PICKLE: A protein-protein interaction meta-database for human and mouse

PICKLE (Protein InteraCtion KnowLedgebasE) is a meta-database for the direct protein-protein interactome of the human and the mouse proteomes, integrating publicly available source protein-protein interaction (PPI) databases via genetic information ontology. PICKLE integrates the primary PPI datasets by superimposing them on the UniProtKB/Swiss-Prot reviewed complete proteome of the human (RHCP) and the mouse (RMCP) ontology network without any a priori transformations.

This is a major novelty over the most commonly used methodology of primary PPI dataset integration after their normalization to a pre-selected level of genetic reference. Importantly, the ontological PPI dataset integration allows the PICKLE heterogeneous integrated network to be reversibly normalized to any level of genetic reference without any loss of the original PPI information, the latter being used for the identification of normalization biases. Moreover, it enables the appraisal of potential false positive interactions through PPI source database cross-checking.

The PICKLE interface allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein (UniProt) or the gene level, at three PPI filtering modes: unfiltered, standard and cross-checked (default), using a standardized confidence scoring protocol for PPIs being direct, based on the quality of the supporting experimental evidence.

General Statistics

PICKLE Release 3.2 (Mar 1, 2021)

The default PICKLE network contains:

Human PICKLE
Protein (UniProt) level
Nodes16384
Interactions214446
Publications44634
Gene level
Nodes16197
Interactions215372
Publications44575
Mouse PICKLE
mouse-mouse PPI subnetwork
Protein (UniProt) level
Nodes5609
Interactions12919
Publications5027
Gene level
Nodes6090
Interactions12381
Publications4834
mouse-human PPI subnetwork
Protein (UniProt) level
Nodes (mouse - human)2709 - 2295
Interactions6106
Publications2582
Gene level
Nodes (mouse - human)2642 - 2227
Interactions5981
Publications2506