Learning signaling network structures with sparsely distributed data

Journal of Computational Biology

Volumn 16, Issue 2, 2009, Pages 201-212

  Sachs, Karen ^a   Itani, Solomon ^b   Carlisle, Jennifer ^b   Nolan, Garry P ^a   Pe'er, Dana ^d   Lauffenburger, Douglas A ^c  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Department of Electrical Engineering and Computer Science   (United States)

^c Massachusetts Institute of Technology   (United States)

^d NONE   (United States)

Author keywords

Bayesian networks; Flow cytometry; Graphical models; Proteomics signaling path ways

Indexed keywords

CYCLIC AMP DEPENDENT PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE KINASE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE; PHOSPHATIDYLINOSITOL 4,5 BISPHOSPHATE; PHOSPHOLIPASE; PROTEIN KINASE B; PROTEIN KINASE C; PROTEIN PLC GAMMA; RAF PROTEIN; STRESS ACTIVATED PROTEIN KINASE; SYNAPTOPHYSIN; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; FLOW CYTOMETRY; PRIORITY JOURNAL; PROBABILITY; PROTEOMICS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BAYES THEOREM; FLOW CYTOMETRY; MARKOV CHAINS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION;

EID: 59649098900     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2008.07TT     Document Type: Article

References (19)

1. Friedman, N. 1998. The Bayesian structural EM algorithm. Proc. 14th Annu. Conf. Uncertainty AI, pgs. 129-138.
2. Friedman, N. 2004. Inferring cellular networks using probabilistic graphical models. Science 303:799-805.
3. Friedman, N., Linial, M., Nachman, I., et al. 2000. Using Bayesian networks to analyze expression data. J. Comput. Biol. 7, 3-4.
4. Hartemink, A.J., Gifford, D.K., Jaakkola, T.S., et al. 2001. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac. Symp. Biocomput. 422-433.
5. Heckerman, D., Meek, C., and Cooper, G.F. 1999. Computation, Causation, and Discovery, Glymour, C., and Cooper, G.F., eds., MIT Press, Cambridge, MA.
6. Herzenberg, L.A., and Sweet, R.G. 1976. Fluorescence-activated cell sorting. Sci. Am. 234, 108-117.
7. Krutzik, P.O., Irish, J.M., Nolan, G.P., et al. 2004. Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications. Clin. Immunol. 110, 206-221.
8. Krutzik, P.O., and Nolan, G.P. 2003. Intracellular phospho-protein staining techniques for flow cytometry: monitoring single cell signaling events. Cytometry A 55, 61-70.
9. Pearl, J. 1988. Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference. Morgan Kauffman Publishers, San Mateo, CA.
10. Pearl, J., and Verma, T.S. 1991. KR-91: Principles of knowledge representation and reasoning: Proc 2nd Intl Conf., Morgan Kaufmann, pgs. 441-452.
11. Perez, O.D., Krutzik, P.O., and Nolan, G.P. 2004. Flow cytometric analysis of kinase signaling cascades. Methods Mol. Biol. 263, 67-94.
12. Perez, O.D., and Nolan, G.P. 2002. Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry. Nat. Biotechnol. 20, 155-162.
13. Perez, O.D., and Nolan, G.P. 2006. Phospho-proteomic immune analysis by flow cytometry: from mechanism to translational medicine at the single-cell level. Immunol. Rev. 210, 208-228.
14. Perfetto, A., Chattopadhyay, P., and Roederer, M. 2004. Seventeen-colour flow cytometry: unravelling the immune system. Nat. Rev. Immunol. 4, 648-655.
15. Sachs, K. 2006. Bayesian network models of biological signaling pathways [Ph.D. dissertation]. Massachussetts Institute of Technology, Cambridge, MA.
16. Sachs, K., Gifford, D., Jakkola, T., et al. 2002. Bayesian network approach to cell signaling pathway modeling. Sci. STKE, 148/38-42.
17. Sachs, K., Perez, O., Pe'er, D., et al. 2005. Causal protein-signaling networks derived from multiparameter single-cell data. Science 308, 523-529.
18. Tanner, S.D., Ornatsky, O., Bandura, D.R., et al. 2007. Multiplex bio-assay with inductively coupled plasma mass spectrometry: towards a massively multivariate single-cell technology. Spectrochim. Acta B: Atomic Spectrosc. 62, 188-195.
19. Woolf, P.J., Prudhomme, W., Daheron, L., et al. 2005. Bayesian analysis of signaling networks governing embryonic stem cell fate decisions. Bioinformatics 21, 741-753.