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human_interactomes_ndex — Molecular interaction networks of two benchmark collections and related studies (NDEx, 2017-2025)

Description

Networks of human genes (or their protein products; a few networks are of other species) from many databases of molecular interactions, from the two collections of harmonized networks used to evaluate how well molecular networks recover disease genes and other biological knowledge, by Huang et al. (2018) and by Wright et al. ("State of the interactomes", 2025), both from the Ideker lab, and deposited on the Network Data Exchange (NDEx). In each network, the nodes are genes (the interactions of the sources were mapped to them), identified by their NCBI Gene identifiers in the networks of Wright et al. and by their HGNC symbols in those of Huang et al., and an edge is an interaction or functional association between two genes, with the attributes given by the source (e.g. scores, evidence, publications). The sources are of many kinds: curated protein-protein interactions (e.g. BioGRID, IntAct, HPRD, DIP, MINT), systematic screens (e.g. HuRI, BioPlex, Hein, Youn, Havugimana, Wan, ProteomeHD), integrated and predicted interactions (e.g. STRING, HumanNet, GeneMANIA, GIANT, FunCoup, ConsensusPathDB, HIPPIE, iRefIndex, IID, Mentha, APID, InBioMap, PrePPI, hu.MAP), pathways and signaling (e.g. Reactome, ReactomeFI, PathwayCommons, PID, SIGNOR, SignaLink, SPIKE, PhosphoSitePlus), and regulation (TFLink); and the Parsimonious Composite Networks (PCNet) built by the authors from the networks that perform best, keeping the interactions supported by at least two of them.

The networks are named by the collection and the source:

  • huang2018_<source>: the 21 networks evaluated by Huang et al. (versions of 2017), with the composite networks huang2018_full_composite (the union of all of them) and huang2018_pcnet (PCNet 1.0), and two variants without text-mined interactions (huang2018_humannet_no_textmining, huang2018_string_no_textmining). These networks have no edge attributes.
  • pcnet_1.1, pcnet_1.2, pcnet_1.3, pcnet_1.4: later versions of PCNet, with updated gene identifiers.
  • wright2025_<source>: the 45 networks of the sources evaluated by Wright et al. (versions of 2016-2024), with the composite networks wright2025_pcnet_2.0, wright2025_pcnet_2.1 and wright2025_pcnet_2.2, and the variants wright2025_string_cocitation_free and wright2025_humannet_cocitation_free without the interactions supported only by co-citation.
  • wright2025_interactome_dependencies: the small directed network of the dependencies between the interactomes evaluated by Wright et al.: the nodes are the interactomes, and an edge goes from an interactome to each interactome whose data it incorporates (the edge attributes source and target give the full names of the incorporated and of the incorporating interactome, and source_category and category their kinds).

The same authors deposited networks of other species and of specific studies, which are also included:

  • pcnet_mouse, pcnet_rat: PCNet (NDEx version 1.1) mapped to the genes of mouse and rat with the HCOP orthology database; string_fly: STRING of the fruit fly (with the combined score as edge weight); string_11.5_rat_all, string_11.5_rat_mid, string_11.5_rat_high: STRING v11.5 of the rat, with all links, and with those of combined score above 400 (medium confidence) and 700 (high confidence). The nodes of these networks are named by the gene symbols of the species.
  • wright2023_bmi_*: the networks of the study of the body mass index (BMI) of Wright et al. (2023), subnetworks of PCNet 1.3 of the genes near the genes of the genome-wide association studies (GWAS) of BMI in humans and rats, found by network propagation (network colocalization, NetColoc): wright2023_bmi_conserved (genes near the GWAS genes of both species), wright2023_bmi_human_specific, wright2023_bmi_rat_specific (near those of one species but not the other) and wright2023_bmi_expanded (near those of either species); and the directed hierarchies of gene systems (communities found with HiDeF, named by enriched GO terms) of the conserved and the expanded network, wright2023_bmi_conserved_systems_map and wright2023_bmi_expanded_systems_map, whose nodes are the systems, with an edge from each system to its subsystems.
  • alzheimers_disease, autism_spectrum_disorder, bipolar_disorder (NDEx user snwright, 2025): networks of the genes near the genes of common and of rare variants associated with Alzheimer's disease, autism spectrum disorder and bipolar disorder, found by network colocalization (unlisted networks on NDEx, linked from their systems maps); and their directed hierarchies of gene systems alzheimers_disease_systems_map, autism_spectrum_disorder_systems_map, bipolar_disorder_systems_map, whose nodes are the systems, with their member genes (hcx_members, NCBI Gene identifiers; hgnc, gene symbols), and with an edge from each system to the larger system that contains it (as stored in NDEx).

The direction of the interactions of directed sources (e.g. kinase to substrate in PhosphoSitePlus, transcription factor to target in TFLink) is kept as the order of the two ends of the edges, but the interaction networks are undirected; only the systems maps and wright2025_interactome_dependencies are directed. The attributes name (e.g. A2M_APP) and Entrez_A, Entrez_B of the edges, which repeat the genes of the edge, are left out.

The networks have the following properties:

  • (Node) name: the name of the node in NDEx: the gene symbol (in pcnet_1.4, alzheimers_disease, autism_spectrum_disorder and bipolar_disorder, the NCBI Gene identifier; in the systems maps, the name or identifier of the system; in wright2025_interactome_dependencies, the short name of the interactome).
  • (Node) represents: the identifier of the gene in NDEx, e.g. ncbigene:2 or hgnc.symbol:A2M (empty if not given).
  • (Node) entrez_id: the NCBI Gene identifier of the gene, from represents, or from name in the networks without represents (-1 if it is not an NCBI Gene identifier).
  • (Node) Other attributes, as given in NDEx, e.g. geneid (the NCBI Gene identifier), hgnc_symbol; in the BMI networks, the network proximity scores nps_h, nps_r, nps_hr (to the human, rat and both GWAS genes) and human_seed, rat_seed (whether the gene is a GWAS gene); in the systems maps, the member genes and sizes of the systems (e.g. community_genes, community_size, hcx_members), their names, and the fractions of the kinds of genes they contain.
  • (Edge) interaction: the kind of interaction, as given in NDEx (e.g. interacts-with).
  • (Edge) Other attributes, as given by each source in NDEx, with their names in lower case and with underscores (e.g. score, experimental_system, publication_source, supporting_databases; columns named only by their number in the source file are named column_<number>); missing values are empty, -1 or NaN.
  • (Graph) ndex_uuid: the identifier of the network in NDEx.
  • (Graph) ndex_<attribute>: the attributes of the network in NDEx, e.g. ndex_name, ndex_version, ndex_description, ndex_reference, ndex_prov_wasderivedfrom (the source of the data).
Tags
Biological Protein interactions Unweighted Metadata
Added
2026-10-31
Citation
  • S. N. Wright, S. Colton, L. V. Schaffer, R. T. Pillich, C. Churas, D. Pratt, T. Ideker, "State of the interactomes: an evaluation of molecular networks for generating biological insights." Molecular Systems Biology 21, 1-29 (2025) 10.1038/s44320-024-00077-y Sci-Hub
  • J. K. Huang, D. E. Carlin, M. K. Yu, W. Zhang, J. F. Kreisberg, P. Tamayo, T. Ideker, "Systematic Evaluation of Molecular Networks for Discovery of Disease Genes." Cell Systems 6, 484-495 (2018) 10.1016/j.cels.2018.03.001 Sci-Hub
  • S. N. Wright, B. S. Leger, S. B. Rosenthal, S. N. Liu, T. Jia, A. S. Chitre, O. Polesskaya, K. Holl, J. Gao, R. Cheng, A. Garcia Martinez, A. George, A. F. Gileta, W. Han, A. H. Netzley, C. P. King, A. Lamparelli, C. Martin, C. L. St. Pierre, T. Wang, H. Bimschleger, J. Richards, K. Ishiwari, H. Chen, S. B. Flagel, P. Meyer, T. E. Robinson, L. C. Solberg Woods, J. F. Kreisberg, T. Ideker, A. A. Palmer, "Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks." Cell Reports 42, 112873 (2023) 10.1016/j.celrep.2023.112873 Sci-Hub
  • D. Pratt, J. Chen, R. Pillich, V. Rynkov, A. Gary, B. Demchak, T. Ideker, "NDEx 2.0: A Clearinghouse for Research on Cancer Pathways." Cancer Research 77, e58-e61 (2017) 10.1158/0008-5472.CAN-17-0606 Sci-Hub
Upstream URL OK
https://www.ndexbio.org/
https://www.ndexbio.org/#/user/7b97c33f-4673-11ed-b7d0-0ac135e8bacf
Upstream license
The licenses of the source databases (open for most; non-commercial use for some); networks of Huang et al.: CC BY-NC 4.0; BMI study: CC BY-NC-SA 4.0, https://www.ndexbio.org/
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
huang2018_bind 7,037 72,780 20.68 105.45 172.20 11.30 -0.36 0.03 9 0.98 Undirected Unipartite represents name entrez_id 120 KiB 296 KiB 289 KiB 262 KiB
huang2018_biogrid 16,702 258,257 30.93 60.41 140.53 6.43 -0.06 0.06 8 1.00 Undirected Unipartite represents name entrez_id 573 KiB 1.1 MiB 1.0 MiB 996 KiB
huang2018_bioplex 10,961 56,553 10.32 13.00 36.36 12.04 -0.12 0.06 11 0.99 Undirected Unipartite represents name entrez_id 185 KiB 285 KiB 280 KiB 289 KiB
huang2018_consensuspathdb 16,301 1,648,426 202.25 380.02 1116.10 13.54 0.32 0.54 8 1.00 Undirected Unipartite represents name entrez_id 1.7 MiB 5.6 MiB 5.7 MiB 4.8 MiB
huang2018_dip 2,983 4,722 3.17 3.76 8.43 182.96 0.00 0.14 19 0.81 Undirected Unipartite represents name entrez_id 35 KiB 46 KiB 45 KiB 45 KiB
huang2018_full_composite 25,355 15,199,639 1198.95 1123.51 2342.91 2.32 0.09 0.27 6 1.00 Undirected Unipartite represents name entrez_id 18.2 MiB 52.0 MiB 50.4 MiB 42.0 MiB
huang2018_giant 17,207 3,631,554 422.10 478.78 1055.18 22.09 0.05 0.40 8 1.00 Undirected Unipartite represents name entrez_id 4.3 MiB 12.2 MiB 12.4 MiB 10.4 MiB
huang2018_genemania 18,103 6,601,644 729.34 414.30 973.71 3.79 0.00 0.14 5 1.00 Undirected Unipartite represents name entrez_id 9.5 MiB 22.1 MiB 22.4 MiB 18.8 MiB
huang2018_hint 14,147 155,459 21.98 40.37 108.30 8.57 -0.03 0.08 10 1.00 Undirected Unipartite represents name entrez_id 375 KiB 692 KiB 668 KiB 638 KiB
huang2018_hprd 9,465 37,039 7.83 14.63 36.91 34.53 -0.03 0.05 14 0.97 Undirected Unipartite represents name entrez_id 138 KiB 205 KiB 193 KiB 205 KiB
huang2018_humaninteractome 4,230 13,427 6.35 15.98 35.88 17.54 -0.21 0.03 11 0.97 Undirected Unipartite represents name entrez_id 61 KiB 88 KiB 87 KiB 84 KiB
huang2018_humannet 16,198 475,959 58.77 86.32 261.34 27.91 0.25 0.22 10 1.00 Undirected Unipartite represents name entrez_id 824 KiB 1.8 MiB 1.8 MiB 1.6 MiB
huang2018_humannet_no_textmining 16,120 471,328 58.48 86.22 261.25 29.87 0.25 0.22 8 1.00 Undirected Unipartite represents name entrez_id 818 KiB 1.8 MiB 1.8 MiB 1.6 MiB
huang2018_irefindex 14,667 133,548 18.21 75.62 112.64 11.02 -0.05 0.02 9 1.00 Undirected Unipartite represents name entrez_id 339 KiB 615 KiB 585 KiB 562 KiB
huang2018_inbiomap 17,262 605,998 70.21 157.39 375.81 16.20 -0.05 0.18 8 1.00 Undirected Unipartite represents name entrez_id 938 KiB 2.2 MiB 2.2 MiB 1.9 MiB
huang2018_intact 13,616 114,572 16.83 35.64 75.20 18.58 -0.12 0.05 9 1.00 Undirected Unipartite represents name entrez_id 303 KiB 543 KiB 510 KiB 500 KiB
huang2018_mentha 16,244 262,876 32.37 64.22 142.60 5.79 -0.09 0.05 8 1.00 Undirected Unipartite represents name entrez_id 575 KiB 1.1 MiB 1.1 MiB 1000 KiB
huang2018_multinet 14,445 109,598 15.17 42.84 99.46 17.76 -0.19 0.04 9 1.00 Undirected Unipartite represents name entrez_id 285 KiB 533 KiB 499 KiB 478 KiB
huang2018_pid 2,576 21,442 16.65 27.57 72.08 15.56 0.03 0.21 11 1.00 Undirected Unipartite represents name entrez_id 50 KiB 95 KiB 94 KiB 85 KiB
huang2018_pcnet 19,781 2,724,724 275.49 340.66 815.53 4.66 0.08 0.23 7 1.00 Undirected Unipartite represents name entrez_id 3.9 MiB 9.3 MiB 9.4 MiB 8.1 MiB
huang2018_pathwaycommons 19,987 824,675 82.52 161.03 306.48 10.18 -0.11 0.12 6 1.00 Undirected Unipartite represents name entrez_id 1.2 MiB 2.9 MiB 2.9 MiB 2.6 MiB
huang2018_reactome 7,926 194,502 49.08 69.04 212.63 700.01 0.16 0.65 35 0.92 Undirected Unipartite represents name entrez_id 176 KiB 658 KiB 716 KiB 593 KiB
huang2018_reactomefi 12,254 229,423 37.44 65.79 178.18 123.86 -0.06 0.33 13 0.98 Undirected Unipartite represents name entrez_id 335 KiB 886 KiB 871 KiB 766 KiB
huang2018_string 18,266 5,135,768 562.33 663.73 1487.90 4.07 0.09 0.30 5 1.00 Undirected Unipartite represents name entrez_id 5.5 MiB 16.5 MiB 16.9 MiB 14.3 MiB
huang2018_string_no_textmining 18,122 4,501,706 496.82 628.84 1459.61 13.66 0.14 0.31 8 1.00 Undirected Unipartite represents name entrez_id 4.6 MiB 14.6 MiB 14.8 MiB 12.6 MiB
pcnet_1.1 18,859 2,695,089 285.81 348.35 821.27 4.32 0.08 0.23 7 1.00 Undirected Unipartite represents name entrez_id 3.9 MiB 9.9 MiB 10.0 MiB 8.3 MiB
pcnet_1.2 18,820 2,693,250 286.21 348.86 821.77 4.30 0.08 0.23 7 1.00 Undirected Unipartite represents name entrez_id 3.9 MiB 9.9 MiB 9.8 MiB 8.3 MiB
pcnet_1.3 18,820 2,693,250 286.21 348.86 821.77 4.30 0.08 0.23 7 1.00 Undirected Unipartite name entrez_id interaction 3.7 MiB 10.1 MiB 9.7 MiB 8.8 MiB
pcnet_1.4 18,630 2,687,393 288.50 349.29 821.60 4.29 0.08 0.23 6 1.00 Undirected Unipartite name hgnc_symbol entrez_id interaction 3.8 MiB 10.5 MiB 10.0 MiB 9.1 MiB
pcnet_mouse 15,399 2,238,029 290.67 333.48 768.34 4.05 0.07 0.23 6 1.00 Undirected Unipartite name entrez_id interaction 3.1 MiB 8.3 MiB 8.0 MiB 7.2 MiB
pcnet_rat 14,963 2,128,991 284.57 325.48 748.36 4.05 0.07 0.23 6 1.00 Undirected Unipartite name entrez_id interaction 2.9 MiB 7.9 MiB 7.5 MiB 6.9 MiB
string_fly 13,046 1,981,482 303.77 311.72 682.12 10.42 0.15 0.28 8 1.00 Undirected Unipartite name entrez_id interaction weight 4.7 MiB 11.1 MiB 10.3 MiB 9.7 MiB
string_11.5_rat_all 22,227 8,391,602 755.08 690.07 1500.28 9.87 0.12 0.24 8 1.00 Undirected Unipartite name entrez_id interaction combined_score 16.8 MiB 44.2 MiB 44.2 MiB 40.7 MiB
string_11.5_rat_mid 21,326 1,207,355 113.23 164.27 680.36 22.99 0.51 0.45 7 1.00 Undirected Unipartite name entrez_id interaction combined_score 2.7 MiB 6.4 MiB 6.3 MiB 6.1 MiB
string_11.5_rat_high 16,787 277,852 33.10 69.18 352.85 286.68 0.50 0.53 16 0.98 Undirected Unipartite name entrez_id interaction combined_score 659 KiB 1.5 MiB 1.5 MiB 1.4 MiB
wright2023_bmi_conserved 657 5,287 16.09 15.88 33.38 45.75 0.07 0.23 7 0.97 Undirected Unipartite nps_hr nps_r rat_seed name nps_h human_seed node_color entrez_id interaction 31 KiB 45 KiB 44 KiB 45 KiB
wright2023_bmi_human_specific 925 10,472 22.64 25.79 58.46 6.47 0.20 0.26 7 0.98 Undirected Unipartite nps_hr nps_r rat_seed name nps_h human_seed node_color entrez_id interaction 45 KiB 70 KiB 69 KiB 72 KiB
wright2023_bmi_rat_specific 688 5,215 15.16 14.79 33.51 29.83 0.26 0.26 8 0.94 Undirected Unipartite nps_hr nps_r rat_seed name nps_h human_seed node_color entrez_id interaction 31 KiB 45 KiB 45 KiB 47 KiB
wright2023_bmi_expanded 6,025 343,615 114.06 130.70 294.11 4.04 0.12 0.22 7 1.00 Undirected Unipartite nps_hr nps_r rat_seed name subgraph nps_h human_seed node_color entrez_id interaction 698 KiB 1.4 MiB 1.4 MiB 1.4 MiB
wright2023_bmi_conserved_systems_map 61 61 1.00 3.39 1.00 30.98 -0.43 0.00 7 1.00 Directed Unipartite community_genes human_rat_seeds community_size human_seeds rat_seeds community_size_log10 name gprofiler_name network_implicated community_id entrez_id interaction 11 KiB 12 KiB 11 KiB 12 KiB
wright2023_bmi_expanded_systems_map 67 67 1.00 4.08 1.00 35.98 -0.48 0.00 7 1.00 Directed Unipartite human_rat_seeds other community_size_log10 human_specific_network_implicated showannotation conserved rat_specific_network_implicated annotation conserved_network_implicated rat_specific community_genes human_specific community_size human_seeds rat_seeds sig_network name entrez_id 47 KiB 49 KiB 48 KiB 58 KiB
alzheimers_disease 526 9,574 36.40 35.56 72.93 3.66 0.04 0.41 6 0.99 Undirected Unipartite nps_r coloc_gene hgnc nps_c inputgene nps_rc name geneclass entrez_id number_of_supporting_databases interaction supporting_databases 44 KiB 79 KiB 78 KiB 69 KiB
autism_spectrum_disorder 871 30,131 69.19 68.04 140.02 4.64 0.03 0.39 6 0.99 Undirected Unipartite nps_r coloc_gene hgnc nps_c inputgene nps_rc name geneclass entrez_id number_of_supporting_databases interaction supporting_databases 100 KiB 199 KiB 198 KiB 171 KiB
bipolar_disorder 387 7,711 39.85 39.14 78.37 4.45 0.00 0.44 6 0.99 Undirected Unipartite nps_r coloc_gene hgnc nps_c inputgene nps_rc name geneclass entrez_id number_of_supporting_databases interaction supporting_databases 35 KiB 62 KiB 61 KiB 53 KiB
alzheimers_disease_systems_map 57 56 0.98 2.35 1.00 72.28 -0.30 0.00 10 1.00 Directed Bipartite cd_memberlist npsr common_fraction community_name c_vs_r hcx_isroot npsrc logsize rare_fraction hgnc shared_fraction sourceterm npsc name hcx_members network_fraction logp entrez_id interaction 16 KiB 18 KiB 17 KiB 20 KiB
autism_spectrum_disorder_systems_map 57 56 0.98 2.91 1.00 46.43 -0.52 0.00 9 1.00 Directed Bipartite cd_memberlist npsr common_fraction community_name c_vs_r hcx_isroot npsrc logsize rare_fraction hgnc shared_fraction sourceterm npsc name hcx_members network_fraction logp entrez_id interaction 19 KiB 21 KiB 21 KiB 24 KiB
bipolar_disorder_systems_map 57 56 0.98 3.08 1.00 26.48 -0.32 0.00 8 1.00 Directed Bipartite cd_memberlist npsr common_fraction community_name c_vs_r hcx_isroot npsrc logsize rare_fraction hgnc shared_fraction sourceterm npsc name hcx_members network_fraction logp entrez_id interaction 13 KiB 15 KiB 14 KiB 16 KiB
wright2025_apid 16,949 258,372 30.49 48.85 103.84 7.01 -0.08 0.05 8 1.00 Undirected Unipartite represents name entrez_id interactionid publications expevidences interaction curationevents uniprotid_a 3dstructures uniprotid_b methods 2.2 MiB 3.5 MiB 3.3 MiB 3.8 MiB
wright2025_bind 6,109 16,726 5.48 38.88 47.32 31.11 -0.20 0.01 11 0.98 Undirected Unipartite represents name entrez_id interaction_pubmed_id interaction_data_source interaction participant_a participant_b 137 KiB 217 KiB 218 KiB 242 KiB
wright2025_biogrid 19,919 823,164 82.65 157.61 356.86 2.91 -0.07 0.09 7 1.00 Undirected Unipartite represents name entrez_id publication_source score biogrid_interaction_id biogrid_id_interactor_a biogrid_id_interactor_b interaction author experimental_system experimental_system_type 8.6 MiB 11.9 MiB 11.9 MiB 15.6 MiB
wright2025_bioplex_293t 13,924 117,930 16.94 23.42 79.66 9.23 -0.03 0.08 9 1.00 Undirected Unipartite represents name entrez_id uniprotb uniprota pw interaction pni pint 3.1 MiB 4.3 MiB 4.2 MiB 4.5 MiB
wright2025_bioplex_hct116 10,093 70,801 14.03 22.84 73.72 20.85 -0.07 0.09 10 0.99 Undirected Unipartite represents name entrez_id uniprotb uniprota pw interaction pni pint 1.9 MiB 2.5 MiB 2.5 MiB 2.7 MiB
wright2025_comppi 17,256 363,732 42.16 78.23 178.27 8.00 -0.07 0.06 8 1.00 Undirected Unipartite represents name entrez_id interaction_experimental_system_type score interaction_source_database interaction interaction_pubmed_id protein_b protein_a interaction_score 6.7 MiB 7.7 MiB 7.6 MiB 8.7 MiB
wright2025_consensuspathdb 17,829 5,201,664 583.51 875.04 2002.69 7.77 0.12 0.49 7 1.00 Undirected Unipartite represents name entrez_id score interaction 5.5 MiB 24.2 MiB 23.6 MiB 19.6 MiB
wright2025_dip 3,202 11,518 7.19 12.16 34.39 124.57 -0.03 0.29 17 0.83 Undirected Unipartite represents name entrez_id interaction_pubmed_id interaction participant_a participant_b 89 KiB 147 KiB 142 KiB 167 KiB
wright2025_funcoup 17,918 5,018,735 560.19 890.29 2011.20 47.44 0.00 0.44 9 1.00 Undirected Unipartite represents name entrez_id score interaction gene2 fbs_max gene1 max_category 36.5 MiB 68.9 MiB 68.3 MiB 65.2 MiB
wright2025_giant 17,095 3,540,302 414.19 471.18 1043.86 22.31 0.05 0.40 8 1.00 Undirected Unipartite represents name entrez_id score interaction 14.1 MiB 28.9 MiB 28.1 MiB 24.6 MiB
wright2025_genemania 19,068 1,164,494 122.14 91.94 215.79 9.60 0.18 0.09 6 1.00 Undirected Unipartite represents name entrez_id score gene_b interaction gene_a 6.3 MiB 10.9 MiB 10.5 MiB 11.8 MiB
wright2025_hint 16,183 241,636 29.86 72.79 137.82 8.24 -0.06 0.04 9 1.00 Undirected Unipartite represents name entrez_id interaction uniprot_a uniprot_b pmid_method_quality 1.7 MiB 2.8 MiB 2.7 MiB 3.3 MiB
wright2025_hippie 19,527 805,622 82.51 146.37 339.83 4.98 -0.06 0.09 7 1.00 Undirected Unipartite represents name entrez_id column_0 score column_2 column_5 column_6 column_7 interaction 5.8 MiB 10.1 MiB 9.1 MiB 11.2 MiB
wright2025_hprd 9,419 36,828 7.82 14.52 36.64 34.53 -0.04 0.05 14 0.97 Undirected Unipartite represents name entrez_id column_0 column_3 column_6 column_7 interaction 410 KiB 585 KiB 565 KiB 672 KiB
wright2025_havugimana 2,994 13,964 9.33 14.67 57.48 59.72 0.37 0.33 14 0.94 Undirected Unipartite represents name entrez_id score interactor_b detection_method_s interactor_a interaction_type_s interaction 126 KiB 200 KiB 194 KiB 203 KiB
wright2025_hein 5,781 28,600 9.89 17.17 50.46 8.21 -0.17 0.07 9 1.00 Undirected Unipartite represents name entrez_id publication_1st_author_s score id_s_interactor_b publication_identifier_s interaction interaction_detection_method_s interaction_type_s id_s_interactor_a 191 KiB 302 KiB 339 KiB 361 KiB
wright2025_huri 9,001 62,720 13.94 29.57 71.03 19.55 -0.13 0.05 11 0.99 Undirected Unipartite represents name entrez_id column_0 column_1 interaction 328 KiB 523 KiB 510 KiB 654 KiB
wright2025_humannet 18,591 1,125,492 121.08 87.98 291.38 9.53 0.42 0.31 6 1.00 Undirected Unipartite represents name entrez_id score interaction 8.3 MiB 12.7 MiB 12.5 MiB 13.0 MiB
wright2025_humannet_cocitation_free 18,457 977,493 105.92 113.97 270.60 14.68 0.01 0.18 7 1.00 Undirected Unipartite represents name entrez_id score interaction 6.0 MiB 10.0 MiB 9.9 MiB 10.5 MiB
wright2025_iid 18,718 1,191,444 127.30 186.39 421.00 31.61 -0.01 0.15 6 1.00 Undirected Unipartite represents name entrez_id n_pred_pmids evidence_type methods pmids n_methods n_exp_pmids interaction uniprot2 uniprot1 db_with_ppi 7.7 MiB 13.6 MiB 12.5 MiB 14.3 MiB
wright2025_inbiomap 17,407 609,241 70.00 157.10 376.09 16.39 -0.05 0.18 8 1.00 Undirected Unipartite represents name entrez_id column_0 column_1 column_12 score column_14 column_6 interaction 3.6 MiB 6.7 MiB 6.1 MiB 7.4 MiB
wright2025_innatedb 15,420 164,596 21.35 96.21 138.13 7.34 -0.06 0.02 8 1.00 Undirected Unipartite represents name entrez_id interaction_detection_method alt_identifier_a alt_identifier_b author interaction interaction_type pmid source_database 1.5 MiB 2.3 MiB 2.3 MiB 2.9 MiB
wright2025_intact 17,194 322,948 37.57 70.75 144.79 7.02 -0.07 0.04 9 1.00 Undirected Unipartite represents name entrez_id publication_1st_author_s id_s_interactor_b publication_identifier_s interaction interaction_detection_method_s id_s_interactor_a 2.4 MiB 4.0 MiB 4.0 MiB 5.0 MiB
wright2025_mint 9,260 36,673 7.92 26.06 44.62 15.00 -0.15 0.02 11 0.99 Undirected Unipartite represents name entrez_id column_0 column_11 column_1 column_7 interaction column_8 381 KiB 536 KiB 509 KiB 682 KiB
wright2025_matrixdb 11,578 75,802 13.09 35.89 75.85 21.25 -0.19 0.03 10 1.00 Undirected Unipartite represents name entrez_id publication_1st_author_s id_s_interactor_b publication_identifier_s source_database_s interaction interaction_detection_method_s interaction_type_s id_s_interactor_a 700 KiB 1.0 MiB 1.0 MiB 1.3 MiB
wright2025_mentha 17,014 329,005 38.67 68.55 154.14 5.03 -0.07 0.06 8 1.00 Undirected Unipartite represents name entrez_id column_0 column_11 column_1 score column_14 column_6 interaction column_8 2.5 MiB 4.4 MiB 4.2 MiB 4.8 MiB
wright2025_multinet 13,969 108,527 15.54 42.99 99.62 12.23 -0.19 0.04 9 1.00 Undirected Unipartite represents name entrez_id phosphorylation num_networks ppi signaling metabolic regulatory score interaction_name interaction genetic 695 KiB 1.2 MiB 1.0 MiB 1.0 MiB
wright2025_pcnet_2.0 19,267 3,852,119 399.87 562.99 1395.03 14.15 0.22 0.34 7 1.00 Undirected Unipartite represents name geneid entrez_id number_of_supporting_databases interaction supporting_databases 10.3 MiB 22.9 MiB 22.9 MiB 19.4 MiB
wright2025_pcnet_2.1 18,839 1,749,784 185.76 247.36 665.10 15.87 0.27 0.26 7 1.00 Undirected Unipartite represents name geneid entrez_id number_of_supporting_databases interaction supporting_databases 3.7 MiB 9.1 MiB 9.1 MiB 7.8 MiB
wright2025_pcnet_2.2 18,558 3,323,928 358.22 563.74 1377.99 22.82 0.15 0.36 7 1.00 Undirected Unipartite represents name geneid entrez_id number_of_supporting_databases interaction supporting_databases 8.5 MiB 19.2 MiB 19.2 MiB 16.0 MiB
wright2025_pid_2.0 2,543 31,881 25.07 46.00 97.21 24.39 -0.13 0.19 8 1.00 Undirected Unipartite represents name entrez_id score relationship_score interaction directed reverse_directed source edge_source target 210 KiB 415 KiB 382 KiB 413 KiB
wright2025_pips 5,326 36,843 13.84 29.59 83.50 47.52 -0.07 0.16 15 0.96 Undirected Unipartite represents name entrez_id score interaction name1 name2 300 KiB 497 KiB 471 KiB 545 KiB
wright2025_proper 8,516 209,829 49.28 199.07 369.97 13.27 -0.37 0.13 9 0.98 Undirected Unipartite represents name entrez_id score potential_background_contamination gene1 cell_line_specificity gene2 bh_corrected_p_value interaction odds_ratio read_count 5.3 MiB 6.5 MiB 6.4 MiB 6.6 MiB
wright2025_ptmcode2 5,535 17,541 6.34 10.12 36.55 103.56 0.06 0.19 16 0.94 Undirected Unipartite represents name entrez_id protein1 interaction ptm2 ptm1 protein2 144 KiB 241 KiB 232 KiB 244 KiB
wright2025_pathwaycommons 19,035 1,038,310 109.09 187.60 376.84 39.68 -0.11 0.13 8 1.00 Undirected Unipartite represents name entrez_id interaction_pubmed_id interaction_data_source interaction participant_a participant_b 5.6 MiB 10.9 MiB 10.8 MiB 12.7 MiB
wright2025_phosphositeplus 2,985 7,345 4.92 18.63 26.23 11.06 -0.38 0.01 9 0.99 Undirected Unipartite represents name entrez_id kin_acc_id substrate kinase interaction sub_acc_id 87 KiB 117 KiB 112 KiB 140 KiB
wright2025_preppi 7,662 9,972 2.60 3.00 4.12 961.06 -0.09 0.00 27 0.86 Undirected Unipartite represents name entrez_id ort_score protpep_score str_score phy_score coexp_score score prot2 prot1 go_score interaction red_score total_score str_max_score 239 KiB 384 KiB 367 KiB 423 KiB
wright2025_proteomehd 1,027 10,744 20.92 30.96 81.24 182.13 0.32 0.55 15 0.87 Undirected Unipartite represents name entrez_id protein_x coreg_with_protein_x interaction 56 KiB 102 KiB 99 KiB 113 KiB
wright2025_reactome 4,693 19,696 8.39 12.60 37.75 91.30 0.08 0.30 15 0.78 Undirected Unipartite represents name entrez_id publication_1st_author_s id_s_interactor_b publication_identifier_s interaction interaction_detection_method_s interaction_type_s id_s_interactor_a 271 KiB 359 KiB 364 KiB 538 KiB
wright2025_reactomefi 13,855 274,571 39.63 65.78 199.36 260.03 -0.01 0.36 15 0.96 Undirected Unipartite represents name entrez_id score gene1 gene2 interaction direction annotation 1.1 MiB 2.3 MiB 2.2 MiB 2.6 MiB
wright2025_signor 5,076 12,039 4.74 10.29 21.38 67.89 -0.13 0.03 14 0.95 Undirected Unipartite represents name entrez_id signor_id score mechanism idb ida interaction effect pmid 208 KiB 279 KiB 271 KiB 325 KiB
wright2025_spike 9,660 45,370 9.39 23.27 45.04 15.90 -0.12 0.03 10 0.99 Undirected Unipartite represents name entrez_id interaction 145 KiB 254 KiB 243 KiB 282 KiB
wright2025_string 18,960 6,583,400 694.45 575.60 1258.61 2.03 0.09 0.21 4 1.00 Undirected Unipartite represents name entrez_id score interaction protein1 protein2 36.0 MiB 59.8 MiB 56.9 MiB 65.1 MiB
wright2025_string_cocitation_free 18,890 5,482,301 580.44 527.20 1136.26 3.11 0.10 0.21 6 1.00 Undirected Unipartite represents name entrez_id cooccurence protein1 protein2 experimental fusion score database interaction neighborhood coexpression textmining 44.8 MiB 82.2 MiB 76.6 MiB 79.8 MiB
wright2025_wan 3,427 16,460 9.61 13.70 61.35 45.41 0.51 0.39 12 0.96 Undirected Unipartite represents name entrez_id score ensg2 ensg1 cofrac_ppi_score in_corum interaction hs 283 KiB 358 KiB 345 KiB 400 KiB
wright2025_youn 5,057 147,165 58.20 197.65 354.69 1.23 -0.88 0.13 4 1.00 Undirected Unipartite represents name entrez_id avgp prey_gene numreplicates maxp bfdr avgspec bait_gene specsum score interaction foldchange spec 1.1 MiB 2.3 MiB 2.1 MiB 2.2 MiB
wright2025_humap 13,896 1,737,628 250.09 379.97 930.58 4.55 0.10 0.32 6 1.00 Undirected Unipartite represents name entrez_id score interaction 7.8 MiB 13.5 MiB 13.5 MiB 11.6 MiB
wright2025_irefindex 17,671 627,565 71.03 120.88 286.43 7.76 -0.03 0.13 7 1.00 Undirected Unipartite represents name entrez_id uidb method interactiontype author pmids uida interaction sourcedb 4.8 MiB 7.6 MiB 7.2 MiB 9.3 MiB
wright2025_interactome_dependencies 47 207 4.40 6.29 11.48 1.55 -0.15 0.29 4 0.91 Directed Unipartite category degree outdegree edgecount indegree name entrez_id target source_category category interaction source 5 KiB 6 KiB 6 KiB 6 KiB