Inferring cell-scale signalling networks via compressive sensing

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Nie, Lei ^a,b,c   Yang, Xian ^a   Adcock, Ian ^d   Xu, Zhiwei ^b   Guo, Yike ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^d NATIONAL HEART AND LUNG INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BAYES THEOREM; CALCULATION; CELL SCALE SIGNALLING NETWORK; CROSS REACTION; IMMUNOPRECIPITATION; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; SENSITIVITY AND SPECIFICITY; SIMULATION; RECEIVER OPERATING CHARACTERISTIC; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

BAYES THEOREM; ROC CURVE; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 84899675693     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0095326     Document Type: Article

References (36)

1. Kolch W (2000) Meaningful relationships: the regulation of the ras/raf/mek/erk pathway by protein interactions. Biochemical Journal 351: 289-305.
2. Swameye I, Müller T, Timmer Jt, Sandra O, Klingmüller U (2003) Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling. Proceedings of the National Academy of Sciences 100: 1028-1033.
3. Hendriks BS, Hua F, Chabot JR (2008) Analysis of mechanistic pathway models in drug discovery: p38 pathway. Biotechnology Progress 24: 96-109. (Pubitemid 351231254)
4. Bonifacino JS, Dell'Angelica EC, Springer TA (2001) Immunoprecipitation. Current Protocols in Immunology 41: 8.3.1-8.3.28.
5. Shuto T, Imasato A, Jono H, Sakai A, Xu H, et al. (2002) Glucocorticoids synergistically enhance nontypeablehaemophilus influenzae-induced toll-like receptor 2 expression via a negative cross-talk with p38 map kinase. Journal of Biological Chemistry 277: 17263-17270. (Pubitemid 34967761)
6. Wang Z, Yang H, Tachado SD, Capó-Aponte JE, Bildin VN, et al. (2006) Phosphatase-mediated crosstalk control of erk and p38 mapk signaling in corneal epithelial cells. Investigative Ophthalmology & Visual Science 47: 5267-5275. (Pubitemid 46723774)
7. Junttila MR, Li SP,Westermarck J (2008) Phosphatase-mediated crosstalk between mapk signaling pathways in the regulation of cell survival. The FASEB Journal 22: 954-965. (Pubitemid 351519953)
8. Guo X,Wang XF (2009) Signaling cross-talk between tgf-b/bmp and other pathways. Cell Research 19: 71-88.
9. Kreeger PK, Lauffenburger DA (2010) Cancer systems biology: a network modeling perspective. Carcinogenesis 31: 2-8.
10. Sontag E, Kiyatkin A, Kholodenko BN (2004) Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics 20: 1877-1886. (Pubitemid 39199051)
11. Schmidt H, Cho KH, Jacobsen EW (2005) Identification of small scale biochemical networks based on general type system perturbations. FEBS Journal 272: 2141-2151. (Pubitemid 40646784)
12. Mendes P, Kell DB (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14: 869-883. (Pubitemid 29041543)
13. Quach M, Brunel N, d'Alché Buc F (2007) Estimating parameters and hidden variables in non-linear state-space models based on odes for biological networks inference. Bioinformatics 23: 3209-3216. (Pubitemid 350187524)
14. Sun X, Jin L, Xiong M (2008) Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks. PloS ONE 3: e3758.
15. Toni T, Welch D, Strelkowa N, Ipsen A, Stumpf MP (2009) Approximate bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of the Royal Society Interface 6: 187-202.
16. Yang X, Guo Y, Guo L (2013) An iterative parameter estimation method for biological systems and its parallel implementation. Concurrency and Computation: Practice and Experience.
17. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S (2002) The protein kinase complement of the human genome. Science 298: 1912-1934. (Pubitemid 35425239)
18. Forrest AR, Ravasi T, Taylor D, Huber T, Hume DA, et al. (2003) Phosphoregulators: protein kinases and protein phosphatases of mouse. Genome Research 13: 1443-1454. (Pubitemid 36827241)
19. Hecker M, Lambeck S, Toepfer S, Van Someren E, Guthke R (2009) Gene regulatory network inference: data integration in dynamic models - a review. Biosystems 96: 86-103.
20. Choudhary C, Mann M (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nature Reviews Molecular Cell Biology 11: 427-439.
21. Dunn JD, Reid GE, Bruening ML (2010) Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. Mass Spectrometry Reviews 29: 29-54.
22. Xiong H, Choe Y (2008) Structural systems identification of genetic regulatory networks. Bioinformatics 24: 553-560. (Pubitemid 351256300)
23. Papin JA, Palsson BO (2004) The jak-stat signaling network in the human b-cell: an extreme signaling pathway analysis. Biophysical journal 87: 37-46. (Pubitemid 38880062)
24. Bhalla US, Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283: 381-387.
25. Weng G, Bhalla US, Iyengar R (1999) Complexity in biological signaling systems. Science 284: 92-96. (Pubitemid 29282052)
26. Frank SA (2002) Chapter 4: specificity and cross-reactivity. In: Immunology and Evolution of Infectious Disease, Princeton University Press.
27. Candès EJ, Romberg J, Tao T (2006) Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information. IEEE Transactions on Information Theory 52: 489-509. (Pubitemid 43174093)
28. Donoho DL (2006) Compressed sensing. IEEE Transactions on Information Theory 52: 1289-1306.
29. Candès EJ, Tao T (2006) Near-optimal signal recovery from random projections: Universal encoding strategies? IEEE Transactions on Information Theory 52: 5406-5425. (Pubitemid 46445381)
30. Tipping ME (2001) Sparse bayesian learning and the relevance vector machine. The Journal of Machine Learning Research 1: 211-244.
31. Ji S, Xue Y, Carin L (2008) Bayesian compressive sensing. IEEE Transactions on Signal Processing 56: 2346-2356. (Pubitemid 351795888)
32. Bishop CM, Tipping ME (2000) Variational relevance vector machines. In: Proceedings of the Sixteenth Conference on Uncertainty in Artificial Intelligence. Morgan Kaufmann Publishers Inc., pp. 46-53.
33. August E, Papachristodoulou A (2009) Efficient, sparse biological network determination. BMC Systems Biology 3: 25.
34. Yeung MKS, Tegnér J, Collins JJ (2002) Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Sciences 99: 6163-6168. (Pubitemid 34493283)
35. Necela BM, Cidlowski JA (2004) Mechanisms of glucocorticoid receptor action in noninflammatory and inflammatory cells. Proceedings of the American Thoracic Society 1: 239-246.
36. Gallager R (1962) Low-density parity-check codes. IRE Transactions on Information Theory 8: 21-28.