title: 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.
authors.affiliation: Department of Clinical Biochemistry & Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
authors.forename: Omer
authors.initials: O
authors.lastname: Basha
authors.affiliation: Department of Computer Science, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
authors.forename: Dvir
authors.initials: D
authors.lastname: Flom
authors.affiliation: Department of Clinical Biochemistry & Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
authors.forename: Ruth
authors.initials: R
authors.lastname: Barshir
authors.affiliation: Department of Computer Science, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
authors.forename: Ilan
authors.initials: I
authors.lastname: Smoly
authors.affiliation: Department of Clinical Biochemistry & Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
authors.forename: Shoval
authors.initials: S
authors.lastname: Tirman
authors.affiliation: Department of Clinical Biochemistry & Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel estiyl@bgu.ac.il.
authors.forename: Esti
authors.initials: E
authors.lastname: Yeger-Lotem
mesh_terms: D030562:Databases, Protein; D020869:Gene Expression Profiling; D063990:Gene Ontology; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software