About


 

About PICKLE

PICKLE (Protein InteraCtion KnowLedgebasE) is a meta-database for the direct protein interaction network in of human and mouse developed and maintained by:

The need for source PPI database integration and related issues

Presently, a vast insight into the known human and mouse interactome can only be achieved by means of integration of source PPI databases collecting experimental PPI data from the literature. This is due to the fact that source PPI databases display limited overlap in their datasets due to different objectives, curation rules and subsets of the literature that they process.

PPI annotation discrepancies between the source databases:

Typically, these heterogeneous primary PPI datasets are integrated via normalization: interactions are first converted to a certain target level of genetic reference and then merged.

Drawbacks:

The PICKLE approach to source PPI database integration

PICKLE introduces the concept of ontological integration as an alternative to the traditional integration via normalization.

The genetic information ontology network:

Focusing primarily on direct physical PPIs, PICKLE introduced a PPI filtering protocol, according to which, only PPIs with at least one supporting experiment capable of suggesting direct interactions are selected from the source PPI databases. Moreover, PICKLE establishes an enhanced confidence scoring protocol for the PPIs being direct based on the "cross-checked" quality of the supporting experimental evidence and provides equivalent integrated human PPI networks at both the protein (UniProt) or the gene level, at three PPI filtering modes:.

  1. cross-checked (default)
  2. standard
  3. unfiltered
PICKLE 3.0: Upgrading PICKLE with the mouse protein interactome

PICKLE is presently upgraded with the laboratory mouse protein interactome. Experimental PPI data between mouse genetic entities are substantially complemented by PPIs between mouse and human genetic entities. The relational scheme of PICKLE 3.0 has been amended to exploit the Mouse Genome Informatics (MGI) mouse-human ortholog gene pair collection, enabling (i) the extension through orthology of the mouse interactome with potentially valid PPIs between mouse entities based on the experimental PPIs between mouse and human entities, and (ii) the comparison between mouse and human PPI networks. PICKLE 3.0 provides a unique comprehensive representation of the mouse protein interactome.

The advantages of the PICKLE structural scheme

The use of the UniProtKB/Swiss-Prot defined reviewed human complete proteome (RHCP) and the reviewed mouse complete proteome (RMCP) as the basis of the instantiation of the respective PICKLE ontological networks offers a standardized point of reference between the PPI networks of successive versions and any future releases of PICKLE. In this way, by comparing the default network of human or mouse PICKLE at the UniProt protein level between two PICKLE versions and/or subsequent releases, we can directly and reliably evaluate the manner of expansion of the RHCP or RMCP PPI network.

Moreover, the reversible normalization process achieved by PICKLE guarantees a direct correspondence between the various normalized instances of the human or mouse integrated PPI network. Hence, one can compare a PPI in the integrated network with all the different ways in which it was originally represented in the primary PPI datasets. This feature enables the identification of any potential normalization artifacts through the comparison of the human or the mouse protein interactome at the protein (UniProt) and gene levels and a PPI reliability assessment through cross-checking of the available experimental evidence sets contributed by the various primary datasets.

In addition, PICKLE 3.1 enables the storage of interactions between protein and gene or nucleotide sequence (mRNA) entities, e.g. those derived from protein-RNA or chromatin immunoprecipitation arrays/assays, as reported by certain sources, which can be used for purposes of cross-evaluating the supporting evidences provided in other primary datasets. In the same context, it is possible for assorted types of data (e.g. disease-related genes, genomic, transcriptomic or proteomic data) to be consistently integrated, viewed and interpreted in the context of the protein interaction network.

PICKLE Ontological network


 

Contributing Databases

PPI Databases
Biological Databases
IntAct UniProt
BioGRID GenBank
HPRD Ensembl
DIP The European Nucleotide Archive
Gene Ontology Consortium
HUPO Proteomics Standards Inititative
Mouse Genome Informatics - Vertebrate Homology

 

PICKLE statistics - release 3.1

Statistics about the default (cross-checked) network at protein (UniProt) level regarding the primary databases:

Human PICKLE
Database UniProt IDs PPIs References
HPRD release 9 9358 37538 19519
IntAct release 227 14274 95806 2891
MINT (via IntAct) 5826 14333 2997
DIP release 20170205 3133 5929 2431
BioGRID release 3.5.178 13613 107593 28847
PICKLE release 3.1 16418 191113 42121
Mouse PICKLE
Database UniProt IDs PPIs References
mouse-mouse PPI subnetwork
BioGRID release 3.5.179 3477 6834 2831
DIP release 20170205 1103 1214 655
IntAct release 228 3395 5194 2352
PICKLE release 3.1 5087 11026 4946
mouse-human PPI subnetwork
BioGRID release 3.5.179 2444 2543 1016
DIP release 20170205 836 704 399
IntAct release 228 2952 3034 1596
PICKLE release 3.1 4464 5396 2552
 

The PICKLE team

Nicholas K. Moschonas, Professor and Head
Department of General Biology
School of Medicine
University of Patras
Rio, Patras
&
Collaborating Faculty Member
Institute of Chemical Engineering Sciences (ICE-HT)
Foundation for Research & Technology - Hellas (FORTH)
Rio, Patras
GREECE
Phone: +30-2610-997602
e-mail: n_moschonas [a.t.] med [DOT] upatras [DOT] gr

Maria I. Klapa, Principal Researcher (Rank B) and Head
Metabolic Engineering and Systems Biology Laboratory (MESBL)
Institute of Chemical Engineering Sciences (ICE-HT)
Foundation for Research & Technology - Hellas (FORTH)
Rio, Patras
GREECE
Phone: +30-2610-965249
e-mail: mklapa [a.t.] iceht [DOT] forth [DOT] gr

Aris G. Gioutlakis, PhD Candidate
Department of General Biology, School of Medicine
University of Patras
&
Metabolic Engineering and Systems Biology Laboratory (MESBL)
Institute of Chemical Engineering Sciences (ICE-HT)
Foundation for Research & Technology - Hellas (FORTH)
Rio, Patras
GREECE
Phone: +30-2610-997603
e-mail: gioutlakis [a.t.] upatras [DOT] gr

Georgios N. Dimitrakopoulos, PhD
Department of General Biology, School of Medicine
University of Patras
&
Metabolic Engineering and Systems Biology Laboratory (MESBL)
Institute of Chemical Engineering Sciences (ICE-HT)
Foundation for Research & Technology - Hellas (FORTH)
Rio, Patras
GREECE
Phone: +30-2610-997603
e-mail: geodimitrak [a.t.] upatras [DOT] gr


 

PICKLE publications

Citing PICKLE

If you are using PICKLE, please cite:


 

PICKLE citations

Publications citing PICKLE

 

PICKLE usage

Last 6 months statistics according to Google Analytics:

users map
users number