title: Method for analyzing signaling networks in complex cellular systems.
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-kappaBorRAS/mitogen-activated protein kinase pathways and defining additional interactions between these pathways.
authors.affiliation: Bioseek, Inc., Burlingame, CA 94010, USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Plavec
authors.forename: Oksana
authors.initials: O
authors.lastname: Sirenko
authors.forename: Sylvie
authors.initials: S
authors.lastname: Privat
authors.forename: Yuker
authors.initials: Y
authors.lastname: Wang
authors.forename: Maya
authors.initials: M
authors.lastname: Dajee
authors.forename: Jennifer
authors.initials: J
authors.lastname: Melrose
authors.forename: Brian
authors.initials: B
authors.lastname: Nakao
authors.forename: Evangelos
authors.initials: E
authors.lastname: Hytopoulos
authors.forename: Ellen L
authors.initials: EL
authors.lastname: Berg
authors.forename: Eugene C
authors.initials: EC
authors.lastname: Butcher
mesh_terms: D002478:Cells, Cultured; D042783:Endothelial Cells / Q000378:metabolism; D006801:Humans; D007371:Interferon-gamma / Q000494:pharmacology; D007375:Interleukin-1 / Q000494:pharmacology; D020935:MAP Kinase Signaling System; D015398:Signal Transduction / Q000502:physiology*; D014409:Tumor Necrosis Factor-alpha / Q000494:pharmacology
chemical_list: D007375:Interleukin-1; D014409:Tumor Necrosis Factor-alpha; D007371:Interferon-gamma