mist — MIST protein interaction database (2020)

Description

The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from several primary sources. This dataset contains the networks of the following species:

1. Homo sapiens (Human)
2. Drosophila melanogaster (Fly)
3. Mus musculus (Mouse)
4. Caenorhabditis elegans (Worm)
5. Rattus norvegicus (Rat)
6. Saccharomyces cerevisiae (Baker's yeast)
7. Schizosaccharomyces pombe (Fission yeast)
8. Danio rerio (Zebrafish)
9. Xenopus tropicalis (Western clawed frog)

The database contains four kinds of interactions:

1. Protein-protein interaction (PPI): “PPI” refers to physical interactions between two or more proteins.
2. Interologs (PPI): Interactions predicted based on PPI data obtained for orthologous proteins.
3. Genetic Interactions: Indicate that the effects of mutations in one gene can be modified by mutation of another gene.
4. Genetic Interologs: Interactions predicted based on genetic interaction data obtained for orthologous proteins

There is one network for each species and kind of interaction, named as <kind>_<species> (e.g. ppi_human or genetic_interolog_fly), with the kinds ppi, ppi_interolog, genetic and genetic_interolog (there is no genetic network for the western clawed frog, and no genetic interolog network for the fission yeast). Nodes are genes (or the proteins they encode), identified by their NCBI Entrez Gene IDs, and an undirected edge connects two genes for which MIST lists an interaction of the given kind; when the same pair is listed in several records, only one of them is kept. The files of a species also contain some interactions with genes of other species (e.g. about 8% of the records of the human PPI file), which are included. The interolog files of a species contain both the interactions predicted for its genes and those predicted for the genes of other species (including Xenopus laevis) from its data, and all of them are included. The species of each gene is given by the vertex property tax_id (NCBI Taxonomy ID).

Tags

Biological Protein interactions Unweighted

Citation

• Yanhui Hu, Arunachalam Vinayagam, Ankita Nand, Aram Comjean, Verena Chung, Tong Hao, Stephanie E Mohr, and Norbert Perrimon, “Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data.” Nucleic Acids Res, 46, D1, Pp. D567-D574 (2017) dx.doi.org

Upstream URL OK

https://fgrtools.hms.harvard.edu/MIST/index.jsp

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

Show all columns

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
ppi_fission_yeast	3,705	15,167	8.19	26.07	40.57	21.00	-0.24	0.03	9	0.97	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	150 KiB	229 KiB	225 KiB	212 KiB
ppi_yeast	7,272	165,705	45.57	129.89	202.31	4.13	-0.18	0.06	6	1.00	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	1.0 MiB	1.8 MiB	1.7 MiB	1.7 MiB
ppi_worm	8,874	42,541	9.59	28.54	82.41	107.49	-0.11	0.11	13	0.97	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	386 KiB	562 KiB	553 KiB	525 KiB
ppi_fly	11,352	135,037	23.79	45.80	104.49	90.14	-0.15	0.08	10	1.00	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	938 KiB	1.5 MiB	1.4 MiB	1.4 MiB
ppi_zebrafish	452	458	2.03	5.39	4.79	46.61	-0.26	0.02	9	0.44	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	13 KiB	17 KiB	16 KiB	15 KiB
ppi_western_clawed_frog	50	41	1.64	3.06	1.00	0.03	-0.49	0.00	2	0.46	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	2 KiB	3 KiB	3 KiB	2 KiB
ppi_human	27,594	526,471	38.16	91.50	238.56	8.26	-0.08	0.06	8	1.00	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	4.1 MiB	6.5 MiB	6.3 MiB	6.4 MiB
ppi_mouse	18,838	75,110	7.97	44.25	72.44	27.72	-0.10	0.01	11	0.99	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	781 KiB	1.1 MiB	1.1 MiB	1.1 MiB
ppi_rat	7,050	14,969	4.25	19.09	30.03	39.03	-0.20	0.01	12	0.96	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	228 KiB	316 KiB	309 KiB	283 KiB
ppi_interolog_fission_yeast	21,912	266,887	24.36	82.13	282.81	1.58	-0.09	0.16	5	0.18	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	2.9 MiB	4.6 MiB	4.3 MiB	4.6 MiB
ppi_interolog_yeast	35,355	958,936	54.25	125.44	210.83	2.69	-0.20	0.08	5	0.14	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	7.8 MiB	14.1 MiB	12.9 MiB	13.9 MiB
ppi_interolog_worm	46,404	643,319	27.73	82.42	322.00	3.93	-0.02	0.12	5	0.16	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	6.3 MiB	9.9 MiB	9.3 MiB	10.0 MiB
ppi_interolog_fly	58,896	1,180,954	40.10	85.40	352.42	3.90	0.05	0.12	6	0.13	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	9.9 MiB	17.4 MiB	15.7 MiB	16.7 MiB
ppi_interolog_zebrafish	17,845	789,779	88.52	170.12	374.45	2.95	-0.09	0.10	6	0.94	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	7.8 MiB	12.2 MiB	11.6 MiB	12.4 MiB
ppi_interolog_western_clawed_frog	13,271	550,375	82.94	147.96	314.26	2.90	-0.09	0.10	7	1.00	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	5.7 MiB	8.8 MiB	8.3 MiB	8.8 MiB
ppi_interolog_human	109,706	2,864,523	52.22	102.93	252.64	5.34	-0.10	0.07	7	0.15	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	25.7 MiB	42.4 MiB	39.6 MiB	42.7 MiB
ppi_interolog_mouse	71,318	933,081	26.17	92.61	342.00	5.18	-0.11	0.08	6	0.24	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	9.7 MiB	15.0 MiB	14.2 MiB	14.9 MiB
ppi_interolog_rat	35,093	747,063	42.58	114.96	334.60	3.68	-0.07	0.09	7	0.49	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	7.7 MiB	12.1 MiB	11.4 MiB	12.1 MiB
genetic_fission_yeast	3,563	52,013	29.20	55.04	108.62	9.23	-0.28	0.09	9	0.99	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	249 KiB	509 KiB	499 KiB	468 KiB
genetic_yeast	5,936	442,019	148.93	172.55	336.99	11.72	-0.08	0.14	8	1.00	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	1.6 MiB	3.7 MiB	3.7 MiB	3.5 MiB
genetic_worm	3,178	8,011	5.04	17.50	29.90	42.99	-0.20	0.03	13	0.96	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	82 KiB	126 KiB	125 KiB	115 KiB
genetic_fly	4,209	13,882	6.60	15.32	36.04	19.19	-0.10	0.08	12	0.96	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	185 KiB	269 KiB	265 KiB	255 KiB
genetic_zebrafish	66	65	1.97	1.73	2.05	9.15	-0.20	0.15	5	0.32	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	3 KiB	4 KiB	3 KiB	3 KiB
genetic_human	3,751	9,034	4.82	19.83	35.45	141.13	-0.16	0.04	11	0.95	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	101 KiB	155 KiB	145 KiB	134 KiB
genetic_mouse	368	357	1.94	3.06	2.83	270.87	-0.18	0.05	17	0.58	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	11 KiB	14 KiB	14 KiB	12 KiB
genetic_rat	39	24	1.23	0.58	1.00	0.02	-0.33	0.00	2	0.10	Undirected	Bipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	2 KiB	3 KiB	2 KiB	2 KiB
genetic_interolog_yeast	33,399	2,028,834	121.49	139.71	300.98	4.95	-0.07	0.17	7	0.14	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	10.9 MiB	26.1 MiB	21.8 MiB	22.9 MiB
genetic_interolog_worm	23,826	285,752	23.99	66.26	257.37	248.65	0.17	0.16	8	0.21	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	1.9 MiB	3.9 MiB	3.4 MiB	3.5 MiB
genetic_interolog_fly	27,105	334,495	24.68	69.32	286.14	10.98	0.23	0.18	8	0.19	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	2.5 MiB	5.0 MiB	4.3 MiB	4.6 MiB
genetic_interolog_zebrafish	8,699	317,814	73.07	131.92	317.11	17.76	-0.00	0.17	8	0.96	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	2.0 MiB	4.4 MiB	3.7 MiB	3.8 MiB
genetic_interolog_western_clawed_frog	6,618	185,239	55.98	97.44	229.63	11.09	-0.02	0.16	8	1.00	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	1.2 MiB	2.6 MiB	2.2 MiB	2.3 MiB
genetic_interolog_human	27,707	363,570	26.24	80.04	310.02	25.36	0.11	0.17	10	0.24	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	2.5 MiB	5.2 MiB	4.5 MiB	4.6 MiB
genetic_interolog_mouse	9,815	318,298	64.86	127.09	315.70	11.00	-0.03	0.17	8	0.82	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	2.0 MiB	4.3 MiB	3.7 MiB	3.9 MiB
genetic_interolog_rat	7,946	250,780	63.12	114.43	272.56	18.54	-0.03	0.16	10	0.98	Undirected	Unipartite	gene tax_id	MasterNetID Rank Interaction_type Exp_Direct Exp_Indirect TaxID_interolog Source_databases Reference Reference_type Count_direct Count_indirect Count_paper Source_Interolog Comment	1.6 MiB	3.5 MiB	2.9 MiB	3.0 MiB

Ridiculograms^*

^* 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.