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hint_interactomes — HINT high-quality protein interactomes (2026)

Description

Networks of high-quality protein-protein interactions of ten organisms, from HINT (High-quality INTeractomes), a database of the Yu lab (Cornell University) that compiles interactions from several public databases and filters them for quality. An interaction is included if it was found in a high-throughput (HT) study that validated its screen with orthogonal assays (studies are inspected manually), or if it was reported by at least two independent small-scale, literature-curated (LC) publications. Post-translational modifications are not considered interactions. This is the HINT release of July 2026.

For each organism there are two networks. In both, nodes are proteins (UniProt entries), and an undirected edge connects two proteins that interact:

  • <organism>_binary: binary interactions, i.e. direct physical contacts between two proteins (e.g. from yeast two-hybrid assays).
  • <organism>_cocomplex: co-complex associations, i.e. two proteins found in the same protein complex (e.g. by affinity purification followed by mass spectrometry), which need not be in direct contact. Not available for rice.

The organisms are: human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), fly (Drosophila melanogaster), worm (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), fission_yeast (Schizosaccharomyces pombe), arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and ecoli (Escherichia coli). Self-loops are proteins that interact with themselves (homodimers).

The networks have the following properties:

  • name: the UniProt accession of the protein.
  • gene: the gene name (empty if not available).
  • evidence (edges): the supporting evidence, a list separated by "|" of entries "PubMed ID:PSI-MI method code:HT or LC:binary or co-complex".
  • in_pdb (edges): whether the interaction is supported by a structure in the Protein Data Bank.
  • pdb_ids (edges): the PDB structures and chains supporting the interaction (empty if none).
Tags
Biological Protein interactions Unweighted Metadata
Citation
  • J. Das, H. Yu, "HINT: High-quality protein interactomes and their applications in understanding human disease." BMC Systems Biology 6, 92 (2012) 10.1186/1752-0509-6-92 Sci-Hub
Upstream URL OK
https://hint.yulab.org/download
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
human_binary 21,412 167,786 15.67 34.33 85.99 55.62 -0.11 0.04 14 0.97 Undirected Unipartite name gene evidence in_pdb pdb_ids 1.3 MiB 2.0 MiB 1.9 MiB 2.0 MiB
human_cocomplex 22,887 595,281 52.02 128.32 298.96 5.00 -0.10 0.06 7 1.00 Undirected Unipartite name gene evidence in_pdb pdb_ids 1.6 MiB 3.6 MiB 3.5 MiB 2.9 MiB
mouse_binary 2,713 4,277 3.15 3.65 10.54 672.76 0.06 0.16 21 0.55 Undirected Unipartite name gene evidence in_pdb pdb_ids 90 KiB 113 KiB 111 KiB 123 KiB
mouse_cocomplex 6,311 19,495 6.18 44.25 57.75 14.23 -0.37 0.01 9 1.00 Undirected Unipartite name gene evidence in_pdb pdb_ids 85 KiB 150 KiB 145 KiB 129 KiB
rat_binary 585 807 2.76 2.55 10.31 221.41 0.64 0.45 10 0.15 Undirected Unipartite name gene evidence in_pdb pdb_ids 33 KiB 38 KiB 37 KiB 43 KiB
rat_cocomplex 1,998 2,937 2.94 24.05 20.41 9.53 -0.68 0.00 7 0.99 Undirected Unipartite name gene evidence in_pdb pdb_ids 20 KiB 32 KiB 31 KiB 30 KiB
fly_binary 9,395 41,804 8.90 14.56 31.10 16.94 -0.09 0.02 11 0.99 Undirected Unipartite name gene evidence in_pdb pdb_ids 197 KiB 344 KiB 335 KiB 323 KiB
fly_cocomplex 7,373 53,845 14.61 36.45 119.66 53.36 -0.16 0.25 11 0.98 Undirected Unipartite name gene evidence in_pdb pdb_ids 145 KiB 318 KiB 313 KiB 264 KiB
worm_binary 4,676 12,326 5.27 11.27 33.24 42.25 -0.07 0.06 13 0.94 Undirected Unipartite name gene evidence in_pdb pdb_ids 79 KiB 128 KiB 126 KiB 118 KiB
worm_cocomplex 2,496 2,947 2.36 41.64 12.66 16.14 -0.56 0.00 8 0.96 Undirected Unipartite name gene evidence in_pdb pdb_ids 22 KiB 35 KiB 35 KiB 35 KiB
yeast_binary 5,429 26,038 9.59 15.40 36.51 18.47 -0.11 0.09 10 0.98 Undirected Unipartite name gene evidence in_pdb pdb_ids 324 KiB 432 KiB 428 KiB 501 KiB
yeast_cocomplex 5,690 139,741 49.12 142.14 211.09 3.03 -0.22 0.08 5 1.00 Undirected Unipartite name gene evidence in_pdb pdb_ids 401 KiB 893 KiB 879 KiB 754 KiB
fission_yeast_binary 1,707 3,326 3.90 6.95 16.79 168.85 -0.07 0.07 14 0.78 Undirected Unipartite name gene evidence in_pdb pdb_ids 33 KiB 46 KiB 46 KiB 45 KiB
fission_yeast_cocomplex 539 752 2.79 6.58 10.87 163.56 -0.19 0.07 17 0.72 Undirected Unipartite name gene evidence in_pdb pdb_ids 8 KiB 11 KiB 11 KiB 10 KiB
arabidopsis_binary 7,421 35,985 9.70 23.82 66.58 45.67 -0.18 0.04 14 0.94 Undirected Unipartite name gene evidence in_pdb pdb_ids 166 KiB 290 KiB 286 KiB 270 KiB
arabidopsis_cocomplex 1,796 3,434 3.82 10.59 18.49 129.93 -0.35 0.03 14 0.88 Undirected Unipartite name gene evidence in_pdb pdb_ids 21 KiB 34 KiB 33 KiB 30 KiB
rice_binary 242 261 2.16 2.11 4.74 396.44 -0.17 0.10 17 0.47 Undirected Unipartite name gene evidence in_pdb pdb_ids 5 KiB 7 KiB 7 KiB 7 KiB
ecoli_binary 2,552 4,650 3.64 4.31 11.17 67.32 0.10 0.09 13 0.53 Undirected Unipartite name gene evidence in_pdb pdb_ids 157 KiB 185 KiB 184 KiB 221 KiB
ecoli_cocomplex 3,066 17,678 11.53 26.71 55.93 16.18 -0.14 0.06 9 0.99 Undirected Unipartite name gene evidence in_pdb pdb_ids 85 KiB 149 KiB 145 KiB 138 KiB