MyProteinNet: Build up-to-date protein interaction networks for organisms, tissues and user-defined contexts

Omer Basha, Dvir Flom, Ruth Barshir, Ilan Smoly, Shoval Tirman, Esti Yeger-Lotem

Research output: Contribution to journalArticlepeer-review

29 Scopus citations

Abstract

The identification of the molecular pathways active in specific contexts, such as disease states or drug responses, often requires an extensive view of the potential interactions between a subset of proteins. This view is not easily obtained: it requires the integration of context-specific protein list or expression data with up-to-date data of protein interactions that are typically spread across multiple databases. The MyProteinNet web server allows users to easily create such context-sensitive protein interaction networks. Users can automatically gather and consolidate data from up to 11 different databases to create a generic protein interaction network (interactome). They can score the interactions based on reliability and filter them by user-defined contexts including molecular expression and protein annotation. The output of MyProteinNet includes the generic and filtered interactome files, together with a summary of their network attributes. MyProteinNet is particularly geared toward building human tissue interactomes, by maintaining tissue expression profiles from multiple resources. The ability of MyProteinNet to facilitate the construction of up-to-date, context-specific interactomes and its applicability to 11 different organisms and to tens of human tissues, make it a powerful tool in meaningful analysis of protein networks. MyProteinNet is available at http://netbio.bgu.ac.il/myproteinnet.

Original languageEnglish
Pages (from-to)W258-W263
JournalNucleic Acids Research
Volume43
Issue numberW1
DOIs
StatePublished - 1 Jan 2015

ASJC Scopus subject areas

  • Genetics

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