is a Data Source.
BioPlex is a proteome-scale map of human protein-protein interactions built by affinity purification-mass spectrometry (AP-MS) of tagged proteins expressed from the human ORFeome. It is a collaboration between the Gygi and Harper labs at Harvard Medical School. BioPlex 3.0 covers nearly 120,000 interactions among nearly 15,000 proteins in HEK293T cells, and a companion network covers about 71,000 interactions in HCT116 cells. Interaction tables for each network version can be downloaded, and the networks can be explored on the web or through R and Python packages.
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| bioplex.explorer | BioPlex Explorer | explorer | Graphical Interface | http | Interactive web explorer (BioPlex Dis... |
| bioplex.3.0-293t | BioPlex 3.0 Interactions (HEK293T) | BioPlex_293T_Network_10K_Dec_2019.tsv (12.3 MB) | Graph | tsv | BioPlex 3.0 human protein-protein int... |
| bioplex.3.0-hct116 | BioPlex 3.0 Interactions (HCT116) | BioPlex_HCT116_Network_5.5K_Dec_2019.tsv (7.4 MB) | Graph | tsv | BioPlex human protein-protein interac... |
| bioplex.2.0-293t | BioPlex 2.0 Interactions (HEK293T) | BioPlex_interactionList_v4a.tsv (5.2 MB) | Graph | tsv | BioPlex 2.0 human protein-protein int... |
| bioplex.1.0-293t | BioPlex 1.0 Interactions (HEK293T) | BioPlex_interactionList_v2.tsv (2.2 MB) | Graph | tsv | BioPlex 1.0 human protein-protein int... |
| bioplex.3.0-293t-directed | BioPlex 3.0 Directed Edges (HEK293T) | BioPlex_3.0_293T_DirectedEdges.tsv (4.1 MB) | Graph | tsv | BioPlex 3.0 network (HEK293T) as dire... |
| bioplex.3.0-hct116-directed | BioPlex 3.0 Directed Edges (HCT116) | BioPlex_3.0_HCT116_DirectedEdges.tsv (2.4 MB) | Graph | tsv | BioPlex 3.0 network (HCT116) as direc... |
| bioplex.2.0-293t-directed | BioPlex 2.0 Directed Edges (HEK293T) | BioPlex_2.0_293T_DirectedEdges.tsv (1.9 MB) | Graph | tsv | BioPlex 2.0 network (HEK293T) as dire... |
| bioplex.1.0-293t-directed | BioPlex 1.0 Directed Edges (HEK293T) | BioPlex_1.0_293T_DirectedEdges.tsv (786.7 KB) | Graph | tsv | BioPlex 1.0 network (HEK293T) as dire... |
| bioplex.3.0-293t-unfiltered | BioPlex 3.0 Unfiltered Bait-Prey Pairs (HEK293T) | BioPlex_BaitPreyPairs_noFilters_293T_10K_Dec_2019.tsv (1.1 GB) | Product | tsv | All candidate bait-prey pairs before ... |
| bioplex.hct116-unfiltered | BioPlex HCT116 Unfiltered Bait-Prey Pairs | BioPlex_BaitPreyPairs_noFilters_HCT116_5.5K_Dec_2019.tsv (774.1 MB) | Product | tsv | All candidate bait-prey pairs before ... |
| bioplex.2.0-293t-unfiltered | BioPlex 2.0 Unfiltered Bait-Prey Pairs (HEK293T) | BaitPreyPairs_noFilters_BP2a.tsv (593.1 MB) | Product | tsv | All candidate bait-prey pairs before ... |
| bioplex.proteome-comparison | HEK293T-HCT116 Proteome Comparison | 293T_HCT116_ProteomeComparison.tsv (1.7 MB) | Product | tsv | TMT-based protein abundance compariso... |
| bioplex.raw-data | BioPlex Raw MS Data Download | download.php | Graphical Interface | http | Web tool for downloading raw mass spe... |
| bioplex.comppass | CompPASS | cRomppass | Process | r | Comparative Proteomic Analysis Softwa... |
| bioplex.bioconductor | BioPlex R Package (Bioconductor) | BioPlex | Programming Interface | r | Bioconductor data package giving R ac... |
| bioplex.bioplexpy | BioPlexPy | bioplexpy | Programming Interface | python | Python package for accessing and anal... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| spoke.graph | SPOKE Graph | data-tools | Graph | http | had primary source | The SPOKE knowledge graph containing ... |
BioPlex (the BioPlex Interactome) maps human protein-protein interactions at proteome scale. Each bait protein is expressed from the human ORFeome (v8.1) with a C-terminal HA-FLAG tag, its interacting partners are captured by affinity purification and identified by mass spectrometry, and high-confidence interactions are scored with CompPASS. The project is a collaboration between the Gygi and Harper labs at Harvard Medical School, funded in part by NHGRI.
Interaction tables identify proteins by Entrez Gene ID and UniProt accession. The site also offers unfiltered bait-prey pairs, directed bait-prey edges, bait lists, and unpublished quarterly releases for further cell lines (U2OS and RPE-1). For those unpublished releases, the site asks users not to publish large-scale analyses until the data appear in a peer-reviewed paper.
The networks can be browsed in the BioPlex Explorer, downloaded as tab-separated files, or loaded with the BioPlex Bioconductor package (R) and BioPlexPy (Python), both maintained by the Center for Computational Biomedicine at Harvard Medical School. The site states no license for the published interaction data. It asks users to cite the corresponding publication for each network.
Created: October 10, 2026 | Last modified: October 10, 2026