Header

UZH-Logo

Maintenance Infos

Context-based retrieval of functional modules in protein-protein interaction networks


Dobay, Maria Pamela; Stertz, Silke; Delorenzi, Mauro (2017). Context-based retrieval of functional modules in protein-protein interaction networks. Briefings in Bioinformatics:Epub ahead of print.

Abstract

Various techniques have been developed for identifying the most probable interactants of a protein under a given biological context. In this article, we dissect the effects of the choice of the protein–protein interaction network (PPI) and the manipulation of PPI settings on the network neighborhood of the influenza A virus (IAV) network, as well as hits in genome-wide small interfering RNA screen results for IAV host factors. We investigate the potential of context filtering, which uses text mining evidence linked to PPI edges, as a complement to the edge confidence scores typically provided in PPIs for filtering, for obtaining more biologically relevant network neighborhoods. Here, we estimate the maximum performance of context filtering to isolate a Kyoto Encyclopedia of Genes and Genomes (KEGG) network Ki from a union of KEGG networks and its network neighborhood. The work gives insights on the use of human PPIs in network neighborhood approaches for functional inference.

Abstract

Various techniques have been developed for identifying the most probable interactants of a protein under a given biological context. In this article, we dissect the effects of the choice of the protein–protein interaction network (PPI) and the manipulation of PPI settings on the network neighborhood of the influenza A virus (IAV) network, as well as hits in genome-wide small interfering RNA screen results for IAV host factors. We investigate the potential of context filtering, which uses text mining evidence linked to PPI edges, as a complement to the edge confidence scores typically provided in PPIs for filtering, for obtaining more biologically relevant network neighborhoods. Here, we estimate the maximum performance of context filtering to isolate a Kyoto Encyclopedia of Genes and Genomes (KEGG) network Ki from a union of KEGG networks and its network neighborhood. The work gives insights on the use of human PPIs in network neighborhood approaches for functional inference.

Statistics

Altmetrics

Downloads

1 download since deposited on 10 Oct 2017
1 download since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Institute of Medical Virology
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Uncontrolled Keywords:context filtering; information content bias; protein–protein networks; text mining evidence evaluation
Language:English
Date:27 March 2017
Deposited On:10 Oct 2017 14:36
Last Modified:12 Oct 2017 11:40
Publisher:Oxford University Press
ISSN:1467-5463
Funders:This work was supported by the Swiss Initiative in Systems Biology, SystemsX, through a fellowship (2013/137) provided to M.P.D.
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/bib/bbx029
PubMed ID:28369159

Download

Content: Accepted Version
Filetype: PDF - Registered users only until 1 April 2018
Size: 7MB
Embargo till: 2018-04-01