Reactome

This is a network of protein–protein interactions in the species Homo sapiens, i.e., in Humans. The data is curated by the Reactome project, an open online database of biological pathways.

Metadata

CodeRC
Internal namereactome
NameReactome
Data sourcehttp://www.reactome.org/pages/download-data/
AvailabilityDataset is available for download
Consistency checkDataset passed all tests
Category
Metabolic network
Dataset timestamp 2014
Node meaningProtein
Edge meaningInteraction
Network formatUnipartite, undirected
Edge typeUnweighted, no multiple edges
LoopsContains loops

Statistics

Size n =6,327
Volume m =147,547
Loop count l =1,387
Wedge count s =20,746,788
Claw count z =1,500,721,941
Cross count x =114,486,893,851
Triangle count t =4,187,734
Square count q =521,539,475
4-Tour count T4 =4,255,595,272
Maximum degree dmax =855
Average degree d =46.640 4
Fill p =0.007 370 49
Size of LCC N =5,973
Diameter δ =24
50-Percentile effective diameter δ0.5 =3.497 02
90-Percentile effective diameter δ0.9 =5.390 42
Median distance δM =4
Mean distance δm =4.142 04
Gini coefficient G =0.656 737
Relative edge distribution entropy Her =0.911 682
Power law exponent γ =1.364 51
Tail power law exponent γt =1.741 00
Degree assortativity ρ =+0.244 874
Degree assortativity p-value pρ =0.000 00
Clustering coefficient c =0.605 549
Spectral norm α =208.170
Algebraic connectivity a =0.013 403 5
Non-bipartivity bA =0.553 695
Normalized non-bipartivity bN =0.027 970 9
Spectral bipartite frustration bK =0.000 437 614

Plots

Fruchterman–Reingold graph drawing

Degree distribution

Cumulative degree distribution

Lorenz curve

Spectral distribution of the adjacency matrix

Spectral distribution of the normalized adjacency matrix

Spectral distribution of the Laplacian

Spectral graph drawing based on the adjacency matrix

Spectral graph drawing based on the Laplacian

Spectral graph drawing based on the normalized adjacency matrix

Degree assortativity

Zipf plot

Hop distribution

Double Laplacian graph drawing

Delaunay graph drawing

Clustering coefficient distribution

Average neighbor degree distribution

SynGraphy

Matrix decompositions plots

Downloads

References

[1] Jérôme Kunegis. KONECT – The Koblenz Network Collection. In Proc. Int. Conf. on World Wide Web Companion, pages 1343–1350, 2013. [ http ]
[2] Geeta Joshi-Topé, Marc Gillespie, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Bernard de Bono, Bijay Jassal, Gopal Gopinath, Guanming Wu, Lisa Matthews, Suzanna Lewis, Ewan Birney, and Lincoln Stein. Reactome: A knowledgebase of biological pathways. Nucleic Acids Res., 33(Database):D428–D432, 2005.