Human proteins (Vidal)

This network represens an initial version of a proteome-scale map of Human binary protein–protein interactions

Metadata

CodeMV
Internal namemaayan-vidal
NameHuman proteins (Vidal)
Data sourcehttp://research.mssm.edu/maayan/datasets/qualitative_networks.shtml
AvailabilityDataset is available for download
Consistency checkDataset passed all tests
Category
Metabolic network
Node meaningProtein
Edge meaningInteraction
Network formatUnipartite, undirected
Edge typeUnweighted, no multiple edges
LoopsContains loops

Statistics

Size n =3,133
Volume m =6,726
Loop count l =577
Wedge count s =88,809
Claw count z =1,399,841
Cross count x =27,308,384
Triangle count t =1,047
Square count q =10,216
4-Tour count T4 =449,262
Maximum degree dmax =129
Average degree d =4.293 65
Fill p =0.001 370 02
Size of LCC N =2,783
Diameter δ =13
50-Percentile effective diameter δ0.5 =4.264 35
90-Percentile effective diameter δ0.9 =5.872 22
Median distance δM =5
Mean distance δm =4.803 13
Gini coefficient G =0.540 534
Balanced inequality ratio P =0.294 826
Relative edge distribution entropy Her =0.926 225
Power law exponent γ =2.114 32
Tail power law exponent γt =3.031 00
Tail power law exponent with p γ3 =3.031 00
p-value p =0.869 000
Degree assortativity ρ =−0.125 658
Degree assortativity p-value pρ =1.817 28 × 10−44
Clustering coefficient c =0.035 368 0
Spectral norm α =16.614 4
Algebraic connectivity a =0.069 808 5
Non-bipartivity bA =0.186 364
Normalized non-bipartivity bN =0.060 887 7
Algebraic non-bipartivity χ =0.107 163
Spectral bipartite frustration bK =0.005 790 50

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] Jean-François Rual, Kavitha Venkatesan, Tong Hao, Tomoko Hirozane-Kishikawa, Amélie Dricot, Ning Li, Gabriel F. Berriz, Francis D. Gibbons, Matija Dreze, and Nono Ayivi-Guedehoussou. Towards a proteome-scale map of the human protein–protein interaction network. Nature, (7062):1173–1178, 2005.