Large-scale signaling network reconstruction

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 6, 2012, Pages 1696-1708

  Hashemikhabir, Seyedsasan ^a   Ayaz, Eyup Serdar ^b   Kavurucu, Yusuf ^b   Can, Tolga ^a   Kahveci, Tamer ^b  

^a MIDDLE EAST TECHNICAL UNIVERSITY   (Turkey)

^b J Crayton Pruitt Family Department of Biomedical Engineering   (United States)

Author keywords

Network editing; RNAi; Signaling network

Indexed keywords

PHYSICAL INTERACTIONS; REFERENCE NETWORK; RNA INTERFERENCE; RNAI; SEARCH SPACES; SIGNALING NETWORKS; STATE OF THE ART; SYNTHETIC AND REAL DATA;

GENES;

SIGNALING;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; GENE REGULATORY NETWORK; GENETIC DATABASE; HUMAN; METHODOLOGY; PHYSIOLOGY; PROTEIN PROTEIN INTERACTION; RNA INTERFERENCE; SIGNAL TRANSDUCTION;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE REGULATORY NETWORKS; HUMANS; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPS; RNA INTERFERENCE; SIGNAL TRANSDUCTION;

EID: 84880386433     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2012.128     Document Type: Article

References (29)

1. T. Akutsu, M. Hayashida, W.-K. Ching, and M.K. Ng, "Control of Boolean Networks: Hardness Results and Algorithms for Tree Structured Networks," J. Theoretical Biology, vol. 244, no. 4, pp. 670-679, 2007.
2. T. Cormen, C. Leiserson, R. Rivest, and C. Stein, Introduction to Algorithms. MIT Press, 2001.
3. E.A. Dinic, "An Algorithm for the Solution of the Max-Flow Problem with the Polynomial Estimation," Soviet Math. Dokl., vol. 11, pp. 1277-1280, 1970.
4. M.R. Garey and D.S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. Freeman, 1979.
5. A. George and J.W.H. Liu, Computer Solutions of Large Sparse Positive Definite Systems. Prentice-Hall, 1990.
6. J. Hirosumi, G. Tuncman, L. Chang, C.Z. Gorgun, K.T. Uysal, K. Maeda, M. Karin, and G.S. Hotamisligil, "A Central Role for JNK in Obesity and Insulin Resistance," Nature, vol. 420, pp. 333-336, 2002.
7. L. Kaderali, E. Dazert, U. Zeuge, M. Frese, and R. Bartenschlager, "Reconstructing Signaling Pathways from Rnai Data Using Probabilistic Boolean Threshold Networks," Bioinformatics, vol. 25, no. 17, pp. 2229-2235, 2009.
8. M. Kanehisa and S. Goto, "Kegg: Kyoto Encyclopedia of Genes and Genomes," Nucleic Acids Research, vol. 28, no. 1, pp. 27-30, 2000.
9. S. Kerrien, B. Aranda, L. Breuza, A. Bridge, F. Broackes-Carter, C. Chen, M. Duesbury, M. Dumousseau, M. Feuermann, U. Hinz, C. Jandrasits, R.C. Jimenez, J. Khadake, U. Mahadevan, P. Masson, I. Pedruzzi, E. Pfeiffenberger, P. Porras, A. Raghunath, B. Roechert, S. Orchard, and H. Hermjakob, "The Intact Molecular Interaction Database in 2012," Nucleic Acids Research, vol. 40, no. D1, pp. D841-D846, 2012.
10. A. Lan, I.Y. Smoly, G. Rapaport, S. Lindquist, E. Fraenkel, and E. Yeger-Lotem, "Responsenet: Revealing Signaling and Regulatory Networks Linking Genetic and Transcriptomic Screening Data," Nucleic Acids Research, vol. 39, no. suppl 2, pp. W424-W429, 2011.
11. C. Langmead and S. Jha, "Symbolic Approaches to Finding Control Strategies in Boolean Networks," J. Bioinformatics and Computational Biology, vol. 7, no. 2, pp. 323-338, 2009.
12. R. Milo, N. Kashtan, S. Itzkovitz, M.E.J. Newman, and U. Alon, "On the Uniform Generation of Random Graphs with Prescribed Degree Sequences," arXiv:cond-mat/0312028, 2003.
13. O. Ourfali, T. Shlomi, T. Ideker, E. Ruppin, and R. Sharan, "Spine: A Framework for Signaling-Regulatory Pathway Inference from Cause-Effect Experiments," Bioinformatics, vol. 23, no. 13, pp. i359-i366, 2007.
14. O.E. Ozsoy and T. Can, "Construction of Signaling Pathways from PPI and RNAi Data Using Linear Programming," technical report, Dept. of Computer Eng., Middle East Technical Univ., http://www.ceng.metu.edu.tr/tcan/TR/ TR-erenOzsoy-March2012.pdf. 2012.
15. L.C. Platanias, "Mechanisms of Type-i-and Type-ii-Interferon- Mediated Signalling," Nature Rev. Immunology, vol. 5, pp. 375-386, 2005.
16. P. Polakis, "The Many Ways of Wnt in Cancer," Current Opinion in Genetics and Development, vol. 17, no. 1, pp. 45-51, 2007.
17. D. Ruths, J.-T. Tseng, L. Nakhleh, and P.T. Ram, "De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis," Proc. Satellite Conf. Systems Biology and Computational Proteomics (RECOMB-SAT), pp. 108-118, 2007.
18. O. Sahin, H. Frohlich, C. Lobke, U. Korf, S. Burmester, M. Majety, J. Mattern, I. Schupp, C. Chaouiya, D. Thieffry, A. Poustka, S. Wiemann, T. Beissbarth, and D. Arlt, "Modeling Erbb Receptor-Regulated g1/s Transition to Find Novel Targets for de Novo Trastuzumab Resistance," BMC Systems Biology, vol. 3, no. 1, p. 1, 2009.
19. J. Scott, T. Ideker, R.M. Karp, and R. Sharan, "Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks," J. Computational Biology, vol. 13, no. 2, pp. 133-144, 2006.
20. T. Shlomi, D. Segal, E. Ruppin, and R. Sharan, "QPath: A Method for Querying Pathways in a Protein-Protein Interaction Network," BMC Bioinformatics, vol. 7, no. 1, p. 199, 2006.
21. R. Singh, "Algorithms for the Analysis of Protein Interaction Networks," PhD thesis, MIT, 2011.
22. S.W. Sloan, "An Algorithm for Profile and Wavefront Reduction of Sparse Matrices," Int'l J. Numerical Methods in Eng., vol. 23, pp. 239-251, 1986.
23. D. Szklarczyk, A. Franceschini, M. Kuhn, M. Simonovic, A. Roth, P. Minguez, T. Doerks, M. Stark, J. Muller, P. Bork, L.J. Jensen, and C. von Mering, "The STRING Database in 2011: Functional Interaction Networks of Proteins, Globally Integrated and Scored," Nucleic Acids Research, vol. 39, pp. 561-568, 2011.
24. The Gene Ontology Consortium, "The Gene Ontology Project in 2008," Nucleic Acids Research, vol. 36, no. suppl 1, pp. D440-D444, 2008.
25. Z. Tu, C. Argmann, K.K. Wong, L.J. Mitnaul, S. Edwards, I.C. Sach, J. Zhu, and E.E. Schadt, "Integrating Sirna and Protein-Protein Interaction Data to Identify an Expanded Insulin Signaling Network," Genome Research, vol. 19, no. 6, pp. 1057-1067, 2009.
26. A. Vinayagam, U. Stelzl, R. Foulle, S. Plassmann, M. Zenkner, J. Timm, H.E. Assmus, M.A. Andrade-Navarro, and E.E. Wanker, "A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction," Science Signaling, vol. 4, no. 189, p. rs8, 2011.
27. H.S. Wiley, "Integrating Multiple Types of Data for Signaling Research: Challenges and Opportunities," Science Signaling, vol. 4, no. 160, p. pe9, 2011.
28. C.H. Yeang, T. Ideker, and T. Jaakkola, "Physical Network Models," J. Computational Biology, vol. 11, nos. 2/3, pp. 243-262, 2004.
29. C.H. Yeang, H.C. Mak, S. McCuine, C. Workman, T. Jaakkola, and T. Ideker, "Validation and Refinement of Gene-Regulatory Pathways on a Network of Physical Interactions," Genome Biology, vol. 6, no. 7, pp. R62.1-R62.10, 2005.