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humannet — HumanNet human functional gene networks (v2 and v3)

Description

Networks of human genes from HumanNet (Network Biomedicine Lab, Yonsei University, and Marcotte Lab, University of Texas at Austin), in which an edge links two genes that are likely to work in the same biological process (co-functional links), weighted by a log-likelihood score (LLS) of their association. The scores are obtained from a Bayesian framework that measures how well each kind of evidence (protein interactions, co-expression, co-citation, pathway databases, protein domains, genetic interactions, gene neighborhood, phylogenetic profiles, interactions of orthologs in other organisms, ...) recovers known co-functional gene pairs (the gold standard). The component networks, each from one kind of evidence, are integrated into the networks HumanNet-FN (functional network) and the extended networks. The genes are identified by their NCBI Gene (Entrez) identifiers.

The networks of HumanNet v3 (2021) are v3_xc (HumanNet-XC, the functional network extended by co-citation), v3_fn (HumanNet-FN, integrating the components CX, DB, DP, GI, GN, PG and PI) and the component networks v3_cc (co-citation), v3_cx (co-expression), v3_db (pathway databases), v3_dp (protein domain profiles), v3_gi (genetic interactions), v3_gn (gene neighborhood), v3_pg (phylogenetic profiles) and v3_pi (protein-protein interactions); v3_gsp is the network of the gold standard positive gene pairs (unweighted).

The networks of HumanNet v2 (2018) are v2_xn (HumanNet-XN, the fully extended functional network), v2_xc (extended by co-citation), v2_xi (extended by interologs), v2_fn (functional network), v2_cf (co-functional network), v2_pi (protein-protein interaction network), the component networks v2_cc (co-citation), v2_ce (co-essentiality), v2_cx (co-expression), v2_db (pathway databases), v2_dp (protein domain profiles), v2_gn (gene neighborhood), v2_ht (high-throughput protein interactions), v2_il (protein interactions transferred from other organisms), v2_lc (literature-curated protein interactions), v2_pg (phylogenetic profiles), and the networks of human genes derived from the interactions of their orthologs in other organisms (interologs): v2_ce_ht, v2_ce_lc (high-throughput and literature-curated protein interactions in C. elegans), v2_dm_ht, v2_dm_lc (D. melanogaster), v2_dr_lc (D. rerio), v2_mm_lc (M. musculus), v2_sc_gt (genetic interactions in S. cerevisiae), v2_sc_ht, v2_sc_lc (protein interactions in S. cerevisiae), v2_sc_ts (3D-structure-based interactions in S. cerevisiae), v2_clf_lc (C. lupus familiaris), v2_bt_lc (B. taurus), v2_rn_lc (R. norvegicus) and v2_gg_lc (G. gallus).

The networks have the following properties:

  • (Node) entrez_id: the NCBI Gene identifier of the gene.
  • (Node) name: the gene symbol, as given by HumanNet v3 (empty for the genes of v2 that are not in the v3 networks).
  • (Edge) lls (all networks but v3_gsp): the log-likelihood score of the link.
  • (Edge) score2 (v2_sc_ht, v2_sc_lc, v2_sc_ts): a second score given in the files of these networks, without documentation (slightly lower than lls).
Tags
Biological Genetic Protein interactions Weighted Metadata
Added
2026-10-31
Citation
  • C. Y. Kim, S. Baek, J. Cha, S. Yang, E. Kim, E. M. Marcotte, T. Hart, I. Lee, "HumanNet v3: an improved database of human gene networks for disease research." Nucleic Acids Research 50, D632-D639 (2022) 10.1093/nar/gkab1048 Sci-Hub
  • S. Hwang, C. Y. Kim, S. Yang, E. Kim, T. Hart, E. M. Marcotte, I. Lee, "HumanNet v2: human gene networks for disease research." Nucleic Acids Research 47, D573-D580 (2019) 10.1093/nar/gky1126 Sci-Hub
Upstream URL OK
https://www.inetbio.org/humannet/
https://www.inetbio.org/humannetv2/
Upstream license
Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0), https://creativecommons.org/licenses/by-sa/4.0/
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
v3_xc 18,593 1,125,494 121.07 87.97 291.37 9.54 0.42 0.31 6 1.00 Undirected Unipartite entrez_id name lls 8.3 MiB 12.2 MiB 11.9 MiB 12.4 MiB
v3_fn 18,459 977,495 105.91 113.97 270.60 14.68 0.01 0.18 7 1.00 Undirected Unipartite entrez_id name lls 6.0 MiB 9.6 MiB 9.4 MiB 10.0 MiB
v3_cc 18,300 1,081,518 118.20 92.16 339.57 8.03 0.57 0.37 6 1.00 Undirected Unipartite entrez_id name lls 9.4 MiB 12.0 MiB 11.9 MiB 12.2 MiB
v3_cx 12,180 81,064 13.31 23.20 123.00 40.12 0.56 0.40 15 0.96 Undirected Unipartite entrez_id name lls 786 KiB 1.0 MiB 1.0 MiB 1013 KiB
v3_db 8,540 135,327 31.69 24.57 96.61 374.72 0.51 0.64 12 0.97 Undirected Unipartite entrez_id name lls 474 KiB 853 KiB 828 KiB 865 KiB
v3_dp 12,700 73,414 11.56 15.83 80.58 9347.94 0.51 0.72 26 0.39 Undirected Unipartite entrez_id name lls 236 KiB 478 KiB 473 KiB 472 KiB
v3_gi 10,478 174,509 33.31 79.62 261.83 91.10 0.12 0.50 13 0.97 Undirected Unipartite entrez_id name lls 1.5 MiB 2.0 MiB 1.9 MiB 1.9 MiB
v3_gn 2,339 97,565 83.42 114.84 232.23 24.03 -0.10 0.45 8 0.98 Undirected Unipartite entrez_id name lls 559 KiB 853 KiB 827 KiB 914 KiB
v3_pg 2,126 16,465 15.49 22.07 63.63 502.07 -0.01 0.29 14 0.91 Undirected Unipartite entrez_id name lls 137 KiB 188 KiB 183 KiB 181 KiB
v3_pi 17,849 633,460 70.98 94.96 201.42 7.33 -0.16 0.12 7 1.00 Undirected Unipartite entrez_id name lls 3.7 MiB 6.3 MiB 6.2 MiB 6.6 MiB
v3_gsp 8,779 260,962 59.45 73.83 174.50 18.20 0.12 0.30 9 0.99 Undirected Unipartite entrez_id name 524 KiB 947 KiB 925 KiB 887 KiB
v2_xn 17,929 525,537 58.62 63.65 202.71 26.93 0.28 0.24 10 1.00 Undirected Unipartite entrez_id name lls 3.0 MiB 5.0 MiB 4.9 MiB 5.3 MiB
v2_xc 17,790 424,501 47.72 48.53 175.98 32.63 0.24 0.26 10 1.00 Undirected Unipartite entrez_id name lls 2.4 MiB 4.0 MiB 3.9 MiB 4.3 MiB
v2_xi 17,303 418,525 48.38 54.67 175.32 18.95 0.23 0.25 8 1.00 Undirected Unipartite entrez_id name lls 2.2 MiB 3.8 MiB 3.7 MiB 4.1 MiB
v2_fn 17,247 371,502 43.08 46.81 173.87 18.92 0.24 0.28 8 1.00 Undirected Unipartite entrez_id name lls 1.9 MiB 3.3 MiB 3.2 MiB 3.6 MiB
v2_cf 14,739 252,590 34.28 42.51 198.57 121.69 0.52 0.46 11 0.98 Undirected Unipartite entrez_id name lls 1.2 MiB 2.0 MiB 2.0 MiB 2.2 MiB
v2_pi 15,352 158,499 20.65 26.23 60.99 12.37 -0.18 0.13 11 1.00 Undirected Unipartite entrez_id name lls 1.0 MiB 1.6 MiB 1.5 MiB 1.7 MiB
v2_cc 10,303 72,819 14.14 16.26 54.12 217.70 0.33 0.36 14 0.96 Undirected Unipartite entrez_id name lls 506 KiB 787 KiB 751 KiB 867 KiB
v2_ce 4,052 71,243 35.16 68.16 242.88 185.77 0.66 0.71 16 0.95 Undirected Unipartite entrez_id name lls 281 KiB 564 KiB 523 KiB 509 KiB
v2_cx 6,658 29,481 8.86 18.58 105.72 184.59 0.70 0.58 20 0.85 Undirected Unipartite entrez_id name lls 295 KiB 402 KiB 393 KiB 382 KiB
v2_db 7,512 125,550 33.43 31.61 111.55 179.38 0.28 0.48 10 0.98 Undirected Unipartite entrez_id name lls 441 KiB 802 KiB 778 KiB 821 KiB
v2_dp 9,454 45,958 9.72 11.62 77.63 15757.90 0.83 0.81 30 0.41 Undirected Unipartite entrez_id name lls 165 KiB 307 KiB 302 KiB 312 KiB
v2_gn 2,403 24,862 20.69 23.17 53.84 39.58 0.08 0.09 11 0.95 Undirected Unipartite entrez_id name lls 169 KiB 253 KiB 242 KiB 245 KiB
v2_ht 12,641 78,627 12.44 15.93 59.64 8.48 0.19 0.22 10 1.00 Undirected Unipartite entrez_id name lls 737 KiB 1018 KiB 982 KiB 988 KiB
v2_il 9,077 113,499 25.01 50.28 171.33 16.89 0.18 0.27 11 0.99 Undirected Unipartite entrez_id name lls 726 KiB 1.1 MiB 1.0 MiB 1.1 MiB
v2_lc 13,790 122,444 17.76 23.41 41.42 23.48 -0.25 0.11 11 1.00 Undirected Unipartite entrez_id name lls 684 KiB 1.1 MiB 1.1 MiB 1.3 MiB
v2_pg 1,552 10,888 14.03 20.34 46.99 1837.21 -0.07 0.23 15 0.91 Undirected Unipartite entrez_id name lls 94 KiB 127 KiB 124 KiB 122 KiB
v2_ce_ht 868 1,041 2.40 2.95 7.07 1048.95 -0.15 0.00 30 0.29 Undirected Unipartite entrez_id name lls 9 KiB 13 KiB 13 KiB 13 KiB
v2_ce_lc 575 860 2.99 4.00 6.52 132.36 -0.27 0.04 14 0.18 Undirected Unipartite entrez_id name lls 6 KiB 10 KiB 9 KiB 9 KiB
v2_dm_ht 3,912 6,383 3.26 3.07 8.31 51.04 -0.32 0.01 15 0.97 Undirected Unipartite entrez_id name lls 56 KiB 85 KiB 83 KiB 82 KiB
v2_dm_lc 1,299 3,196 4.92 4.96 11.31 262.83 -0.12 0.06 19 0.78 Undirected Unipartite entrez_id name lls 30 KiB 44 KiB 43 KiB 41 KiB
v2_dr_lc 169 179 2.12 6.11 4.42 5.25 -0.35 0.02 4 0.52 Undirected Unipartite entrez_id name lls 3 KiB 4 KiB 3 KiB 3 KiB
v2_mm_lc 5,120 11,336 4.43 18.62 22.11 69.31 -0.13 0.01 14 0.96 Undirected Unipartite entrez_id name lls 72 KiB 118 KiB 114 KiB 118 KiB
v2_sc_gt 2,671 44,222 33.11 33.03 78.95 7.13 0.14 0.30 8 1.00 Undirected Unipartite entrez_id name lls 294 KiB 448 KiB 438 KiB 478 KiB
v2_sc_ht 2,326 39,536 33.99 57.27 150.04 21.34 0.24 0.41 11 0.98 Undirected Unipartite entrez_id name lls score2 418 KiB 543 KiB 540 KiB 570 KiB
v2_sc_lc 2,580 23,974 18.58 19.25 55.97 8.39 0.24 0.13 9 1.00 Undirected Unipartite entrez_id name lls score2 245 KiB 321 KiB 320 KiB 385 KiB
v2_sc_ts 857 6,005 14.01 20.04 67.97 196.48 0.78 0.80 12 0.20 Undirected Unipartite entrez_id name lls score2 57 KiB 78 KiB 76 KiB 79 KiB
v2_clf_lc 9 5 1.11 0.31 1.00 nan -0.25 0.00 2 0.33 Undirected Bipartite entrez_id name lls 1 KiB 2 KiB 1 KiB 2 KiB
v2_bt_lc 275 2,230 16.22 16.77 44.13 7.88 0.80 0.86 3 0.30 Undirected Unipartite entrez_id name lls 6 KiB 12 KiB 11 KiB 11 KiB
v2_rn_lc 1,129 5,135 9.10 17.15 51.51 140.70 0.06 0.53 12 0.80 Undirected Unipartite entrez_id name lls 26 KiB 43 KiB 41 KiB 40 KiB
v2_gg_lc 123 1,000 16.26 17.37 38.98 14.08 0.91 0.96 4 0.46 Undirected Unipartite entrez_id name lls 3 KiB 5 KiB 5 KiB 5 KiB