Measuring the physical cohesiveness of proteins using physical interaction enrichment.

ABSTRACT:

Motivation

Protein-protein interaction (PPI) networks are a valuable resource for the interpretation of genomics data. However, such networks have interaction enrichment biases for proteins that are often studied. These biases skew quantitative results from comparing PPI networks with genomics data. Here, we introduce an approach named physical interaction enrichment (PIE) to eliminate these biases.

Methodology

PIE employs a normalization that ensures equal node degree (edge) distribution of a test set and of the random networks it is compared with. It quantifies whether a set of proteins have more interactions between themselves than proteins in random networks, and can therewith be regarded as physically cohesive.

Results

Among other datasets, we applied PIE to gene

SUBMITTER: Sama IE 

PROVIDER: S-EPMC2958743 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature