A novel framework for the comparative analysis of biological networks

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Pache, Roland A ^a   Aloy, Patrick ^a,b  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE 2; CYCLINE; DNA DIRECTED DNA POLYMERASE ALPHA; PROTEASOME; REGULATOR PROTEIN;

ARTICLE; CONTROLLED STUDY; GENE INTERACTION; GENE REGULATORY NETWORK; GENETIC CONSERVATION; GENETIC DISTANCE; HUMAN; MOLECULAR BIOLOGY; NONHUMAN; PREDICTION; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; ALGORITHM; ANIMAL; COMPARATIVE STUDY; DROSOPHILA MELANOGASTER; METABOLISM; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; ANIMALS; DROSOPHILA MELANOGASTER; GENE REGULATORY NETWORKS; HUMANS; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

EID: 84857402984     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031220     Document Type: Article

References (53)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. (2001) The sequence of the human genome. Science 291: 1304-1351.
3. Rual J-F, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
4. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968.
5. Ewing RM, Chu P, Elisma F, Li H, Taylor P, et al. (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular Systems Biology 3: 89.
6. Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, et al. (2010) Rewiring of genetic networks in response to DNA damage. Science 330: 1385-1389.
7. Califano A, (2011) Rewiring makes the difference. Mol Syst Biol 7: 463.
8. Beltrao P, Serrano L, (2007) Specificity and evolvability in eukaryotic protein interaction networks. PLoS Computational Biology 3: e25.
9. Kiemer L, Cesareni G, (2007) Comparative interactomics: comparing apples and pears? Trends Biotechnol 25: 448-454.
10. Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci USA 100: 11394-11399.
11. Sharan R, Ideker T, (2006) Modeling cellular machinery through biological network comparison. Nat Biotechnol 24: 427-433.
12. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, et al. (2005) Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA 102: 1974-1979.
13. Koyutürk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, et al. (2006) Pairwise alignment of protein interaction networks. J Comput Biol 13: 182-199.
14. Singh R, Xu J, Berger B, (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acad Sci USA 105: 12763-12768.
15. Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S, (2009) Automatic parameter learning for multiple local network alignment. J Comput Biol 16: 1001-1022.
16. Venkatesan K, Rual J-F, Vazquez A, Stelzl U, Lemmens I, et al. (2009) An empirical framework for binary interactome mapping. Nat Methods 6: 83-90.
17. Zhang S, Zhang X-S, Chen L, (2008) Biomolecular network querying: a promising approach in systems biology. BMC systems biology 2: 5.
18. Flicek P, Aken BL, Ballester B, Beal K, Bragin E, et al. (2010) Ensembl's 10th year. Nucleic Acids Research 38: D557-562.
19. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
20. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110.
21. Teichmann SA, (2002) The constraints protein-protein interactions place on sequence divergence. Journal of Molecular Biology 324: 399-407.
22. Cesareni G, Ceol A, Gavrila C, Palazzi LM, Persico M, et al. (2005) Comparative interactomics. FEBS LETTERS 579: 1828-1833.
23. Pazos F, Valencia A, (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47: 219-227.
24. Juan D, Pazos F, Valencia A, (2008) Co-evolution and co-adaptation in protein networks. FEBS LETTERS 582: 1225-1230.
25. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW, (2002) Evolutionary rate in the protein interaction network. Science 296: 750-752.
26. Chen Y, Dokholyan NV, (2006) The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet 22: 416-419.
27. Cootes AP, Muggleton SH, Sternberg MJE, (2007) The identification of similarities between biological networks: application to the metabolome and interactome. Journal of Molecular Biology 369: 1126-1139.
28. Pache RA, Zanzoni A, Naval J, Mas JM, Aloy P, (2008) Towards a molecular characterisation of pathological pathways. FEBS LETTERS 582: 1259-1265.
29. Zhenping L, Zhang S, Wang Y, Zhang X-S, Chen L, (2007) Alignment of molecular networks by integer quadratic programming. Bioinformatics 23: 1631-1639.
30. Barabási A-L, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
31. Dijkstra EW, (1959) A note on two problems in connexion with graphs. Numerische Mathematik 1: 269-271.
32. Hirsh E, Sharan R, (2007) Identification of conserved protein complexes based on a model of protein network evolution. Bioinformatics 23: e170-176.
33. Cheng Y, (2009) Toward an atomic model of the 26S proteasome. Curr Opin Struct Biol 19: 203-208.
34. Cope GA, Deshaies RJ, (2003) COP9 signalosome: a multifunctional regulator of SCF and other cullin-based ubiquitin ligases. Cell 114: 663-671.
35. Wei N, Serino G, Deng X-W, (2008) The COP9 signalosome: more than a protease. Trends Biochem Sci 33: 592-600.
36. Foiani M, Lucchini G, Plevani P, (1997) The DNA polymerase alpha-primase complex couples DNA replication, cell-cycle progression and DNA-damage response. Trends Biochem Sci 22: 424-427.
37. Pavlov YI, Frahm C, Nick McElhinny SA, Niimi A, Suzuki M, et al. (2006) Evidence that errors made by DNA polymerase alpha are corrected by DNA polymerase delta. Curr Biol 16: 202-207.
38. Altomare DA, Testa JR, (2005) Perturbations of the AKT signaling pathway in human cancer. Oncogene 24: 7455-7464.
39. Häcker H, Karin M, (2006) Regulation and function of IKK and IKK-related kinases. Sci STKE 2006: re13.
40. Nicholson KM, Anderson NG, (2002) The protein kinase B/Akt signalling pathway in human malignancy. Cell Signal 14: 381-395.
41. Consortium U, (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37: D169-174.
42. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, et al. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Research 35: D561-565.
43. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, et al. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Research 35: D572-574.
44. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37: D767-772.
45. Grishin NV, (1995) Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J Mol Evol 41: 675-679.
46. Güldener U, Münsterkötter M, Oesterheld M, Pagel P, Ruepp A, et al. (2006) MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res 34: D436-441.
47. Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, et al. (2010) CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res 38: D497-501.
48. Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
49. Narayanan M, Karp RM, (2007) Comparing protein interaction networks via a graph match-and-split algorithm. J Comput Biol 14: 892-907.
50. Pawson T, Linding R, (2005) Synthetic modular systems-reverse engineering of signal transduction. FEBS LETTERS 579: 1808-1814.
51. Kalaev M, Bafna V, Sharan R, (2009) Fast and accurate alignment of multiple protein networks. J Comput Biol 16: 989-999.
52. Liao C-S, Lu K, Baym M, Singh R, Berger B, (2009) IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 25: i253-i258.
53. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T, (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.