From Human Salivary Proteome Wiki

Protein Interactions

Many of the important biological processes involve interactions of many different molecules. Protein-protein interactions are especially critical in many aspects of cell functioning. A lot of studies have been carried out to characterize these interactions, which are essential to our understanding of how cells work and how diseases develop. IntAct is a molecular interaction database that stores data extracted from the literature or from direct expert annotations. In addition to the set of molecules that interacts with a protein, for each interaction, IntAct also provides all the relevant experimental details described in the original source. Most of the values used to populate the IntAct records are controlled-vocabulary terms from the PSI-MI Molecular Interaction ontology.

See also: Help:Ontology Lookup

Contents 1 Protein Interactions 1.1 Link from Protein Pages 1.2 Interactor List 1.3 Binary Interaction Details 1.4 Reference

Link from Protein Pages

You can retrieve IntAct interaction data for any proteins on the wiki by clicking the "Protein Interactions" link in the Tools panel on the protein page. Note that many of the proteins have no binary interaction data in the database. If that's the case, an error message will be shown on the result page.

See also: Help:Salivary Proteins

Interactor List

The interactor list consists of two parts. The first part is a network showing the molecules known to interact with the protein. Figure 1 illustrates the interactor network for the Keratin, type II cytoskeletal 6B (KRT6B) protein. You can also visualize the network in Cytoscape by clicking the "Open network in Cytoscape" link beneath the diagram. A Java applet will open up and you can re-arrange the nodes or run other operations.

The second part is a table (Figure 2) showing more details about each of the interactors:

• Molecule Accession - the accession number of the molecule in a certain database. For proteins, the UniProt accessions are used and have links to the corresponding protein page on the wiki.
• Molecule Alias - it is usually the gene symbol of a protein.
• Molecule Type - protein-protein interactions are the most common type of interactions in the database, but interactions with other types of molecules (e.g. ribonucleic acid) are also captured.
• Species - origin of the molecule.
• Interaction Count - the number of interactions documented between the molecule and the protein of interest. Click on the count to see more details about the individual interactions as described in the next section.

Binary Interaction Details

The interaction details page display specific interactions between two molecules. Like the interactor list, a diagram is shown connecting the two molecules in conjunction with all the other molecules that interact with them. The interaction details table (Figure 3) lists all the binary interactions, with evidences, between the two molecules as described in the literature. Some of the interactions may be generated through spoke expansion.

• Interaction AC - the accession number of the interaction in the IntAct database. You can see the record of this interaction on the IntAct Website by clicking on the accession number.
• Molecule A - the accession number or gene symbol of the molecule.
• Molecule B - the accession number or gene symbol of the other molecule.
• Interaction Type - the type of connection between the molecules.
• Detection Method - the experimental method used to detect the interaction.
• Reference - the original source that describes the interaction. The source is usually a PubMed article, in which case clicking on the source PMID will take you to the corresponding PubMed page on the wiki.

See also: Help:PubMed Citations

Reference

Aranda B, et al. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38(Database issue):D525-31 [PubMed:19850723]