Table 1

Top 20 protein-protein interactions from IDBOS ranking
Proteini Proteinj Protein-protein interactioni-j
Symbol Occurrence Name Symbol Occurrence Name

Occurrence

Oij

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

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.

Yu et al.

Yu et al. BMC Bioinformatics 2012 13:79   doi:10.1186/1471-2105-13-79

Open Data