

R

5

Ssc.28305.1.A1_at

1

TACC1

0.000376

1585

750

none

 

Ssc.18850.1.S1_at

2

GOLPH2

0.000442

1640

758

none

 

Ssc.1911.1.A1_at

9

PSMC1

0.001044

1893

788

none

 

Ssc.28305.1.A1_at

8

TACC1

0.001842

2108

797

none

 

Ssc.1911.1.A1_at

10

PSMC1

0.005343

2571

816

none

 
  1. This table summarizes the results of sequencing of randomly selected predicted SFPs meeting the criteria of q ≤ 0.05 and a 2-fold expression difference between interacting probes. We estimate the unbiased confirmation rate from this random sample to be 70% using 6 arrays.
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BMC Genomics

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