The mEPN scheme: An intuitive and flexible graphical system for rendering biological pathways

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Freeman, Tom C ^a,b   Raza, Sobia ^a,b   Theocharidis, Athanasios ^a,b   Ghazal, Peter ^a,c  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c Centre for Systems Biology at Edinburgh CSBE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALIA;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETICS; HUMAN; IMMUNE SYSTEM; MAJOR HISTOCOMPATIBILITY COMPLEX; METHODOLOGY; MOUSE; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; COMPUTER SIMULATION; HUMANS; IMMUNE SYSTEM; MAJOR HISTOCOMPATIBILITY COMPLEX; MICE; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION; SOFTWARE; SYSTEMS BIOLOGY; USER-COMPUTER INTERFACE;

EID: 77952196907     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-65     Document Type: Article

References (46)

1. Bader GD, Cary MP, Sander C. Pathguide: a pathway resource list. Nucleic Acids Res 2006, 34:D504-506. 10.1093/nar/gkj126, 1347488, 16381921.
2. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, 36:D480-484. 10.1093/nar/gkm882, 2238879, 18077471.
3. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
4. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. PID: the Pathway Interaction Database. Nucleic Acids Res 2009, 37:D674-679. 10.1093/nar/gkn653, 2686461, 18832364.
5. Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, et al. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res 2003, 31:334-341. 10.1093/nar/gkg115, 165562, 12520017.
6. Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, 33:D428-432. 10.1093/nar/gki072, 540026, 15608231.
7. Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol 2008, 6:e184. 10.1371/journal.pbio.0060184, 2475545,2475545, 18651794.
8. Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol 2007, 8:R39. 10.1186/gb-2007-8-3-r39, 1868929, 17367534.
9. Kitano H, Funahashi A, Matsuoka Y, Oda K. Using process diagrams for the graphical representation of biological networks. Nat Biotechnol 2005, 23:961-966. 10.1038/nbt1111, 16082367.
10. Kohn KW. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol Biol Cell 1999, 10:2703-2734. 25504, 10436023.
11. Moodie SL, Sorokin A, Goryanin I, Ghazal P. A Graphical Notation to Describe the Logical Interactions of Biological Pathways. Journal of Integrative Bioinformatics 2006, 3:11.
12. Novere NL, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, et al. The systems biology graphical notation. Nat Biotechnol 2009, 27:735-741. 10.1038/nbt.1558, 19668183.
13. Oda K, Kitano H. A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol 2006, 2:2006 0015. 10.1038/msb4100057, 1681489, 16738560.
14. 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. 10.1038/msb4100014, 1681468, 16729045.
15. Calzone L, Gelay A, Zinovyev A, Radvanyi F, Barillot E. A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol Syst Biol 2008, 4:173. 10.1038/msb.2008.7, 2290939, 18319725.
16. Raza S, Robertson KA, Lacaze PA, Page D, Enright AJ, Ghazal P, Freeman TC. A logic-based diagram of signalling pathways central to macrophage activation. BMC Syst Biol 2008, 2:36. 10.1186/1752-0509-2-36, 2383880, 18433497.
17. Raza S, McDerment N, Lacaze P, Robertson K, Watterson S, Chen Y, Chisholm M, Eleftheriadis G, Monk S, O'Sullivan M, Turnbull A, Roy D, Theocharidis T, Ghazal P, Freeman TC. Construction of a Large Scale Integrated Map of Macrophage Pathogen Recognition and Effector Systems. BMC Syst Biol 2010, 4:63. 10.1186/1752-0509-4-63, 20470404.
18. Macrophages - Resources for the Analysis of Macrophage Pathways. , http://www.macrophages.com/index_pathways.html
19. Marcucci F, Waller M, Kirchner H, Krammer P. Production of immune interferon by murine T-cell clones from long-term cultures. Nature 1981, 291:79-81. 10.1038/291079a0, 6164925.
20. O'Malley JA, Nussbaum-Blumenson A, Sheedy D, Grossmayer BJ, Ozer H. Identification of the T cell subset that produces human gamma interferon. J Immunol 1982, 128:2522-2526.
21. Munakata T, Semba U, Shibuya Y, Kuwano K, Akagi M, Arai S. Induction of interferon-gamma production by human natural killer cells stimulated by hydrogen peroxide. J Immunol 1985, 134:2449-2455.
22. Walter MR, Windsor WT, Nagabhushan TL, Lundell DJ, Lunn CA, Zauodny PJ, Narula SK. Crystal structure of a complex between interferon-gamma and its soluble high-affinity receptor. Nature 1995, 376:230-235. 10.1038/376230a0, 7617032.
23. Sakatsume M, Igarashi K, Winestock KD, Garotta G, Larner AC, Finbloom DS. The Jak kinases differentially associate with the alpha and beta (accessory factor) chains of the interferon gamma receptor to form a functional receptor unit capable of activating STAT transcription factors. J Biol Chem 1995, 270:17528-17534. 10.1074/jbc.270.29.17528, 7615558.
24. Watling D, Guschin D, Muller M, Silvennoinen O, Witthuhn BA, Quelle FW, Rogers NC, Schindler C, Stark GR, Ihle JN, et al. Complementation by the protein tyrosine kinase JAK2 of a mutant cell line defective in the interferon-gamma signal transduction pathway. Nature 1993, 366:166-170. 10.1038/366166a0, 7901766.
25. Igarashi K, Garotta G, Ozmen L, Ziemiecki A, Wilks AF, Harpur AG, Larner AC, Finbloom DS. Interferon-gamma induces tyrosine phosphorylation of interferon-gamma receptor and regulated association of protein tyrosine kinases, Jak1 and Jak2, with its receptor. J Biol Chem 1994, 269:14333-14336.
26. Endo TA, Masuhara M, Yokouchi M, Suzuki R, Sakamoto H, Mitsui K, Matsumoto A, Tanimura S, Ohtsubo M, Misawa H, et al. A new protein containing an SH2 domain that inhibits JAK kinases. Nature 1997, 387:921-924. 10.1038/43213, 9202126.
27. Schroder K, Hertzog PJ, Ravasi T, Hume DA. Interferon-gamma: an overview of signals, mechanisms and functions. J Leukoc Biol 2004, 75:163-189. 10.1189/jlb.0603252, 14525967.
28. ten Hoeve J, de Jesus Ibarra-Sanchez M, Fu Y, Zhu W, Tremblay M, David M, Shuai K. Identification of a nuclear Stat1 protein tyrosine phosphatase. Mol Cell Biol 2002, 22:5662-5668. 10.1128/MCB.22.16.5662-5668.2002, 133976, 12138178.
29. Simoncic PD, Lee-Loy A, Barber DL, Tremblay ML, McGlade CJ. The T cell protein tyrosine phosphatase is a negative regulator of janus family kinases 1 and 3. Curr Biol 2002, 12:446-453. 10.1016/S0960-9822(02)00697-8, 11909529.
30. Uddin S, Sassano A, Deb DK, Verma A, Majchrzak B, Rahman A, Malik AB, Fish EN, Platanias LC. Protein kinase C-delta (PKC-delta) is activated by type I interferons and mediates phosphorylation of Stat1 on serine 727. J Biol Chem 2002, 277:14408-14416. 10.1074/jbc.M109671200, 11839738.
31. Gilmore TD, Koedood M, Piffat KA, White DW. Rel/NF-kappaB/IkappaB proteins and cancer. Oncogene 1996, 13:1367-1378.
32. Naka T, Narazaki M, Hirata M, Matsumoto T, Minamoto S, Aono A, Nishimoto N, Kajita T, Taga T, Yoshizaki K, et al. Structure and function of a new STAT-induced STAT inhibitor. Nature 1997, 387:924-929. 10.1038/43219, 9202127.
33. Alexander WS. Suppressors of cytokine signalling (SOCS) in the immune system. Nat Rev Immunol 2002, 2:410-416.
34. Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005, 33:D418-424. 10.1093/nar/gki051, 540005, 15608229.
35. Reith W, LeibundGut-Landmann S, Waldburger JM. Regulation of MHC class II gene expression by the class II transactivator. Nat Rev Immunol 2005, 5:793-806. 10.1038/nri1708, 16200082.
36. Boss JM, Jensen PE. Transcriptional regulation of the MHC class II antigen presentation pathway. Curr Opin Immunol 2003, 15:105-111. 10.1016/S0952-7915(02)00015-8, 12495741.
37. Freeman TC, Goldovsky L, Brosch M, van Dongen S, Maziere P, Grocock RJ, Freilich S, Thornton J, Enright AJ. Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol 2007, 3:2032-2042. 10.1371/journal.pcbi.0030206, 2041979, 17967053.
38. Theocharidis A, van Dongen S, Enright AJ, Freeman TC. Network Visualisation and Analysis of Gene Expression Data using BioLayout Express3D. Nature Protocols 2009, 4:1535-1550. 10.1038/nprot.2009.177, 19798086.
39. Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell 2006, 17:1-13. 10.1091/mbc.E05-09-0824, 1345641, 16267266.
40. Kwiatkowska MZ, Heath JK. Biological pathways as communicating computer systems. J Cell Sci 2009, 122:2793-2800. 10.1242/jcs.039701, 19657015.
41. Eungdamrong NJ, Iyengar R. Modeling cell signaling networks. Biol Cell 2004, 96:355-362. 10.1016/j.biolcel.2004.03.004, 15207904.
42. Ruths D, Muller M, Tseng JT, Nakhleh L, Ram PT. The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks. PLoS Comput Biol 2008, 4:e1000005. 10.1371/journal.pcbi.1000005, 2265486, 18463702.
43. Le Novère N, Hucka M, Mi H, Moodie S, Shreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nature Biotechnology 2009, 27:735-741. 10.1038/nbt.1558, 19668183.
44. Yeung N, Cline MS, Kuchinsky A, Smoot ME, Bader GD. Exploring biological networks with Cytoscape software. Curr Protoc Bioinformatics 2008, Chapter 8(Unit 8):13.
45. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
46. yEd Graph Editior - yWorks the diagramming company. , http://www.yworks.com