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bioplex — BioPlex human protein co-complex interactomes (2015-2022)

Description

Networks of protein interactions in human cell lines from the BioPlex project of the Gygi and Harper labs (Harvard Medical School). BioPlex maps the human interactome by affinity purification and mass spectrometry (AP-MS): each of thousands of human proteins (the baits, expressed from the ORFeome collection with an epitope tag) is purified from the cells together with the proteins bound to it (the preys), which are identified by mass spectrometry. The candidate bait-prey pairs are scored with the CompPASS-Plus classifier, which estimates for each pair the probabilities of a wrong protein identification, of a nonspecific (background) association, and of a genuine interaction; the published networks keep the pairs classified as interactions. Since the proteins in a purification may be bound indirectly, through other members of the same complex, the interactions are co-complex associations rather than necessarily direct (binary) contacts. Nodes are proteins, identified by the Entrez (NCBI) Gene IDs of the genes that encode them.

The entry contains every network offered for download on the BioPlex site:

  • 1.0_293T, 2.0_293T, 3.0_293T, 3.0_HCT116: the official undirected networks of BioPlex 1.0 (2,594 baits in HEK293T cells, Huttlin et al. 2015), BioPlex 2.0 (5,891 baits in HEK293T cells, Huttlin et al. 2017), and BioPlex 3.0 (10,128 baits in HEK293T cells and 5,522 baits in HCT116 cells, Huttlin et al. 2021). An undirected edge joins two proteins found to interact, whichever was the bait.
  • 1.0_293T_directed, 2.0_293T_directed, 3.0_293T_directed, 3.0_HCT116_directed: the same networks as directed bait-prey interactions, with a directed edge from the bait to each of its interacting preys (as distributed separately by the BioPlex site; a pair of proteins that found each other as baits is joined by two opposite edges, so that the numbers of edges differ slightly from the undirected networks).
  • 2.0_293T_unfiltered, 3.0_293T_unfiltered, 3.0_HCT116_unfiltered: all the candidate bait-prey pairs of BioPlex 2.0 and of BioPlex 3.0 (HEK293T and HCT116 cells) before filtering, i.e. every protein detected in the purification of every bait, with the CompPASS scores and classifier probabilities (the BioPlex site warns that these lists contain background and nonspecific interactors). A directed edge goes from the bait to each protein detected with it, so that the bait's own detection is a self-loop. Each edge is one identified protein (database entry), so that several isoforms or entries of the same gene give multiple edges between the same pair of nodes.
  • 293T_2015-12, 293T_2016-05, 293T_2016-08, 293T_2016-12, 293T_2017-04, 293T_2017-10: the quarterly releases of interactions of new baits in HEK293T cells (U41 grant), released before their publication in BioPlex 3.0.
  • HCT116_2018-11, HCT116_2019-03, HCT116_2019-05, HCT116_2019-08, HCT116_2019-11, HCT116_2020-02, HCT116_2020-05, HCT116_2021-02, HCT116_2021-05, HCT116_2021-08, HCT116_2021-11: the quarterly releases of interactions of new baits in HCT116 cells (U24 grant); the releases of August and November 2020 were not made because of the COVID-19 shutdown.
  • U2OS_0.1, RPE1_0.1: preliminary networks (version 0.1) of 2,279 baits in U2OS cells (released in August 2021) and of 1,925 baits in RPE-1 cells (released in February 2022).

In the quarterly releases and the preliminary networks, a directed edge goes from the bait to each interacting prey (as classified by CompPASS-Plus), including the bait itself as a self-loop when it was detected, and, in the quarterly releases, each edge is one identified protein, so that several isoforms or entries of the same gene give multiple edges. The BioPlex site describes the quarterly releases and the preliminary networks as unpublished data, and asks users not to publish large-scale analyses of them before they are published by the authors. In the unfiltered lists and the quarterly releases, the few detected proteins without a Gene ID are identified by their UniProt entry instead (e.g. sp|P01891|1A68_HUMAN). Baits that were not found to interact with anything do not appear in the networks. The descriptions of the proteins in the unfiltered lists (taken from UniProt) and the proteome comparison of HEK293T and HCT116 cells (also available on the site) are not included.

The networks have the following properties:

  • name: the Entrez Gene ID of the protein (or the UniProt entry of a detected protein without a Gene ID); symbol: the gene symbol; is_bait: whether the protein was used as a bait (from the lists of baits of the official networks, and otherwise whether the node is the source of edges).
  • In the official undirected networks, uniprot: the UniProt accession of the protein (or isoform) identified; edge p_wrong_id, p_no_interaction, p_interaction: the CompPASS-Plus probabilities that the pair is a wrong identification, a nonspecific (background) association, or a genuine interaction.
  • In the unfiltered lists, the quarterly releases and the preliminary networks, edge p_wrong_id, p_no_interaction, p_interaction as above.
  • In the unfiltered lists and the quarterly releases, edge protein_id: the UniProt entry of the identified protein (e.g. sp|P05387|RLA2_HUMAN).
  • In the unfiltered lists, the CompPASS scores of the pair (Sowa et al. 2009, Huttlin et al. 2015): edge ave_apsm (the average number of assembled peptide spectral matches of the prey), nwd_score (normalized weighted D score), z_score, plate_z_score, entropy, unique_peptides, ratio, total_psms, ratio_total_psms, unique_to_total_ratio (named ave_apsm, nwdscore, zscore, plate_zscore, entropy, uPeps, ratio, total_psms, ratioTotalPSMs and UtoTratio upstream); vertex compass_id: the CompPASS id of the bait's purification (-1 for proteins that were not baits).
  • In the quarterly releases and the preliminary networks, edge plate and well: the plate and well of the purification.
Tags
Biological Protein interactions Unweighted Multigraph Metadata
Citation
  • E. L. Huttlin, L. Ting, R. J. Bruckner, F. Gebreab, M. P. Gygi, J. Szpyt, et al., "The BioPlex Network: A Systematic Exploration of the Human Interactome." Cell 162, 425-440 (2015) 10.1016/j.cell.2015.06.043 Sci-Hub
  • E. L. Huttlin, R. J. Bruckner, J. A. Paulo, J. R. Cannon, L. Ting, K. Baltier, et al., "Architecture of the human interactome defines protein communities and disease networks." Nature 545, 505-509 (2017) 10.1038/nature22366 Sci-Hub
  • E. L. Huttlin, R. J. Bruckner, J. Navarrete-Perea, J. R. Cannon, K. Baltier, F. Gebreab, et al., "Dual proteome-scale networks reveal cell-specific remodeling of the human interactome." Cell 184, 3022-3040 (2021) 10.1016/j.cell.2021.04.011 Sci-Hub
Upstream URL OK
https://bioplex.hms.harvard.edu/interactions.php
Networks
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
1.0_293T 7,668 23,744 6.19 9.44 20.70 15.78 -0.30 0.04 11 0.99 Undirected Unipartite name symbol uniprot is_bait p_wrong_id p_no_interaction p_interaction 756 KiB 985 KiB 971 KiB 902 KiB
2.0_293T 10,961 56,553 10.32 13.00 36.36 12.04 -0.12 0.06 11 0.99 Undirected Unipartite name symbol uniprot is_bait p_wrong_id p_no_interaction p_interaction 1.6 MiB 2.1 MiB 2.0 MiB 1.9 MiB
3.0_293T 13,957 118,162 16.93 23.41 79.66 9.23 -0.03 0.08 10 1.00 Undirected Unipartite name symbol uniprot is_bait p_wrong_id p_no_interaction p_interaction 3.1 MiB 4.0 MiB 4.0 MiB 3.8 MiB
3.0_HCT116 10,115 70,966 14.03 22.86 73.72 20.85 -0.07 0.09 10 0.99 Undirected Unipartite name symbol uniprot is_bait p_wrong_id p_no_interaction p_interaction 1.9 MiB 2.5 MiB 2.4 MiB 2.3 MiB
1.0_293T_directed 7,668 24,296 3.17 9.81 20.70 16.72 -0.28 0.05 11 0.99 Directed Unipartite name symbol is_bait 214 KiB 289 KiB 284 KiB 247 KiB
2.0_293T_directed 10,961 59,584 5.44 14.14 36.36 13.03 -0.07 0.08 11 0.99 Directed Unipartite name symbol is_bait 347 KiB 512 KiB 503 KiB 433 KiB
3.0_293T_directed 13,957 129,687 9.29 27.68 79.66 10.93 0.07 0.12 10 1.00 Directed Unipartite name symbol is_bait 527 KiB 857 KiB 809 KiB 715 KiB
3.0_HCT116_directed 10,115 77,184 7.63 25.96 73.72 24.06 0.01 0.14 10 0.99 Directed Unipartite name symbol is_bait 348 KiB 526 KiB 520 KiB 451 KiB
2.0_293T_unfiltered 12,431 3,085,484 248.21 872.02 1453.44 1.33 -0.43 0.16 4 1.00 Directed Unipartite name symbol is_bait compass_id protein_id ave_apsm nwd_score z_score plate_z_score entropy unique_peptides ratio total_psms ratio_total_psms unique_to_total_ratio p_wrong_id p_no_interaction p_interaction 52.8 MiB 86.6 MiB 81.2 MiB 110.1 MiB
3.0_293T_unfiltered 15,126 5,851,900 386.88 1404.76 2028.22 1.28 -0.45 0.16 4 1.00 Directed Unipartite name symbol is_bait compass_id protein_id ave_apsm nwd_score z_score plate_z_score entropy unique_peptides ratio total_psms ratio_total_psms unique_to_total_ratio p_wrong_id p_no_interaction p_interaction 99.8 MiB 165.8 MiB 155.5 MiB 209.9 MiB
3.0_HCT116_unfiltered 11,333 4,006,565 353.53 1126.71 1827.90 1.08 -0.44 0.21 4 1.00 Directed Unipartite name symbol is_bait compass_id protein_id ave_apsm nwd_score z_score plate_z_score entropy unique_peptides ratio total_psms ratio_total_psms unique_to_total_ratio p_wrong_id p_no_interaction p_interaction 66.1 MiB 111.0 MiB 103.8 MiB 143.9 MiB
293T_2015-12 2,825 4,140 1.47 6.39 9.71 134.92 -0.36 0.01 17 0.95 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 191 KiB 243 KiB 240 KiB 232 KiB
293T_2016-05 3,198 4,955 1.55 7.46 8.80 142.56 -0.44 0.01 14 0.98 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 222 KiB 283 KiB 279 KiB 272 KiB
293T_2016-08 2,838 4,305 1.52 6.67 7.70 68.13 -0.40 0.01 13 0.95 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 196 KiB 249 KiB 246 KiB 238 KiB
293T_2016-12 2,311 3,160 1.37 6.55 6.98 128.15 -0.37 0.01 15 0.92 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 151 KiB 191 KiB 189 KiB 181 KiB
293T_2017-04 2,702 4,046 1.50 6.89 8.63 109.92 -0.42 0.01 17 0.97 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 184 KiB 234 KiB 231 KiB 226 KiB
293T_2017-10 2,819 4,464 1.58 7.51 10.89 52.20 -0.50 0.02 14 0.98 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 198 KiB 254 KiB 251 KiB 243 KiB
HCT116_2018-11 2,612 12,845 4.92 21.54 54.00 97.65 -0.21 0.25 12 0.99 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 399 KiB 546 KiB 536 KiB 543 KiB
HCT116_2019-03 2,883 5,474 1.90 8.76 14.44 163.84 -0.24 0.10 14 0.95 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 225 KiB 293 KiB 290 KiB 281 KiB
HCT116_2019-05 3,242 5,774 1.78 9.69 12.01 65.81 -0.27 0.01 13 0.95 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 244 KiB 316 KiB 312 KiB 305 KiB
HCT116_2019-08 3,080 5,581 1.81 13.12 17.50 53.91 -0.23 0.00 13 0.95 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 236 KiB 306 KiB 302 KiB 295 KiB
HCT116_2019-11 2,790 4,728 1.69 8.60 12.17 89.50 -0.26 0.00 15 0.93 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 206 KiB 265 KiB 261 KiB 255 KiB
HCT116_2020-02 3,203 5,805 1.81 11.36 13.50 49.78 -0.27 0.00 13 0.95 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 246 KiB 320 KiB 316 KiB 308 KiB
HCT116_2020-05 3,115 6,122 1.97 12.02 15.39 70.35 -0.31 0.01 13 0.95 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 251 KiB 326 KiB 322 KiB 317 KiB
HCT116_2021-02 3,101 6,250 2.02 11.95 18.83 68.05 -0.18 0.05 14 0.96 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 254 KiB 331 KiB 327 KiB 321 KiB
HCT116_2021-05 2,935 4,764 1.62 9.54 15.18 69.88 -0.25 0.01 14 0.94 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 210 KiB 272 KiB 268 KiB 259 KiB
HCT116_2021-08 2,896 5,225 1.80 9.50 15.33 70.72 -0.29 0.01 12 0.93 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 220 KiB 286 KiB 282 KiB 276 KiB
HCT116_2021-11 2,877 4,908 1.71 9.22 11.11 111.83 -0.26 0.01 14 0.94 Directed Unipartite name symbol is_bait plate well protein_id p_wrong_id p_no_interaction p_interaction 214 KiB 277 KiB 273 KiB 264 KiB
U2OS_0.1 7,639 41,133 5.38 17.89 32.73 18.99 -0.20 0.03 9 0.99 Directed Unipartite name symbol is_bait plate well p_wrong_id p_no_interaction p_interaction 1.1 MiB 1.5 MiB 1.4 MiB 1.4 MiB
RPE1_0.1 6,832 35,914 5.26 17.68 33.51 17.84 -0.23 0.04 11 0.99 Directed Unipartite name symbol is_bait plate well p_wrong_id p_no_interaction p_interaction 967 KiB 1.3 MiB 1.3 MiB 1.2 MiB