huri — Human Reference Interactome HuRI (2020)

Description

Networks of binary interactions between human proteins from the Human Reference Interactome (HuRI) mapping project of the Center for Cancer Systems Biology (CCSB) at the Dana-Farber Cancer Institute, with the Roth, Tavernier and Bader labs (Luck et al. 2020). HuRI is a systematic map of the binary interactome: the products of about 17,500 protein-coding genes ("Space III" of the human ORFeome) were screened pairwise by yeast two-hybrid (Y2H) assays, with three versions of the assay, and the detected pairs were verified by pairwise retesting (with samples validated by orthogonal assays). In all networks, nodes are proteins, identified by the Ensembl gene IDs of the genes that encode them (gene names are not given in these files), and an undirected edge represents a binary (direct) protein-protein interaction; self-loops are proteins that interact with themselves. The files have not changed since 2020.

HuRI: the HuRI map proper, the interactions detected in the screens of Space III (52,548 interactions among 8,272 proteins; the download page gives 52,569 interactions for this dataset).
HI-union: the union of all the systematic binary maps of the CCSB: HuRI, the earlier maps H-I-05 (CCSB-HI1, Rual et al. 2005), Venkatesan-09, Yu-11, HI-II-14 (Rolland et al. 2014) and Yang-16, and the test-space screens of 2019 (all of which are also available separately on the HuRI site).
Lit-BM: binary interactions curated from the literature and supported by at least two pieces of evidence (multiple publications or methods), as updated by Luck et al. for comparison with HuRI.
Test_space_screens-19: the interactions found in the screens of a smaller test space of genes with the assay versions of HuRI, used by Luck et al. to benchmark the screening pipeline.
H-I-05, Venkatesan-09, Yu-11, HI-II-14, Yang-16: the earlier systematic maps of the CCSB that make up HI-union besides HuRI, each on its own, with the proteins mapped to Ensembl gene IDs as in the other networks: H-I-05 (CCSB-HI1, Rual et al. 2005), the second-generation screens of Venkatesan et al. (2009) and Yu et al. (2011), HI-II-14 (Rolland et al. 2014) and the isoform screens of Yang et al. (2016).

H-I-05 (CCSB-HI1) is also in the entry interactome_vidal, and HI-II-14 and Lit-BM-13 in the entry human_interactome_2014, with the identifiers of the original publications. The PSI-MI files of the site (with protein isoforms, scores and the screens in which each interaction was found) are not included either.

The networks have the following properties:

name: the Ensembl gene ID.

Tags

Biological Protein interactions Unweighted

Citation

K. Luck, D.-K. Kim, L. Lambourne, K. Spirohn, B. E. Begg, W. Bian, et al., "A reference map of the human binary protein interactome." Nature 580, 402-408 (2020) 10.1038/s41586-020-2188-x Sci-Hub

Upstream URL OK

https://interactome-atlas.org/download

Upstream license

Creative Commons Attribution 4.0 International (CC BY 4.0), https://creativecommons.org/licenses/by/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	gt	GraphML	GML	csv
HuRI	8,272	52,548	12.71	25.58	61.47	26.70	-0.11	0.06	12	0.99	Undirected	Unipartite	name	236 KiB	368 KiB	364 KiB	312 KiB
HI-union	9,094	64,006	14.08	29.75	72.03	23.01	-0.13	0.05	11	0.99	Undirected	Unipartite	name	267 KiB	428 KiB	409 KiB	361 KiB
Lit-BM	6,047	13,441	4.45	10.84	20.10	46.63	-0.08	0.02	13	0.92	Undirected	Unipartite	name	142 KiB	192 KiB	191 KiB	161 KiB
Test_space_screens-19	672	1,159	3.45	5.20	8.27	51.04	-0.20	0.00	12	0.91	Undirected	Bipartite	name	16 KiB	21 KiB	20 KiB	17 KiB
H-I-05	1,530	2,709	3.54	7.25	13.24	26.90	-0.17	0.02	12	0.84	Undirected	Unipartite	name	34 KiB	44 KiB	43 KiB	38 KiB
Venkatesan-09	196	193	1.97	3.15	3.24	30.45	-0.29	0.00	10	0.66	Undirected	Unipartite	name	5 KiB	7 KiB	6 KiB	6 KiB
Yu-11	1,149	1,169	2.03	4.91	3.36	111.48	-0.10	0.00	17	0.69	Undirected	Unipartite	name	25 KiB	31 KiB	31 KiB	27 KiB
HI-II-14	4,182	13,633	6.52	15.41	35.33	56.05	-0.19	0.04	11	0.95	Undirected	Unipartite	name	103 KiB	142 KiB	140 KiB	119 KiB
Yang-16	506	728	2.88	5.56	8.71	27.71	-0.26	0.01	11	0.81	Undirected	Unipartite	name	12 KiB	16 KiB	15 KiB	13 KiB

Ridiculograms^*

Test_space_screens-19 drawing — Test_space_screens-19

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.