BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats

BMC Systems Biology

Volumn 7, Issue , 2013, Pages

  Bonnet, Eric ^a,b,c   Calzone, Laurence ^a,b,c   Rovera, Daniel ^a,b,c   Stoll, Gautier ^a,b,c   Barillot, Emmanuel ^a,b,c   Zinovyev, Andrei ^a,b,c  

^a INSTITUT CURIE   (France)

^b INSERM U900   (France)

^c PSL RESEARCH UNIVERSITY   (France)

Author keywords

BioPAX; CellDesigner; Conversion; Cytoscape; Molecular maps; Network analysis; Path analysis; Pathways; Reactome; SBGN; SBML; Software; Systems biology

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CELL CYCLE; COMPUTER PROGRAM; GENETICS; HIGH THROUGHPUT SCREENING; HUMAN; METABOLISM; METHODOLOGY; PHYSIOLOGY; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ALGORITHMS; CELL CYCLE; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SOFTWARE; SYSTEMS BIOLOGY;

MLCS; MLOWN;

EID: 84874398455     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-18     Document Type: Article

References (43)

1. Adriaens M, Jaillard M, Waagmeester A, Coort S, Pico A, Evelo C. The public road to high-quality curated biological pathways. Drug Discov Today 2008, 13(19-20):856-862. 10.1016/j.drudis.2008.06.013, 18652912.
2. Cary M, Bader G, Sander C. Pathway information for systems biology. FEBS Lett 2005, 579(8):1815-1820. 10.1016/j.febslet.2005.02.005, 15763557.
3. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto encyclopedia of genes and genomes. 27 1999, 29-34.
4. Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath G, Wu G, Matthews L. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, 33(suppl 1):D428. 540026, 15608231.
5. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. MINT: a Molecular INTeraction database. FEBS Lett 2002, 513:135-140. 10.1016/S0014-5793(01)03293-8, 11911893.
6. Saraiya P, North C, Duca K. Visualizing biological pathwaysrequirements analysis, systems evaluation and research agenda. Inf Vis 2005, 4(3):191-205.
7. Gehlenborg N, O'Donoghue S, Baliga N, Goesmann A H, Kitano H, Neuweger H, Schneider R, Tenenbaum D, . Kohlbacher O Visualization of omics data for systems biology. Nat Methods 2010, 7:S56-S68. 10.1038/nmeth.1436, 20195258, Kohlbacher O.
8. Demir E, Cary M, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J. The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010, 28(9):935-942. 10.1038/nbt.1666, 3001121, 20829833.
9. Hucka M, Finney A, Sauro H, Bolouri H, Doyle J, Kitano H, Arkin A, Bornstein B, Bray D, Cornish-Bowden A. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524. 10.1093/bioinformatics/btg015, 12611808.
10. Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem M, Wimalaratne S. The systems biology graphical notation. Nat Biotechnol 2009, 27(8):735-741. 10.1038/nbt.1558, 19668183.
11. Bader G, Cary M, Sander C. Pathguide: a pathway resource list. Nucleic Acids Res 2006, 34(suppl 1):D504-D506. 1347488, 16381921.
12. Karlebach G, Shamir R. Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 2008, 9(10):770-780. 10.1038/nrm2503, 18797474.
13. Kitano H. Systems biology: a brief overview. Science 2002, 295(5560):1662-1664. 10.1126/science.1069492, 11872829.
14. Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2001, 2:343-372. 10.1146/annurev.genom.2.1.343, 11701654.
15. Bauer-Mehren A, Furlong L, Sanz F. Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol Syst Biol 2009, 5(290).
16. Oda K, Matsuoka Y, Funahashi A, Kitano H. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 2005, 1:2005.0010. 1681468, 16729045.
17. Oda K, Kitano H. A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol 2006, 2:2006.0015. 1681489, 16738560.
18. Calzone L, Gelay A, Zinovyev A, Radvanyl F, Barillot E. A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol Syst Biol 2008, 4(174).
19. Caron E, Ghosh S, Matsuoka Y, Ashton-Beaucage D, Therrien M, Lemieux S, Perreault C, Roux P, Kitano H. A comprehensive map of the mTOR signaling network. Mol Syst Biol 2010, 6:453. 3018167, 21179025.
20. Funahashi A, Tanimura N, Morohashi M, Kitano H. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 2003, 1:159-162.
21. Zinovyev A, Viara E, Calzone L, Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 2008, 24(6):876. 10.1093/bioinformatics/btm553, 18024474.
22. Cline M, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2(10):2366. 10.1038/nprot.2007.324, 17947979.
23. Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas P. BioPAX support in CellDesigner. Bioinformatics 2011, 27(24):3437-3438. 10.1093/bioinformatics/btr586, 3232372, 22021903.
24. Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, Zell A. Qualitative translation of relations from BioPAX to SBML qual. Bioinformatics 2012,
25. Ruebenacker O, Moraru I, Schaff J, Blinov M. Integrating BioPAX pathway knowledge with SBML models. Syst Biol, IET 2009, 3(5):317-328.
26. König M, Dräger A, Holzhütter H. CySBML: a Cytoscape plugin for SBML. Bioinformatics 2012, 28(18):2402-2403. 10.1093/bioinformatics/bts432, 22772946.
27. Su G, Kuchinsky A, Morris J, Meng F. GLay: community structure analysis of biological networks. Bioinformatics 2010, 26(24):3135-3137. 10.1093/bioinformatics/btq596, 2995124, 21123224.
28. Bader G, Hogue C. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 10.1186/1471-2105-4-2, 149346, 12525261.
29. Palotai R, Szappanos B, Kovács I, Papp B, Csermely P, . Szalay-Beko{combining double acute accent} M ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality. Bioinformatics 2012, 28(16):2202-2204. 10.1093/bioinformatics/bts352, 22718784, Szalay-Beko{combining double acute accent} M.
30. Morris J, Apeltsin L, Newman A, Baumbach J, Wittkop T, Su G, Bader G, Ferrin T. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics 2011, 12(436).
31. Rivera C, Vakil R, Bader J. NeMo: network module identification in Cytoscape. BMC Bioinformatics 2010, 11(Suppl 1):S61. 10.1186/1471-2105-11-S1-S61, 3009535, 20122237.
32. Gonzalez A, Naldi A, Sanchez L, Thieffry D, Chaouiya C. GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems 2006, 84(2):91-100. 10.1016/j.biosystems.2005.10.003, 16434137.
33. Tarjan R. Depth-first search and linear graph algorithms. SIAM J Comput 1972, 1(2):146-160.
34. Broder A, Kumar R, Maghoul F, Raghavan P, Rajagopalan S, Stata R, Tomkins A, Wiener J. Graph structure in the web. Comput Netw 2000, 33(1-6):309-320.
35. Novak B, Csikasz-Nagy A, Gyorffy B, Nasmyth K, Tyson J. Model scenarios for evolution of the eukaryotic cell cycle. Philos Trans R Soc Lond B Biol Sci 1998, 353(1378):2063. 10.1098/rstb.1998.0352, 1692434, 10098216.
36. Gleiss P, Stadler P, Wagner A, Fell D. Relevant cycles in chemical reaction networks. Adv Complex Syst 2001, 4(2/3):207-226.
37. Vismara P. Union of all the minimum cycle bases of a graph. Electr J Comb 1997, 4:73-87.
38. Weinberg R. The retinoblastoma protein and cell cycle control. Cell 1995, 81(3):323-330. 10.1016/0092-8674(95)90385-2, 7736585.
39. Calzone L, Fages F, Soliman S. BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 2006, 22(14):1805-1807. 10.1093/bioinformatics/btl172, 16672256.
40. Fage F, Soliman S. From reaction models to influence graphs and back: a theorem. Formal Methods Syst Biol FMSB'08, Lect Notes Comput Sci 2008, 5054:90-102.
41. Calzone L, Chaouiya C, Remy E, Soliman S. Qualitative modelling of the RB/E2F network, deliverable D3.1. ANR CALAMAR (ANR-08-SYSC-003) 2011, [Https://tagc.univ-mrs.fr/welcome/IMG/pdf/livrable-3-1.pdf].
42. Stransky N, Vallot C, Reyal F, Bernard-Pierrot I, de Medina S, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C. Regional copy number-independent deregulation of transcription in cancer. Nature Genet 2006, 38(12):1386-1396. 10.1038/ng1923, 17099711.
43. Kairov U, Karpenyuk T, Ramanculov E, Zinovyev A. Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures. Bioinformation 2012, 18(6):773-776.