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Journal of Computational Biology
Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data
To cite this article:
Kevin A. Janes, Jason R. Kelly, Suzanne Gaudet, John G. Albeck, Peter K. Sorger, Douglas A. Lauffenburger.
Journal of Computational Biology.
2004,
11(4): 544-561.
doi:10.1089/cmb.2004.11.544.
Kevin A. Janes Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139. Jason R. Kelly Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139. Suzanne Gaudet Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139. John G. Albeck Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139. Peter K. Sorger Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139. Douglas A. Lauffenburger Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139. Biological signaling networks process extracellular cues to control important cell decisions such as death–survival, growth–quiescence, and proliferation–differentiation. After receptor activation, intracellular signaling proteins change in abundance, modification state, and enzymatic activity. Many of the proteins in signaling networks have been identified, but it is not known how signaling molecules work together to control cell decisions. To begin to address this issue, we report the use of partial least squares regression as an analytical method to glean signal–response relationships from heterogeneous multivariate signaling data collected from HT-29 human colon carcinoma cells stimulated to undergo programmed cell death. By partial least squares modeling, we relate dynamic and quantitative measurements of 20–30 intracellular signals to cell survival after treatment with tumor necrosis factor alpha (a death factor) and insulin (a survival factor). We find that partial least squares models can distinguish highly informative signals from redundant uninformative signals to generate a reduced model that retains key signaling features and signal–response relationships. In these models, measurements of biochemical characteristics, based on very different techniques (Western blots, kinase assays, etc.), are grouped together as covariates, showing that heterogenous data have been effectively fused. Importantly, informative protein predictors of cell responses are always multivariate, demonstrating the multicomponent nature of the decision process.  This paper was cited by:Translating Biomaterial Properties to Intracellular Signaling Michael R. Caplan, Miti M. Shah Cell Biochemistry and Biophysics. Aug 2009, Vol. 54, No. 1-3: 1-10 CrossRef Illuminating signaling network functional biology through quantitative phosphoproteomic mass spectrometry N. C. Tedford, F. M. White, J. A. Radding Briefings in Functional Genomics and Proteomics. Jul 2008, Vol. 7, No. 5: 383-394 CrossRef Common effector processing mediates cell-specific responses to stimuli Kathryn Miller-Jensen, Kevin A. Janes, Joan S. Brugge, Douglas A. Lauffenburger Nature. Sep 2007, Vol. 448, No. 7153: 604-608 CrossRef A high-throughput microfluidic real-time gene expression living cell array Kevin R. King, Sihong Wang, Daniel Irimia, Arul Jayaraman, Mehmet Toner, Martin L. Yarmush Lab on a Chip. Feb 2007, Vol. 7, No. 1: 77 CrossRef Linking data to models: data regression Khuloud Jaqaman, Gaudenz Danuser Nature Reviews Molecular Cell Biology. Dec 2006, Vol. 7, No. 11: 813-819 CrossRef Data-driven modelling of signal-transduction networks Kevin A. Janes, Michael B. Yaffe Nature Reviews Molecular Cell Biology. Dec 2006, Vol. 7, No. 11: 820-828 CrossRef Effects of HER2 overexpression on cell signaling networks governing proliferation and migration Alejandro Wolf-Yadlin, Neil Kumar, Yi Zhang, Sampsa Hautaniemi, Muhammad Zaman, Hyung-Do Kim, Viara Grantcharova, Douglas A Lauffenburger, Forest M White Molecular Systems Biology. Nov 2006, Vol. 2 CrossRef Bioengineering and Systems Biology Trey Ideker, L. Raimond Winslow, A. Douglas Lauffenburger Annals of Biomedical Engineering. Mar 2006, Vol. 34, No. 2: 257-264 CrossRef
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