Editing Interactome (section)

==Network properties==
Protein interaction networks can be analyzed with the same tool as other networks. In fact, they share many properties with biological or [[social networks]]. Some of the main characteristics are as follows.

[[File:The protein interaction network of Treponema pallidum.png|300px|right|thumb|The ''[[Treponema pallidum]]'' protein interactome.<ref name="Titz2008"/>]]

===Degree distribution===
The degree distribution describes the number of proteins that have a certain number of connections. Most protein interaction networks show a [[Scale-free network|scale-free]] ([[power law]]) degree distribution where the connectivity distribution P(k) ~ k<sup>−γ</sup> with k being the degree. This relationship can also be seen as a straight line on a [[log-log plot]] since, the above equation is equal to log(P(k)) ~ —y•log(k). One characteristic of such distributions is that there are many proteins with few interactions and few proteins that have many interactions, the latter being called "hubs".

===Hubs===
Highly connected nodes (proteins) are called hubs. Han et al.<ref name="Han2004">{{Cite journal | pmid = 15190252 | year = 2004 | last1 = Han | first1 = J. D. | title = Evidence for dynamically organized modularity in the yeast protein–protein interaction network | journal = Nature | volume = 430 | issue = 6995 | pages = 88–93 | last2 = Bertin | first2 = N | last3 = Hao | first3 = T | last4 = Goldberg | first4 = D. S. | last5 = Berriz | first5 = G. F. | last6 = Zhang | first6 = L. V. | last7 = Dupuy | first7 = D | last8 = Walhout | first8 = A. J. | last9 = Cusick | first9 = M. E. | last10 = Roth | first10 = F. P. | last11 = Vidal | first11 = M | doi = 10.1038/nature02555 | bibcode = 2004Natur.430...88H | s2cid = 4426721 }}</ref> have coined the term "'''party hub'''" for hubs whose expression is correlated with its interaction partners. Party hubs also connect proteins within functional modules such as protein complexes. In contrast, "'''date hubs'''" do not exhibit such a correlation and appear to connect different functional modules. Party hubs are found predominantly in AP/MS data sets, whereas date hubs are found predominantly in binary interactome network maps.<ref name="Yu2008">{{Cite journal | pmid = 18719252 | year = 2008 | last1 = Yu | first1 = H | title = High-quality binary protein interaction map of the yeast interactome network | journal = Science | volume = 322 | issue = 5898 | pages = 104–10 | last2 = Braun | first2 = P | last3 = Yildirim | first3 = M. A. | last4 = Lemmens | first4 = I | last5 = Venkatesan | first5 = K | last6 = Sahalie | first6 = J | last7 = Hirozane-Kishikawa | first7 = T | last8 = Gebreab | first8 = F | last9 = Li | first9 = N | last10 = Simonis | first10 = N | last11 = Hao | first11 = T | last12 = Rual | first12 = J. F. | last13 = Dricot | first13 = A | last14 = Vazquez | first14 = A | last15 = Murray | first15 = R. R. | last16 = Simon | first16 = C | last17 = Tardivo | first17 = L | last18 = Tam | first18 = S | last19 = Svrzikapa | first19 = N | last20 = Fan | first20 = C | last21 = De Smet | first21 = A. S. | last22 = Motyl | first22 = A | last23 = Hudson | first23 = M. E. | last24 = Park | first24 = J | last25 = Xin | first25 = X | last26 = Cusick | first26 = M. E. | last27 = Moore | first27 = T | last28 = Boone | first28 = C | last29 = Snyder | first29 = M | last30 = Roth | first30 = F. P. | doi = 10.1126/science.1158684 | pmc = 2746753 | bibcode = 2008Sci...322..104Y }}</ref> Note that the validity of the date hub/party hub distinction was disputed.<ref name="Batada2006">{{Cite journal | pmid = 16984220 | year = 2006 | last1 = Batada | first1 = N. N. | title = Stratus not altocumulus: A new view of the yeast protein interaction network | journal = PLOS Biology | volume = 4 | issue = 10 | pages = e317 | last2 = Reguly | first2 = T | last3 = Breitkreutz | first3 = A | last4 = Boucher | first4 = L | last5 = Breitkreutz | first5 = B. J. | last6 = Hurst | first6 = L. D. | last7 = Tyers | first7 = M | doi = 10.1371/journal.pbio.0040317 | pmc = 1569888 | doi-access = free }}</ref><ref name="Bertin2007">{{Cite journal | pmid = 17564493 | year = 2007 | last1 = Bertin | first1 = N | title = Confirmation of organized modularity in the yeast interactome | journal = PLOS Biology | volume = 5 | issue = 6 | pages = e153 | last2 = Simonis | first2 = N | last3 = Dupuy | first3 = D | last4 = Cusick | first4 = M. E. | last5 = Han | first5 = J. D. | last6 = Fraser | first6 = H. B. | last7 = Roth | first7 = F. P. | last8 = Vidal | first8 = M | doi = 10.1371/journal.pbio.0050153 | pmc = 1892830 | doi-access = free }}</ref> Party hubs generally consist of multi-interface proteins whereas date hubs are more frequently single-interaction interface proteins.<ref name="Kim2006">{{Cite journal | pmid = 17185604 | year = 2006 | last1 = Kim | first1 = P. M. | title = Relating three-dimensional structures to protein networks provides evolutionary insights | journal = Science | volume = 314 | issue = 5807 | pages = 1938–41 | last2 = Lu | first2 = L. J. | last3 = Xia | first3 = Y | last4 = Gerstein | first4 = M. B. | s2cid = 2489619 | doi = 10.1126/science.1136174 | bibcode = 2006Sci...314.1938K }}</ref> Consistent with a role for date-hubs in connecting different processes, in yeast the number of binary interactions of a given protein is correlated to the number of phenotypes observed for the corresponding mutant gene in different physiological conditions.<ref name="Yu2008" />

===Modules===
Nodes involved in the same biochemical process are highly interconnected.<ref name="Barabasi"/>