Dataset Information

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

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.

SUBMITTER: Basha O

PROVIDER: S-EPMC4489290 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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

Basha Omer O Flom Dvir D Barshir Ruth R Smoly Ilan I Tirman Shoval S Yeger-Lotem Esti E

Nucleic acids research 20150518 W1

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-sensitiv ...[more]

PMID: 25990735

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Project description:BackgroundProtein-protein interaction (PPI) data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or 'interologs'. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for 'on-the-fly' interolog prediction.ResultsWe introduce Bio::Homology::InterologWalk, a Perl module to retrieve, prioritise and visualise putative protein-protein interactions through an orthology-walk method. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an Interaction Prioritisation Index that can be used to help prioritise interologs for further analysis. We show the application of our interolog prediction method to the genomic interactome of the fruit fly, Drosophila melanogaster. We analyse the resulting interaction networks and show that the method proposes new interactome members and interactions that are candidates for future experimental investigation.ConclusionsOur interolog prediction tool employs the Ensembl Perl API and PSICQUIC enabled protein interaction data sources to generate up to date interologs 'on-the-fly'. This represents a significant advance on previous methods for interolog prediction as it allows the use of the latest orthology and protein interaction data for all of the genomes in Ensembl. The module outputs simple text files, making it easy to customise the results by post-processing, allowing the putative PPI datasets to be easily integrated into existing analysis workflows. The Bio::Homology::InterologWalk module, sample scripts and full documentation are freely available from the Comprehensive Perl Archive Network (CPAN) under the GNU Public license.

Dataset Information

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

Publications

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

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