Summary of the Downloads page
On the Downloads page the user can download the following predefined custom datasets and the full database:
Compartmentalized Interactome
The Compartmentalized Interactome is the protein-protein interaction network of the selected major subcellular localization.
This dataset contains only those interactions in which both interactors share at least one common subcellular localization.
Customization options:
- Choose species
- All species: contains the compartmentalized data for the selected compartment for all species
- H. sapiens: contains the compartmentalized data for the selected compartment only for Human
- D. melanogaster: contains the compartmentalized data for the selected compartment only for Fruit fly
- C. elegans: contains the compartmentalized data for the selected compartment only for the C. elegans
- S. cerevisiae: contains the compartmentalized data for the selected compartment only for Yeast
- Choose subcellular localization
- All localizations: contains the compartmentalized data for the all major localizations for the choosen species
- Cytosol: contains the compartmentalized data only for the cytosol major localization for the choosen species
- Mitochondrion: contains the compartmentalized data only for the mitochondrion major localization for the choosen species
- Nucleus: contains the compartmentalized data only for the nucleus major localization for the choosen species
- Extracellular: contains the compartmentalized data only for the extracellular major localization for the choosen species
- Secretory-Pathway: contains the compartmentalized data only for the secretory-pathway major localization for the choosen species
- Membrane: contains the compartmentalized data only for the membrane major localization for the choosen species
Note that the user could choose only one subcellular localization. Download of multiple localization datasets is not available yet.
The Compartmentalized Interactome contains the following data columns (the entries are separated by |):
- Interactor A: UniProt accession of the interactor protein A
- Naming Convention A: naming convention for the interactor protein A
- Major Loc A With Loc Score: list of the major subcellular localizations where the protein exists and the corresponding localization score for the interactor protein A
- Minor Loc A: list of the minor localizations where the protein exists for the interactor protein A
- Loc Experimental System Type A: list of the experimental system types for the given major or minor localizations for the interactor protein A
- Loc Source DB A: list of the source databases for the given major or minor localizations for the interactor protein A
- Loc PubMed ID A: list of the PubMed IDs for the sources of the given major or minor localizations for the interactor protein A
- Taxonomy ID A: the taxonomy ID of the interactor protein A
- Interactor B: UniProt accession of the interactor protein B
- Naming Convention B: naming convention for the interactor protein B
- Major Loc B With Loc Score: list of the major subcellular localizations where the protein exists and the corresponding localization score for the interactor protein B
- Minor Loc B: list of the minor localizations where the protein exists for the interactor protein B
- Loc Experimental System Type B: list of the experimental system types for the given major or minor localizations for the interactor protein B
- Loc Source DB B: list of the source databases for the given major or minor localizations for the interactor protein B
- Loc PubMed ID B: list of the PubMed IDs for the source of the given major or minor localizations for the interactor protein B
- Taxonomy ID B: the taxonomy ID of the interactor protein B
- Interaction Score: the interaction score gives the probability of the interaction in a compartment dependent manner
- Interaction Experimental System Type: list of the experimental system types for the given interaction
- Interaction Source Database: list of the source databases for the given interaction
- Interaction PubMed ID: list of the PubMed Ids for the sources of the given interaction
Integrated Protein-Protein Interaction Dataset
The Integrated Protein-Protein Interaction Dataset contains all the interactions for the choosen species excluding the subcellular localizations.
Customization options:
- Choose species
- All species: contains the integrated protein-protein interaction data for all species
- H. sapiens: contains the integrated protein-protein interaction data for Human
- D. melanogaster: contains the integrated protein-protein interaction data for Fruit fly
- C. elegans: contains the integrated protein-protein interaction data for the C. elegans
- S. cerevisiae: contains the integrated protein-protein interaction data for Yeast
The Integrated Protein-Protein Interaction Dataset contains the following data columns (the entries are separated by |):
- Protein A: UniProt accession of the interactor protein A
- Synonyms A: list of the protein name synonyms for the interactor protein A
- Naming Convention A: naming convention for the interactor protein A
- Taxonomy ID A: the taxonomy ID of the interactor protein B
- Protein B: UniProt accession of the interactor protein B
- Synonyms B: list of the protein name synonyms for the interactor protein B
- Naming Convention A: naming convention for the interactor protein A
- Taxonomy ID B: the taxonomy ID of the interactor protein B
- Interaction Score: the interaction score gives the probability of the interaction in a compartment dependent manner
(Note that the interaction score is 0, if there was no localization information for one, or both of the interactors.)
- Interaction Experimental System Type: list of the experimental system types for the given interaction
- Interaction Source Database: list of the source databases for the given interaction
- Interaction PubMed ID: list of the PubMed Ids for the sources of the given interaction
Integrated Subcellular Localization Dataset
The Integrated Subcellular Localization Dataset contains all the localization data for the proteins excluding the interactions.
Customization options:
- Choose species
- All species: contains the integrated subcellular localization data for all species
- H. sapiens: contains the integrated subcellular localization data for Human
- D. melanogaster: contains the integrated subcellular localization data for Fruit fly
- C. elegans: contains the integrated subcellular localization data for the C. elegans
- S. cerevisiae: contains the integrated subcellular localization data for Yeast
- Choose subcellular localization
- All localizations: contains the subcellular localization data for the all major localizations for the choosen species
- Cytosol: contains the subcellular localization data only for the cytosol major localization for the choosen species
- Mitochondrion: contains the subcellular localization data only for the mitochondrion major localization for the choosen species
- Nucleus: contains the subcellular localization data only for the nucleus major localization for the choosen species
- Extracellular: contains the subcellular localization data only for the extracellular major localization for the choosen species
- Secretory-Pathway: contains the subcellular localization data only for the secretory-pathway major localization for the choosen species
- Membrane: contains the subcellular localization data only for the membrane major localization for the choosen species
The Integrated Subcellular Localization Dataset contains the following data columns (the entries are separated by |):
- Protein Name: UniProt accession of the protein
- Naming Convention: naming convention for the protein
- Synonyms: list of the protein name synonyms for the protein
- Major Loc With Loc Score: list of the major subcellular localizations where the protein exists and the corresponding localization score for the protein
- Minor Loc: list of the minor localizations where the protein exists for the protein
- Experimental System Type: list of the experimental system types for the given major or minor localizations for the protein
- Localization Source Database: list of the source databases for the given major or minor localizations for the protein
- PubmedID: list of the PubMed IDs for the source of the given major or minor localizations for the protein
- TaxID: the taxonomy ID of the protein
Full database - Current and Previous Releases
The ComPPI Full Database download allows the user o download the current or previous releases of the ComPPI database.
The downloaded database is in SQL format and contains all the information stored in the ComPPI database.
More information about the output formats on the Downloads page here.
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