The dichotomy in degree correlation of biological networks

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Hao, Dapeng ^a   Li, Chuanxing ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE;

ARTICLE; ASSORTATIVE NETWORK; BIOLOGICAL NETWORK; CLUSTER ANALYSIS; COMPUTER NETWORK; CONTROLLED STUDY; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; DISASSORTATIVE NETWORK; GENE INTERACTION; NONHUMAN; PROTEIN INTERACTION; SOCIAL NETWORK; ALGORITHM; BIOLOGICAL MODEL; CELL COMMUNICATION; COMPUTER SIMULATION; METABOLISM; SOCIAL SUPPORT; THEORETICAL MODEL;

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; ALGORITHMS; CELL COMMUNICATION; CLUSTER ANALYSIS; COMPUTER SIMULATION; FUNGAL PROTEINS; MODELS, BIOLOGICAL; MODELS, THEORETICAL; SOCIAL SUPPORT;

EID: 82555187456     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028322     Document Type: Article

References (47)

1. Barabasi AL, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
2. Jeong H, Mason SP, Barabasi AL, Oltvai ZN, (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
3. Newman ME, (2002) Assortative mixing in networks. Phys Rev Lett 89: 208701.
4. Maslov S, Sneppen K, (2002) Specificity and stability in topology of protein networks. Science 296: 910-913.
5. Park J, Newman ME, (2004) Statistical mechanics of networks. Phys Rev E Stat Nonlin Soft Matter Phys 70: 066117.
6. Newman ME, (2003) Mixing patterns in networks. Phys Rev E Stat Nonlin Soft Matter Phys 67: 026126.
7. Maslov S, Sneppen K, (2002) Protein interaction networks beyond artifacts. FEBS Lett 530: 255-256.
8. Song C, Havlin S, Makse HA, (2006) Origins of fractality in the growth of complex networks. Nature Physics 2: 275-281.
9. Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, et al. (2007) Still stratus not altocumulus: further evidence against the date/party hub distinction. PLoS Biol 5: e154.
10. Leskovec J, Kleinberg J, Faloutsos C, (2005) Graphs over Time: Densification Laws, Shrinking Diameters and Possible Explanations. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD).
11. Leskovec J, Kleinberg J, Faloutsos C, (2007) Graph Evolution: Densification and Shrinking Diameters. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD).
12. Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, et al. (2006) Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol 4: e317.
13. Yamada T, Bork P, (2009) Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 10: 791-803.
14. Zhu D, Qin ZS, (2005) Structural comparison of metabolic networks in selected single cell organisms. BMC Bioinformatics 6: 8.
15. Durek P, Walther D, (2008) The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. BMC Syst Biol 2: 100.
16. Folger O, Jerby L, Frezza C, Gottlieb E, Ruppin E, et al. (2011) Predicting selective drug targets in cancer through metabolic networks. Mol Syst Biol 7: 527.
17. Tong AH, Lesage G, Bader GD, Ding H, Xu H, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303: 808-813.
18. Aloy P, Russell RB, (2002) Potential artefacts in protein-interaction networks. FEBS Lett 530: 253-254.
19. Pu S, Wong J, Turner B, Cho E, Wodak SJ, (2009) Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res 37: 825-831.
20. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32: D449-451.
21. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
22. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
23. Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, et al. (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 27: 199-204.
24. Bertin N, Simonis N, Dupuy D, Cusick ME, Han JD, et al. (2007) Confirmation of organized modularity in the yeast interactome. PLoS Biol 5: e153.
25. Pastor-Satorras R, Vazquez A, Vespignani A, (2001) Dynamical and correlation properties of the internet. Phys Rev Lett 87: 258701.
26. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL, (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
27. Soffer SN, Vazquez A, (2005) Network clustering coefficient without degree-correlation biases. Phys Rev E Stat Nonlin Soft Matter Phys 71: 057101.
28. Maslov S, Sneppen K, Zaliznyak A, (2003) Detection of topological patterns in complex networks: correlation profile of the internet. Physica A 333: 529-540.
29. Sales-Pardo M, Guimera R, Moreira AA, Amaral LA, (2007) Extracting the hierarchical organization of complex systems. Proc Natl Acad Sci U S A 104: 15224-15229.
30. Newman ME, Girvan M, (2004) Finding and evaluating community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys 69: 026113.
31. Guimera R, Sales-Pardo M, Amaral LA, (2004) Modularity from fluctuations in random graphs and complex networks. Phys Rev E Stat Nonlin Soft Matter Phys 70: 025101.
32. Girvan M, Newman ME, (2002) Community structure in social and biological networks. Proc Natl Acad Sci U S A 99: 7821-7826.
33. Albert R, Jeong H, Barabasi AL, (2000) Error and attack tolerance of complex networks. Nature 406: 378-382.
34. Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M, (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3: e59.
35. Agarwal S, Deane CM, Porter MA, Jones NS, (2010) Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks. PLoS Comput Biol 6: e1000817.
36. Kamada Y, Funakoshi T, Shintani T, Nagano K, Ohsumi M, et al. (2000) Tor-mediated induction of autophagy via an Apg1 protein kinase complex. J Cell Biol 150: 1507-1513.
37. Ubersax JA, Woodbury EL, Quang PN, Paraz M, Blethrow JD, et al. (2003) Targets of the cyclin-dependent kinase Cdk1. Nature 425: 859-864.
38. Guimera R, Nunes Amaral LA, (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
39. Pereira-Leal JB, Audit B, Peregrin-Alvarez JM, Ouzounis CA, (2005) An exponential core in the heart of the yeast protein interaction network. Mol Biol Evol 22: 421-425.
40. He X, Zhang J, (2006) Why do hubs tend to be essential in protein networks? PLoS Genet 2: e88.
41. Redner S, (2008) Networks: teasing out the missing links. Nature 453: 47-48.
42. Hartwell LH, Hopfield JJ, Leibler S, Murray AW, (1999) From molecular to modular cell biology. Nature 402: C47-52.
43. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, et al. (2010) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39: D698-704.
44. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL, (2000) The large-scale organization of metabolic networks. Nature 407: 651-654.
45. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-360.
46. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569-4574.
47. Molloy M, Reed B, (1995) A Critical Point For Random Graphs With A Given Degree Sequence. Random structures and Algorithms 6: 161-179.