SLiMScape 3

SLiMScape 3 analyzes short linear motifs (SLiMs) within protein interaction networks to support de novo motif discovery and enrichment analysis of motif occurrences.

Key Features:

• De Novo Discovery: Uses SLiMFinder and QSLiMFinder from the SLiMSuite package to discover novel SLiMs from protein interaction networks or sets of UniProt identifiers.
• Enrichment Analysis: Uses SLiMProb to identify occurrences and test enrichment of known SLiMs given user-supplied query motifs.
• Network Visualization in Cytoscape: Displays predicted SLiM occurrences within the context of protein interaction networks via integration with Cytoscape.
• Statistical Models for Enrichment: Applies statistical models leveraging evolutionary relationships, amino acid composition, and predicted disorder to predict SLiM enrichment in non-homologous proteins.
• Remote Job Execution: Supports submission of analysis jobs to the SLiMSuite REST server at http://rest.slimsuite.unsw.edu.au for remote processing and subsequent retrieval.

Scientific Applications:

• De novo motif discovery and annotation: Generation of candidate SLiMs from protein interaction datasets and UniProt identifier lists.
• Motif occurrence and enrichment analysis: Assessment of the presence and statistical enrichment of known SLiMs across protein networks and non-homologous protein sets.
• Functional analysis of protein interaction networks: Linking SLiM occurrences to processes such as complex formation, signal transduction, localization, and stabilization.
• Study of molecular mimicry by pathogens: Detection of potential pathogen-derived motifs that mimic host SLiMs.

Methodology:

Integrates SLiMSuite tools (SLiMFinder, QSLiMFinder, SLiMProb) within Cytoscape; analyzes protein interaction networks or UniProt identifier sets; applies statistical models based on evolutionary relationships, amino acid composition, and predicted disorder to assess SLiM enrichment in non-homologous proteins; supports remote execution via the SLiMSuite REST server (http://rest.slimsuite.unsw.edu.au).