Setting the standards for signal transduction research

Science Signaling

Volumn 4, Issue 160, 2011, Pages

  Saez Rodriguez, Julio ^a,b   Alexopoulos, Leonidas G ^c   Stolovitzky, Gustavo ^d  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c NATIONAL TECHNICAL UNIVERSITY OF ATHENS   (Greece)

^d IBM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; CELL ASSAY; COMPUTER SIMULATION; DATA ANALYSIS; FLOW CYTOMETRY; GENE EXPRESSION; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEOMICS; REVIEW; SIGNAL TRANSDUCTION; ARTICLE; DATA BASE; HUMAN; METHODOLOGY; RESEARCH; STANDARD; STATISTICS;

PROTEOME;

DATABASE MANAGEMENT SYSTEMS; HUMANS; PROTEOME; PROTEOMICS; REFERENCE STANDARDS; RESEARCH; SIGNAL TRANSDUCTION;

EID: 79951871564     PISSN: 19450877     EISSN: 19379145     Source Type: Journal    
DOI: 10.1126/scisignal.2001844     Document Type: Review

References (42)

1. T. R. Golub, D. K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J. P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, C. D. Bloomfield, E. S. Lander, Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531-537 (1999).
2. P. I. Wang, E. M. Marcotte, It's the machine that matters: Predicting gene function and phenotype from protein networks. J. Proteomics 73, 2277-2289 (2010).
3. C. Choudhary, M. Mann, Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. Mol. Cell Biol. 11, 427-439 (2010).
4. M. Gstaiger, R. Aebersold, Applying mass spectrometry- based proteomics to genetics, genomics and network biology. Nat. Rev. Genet. 10, 617-627 (2009).
5. P. H. Huang, A. M. Xu, F. M. White, Oncogenic EGFR signaling networks in glioma. Sci. Signal. 2, re6 (2009).
6. B. Bodenmiller, S. Wanka, C. Kraft, J. Urban, D. Campbell, P. G. Pedrioli, B. Gerrits, P. Picotti, H. Lam, O. Vitek, M.-Y. Brusniak, B. Roschitzki, C. Zhang, K. M. Shokat, R. Schlapbach, A. Colman- Lerner, G. P. Nolan, A. I. Nesvizhskii, M. Peter, R. Loewith, C. von Mering, R. Aebersold, Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci. Signal. 3, rs4 (2010).
7. J. Villén, S. A. Beausoleil, S. A. Gerber, S. P. Gygi, Large-scale phosphorylation analysis of mouse liver. Proc. Natl. Acad. Sci. U.S.A. 104, 1488-1493 (2007).
8. J. V. Olsen, M. Vermeulen, A. Santamaria, C. Kumar, M. L. Miller, L. J. Jensen, F. Gnad, J. Cox, T. S. Jensen, E. A. Nigg, S. Brunak, M. Mann, Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci. Signal. 3, ra3 (2010).
9. L. G. Alexopoulos, J. Saez-Rodriguez, B. D. Cosgrove, D. A. Lauffenburger, P. K. Sorger, Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Mol. Cell. Proteomics 9, 1849-1865 (2010).
10. A. Wolf-Yadlin, M. Sevecka, G. MacBeath, Dissecting protein function and signaling using protein microarrays. Curr. Opin. Chem. Biol. 13, 398-405 (2009).
11. C. Harrison, High-content screening: Integrating information. Nat. Rev. Drug Discov. 7, 121 (2008).
12. P. O. Krutzik, M. R. Clutter, A. Trejo, G. P. Nolan, Fluorescent cell barcoding for multiplex flow cytometry. Curr. Protoc. Cytom. 6, Unit 6.31(2011).
13. O. Ornatsky, D. Bandura, V. Baranov, Multiplex bio-assay with inductively coupled plasma mass spectrometry: Towards a massively multivariate single-cell technology. Spectrochimica Acta Part B 62, 188-195 (2007).
14. M. F. Ciaccio, J. P. Wagner, C.-P. Chuu, D. A. Lauffenburger, R. B. Jones, Systems analysis of EGF receptor signaling dynamics with microwestern arrays. Nat. Methods 7, 148-155 (2010).
15. E. E. Schadt, M. D. Linderman, J. Sorenson, L. Lee, G. P. Nolan, Computational solutions to large-scale data management and analysis. Nat. Rev. Genet. 11, 647-657 (2010).
16. R. C. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. Yang, J. Zhang, Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5, R80-R80 (2004).
17. A. Floratos, K. Smith, Z. Ji, J. Watkinson, A. Califano, geWorkbench: An open source platform for integrative genomics. Bioinformatics 26, 1779-1780 (2010).
18. M. Reich, T. Liefeld, J. Gould, J. Lerner, P. Tamayo, J. P. Mesirov, GenePattern 2.0. Nat Genet. 38, 500-501 (2006).
19. P. T. Shannon, D. J. Reiss, R. Bonneau, N. S. Baliga, The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics 7, 176 (2006).
20. A. R. Shah, M. Singhal, K. R. Klicker, E. G. Stephan, H. S. Wiley, K. M. Waters, Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager. Bioinformatics 23, 906-909 (2007).
21. M. S. Cline, M. Smoot, E. Cerami, A. Kuchinsky, N. Landys, C. Workman, R. Christmas, I. Avila- Campilo, M. Creech, B. Gross, K. Hanspers, R. Isserlin, R. Kelley, S. Killcoyne, S. Lotia, S. Maere, J. Morris, K. Ono, V. Pavlovic, A. R. Pico, A. Vailaya, P.-L. Wang, A. Adler, B. R. Conklin, L. Hood, M. Kuiper, C. Sander, I. Schmulevich, B. Schwikowski, G. J. Warner, T. Ideker, G. D. Bader, Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2, 2366-2382 (2007).
22. M. P. van Iersel, T. Kelder, A. R. Pico, K. Hanspers, S. Coort, B. R. Conklin, C. Evelo, Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 9, 399 (2008).
23. D. Hull, K. Wolstencroft, R. Stevens, C. Goble, M. R. Pocock, P. Li, T. Oinn, Taverna: A tool for building and running workflows of services. Nucleic Acids Res. 34 (Web Server issue), W729-W732 (2006).
24. J. Saez-Rodriguez, A. Goldsipe, J. Muhlich, L. G. Alexopoulos, B. Millard, D. A. Lauffenburger, P. K. Sorger, Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics 24, 840-847 (2008).
25. J. Goecks, A. Nekrutenko, J. Taylor, T. Galaxy TeamGalaxy Team, Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
26. B. Marzolf, E. W. Deutsch, P. Moss, D. Campbell, M. H. Johnson, T. Galitski, SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7, 286 (2006).
27. K. A. Janes, J. G. Albeck, S. Gaudet, P. K. Sorger, D. A. Lauffenburger, M. B. Yaffe, A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310, 1646-1653 (2005).
28. M. Bansal, V. Belcastro, A. Ambesi-Impiombato, D. di Bernardo, How to infer gene networks from expression profiles. Mol. Syst. Biol. 3, 78 (2007).
29. R. J. Prill, D. Marbach, J. Saez-Rodriguez, P. K. Sorger, L. G. Alexopoulos, X. Xue, N. D. Clarke, G. Altan-Bonnet, G. Stolovitzky, Towards a rigorous assessment of systems biology models: The DREAM3 challenges. PLoS ONE 5, e9202 (2010).
30. K. Jaqaman, G. Danuser, Linking data to models: Data regression. Nat. Rev. Mol. Cell Biol. 7, 813-819 (2006).
31. A. Brazma, M. Krestyaninova, U. Sarkans, Standards for systems biology. Nat. Rev. Genet. 7, 593-605 (2006).
32. J. Quackenbush, Standardizing the standards. Mol. Syst. Biol. 2, 2006.0010 (2006).
33. A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C. A. Ball, H. C. Causton, T. Gaasterland, P. Glenisson, F. C. Holstege, I. F. Kim, V. Markowitz, J. C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo, M. Vingron, Minimum information about a microarray experiment (MIAME)- toward standards for microarray data. Nat. Genet. 29, 365-371 (2001).
34. H. Hermjakob, L. Montecchi-Palazzi, G. Bader, J. Wojcik, L. Salwinski, A. Ceol, S. Moore, S. Orchard, U. Sarkans, C. von Mering, B. Roechert, S. Poux, E. Jung, H. Mersch, P. Kersey, M. Lappe, Y. Li, R. Zeng, D. Rana, M. Nikolski, H. Husi, C. Brun, K. Shanker, S. G. N. Grant, C. Sander, P. Bork, W. Zhu, A. Pandey, A. Brazma, B. Jacq, M. Vidal, D. Sherman, P. Legrain, G. Cesareni, I. Xenarios, D. Eisenberg, B. Steipe, C. Hogue, R. Apweiler, The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat. Biotechnol. 22, 177-183 (2004).
35. C. F. Taylor, D. Field, S.-A. Sansone, J. Aerts, R. Apweiler, M. Ashburner, C. A. Ball, P.-A. Binz, M. Bogue, T. Booth, A. Brazma, R. R. Brinkman, A. Michael Clark, E. W. Deutsch, O. Fiehn, J. Fostel, P. Ghazal, F. Gibson, T. Gray, G. Grimes, J. M. Hancock, N. W. Hardy, H. Hermjakob, R. K. Julian, Jr, M. Kane, C. Kettner, C. Kinsinger, E. Kolker, M. Kuiper, N. Le Novère, J. Leebens-Mack, S. E. Lewis, P. Lord, A.-M. Mallon, N. Marthandan, H. Masuya, R. McNally, A. Mehrle, N. Morrison, S. Orchard, J. Quackenbush, J. M. Reecy, D. G. Robertson, P. Rocca-Serra, H. Rodriguez, H. Rosenfelder, J. Santoyo-Lopez, R. H. Scheuermann, D. Schober, B. Smith, J. Snape, C. J. Stoeckert, Jr, K. Tipton, P. Sterk, A. Untergasser, J. Vandesompele, S. Wiemann, Promoting coherent minimum reporting guidelines for biological and biomedical investigations: The MIBBI project. Nat. Biotechnol. 26, 889-896 (2008).
36. C. Li, M. Courtot, N. Le Novère, C. Laibe, BioModels. net Web Services, a free and integrated toolkit for computational modelling software. Brief. Bioinform. 11, 270-277 (2010).
37. M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J.-H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novère, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang, SBML Forum, The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531 (2003).
38. J. O. Dada, I. Spasi, N. W. Paton, P. Mendes, SBRML: A markup language for associating systems biology data with models. Bioinformatics 26, 932-938 (2010).
39. P. J. Durka, D. Ircha, SignalML: Metaformat for description of biomedical time series. Comput. Methods Programs Biomed. 76, 253-259 (2004).
40. P. Rocca-Serra, M. Brandizi, E. Maguire, N. Sklyar, C. Taylor, K. Begley, D. Field, S. Harris, W. Hide, O. Hofmann, S. Neumann, P. Sterk, W. Tong, S.-A. Sansone, ISA software suite: Supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics 26, 2354-2356 (2010).
41. A. Abbott, Germans cook up liver project. Nature 468, 879 (2010).
42. Acknowledgements: We thank C. Taylor, N. Le Novere, M. van Iersel, M. Klapa and W. Muller for useful discussions and for critically reading the manuscript.