Interaction - Methods summary

Summary

The Interaction section presents interaction networks for 15026 genes based on protein-protein interaction data from IntAct, BioGRID, BioPlex and OpenCell that has been integrated with data related to protein expression, location and classification from the Human Protein Atlas.The IntAct database relies on experimental molecular interaction data derived from literature curation or direct user submissions, the BioGRID contains curated data derived from publications, BioPlex contributes with interactions based on AP-MS experiments in HEK293T and HCT116 cells and OpenCell provides interaction data based on IP-MS experiments in CRISPR-edited HEK293T cells.

Key publications

Orchard S et al., The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. (2014)
PubMed: 24234451 DOI: 10.1093/nar/gkt1115

Oughtred R et al., The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci. (2021)
PubMed: 33070389 DOI: 10.1002/pro.3978

Huttlin EL et al., The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell. (2015)
PubMed: 26186194 DOI: 10.1016/j.cell.2015.06.043

Cho NH et al., OpenCell: Endogenous tagging for the cartography of human cellular organization. Science. (2022)
PubMed: 35271311 DOI: 10.1126/science.abi6983

What can you learn from the Interaction Section?

Learn about:

• the interaction partners of proteins
• the predicted and subcellular location of the proteins in the network
• the expression specificity of the proteins in the network
• the interaction partners expressed in the same cell type for genes with specific expression

Data overview

How has the data been generated?

Interactions included are direct interaction and physical associations with high and medium confidence from IntAct, physical multivalidated interactions from BioGRID, interactions with>75% probability from BioPlex and significant physical interactions from OpenCell. The consensus network plot consists of interaction pairs present in more than one of the datasets, but since BioPlex and OpenCell data is integrated in the IntAct database interaction pairs present only in IntAct and BioPlex or in Intact and OpenCell will not be shown in the consensus plot.

Figure 1. Genes grouped by the number of first level consensus interaction partners

What is presented in the section?

This section presents interaction data for 11973 genes based on IntAct, 11242 genes based on BioGRID, 6374 genes based on BioPlex and 4654 genes based on OpenCell. The protein-protein interaction data on the gene pages is displayed as a network with nodes representing interaction partners and edges representing the number of datasets in which the interaction is present. The nodes can be coloured according to subcellular location based on data in the Subcellular section, predicted location based on signal peptide and transmembrane region predictions, single cell type specificity based on RNA expression profiles or proteinclass, by using the highlight bar in the top of the plot. For genes classified as single cell type enriched or group enriched there is also an option to highlight interactors expressed in the same cell type. There is also an option for custom highlighting of nodes using the top left Filter option in which a query can be built to for example label all nodes that are tissue enriched in both human and mouse brain or belongs to a certain tissue expression cluster.