Skip to main content

Table 8 Comparison of the predicted SSL network to the known SSL network

From: Mining protein networks for synthetic genetic interactions

Threshold Level (Number of pre dictions)

Gene-pair Characteristic

S∩C

Sonly

Conly

S'∩C'

Odds

P-value

Known SSL Pairs (6074)

Cellular Component

4467

1607

193007

207466

2.988

< 2.2 × 10-16

 

Molecular Function

1464

4610

38865

361608

2.955

< 2.2 × 10-16

 

Biological Process

4074

2000

137827

262646

3.882

< 2.2 × 10-16

 

Protein Complex

197

5877

747

399726

17.937

< 2.2 × 10-16

 

Upstream Regulator

220

5854

10327

390146

1.420

9 × 10-7

0.75 (30087)

Cellular Component

17967

12120

781640

799150

1.516

< 2.2 × 10-16

 

Molecular Function

4115

25972

113100

1467690

2.056

< 2.2 × 10-16

 

Biological Process

12966

17121

314562

1266228

3.048

< 2.2 × 10-16

 

Protein Complex

363

29724

1339

1579451

14.405

< 2.2 × 10-16

 

Upstream Regulator

1052

29035

47294

1533496

1.175

3.76 × 10-7

0.80 (28440)

Component

16942

11498

782665

799772

1.506

< 2.2 × 10-16

 

Function

3826

24614

113389

1469048

2.014

< 2.2 × 10-16

 

Process

12245

16195

315283

1267154

3.039

< 2.2 × 10-16

 

Protein Complex

346

28094

1356

1581081

14.360

< 2.2 × 10-16

 

Upstream Regulator

986

27454

47360

1535077

1.164

3.01 × 10-6

0.850 (5149)

Component

3799

1350

795808

809920

2.864

< 2.2 × 10-16

 

Function

1309

3840

115906

1489822

4.382

< 2.2 × 10-16

 

Process

3221

1928

324307

1281421

6.601

< 2.2 × 10-16

 

Protein Complex

287

4862

1415

1604313

66.927

< 2.2 × 10-16

 

Upstream Regulator

173

4976

48173

1557555

1.124

0.024

0.900 (1398)

Component

1184

214

798423

811056

5.602

< 2.2 × 10-16

 

Function

508

890

116707

1492772

7.301

< 2.2 × 10-16

 

Process

1060

338

326468

1283011

12.325

< 2.2 × 10-16

 

Protein Complex

151

1247

1551

1607928

125.535

< 2.2 × 10-16

 

Upstream Regulator

49

1349

48297

1561182

1.174

0.1525

0.950 (953)

Component

831

122

798776

811148

6.917

< 2.2 × 10-16

 

Function

368

585

116847

1493077

8.038

< 2.2 × 10-16

 

Process

776

177

326752

1283172

17.217

< 2.2 × 10-16

 

Protein Complex

126

827

1576

1608348

155.485

< 2.2 × 10-16

 

Upstream Regulator

29

924

48317

1561607

1.014

0.4958

0.999 (202)

Component

184

18

799423

811252

10.373

< 2.2 × 10-16

 

Function

93

109

117122

1493553

10.880

< 2.2 × 10-16

 

Process

179

23

327349

1283326

30.511

< 2.2 × 10-16

 

Protein Complex

37

165

1665

1609010

216.702

< 2.2 × 10-16

 

Upstream Regulator

5

197

48341

1562334

0.820

0.7274

  1. Association between SSL interaction and gene-pair characteristic, following the framework of [20]. S ∩ C represents the number of gene pairs with both SSL interaction(S) and same gene-pair characteristic(C). Sonly represents the number of gene pairs with SSL interaction only. Conly represents the number of non-SSL gene pairs that share the same characteristic. S' ∩ C' represents the number of gene pairs that neither have SSL interaction nor share a specified characteristic. Odds represents the odds ratio of a SSL pair sharing a given characteristic to a non-SSL pair sharing the same characteristic. The P-value represents the statistical significance of overlap between SSL interaction and the specified characteristic as computed by Fisher's exact test. If a protein corresponding to a gene is not assigned to any of the known protein complexes then the gene and its interacting partner are considered to come from two different protein complexes. Similarly in the case of upstream regulators, if a gene does not have any known upstream regulator then the gene and its interacting partner are treated as if they don't share any common upstream regulator. The P-values are not significant in case of common upstream regulator due to the fact the number of predicted positives that share a common upstream regulator is very small in comparison to the total number of pairs that share a common upstream regulator, which is also reflected in the low odds ratio seen at different levels of threshold.
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us