Method for analyzing signaling networks in complex cellular systems
- Ivan Plavec†,
- Oksana Sirenko†,
- Sylvie Privat†,
- Yuker Wang†,
- Maya Dajee†,
- Jennifer Melrose†,
- Brian Nakao†,
- Evangelos Hytopoulos†,
- Ellen L. Berg†, and
- Eugene C. Butcher‡,§
- †Bioseek, Inc., Burlingame, CA 94010; and ‡Laboratory of Immunology and Vascular Biology, Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
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Communicated by Leroy Hood, Institute for Systems Biology, Seattle, WA, December 10, 2003 (received for review September 25, 2003)
Abstract
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-κBorRAS/mitogen-activated protein kinase pathways and defining additional interactions between these pathways.
Footnotes
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↵ § To whom correspondence should be addressed. E-mail: ebutcher{at}stanford.edu.
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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.
- Copyright © 2004, The National Academy of Sciences
