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Interactions and Post translational modifications
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Intact Interactions: intact-micluster-human.txt
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OmniPath Interactions: omnipath_interactions.tsv.gz
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OmniPath PTMs: omnipath_ptms.tsv.gz
Full monthly report of characterised interactions from the Intact database, filtered on human protein interactions. There is one line per interacting pair with all the evidence collapsed in a single record.
| Column name | Description |
|---|---|
| ID(s) interactor A | Intact ID |
| ID(s) interactor B | Intact ID |
| Alt. ID(s) interactor A | UniProt ID |
| Alt. ID(s) interactor B | UniProt ID |
| Alias(es) interactor A | Aliases |
| Alias(es) interactor B | Aliases |
| Interaction detection method(s) | ditto |
| Publication 1st author(s) | ditto |
| Publication Identifier(s) | ditto |
| Taxid interactor A | NCBI taxonomy ID of first interactor |
| Taxid interactor B | NCBI taxonomy ID of second interactor |
| Interaction type(s) | collapsed interaction types e.g. "direct interaction", "association", "Phage display" |
| Source database(s) | e.g. Intact, MINT |
| Interaction identifier(s) | Intact (with several records) |
| Confidence value(s) | Confidence value derived from Intact scoring system that weights the amount of evidence reported in the literature for a given protein pair. Take a cut-off around 0.6 for highly characterized interactions |
OmniPath is a comprehensive collection of literature curated human signaling pathways.
Open Targets present this information on the target profile page to show the interactors of a protein.
Filename: omnipath_interactions.tsv.gz
| Column name | Description |
|---|---|
| source | source protein |
| target | target protein |
| is_directed | is the interaction directed |
| is_stimulation | stimulating effect of the interaction |
| is_inhibition | inhibiting effect of the interaction |
| dip_url | link to original Database of Interacting Proteins when available |
| sources | database sources for this protein-protein interaction |
| references | bibliographic references |
Post-translational modifications (PTMs) modulate protein function and contribute to the functional diversity of the proteome. PTMs of proteins are tracked as disease markers. PTMs can be used as molecular targets for developing target-specific therapies. Their characterisation is thus important in early drug development.
Protein phosphorylation is one example of a post-translational modification of proteins whereby a phosphate group is covalently attached to either a serine, threonine or tyrosine residue.
Filename: omnipath_ptms.tsv.gz
| Column name | Description |
|---|---|
| enzyme | enzyme in the enzyme-substrate interaction |
| substrate | substrate in the enzyme-substrate interaction |
| residue_type | type of modified residue |
| residue_offset | position of modified residue |
| modification | type of PTM, e.g. phosphorylation, acetylation, methylation, etc. |
| sources | database sources for the described PTM |
| references | bibliographic references |