Table 2

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

Occurrence

Oij

Z-score Z-rank Average rank
MDM2 466 Mouse double minute 2 homolog TP53 1097 Tumor protein p53 130 86.0 3355 2999.8
TP53 1097 Tumor protein p53 UBC 1899 Ubiquitin C 64 18.4 30486 16565.3
HBA2 68 Hemoglobin, alpha 2 HBB 76 Hemoglobin, beta 59 395.5 76 1360.3
CBL 414 Cas-Br-M ecotro- pic sequence EGFR 626 Epidermal growth factor receptor 46 42.6 11054 6849.3
CBL 414 Cas-Br-M ecotro- pic sequence GRB2 916 Growth factor receptor bound 2 44 33.2 15615 9129.8
FANCA 217 Fanconi anemia, complementation A FANCG 143 Fanconi anemia, complementation G 43 117.3 1808 2226.3
EGFR 626 Epidermal growth factor receptor UBC 1899 Ubiquitin C 41 15.8 34796 18720.3
BRCA2 199 Breast cancer 2, early onset RAD51 171 DNA repair protein RAD51 homolog 1 40 104.4 2288 2466.3
HIF1A 207 Hypoxia inducible factor 1, alpha VHL 351 von Hippel-Lindau tumor suppressor 39 69.2 5071 3857.8
HRAS 164 Ha-Ras1 proto-oncoprotein RAF1 281 Proto-oncogene c-RAF 38 84.8 3444 3044.3
SNAP25 131 Synaptosomal-associated protein, 25kDa STX1A 183 Syntaxin 1A 37 114.7 1920 2282.3
MAX 145 MYC associated factor X MYC 382 Proto-oncogene c-Myc 36 73.4 4568 3606.3
BARD1 109 BRCA1 assoc. RING domain 1 BRCA1 448 Breast cancer 1, early onset 35 75.9 4279 3461.8
GRB2 916 Growth factor receptor bound 2 SHC1 317 SHC transforming protein 1 35 30.1 17593 10118.8
CDH1 167 Cadherin 1, type 1 CTNNB1 470 Catenin, beta 1 34 57.8 6876 4760.3
E2F1 168 E2F transcription factor 1 RB1 385 Retinoblastoma 1 34 64.0 5853 4248.8
GRB2 916 Growth factor receptor bound 2 SOS1 125 Son of sevenless homolog 1 32 44.9 10232 6438.3
CCNA2 109 Cyclin A2 CDK2 286 Cyclin-dependent kinase 2 31 84.3 3485 3064.8
EGF 76 Epidermal growth factor EGFR 626 Epidermal growth factor receptor 31 68.2 5211 3927.8
NFKBIA 231 Nucl. factor of kappa light chain gene enhancer in B-cells RELA 314 V-rel reticulo-endotheliosis viral oncogene homolog A 30 53.1 7932 5288.3

Top 20-ranked protein-protein interactions (PPIs), as identified by the number of times they were observed in the aggregated data set. The quantities and calculations are annotated as in Table‚ÄČ1, except that the data were sorted in decreasing order of PPI occurrence Oij. The proteins involved in these interactions are easily recognizable, and this partly reflects an underlying study-bias of focusing research efforts on a smaller set of high-interest proteins.

Yu et al.

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

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