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Table 1 Features considered in the prediction of interactions for each module

From: Probabilistic prediction and ranking of human protein-protein interactions

Module abbreviation

Features considered

Data source

Description

Scoring function

Bins

E

Expression

GDS596 from the Gene Expression Omnibus [70]

Gene expression profiles from 79 physiologically normal tissues obtained from various sources [71]

Pearson correlation of co-expression over all conditions

20 of equal size covering the correlation value range (-1 to +1)

O

Orthology

InParanoid [72], BIND [66], DIP [65] and GRID [69] databases

Interactions of homologous protein pairs from yeast, fly, worm and human

Organism-based using InParanoid score

13

C (Combined)

Localization

PSLT predictions [54]

PSLT is a human subcellular localization predictor that considers nine different compartments (ER, Golgi, cytosol, nucleus, peroxisome, plasma membrane, lysosome, mitochondria and extracellular)

Qualitative score: proximity of compartments

4 (same, neighboring, different compartments, or not localized)

 

Domain co-occurrence

InterPro [73] and Pfam [74]

Protein domains and motifs

Chi-square

5 covering range of Chi-square scores

 

PTM co-occurrence

HPRD [15] and UniProt [76]

Post-translational modifications

P ( PTM [ i ] , PTM [ j ] | I ) P ( PTM [ i ] | I ) ∗ P ( PTM [ j ] | I ) MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaadaWcaaqaaiabbcfaqjabcIcaOiabbcfaqjabbsfaujabb2eanjabcUfaBjabbMgaPjabc2faDjabcYcaSiabbcfaqjabbsfaujabb2eanjabcUfaBjabbQgaQjabc2faDjabcYha8jabbMeajjabcMcaPaqaaiabbcfaqjabcIcaOiabbcfaqjabbsfaujabb2eanjabcUfaBjabbMgaPjabc2faDjabcYha8jabbMeajjabcMcaPiabgEHiQiabbcfaqjabcIcaOiabbcfaqjabbsfaujabb2eanjabcUfaBjabbQgaQjabc2faDjabcYha8jabbMeajjabcMcaPaaaaaa@5C25@

4 covering range of PTM scores

D

Disorder

VLS2 predictions [78]

Prediction of protein intrinsic disorder

Sum of the percent disorder for each protein in a pair

6 covering range of scoring function (0 to 200%)

T

Transitive

-

Module that considers local topology of underlying network predicted using combinations of above features

T = ∑ e ∈ E c s e 1 + | E i \ E c | + | E j \ E c | MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqqGubavcqGH9aqpdaWcaaqaamaaqafabaGaee4Cam3aaSbaaSqaaiabbwgaLbqabaaabaGaeeyzauMaeyicI4Saeeyrau0aaSbaaWqaaiabbogaJbqabaaaleqaniabggHiLdaakeaacqaIXaqmcqGHRaWkcqGG8baFcqqGfbqrdaWgaaWcbaGaeeyAaKgabeaakiabcYfaCjabbweafnaaBaaaleaacqqGJbWyaeqaaOGaeiiFaWNaey4kaSIaeiiFaWNaeeyrau0aaSbaaSqaaiabbQgaQbqabaGccqGGCbaxcqqGfbqrdaWgaaWcbaGaee4yamgabeaakiabcYha8baaaaa@4F06@

5 covering range of scoring function