iRefIndex Manager (iRefR)

iRefIndex Manager (iRefR) provides programmatic access to and manipulation of iRefIndex protein interaction data within R for standardized network and complex analysis.

Key Features:

• Data Access and Selection: Access iRefIndex datasets within R and filter interactions by organism type, source database, experimental methods, protein accession numbers, and publication identifiers (PMIDs).
• Data Representation: Convert interaction data between MITAB, edgeList, and graph formats and interoperate with R packages such as igraph, graph, and RBGL.
• Redundancy Resolution and n-ary Representation: Apply multiple methods to resolve redundant interaction records and to represent n-ary interactions involving more than two proteins.
• Identification of Protein Complexes: Identify binary interaction records that may represent protein complexes to distinguish binary pairs from multi-protein assemblies.
• Impact on Graphical Analysis: Expose parameters for data selection, redundancy resolution, and n-ary representation that influence outcomes of network and graphical analyses.

Scientific Applications:

• Systems Biology: Analyze protein interaction networks and complex membership for systems-level models.
• Molecular Biology: Investigate protein partners and multi-protein assemblies relevant to cellular mechanisms.
• Bioinformatics: Integrate standardized interaction datasets into network analysis and pathway analysis workflows.

Methodology:

Programmatic access to iRefIndex within R; filtering by organism, source database, experimental methods, protein accession numbers, and PMIDs; conversion between MITAB, edgeList, and graph formats; interoperability with igraph, graph, and RBGL; multiple redundancy-resolution methods; representation of n-ary interactions; identification of binary records that may indicate protein complexes.