Method for Analyzing Signaling Networks in Complex Cellular Systems

Now that the human genome has been sequenced, the challenge of assigning function to human genes has become acute. Existing approaches using microarrays or proteomics frequently generate very large volumes of data not directly related to biological function, making interpretation difficult. Here, we...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 101; no. 5; pp. 1223 - 1228
Main Authors Plavec, Ivan, Sirenko, Oksana, Privat, Sylvie, Wang, Yuker, Dajee, Maya, Melrose, Jennifer, Nakao, Brian, Hytopoulos, Evangelos, Berg, Ellen L., Butcher, Eugene C.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 03.02.2004
National Acad Sciences
Subjects
Biological Sciences
Cell culture techniques
Cell lines
Cells
Cells, Cultured
Cellular biology
Correlations
Cytokines
Endothelial cells
Endothelial Cells - metabolism
Genes
Genetic vectors
Genetics
Human umbilical vein endothelial cells
Humans
Interferon-gamma - pharmacology
Interleukin-1 - pharmacology
MAP Kinase Signaling System
Proteins
Receptors
Signal Transduction - physiology
Tumor Necrosis Factor-alpha - pharmacology
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Summary:Now that the human genome has been sequenced, the challenge of assigning function to human genes has become acute. Existing approaches using microarrays or proteomics frequently generate very large volumes of data not directly related to biological function, making interpretation difficult. Here, we describe a technique for integrative systems biology in which: (i) primary cells are cultured under biologically meaningful conditions; (ii) a limited number of biologically meaningful readouts are measured; and (iii) the results obtained under several different conditions are combined for analysis. Studies of human endothelial cells overexpressing different signaling molecules under multiple inflammatory conditions show that this system can capture a remarkable range of functions by a relatively small number of simple measurements. In particular, measurement of seven different protein levels by ELISA under four different conditions is capable of reconstructing pathway associations of 25 different proteins representing four known signaling pathways, implicating additional participants in the NF-κB or RAS/mitogen-activated protein kinase pathways and defining additional interactions between these pathways.
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Abbreviations: BioMAP, biologically multiplexed activity profiling; TNF-α, tumor necrosis factor α; ICAM, intercellular adhesion molecule; VCAM, vascular cell adhesion molecule; MIG, monokine induced by IFN-γ; MCP-1, monocyte chemoattractant protein 1; PI3K, phosphatidylinositol 3-kinase; MAPK, mitogen-activated protein kinase.
To whom correspondence should be addressed. E-mail: ebutcher@stanford.edu.
Communicated by Leroy Hood, Institute for Systems Biology, Seattle, WA, December 10, 2003
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0308221100