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Table 1 Summary of interactions within clusters for GSE13355

From: Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery

 

#gene in cluster

#protein in STRING

#interaction

#expected interaction

Ratio (#interaction/#expected interaction)

p value

Cluster 1

158

152

109

42

2.60

0

Cluster 2

65

62

15

7

2.14

0.0079

Cluster 3

38

36

72

8

9

0

Cluster 4

92

91

19

15

1.27

0.25

Cluster 5

50

49

255

11

23.18

0

Cluster 6

67

65

22

5

4.40

0.0000002

Cluster 7

63

61

463

40

11.58

0

Cluster 8

94

90

19

11

1.73

0.034

Cluster 9

61

61

59

16

3.69

0

Cluster 10

18

18

3

0

NA

0.0048

Up

468

453

1616

633

2.55

0

Down

238

231

235

112

2.10

0

All DE genes

706

684

2407

1274

1.89

0

  1. STRING interactions are shown for each cluster, up or down-regulated genes and all DE genes, how many genes (#gene in cluster), how many proteins (#protein in STRING), how many interactions (#interaction), how many expected interactions (#expected interaction), the ratio of #interactions and #expected interactions, together with the p value to get such a number of interactions by chance
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BMC Genomics

ISSN: 1471-2164

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