Dominating biological networks

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Milenković, Tijana ^a   Memišević, Vesna ^b   Bonato, Anthony ^c   Pržulj, Nataša ^d  

^a University of Notre Dame   (United States)

^b Irvine   (United States)

^c RYERSON UNIVERSITY   (Canada)

^d IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AGING GENE; ALGORITHM; ARTICLE; BIOLOGICALLY CENTRAL GENE; DRUG TARGETING; GENE; HUMAN; PROTEIN PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION NETWORK; AGING; GENETICS; METABOLISM; PROTEIN BINDING; SIGNAL TRANSDUCTION;

DRUG; PROTEIN;

AGING; ALGORITHMS; HUMANS; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; PROTEIN INTERACTION MAPS; PROTEINS; SIGNAL TRANSDUCTION;

EID: 80052047022     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0023016     Document Type: Article

References (71)

1. Ideker T, Sharan R, (2008) Protein networks in disease. Genome Research 18: 644-652.
2. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, et al. (2000) Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A 97: 1143-7.
3. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, et al. (2000) A comprehensive analysis of protein-protein interactions in saccharomyces cerevisiae. Nature 403: 623-627.
4. Li S, Armstrong C, Bertin N, Ge H, Milstein S, et al. (2004) A map of the interactome network of the metazoan c. elegans. Science 303: 540-543.
5. Giot L, Bader J, Brouwer C, Chaudhuri A, Kuang B, et al. (2003) A protein interaction map of drosophila melanogaster. Science 302: 1727-1736.
6. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck F, et al. (2005) A human protein-protein interaction network: A resource for annotating the proteome. Cell 122: 957-968.
7. Rual J, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteomescale map of the human protein-protein interaction network. Nature 437: 1173-78.
8. Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, et al. (2009) Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nature Methods 6: 47-54.
9. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-7.
10. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, et al. (2002) Systematic identification of protein complexes in saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-3.
11. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
12. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
13. Tong AHY, Lesage G, Bader GD, Ding H, Xu H, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303: 808-813.
14. Collins S, Schuldiner M, Krogan N, Weissman J, (2006) A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biology 7: R63.
15. Rain JD, Selig L, De Reuse H, Battaglia V, Reverdy C, et al. (2001) The protein-protein interaction map of helicobacter pylori. Nature 409: 211-215.
16. Parrish JR, Yu J, Liu G, Hines JA, Chan JE, et al. (2007) A proteome-wide protein interaction map for campylobacter jejuni. Genome Biology 8: R130.
17. LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, et al. (2005) A protein interaction network of the malaria parasite plasmodium falciparum. Nature 438: 103-107.
18. Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, et al. (2006) Herpesviral protein networks and their interaction with the human proteome. Science 311: 239-242.
19. von Brunn A, Teepe C, Simpson JC, Pepperkok R, Friedel CC, et al. (2007) Analysis of intraviral protein-protein interactions of the sars coronavirus orfeome. PLoS ONE 2: e459.
20. Chatr-aryamontri A, Ceol A, Peluso D, Nardozza A, Panni S, et al. (2009) Virusmint: a viral protein interaction database. Nucleic Acids Res 37: D669-D673.
21. Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, et al. (1998) SGD: Saccharomyces Genome Database. Nucleic acids research 26: 73-79.
22. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Research 32: D449-51.
23. Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, et al. (2004) Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 32 Database issue: D497-501.
24. Breitkreutz BJ, Stark C, Reguly T, Boucher L, et al. (2008) The BioGRID Interaction Database: 2008 update. Nucleic Acids Research 36: D637-D640.
25. Sharan R, Ulitsky I, Ideker T, (2007) Network-based prediction of protein function. Molecular Systems Biology 3.
26. Schwikowski B, Fields S, (2000) A network of protein-protein interactions in yeast. Nature Biotechnology 18: 1257-1261.
27. Milenković T, Pržulj N, (2008) Uncovering biological network function via graphlet degree signatures. Cancer Informatics 4: 257-273.
28. Radivojac P, Peng K, Clark WT, Peters BJ, Mohan A, et al. (2008) An integrated approach to inferring gene-disease associations in humans. Proteins 72: 1030-7.
29. Goh K, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. PNAS 104: 8685-8690.
30. Yidirim MA, Goh KI, Cusick ME, Barabási AL, Vidal M, (2007) Drugtarget network. Nature Biotechnology 25.
31. Milenković T, Memišević V, Ganesan A, Pržulj N, (2010) Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. Journal of the Royal Society Interface 44: 353-350.
32. Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R, (2010) Associating genes and protein complexes with disease via network propagation. PLoS Computational Biology 6: e1000641.
33. Jonsson P, Bates P, (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22: 2291-2297.
34. Aragues R, Sander C, Oliva B, (2008) Predicting cancer involvement of genes from heterogeneous data. BMC Bioinformatics 9.
35. Sun J, Zhao Z, (2010) A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics 11: S5.
36. Jeong H, Mason SP, Barabási AL, Oltvai ZN, (2001) Lethality and centrality in protein networks. Nature 411: 41-2.
37. Yu H, Braun P, Yi{dotless}ldi{dotless}ri{dotless}m MA, Lemmens I, Venkatesan K, et al. (2008) High-Quality Binary Protein Interaction Map of the Yeast Interactome Network. Science 322: 104-110.
38. Ratmann O, Wiuf C, Pinney J, (2009) From evidence to inference: probing the evolution of protein interaction networks. HFSP Journal 3: 290-306.
39. Reguly T, Breitkreutz A, Boucher L, Breitkreutz B, Hon G, et al. (2006) Comprehensive curation and analysis of global interaction networks in saccharomyces cerevisiae. J Biol 5: 10.
40. Ho H, Milenković T, Memišević V, Aruri J, Pržulj N, et al. (2010) Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets. BMC Systems Biology 4.
41. Promislow DE, (2004) Protein networks, pleiotropy and the evolution of senescence. Proc Biol Sci 1545: 1225-1234.
42. Ferrarini L, Bertelli L, Feala J, McCulloch AD, Paternostro G, (2005) A more efficient search strategy for aging genes based on connectivity. Bioinformatics 21: 338-348.
43. Dyer MD, Murali TM, Sobral BW, (2008) The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog 4: e32.
44. Estrada E, Rodrguez-Velazquez J, (2005) Subgraph centrality in complex networks. Phys Rev E 71: 056103.
45. Estrada E, Hatano N, (2007) Statistical-mechanical approach to subgraph centrality in complex networks. Chemical Physics Letters 439: 247-251.
46. Pržulj N, Corneil DG, Jurisica I, (2004) Modeling interactome: Scale-free or geometric? Bioinformatics 20: 3508-3515.
47. Pržulj N, (2007) Biological network comparison using graphlet degree distribution. Bioinformatics 23: e177-e183.
48. Milo R, Shen-Orr SS, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-827.
49. Watts DJ, Strogatz SH, (1998) Collective dynamics of 'small-world' networks. Nature 393: 440-442.
50. Guerrero C, Milenković T, Pržulj N, Jones JJ, Kaiser P, et al. (2008) Characterization of the yeast proteasome interaction network by qtax-based tag-team mass spectrometry and protein interaction network analysis. Proc Natl Acad Sci U S A 105: 13333-13338.
51. Memišević V, Milenković T, Pržulj N, (2010) Complementarity of network and sequence structure in homologous proteins. Journal of Integrative Bioinformatics 7: 135.
52. Kuchaiev O, Milenković T, Memišević V, Hayes W, Pržulj N, (2010) Topological network alignment uncovers biological function and phylogeny. Journal of the Royal Society Interface 7: 1341-1354.
53. Milenković T, Ng W, Hayes W, Pržulj N, (2010) Optimal network alignment with graphlet degree vectors. Cancer Informatics 9: 121-137.
54. Stojmenovic I, Seddigh M, Zunic J, (2002) Dominating sets and neighbor elimination-based broadcasting algorithms in wireless networks. IEEE Transactions on Parallel and Distributed Systems 13: 14-25.
55. Houmaidi M, Bassiouni M (2003) Dominating set algorithms for sparse placement of full and limited wavelength converters in wdm optical networks. Journal of Optical Networking 2.
56. Gao B, Yang Y, Ma H, (2005) A new distributed approximation algorithm for constructing minimum connected dominating set in wireless ad hoc networks. International Journal of Comunication Systems pp. 743-762.
57. Rai M, Verma S, Tapaswi S, (2009) A power aware minimum connected dominating set for wireless sensor networks. Journal of Networks 4.
58. Wu J, Li H, (1999) On calculating connected dominating set for efficient routing in ad hoc wireless network. Proceedings od 3rd ACM International Workshop on Discrete Algorithms and Methods for Mobile Computing and Communications 18: 7-14.
59. Cooper C, Klasing R, Zito M, (2005) Lower bounds and algorithms for dominating sets in web graphs. Internet Mathematics 2: 275-300.
60. Junker BH, Schreiber F, (2008) Analysis of Biological Networks (Wiley Series in Bioinformatics) Wiley-Interscience.
61. Duckworth W, Wormald N, (2006) On the independent domination number of random regular graphs. Combinatorics, Probability and Computing 15: 513-522.
62. de Magalhaes JP, Budovsky A, Lehmann G, Costa LJ, Fraifeld YV, et al. (2009) The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell 1: 65-72.
63. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, et al. (2004) A census of human cancer genes. Nature Reviews Cancer 4: 177-183.
64. Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, et al. (2002) GeneCards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics 18: 1542-1543.
65. Kanehisa M, Goto S, (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 28: 27-30.
66. Hamosh A, Scott AF, Amberger J, Bocchini C, Valle D, et al. (2002) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Research 30: 52-55.
67. Fu W, Sanders-Beer B, Katz K, Maglott D, Pruitt K, et al. (2009) Human immunodeficiency virus type 1, human protein interaction database at ncbi. Nucleic Acids Research 37: D417-22.
68. Bandyopadhyay S, Chiang Cy, Srivastava J, Gersten M, White S, et al. (2010) A human MAP kinase interactome. Nature Methods 7: 801-805.
69. Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GSS, et al. (2010) NetPath: a public resource of curated signal transduction pathways. Genome biology 11: R3+.
70. Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, et al. (2006) Drugbank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Research 34: D668-D672.
71. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25: 25-29.