Data-driven modeling of cellular stimulation, signaling and output response in RAW 264.7 cells

Journal of Molecular Signaling

Volumn 3, Issue , 2008, Pages

  Wu, Yang ^a   Johnson, Gary L ^a   Gomez, Shawn M ^a,b  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 46749104117     PISSN: None     EISSN: 17502187     Source Type: Journal    
DOI: 10.1186/1750-2187-3-11     Document Type: Article

References (28)

1. de Jong H Modeling and simulation of genetic regulatory systems: A literature review J Comput Biol 2002, 9:67-103. 10.1089/ 10665270252833208 11911796
2. Janes KA Yaffe MB Data-driven modelling of signal-transduction networks Nat Rev Mol Cell Biol 2006, 7(11):820-828. 10.1038/nrm2041 17057752
3. Sachs K Perez O Pe'er D Lauffenburger DA Nolan GP Causal protein-signaling networks derived from multiparameter single-cell data Science 2005, 308(5721):523-529. 10.1126/science.1105809 15845847
4. Janes K Albeck J Gaudet S Sorger P Lauffenburger D Yaffe M A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis Science 2005, 310(5754):1646-53. 10.1126/science.1116598 16339439
5. Janes K Kelly J Gaudet S Albeck J Sorger P Lauffenburger D Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data J Comput Biol 2004, 11(4):544-61. 10.1089/cmb.2004.11.544 15579231
6. Miller-Jensen K Janes KA Brugge JS Lauffenburger DA Common effector processing mediates cell-specific responses to stimuli Nature 2007, 448(7153):604-608. 10.1038/nature06001 17637676
7. Pradervand S Maurya M Subramaniam S Identification of signaling components required for the prediction of cytokine release in RAW 264.7 macrophages Genome biology 2006, 7(2):R11. [M3: 10.1186/ gb-2006-7-2-r11]. 1431720 16507166 10.1186/gb-2006-7-2-r11
8. Smilde A Bro R Geladi P Multi-way analysis with applications in the chemical sciences John Wiley & Sons, Ltd 2004.
9. Abbas A Lichtman A Cellular and molecular immunology Elsevier Inc. 5, 2005.
10. Schuster C Forster K Dierks H Elsasser A Behre G Simon N Danhauser-Riedl S Hallek M Warmuth M The effects of Bcr-Abl on C/EBP transcription-factor regulation and neutrophilic differentiation are reversed by the Abl kinase inhibitor imatinib mesylate Blood 2003, 101(2):655-663. 10.1182/blood-2002-01-0043 12393654
11. Thomson A The cytokine handbook Academic Press 1994.
12. Dunn SM Coles LS Lang RK Gerondakis S Vadas MA Shannon MF Requirement for nuclear factor (NF)-kappa B p65 and NF-interleukin-6 binding elements in the tumor necrosis factor response region of the granulocyte colony-stimulating factor promoter Blood 1994, 83(9):2469-2479. 7513199
13. Akira S Isshiki H Sugita T Tanabe O Kinoshita S Nishio Y Nakajima T Hirano T Kishimoto T A nuclear factor for IL-6 expression (NF-IL6) is a member of a C/EBP family EMBO J 1990, 9(6):1897-1906. 551896 2112087
14. Cho YH Lee CH Kim SG Potentiation of lipopolysaccharide-inducible cyclooxygenase 2 expression by C2-ceramide via c-Jun N-terminal kinase-mediated activation of CCAAT/enhancer binding protein beta in macrophages Mol Pharmacol 2003 63 3 512 523 10.1124/mol.63.3.512 12606757
15. Chen G Goeddel DV TNF-R1 signaling: A beautiful pathway Science 2002, 296(5573):1634-1635. 10.1126/science.1071924 12040173
16. Wajant H Pfizenmaier K Scheurich P Tumor necrosis factor signaling Cell Death Differ 2003, 10:45-65. 10.1038/sj.cdd.4401189 12655295
17. Schall TJ Biology of the RANTES/SIS cytokine family Cytokine 1991, 3(3):165-183. 10.1016/1043-4666(91)90013-4 1715772
18. Guo Z Zhang M Tang H Cao X Fas signal links innate and adaptive immunity by promoting dendritic-cell secretion of CC and CXC chemokines Blood 2005, 106(6):2033-2041. 10.1182/blood-2004-12-4831 15941911
19. Hiura TS Kempiak SJ Nel AE Activation of the human RANTES gene promoter in a macrophage cell line by lipopolysaccharide is dependent on stress-activated protein kinases and the IkappaB kinase cascade: implications for exacerbation of allergic inflammation by environmental pollutants Clin Immunol 1999, 90(3):287-301. 10.1006/clim.1998.4659 10075858
20. Alliance for Cell Signaling Protocols http://www.signaling-gateway.org/ data/ProtocolLinks.html
21. De Jong S SIMPLS - An Alternative approach to partial least-squares regression Chemometrics and Intelligent Laboratory Systems 1993, 18:251-263. 10.1016/0169-7439(93)85002-X
22. Wise B Ricker N Recent advances in multivariate statistical process control: Improving robustness and sensitivity IFAC Symposium on Advanced Control of Chemical Processes. Toulouse, France 1991.
23. Wold S Johansson E Cocchi M PLS: Partial Least Squares Projections to Latent Structures 3D QSAR in Drug Design; Theory, Methods, and Applications ESCOM Science Publishers, Leiden Kubinyi H 1993.
24. Sugiura N Further analysis of the data by Akaike's information criterion and the finite corrections Comunications in Statistics, Theory and Methods 1978, A7:13-26. 10.1080/03610927808827599
25. Hurvich C Tsai CL Regression and time series model selection in small samples Biometrika 1989, 76:297-307. 10.1093/biomet/76.2.297
26. Akaike H A Bayesian analysis of the minimum AIC procedure Annals of the Institute of Statistical Mathematics 1978, 30:9-14. 10.1007/BF02480194
27. Akaike H A Bayesian extension of the minimum AIC procedure of autoregressive model fitting Biometrika 1979, 66:237-242. 10.1093/biomet/ 66.2.237
28. Wold S Exponentially Weighted Moving Principal Components Analysis And Projections To Latent Structures Chemometrics and intelligent laboratory systems 1994, 23:149-161. 10.1016/0169-7439(93)E0075-F