Description
As elementary constituents of cellular protein complexes and pathways, protein–protein interactions (PPIs) are key determinants of protein function. This tool allows building interaction maps by mapping your list of protein or gene identifiers on different public resources; indeed, according to your need and the species of interest, different PPIs resources are available (for details see “Parameters” section). The two result files generated (network and nodes attributes) can be used for viewing and further exploration of the resulting protein interactions network by directly importing those in dedicated software (e.g. Cytoscape).
Input
"Enter IDs": A list of IDs must be entered either via a copy/paste or by choosing a file. The type of identifiers allowed depends on the public resource you select (see below).
In copy/paste mode, the number of IDs considered in input is limited to 5000.
Parameters
"Select database": three databases are currently proposed according to your need and listed below
"Type/source of IDs": correspond to the type of your identifiers you have. Note that only Entrez gene Id and Uniprot Accession number are allowed. If you don't have this type please use the "ID-converter" tool from ProteoRE.
"Species": must be specified if using Biogrid as PPI database (i.e. Homo sapiens, Mus musculus and Rattus norvegicus). If Bioplex or HuMAP are selected, then species is automatically set to Human (Homo sapiens) displaying the release date.
Output:
Two output files are created with the follwing prefix "Network_PPIdatabaseName_" and a "Nodes_PPIdatabaseName_" (where "PPIdatabaseName" correspond to the PPI database selected). The "Network" file contains information related to each interaction between two proteins (one row per binary interaction) while the "Nodes" file contains attributes (i.e. annotation, information) related to each gene/protein. Below is shown a brief example of each output file when BioGRID is selected. Note that a "NA" is added when there is no available information.
"Network" output file (example):
Entrez_Gene_Interactor_A | Entrez Gene Interactor B | Gene symbol Interactor A | Gene symbol Interactor B | Experimental System | Experimental Type | Pubmed ID | Interaction Score | Phenotypes |
---|---|---|---|---|---|---|---|---|
1 | 368 | A1BG | ABCC6 | Two-hybrid | physical | 21988832 | NA | Growth abnormality |
1 | 10549 | A1BG | PRDX4 | Negative Genetic | genetic | 21988832 | NA | NA |
1 | 9923 | A1BG | ZBTB40 | Affinity Capture-MS | physical | 28514442 | 0.99977983 | NA |
"Interaction Score": a positive for negative value recorded by the original publication depicting P-Values, Confidence Score, SGA Score, etc. Will be “NA” if no score is reported.
"Nodes" output file (example):
Entrez gene ID | Official Symbol Interactor | Present in user input ids | ID present in Biogrid Human | Pathway |
---|---|---|---|---|
1 | A1BG | True | True | Platelet degranulation ;Neutrophil degranulation |
10 | NAT2 | False | True | Acetylation |
12 | SERPINA3 | True | False | NA |
These 2 files can be directly imported into a visualization software (such as Cytoscape - https://cytoscape.org/download.html) for further exploration and analysis of the newly created biological network.
Data source (release date)
This tool uses the following public ressources (for more details please check: http://www.proteore.org/static/data_source.html)
Data were downloaded from BioGrid: https://downloads.thebiogrid.org/BioGRID/
Installation date:
06/02/2020
01/03/2019
BioPlex_interactionList_v4a.tsv: http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv
nodeTable.txt: http://proteincomplexes.org/static/downloads/nodeTable.txt
pairsWprob: http://proteincomplexes.org/static/downloads/pairsWprob.txt
Mapping files linking the source database identifier (Entrez gene ID and Uniprot Accession Number) to the Reactome pathways are based on 2018-12-07 version, NCBI2Reactome.txt and UniProt2Reactome.txt (from https://www.reactome.org/download-data).
Galaxy integration
David Christiany, Lisa Perus, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
Sandra Dérozier, Olivier Rué, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
This work has been partially funded through the French National Agency for Research (ANR) IFB project.
Help: contact@proteore.org for any questions or concerns about the Galaxy implementation of this tool.