Inferring high-confidence human protein-protein interactions.

BMC Bioinformatics
Xueping YuJaques Reifman

Abstract

As numerous experimental factors drive the acquisition, identification, and interpretation of protein-protein interactions (PPIs), aggregated assemblies of human PPI data invariably contain experiment-dependent noise. Ascertaining the reliability of PPIs collected from these diverse studies and scoring them to infer high-confidence networks is a non-trivial task. Moreover, a large number of PPIs share the same number of reported occurrences, making it impossible to distinguish the reliability of these PPIs and rank-order them. For example, for the data analyzed here, we found that the majority (>83%) of currently available human PPIs have been reported only once. In this work, we proposed an unsupervised statistical approach to score a set of diverse, experimentally identified PPIs from nine primary databases to create subsets of high-confidence human PPI networks. We evaluated this ranking method by comparing it with other methods and assessing their ability to retrieve protein associations from a number of diverse and independent reference sets. These reference sets contain known biological data that are either directly or indirectly linked to interactions between proteins. We quantified the average effect of using ranked pro...Continue Reading

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Citations

Jan 9, 2013·Nature Reviews. Gastroenterology & Hepatology·Tom J G Gevers, Joost P H Drenth
Jun 27, 2013·Molecular & Cellular Proteomics : MCP·Vesna MemisevićAnders Wallqvist
Mar 21, 2013·Journal of Neurotrauma·Jacob D FealaJaques Reifman
May 9, 2013·BMC Bioinformatics·Vesna MemiševićJaques Reifman
Jun 5, 2014·Annual Review of Biophysics·Donald Petrey, Barry Honig
Nov 8, 2014·PloS One·Mohamed Diwan M AbdulHameedAnders Wallqvist
Mar 5, 2015·PLoS Computational Biology·Vesna MemiševićAnders Wallqvist
Sep 22, 2016·BMC Bioinformatics·Vesna MemiševićJaques Reifman
Oct 12, 2016·BMC Genomics·Mohamed Diwan M AbdulHameedAnders Wallqvist
Sep 12, 2014·Integrative Biology : Quantitative Biosciences From Nano to Macro·Edson Luiz FoladorVasco Azevedo
Aug 8, 2020·Journal of Bioinformatics and Computational Biology·Madhusudan Paul, Ashish Anand
Jul 18, 2014·BMC Bioinformatics·Vesna MemiševićJaques Reifman

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Methods Mentioned

BETA
two-hybrid
affinity purification
surface plasmon resonance

Software Mentioned

Reactome
EMPIRE
IDBOS
Linux
OMIM

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