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Table 1 Top 20 protein-protein interactions from IDBOS ranking

From: Inferring high-confidence human protein-protein interactions

 

Proteini

  

Proteinj

 

Protein-protein interactioni-j

Symbol

Occurrence

Name

Symbol

Occurrence

Name

Occurrence

O ij

Z-score

Z-rank

Average rank

GCAT

2

Glycine C-acetyltransferase

TDH

2

L-threonine dehydrogenase

2

577.4

11.0

1328.0

CXCL16

4

Inducible T cell co-stimulator

CXCR6

4

Inducible T cell co-stimulator ligand

4

565.7

21.0

1333.0

CAPG (NCAPG)

2

Non-SMC condensin I, G

NCAPH

2

Non-SMC condensin I, H

2

534.5

22.0

1333.5

ICOS

5

Inducible T cell co-stimulator

ICOSLG

5

Inducible T cell co-stimulator ligand

5

507.7

23.0

1334.0

GPR103 (QRFPR)

3

QRFP receptor

P518(QRFP)

3

Pyroglutamylated RFamide peptide

3

474.3

28.0

1337.0

BCKDHA

5

Branched chain keto acid dehydro. E1, alpha

BCKDHB

4

Branched chain keto acid dehydro. E1, beta

4

471.4

29.0

1337.5

ARTN

2

Artemin (GDNF family)

GFRA3

2

GDNF family receptor alpha 3

2

458.8

30.0

1338.0

CX3CL1

3

Chemokine (C-X3

-C motif) ligand 1

CX3CR1

3

Chemokine (C-X3-C motif) receptor 1

3

442.3

57.0

1351.5

GIP

7

Gastric inhibitory polypeptide

GIPR

9

Gastric inhibitory polypeptide receptor

7

431.7

58.0

1352.0

POLG

4

Polymerase (DNA directed), gamma

POLG2

3

Polymerase (DNA directed), gamma2

3

428.6

59.0

1352.5

METTL1

5

tRNA(m7G46)-methyltransferase

WDR4

2

tRNA (guanine-N(7)-)-methyltran. subunit WDR4

2

417.0

60.0

1353.0

IL11

3

Interleukin 11

IL11RA

2

Interleukin 11 receptor, alpha

2

408.2

61.0

1353.5

HBA2

68

Hemoglobin, alpha 2

HBB

76

Hemoglobin, beta

59

395.5

76.0

1361.0

CLEC2D

2

C-type lectin domain family 2, member D

KLRB1

3

Killer cell lectin-like receptor subfamily B, 1

2

392.2

77.5

1361.8

LTC4S

2

Leukotriene C4 synthase

MGST1

3

Microsomal glutathione S-transferase 1

2

392.2

77.5

1361.8

CD97

4

Leukocyte antigen CD97

DAF

2

CD55 antigen

2

384.9

79.5

1362.8

D2LIC

2

Dynein, cyto-plasmic 2, light intermed. chain 1

DNCH2

3

Dynein, cytoplasmic 2, heavy chain 1

2

384.9

79.5

1362.8

IL22

6

Interleukin 22

IL22RA1

4

Interleukin 22 receptor, alpha 1

4

383.1

81.0

1363.5

CD200

3

MRC OX-2 antigen

CD200R1

2

CD200 receptor 1

2

378.0

82.0

1364.0

MLN

4

Motilin

MLNR

7

Motilin receptor

4

369.8

98.0

1372.0

  1. The top-20 ranked protein-protein interactions (PPIs) as identified by the interaction detection based on shuffling (IDBOS) method. We also provided the number of times each individual protein was observed in the aggregated data set, the number of times the PPI was observed, and the corresponding Z-score and associated fractional rank. All PPIs in this table have p-values <10−6, i.e., in the 106 randomization shuffles each of these PPIs were never observed to occur more times than they were actually observed in the original data set. In the data set there were 5,288 PPIs with zero p-values and, hence, we assigned their uniform p-value rank to be 2,644.5 (5288/2). This value was used together with each Z-rank to create the average rank in the last column. The estimated Z-score of a PPI depends on the number of times each protein was observed in the original aggregated data set.
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BMC Bioinformatics

ISSN: 1471-2105

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