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.
Using PICKLE
Search for PPIs
Citing PICKLE
- Dimitrakopoulos, GN, Klapa, MI, Moschonas, NK (2022). How Far Are We from the Completion of the Human Protein Interactome Reconstruction?. Biomolecules, 12(1), 140.
- Dimitrakopoulos GN, Klapa MI, Moschonas NK (2021). PICKLE 3.0: Enriching the human Meta-database with the mouse protein interactome extended via mouse-human orthology. Bioinformatics, 37(1), 145-146.
- Gioutlakis A, Klapa MI, Moschonas NK (2017). PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PLoS ONE 12(10), e0186039.
- Klapa MI, Tsafou K, Theodoridis E, Tsakalidis A, Moschonas NK (2013). Reconstruction of the experimentally supported human protein interactome: what can we learn? BMC Systems Biology, 7, 96.
Contributing databases
PPI databases
Biological databases
General Statistics
PICKLE Release 3.3 (Oct 1, 2021)
The default PICKLE network contains:
Human PICKLE
Protein (UniProt) level |
Nodes | 16420 |
Interactions | 218025 |
Publications | 45695 |
Gene level |
Nodes | 16233 |
Interactions | 218891 |
Publications | 45636 |
Mouse PICKLE
mouse-mouse PPI subnetwork |
Protein (UniProt) level |
Nodes | 5666 |
Interactions | 13140 |
Publications | 5156 |
Gene level |
Nodes | 6153 |
Interactions | 12606 |
Publications | 4966 |
mouse-human PPI subnetwork |
Protein (UniProt) level |
Nodes (mouse - human) | 2721 - 2347 |
Interactions | 6211 |
Publications | 2626 |
Gene level |
Nodes (mouse - human) | 2655 - 2282 |
Interactions | 6096 |
Publications | 2551 |