EndoMAP.v1 Interaction Network

Represents proteins as nodes and interactions as edges based on cross-linking and/or co-fractionation experiments.

Protein Information

Select a protein by clicking a node or using the search box to find your protein of interest.

• Gene name, accession number and protein description as retrieved from UniProt.
• Meta-analysis score (0-1): higher scores indicate higher likelihood of endosomal localization. Meta-analysis score was obtained by combination of three individual metrics: identification across multiple datasets in the literature, protein abundance in purified endosomes by Endo-IP, and number of interactions with well-known endosomal proteins. Absence of score indicates proteins not detected in meta-analysis.
• Labeled as endosomal (Y/N): proteins above the minimum meta-analysis score (0.0734) and well-known endosomal proteins are annotated as endosomal. Node shape indicates proteins annotated as endosomal (diamonds) or not (circles).
• Intraprotein cross-links: position of the cross-linked residues identified with each cross-linker (DSSO, DHSO and/or DMTMM).

Interaction Information

Select interactions by clicking an edge. Interactions identified by cross-linking are indicated with solid lines and interactions identified only by co-fractionation with dashed lines.

Protein-Protein Interaction (PPI) Databases

• Previously identified (Y/N): protein interactions identified in at least one of the following databases (BioPlex, STRINGDB, CORUM, PDB) are indicated with red edges.
• CORUM database (Y/N): interaction included in manually annotated protein complexes from mammalian organisms from CORUM.
• PDB (Y/N): experimentally determined 3D structure of the interaction as retrieved from Protein Data Bank (PDB).
• BioPlex pInt (0-1): Probability of the prey being a high-confidence interacting protein as retrieved from Bioplex3.0.
• StringDB combined score: integrated probability from experimentally determined interactions and database annotated interactions (confidence >0.7, 5% FDR) from STRINGDB.

Blue-Native (BN) Gel Co-Fractionation Data

Purified human endosomes purified were subjected to BN co-fractionation to identify possible protein complexes based on correlation profiling.

• SECAT p-value: targeted co-elution analysis of cross-linking PPIs in our BN co-fractionation data. Only available for PPIs identified by cross-linking whose proteins were also identified in BN experiments.
• PCprophet total score: untargeted prediction of PPIs based on our BN co-fractionation data. It indicates the combined scores for each PPI in all three replicates. PPIs were considered with a minimum of 0.7 score in at least two replicates.

Cross-Linking (XL) Data

Purified human endosomes were cross-linked to capture protein interactions and structures in their organellar context.

• Total number of interprotein cross-links identified and the position of the cross-linked residues are indicated for each cross-linker reagent (DSSO, DHSO and/or DMTMM).
• PPI found at 1%FDR: interactions identified with at least one cross-link using Scout at 1% FDR are indicated.

AlphaFold Multimer and AlphaLink2

Large-scale AF-M and AlphaLink2 predictions for protein pairs identified by XL-MS.

• Structure Prediction and Omics informed Classifier (SPOC): prediction quality score based on structural properties of the predicted interface and biological correlations among the interacting proteins (such as colocalization and genetic co-dependency). A SPOC >0.33 is considered acceptable quality for pairwise predictions.
• ipTM interface predicted Template Modelsing score. (Please refer to AlphaFold website for additional information).

Filtering Options

• Interaction level: searching a node/protein shows only direct interactions by default (level=1). The filtering level option can be used to visualize only direct interactions (level=1) or include second order interactions (level=2).
• Show all data: click to show all interactions including non-filtered data. By default, the network is filtered to remove dubious interactions and include only endosomal proteins and their direct interactors. Second order interactors of endosomal proteins were only included when connected to at least one direct interactor by XL and/or two direct interactors by BN. Unfiltered interactions may include proteins and complexes co-purified with the endosomes.