1. Home page
  2. Search

The logic of EGFR/ErbB signaling: Theoretical properties and analysis of high-throughput data

This item is provided by the institution :
National Technical University of Athens   

Repository :
Digital Library of National Technical University of Athens | Dspace@NTUA   

see the original item page
in the repository's web site and access all digital files if the item*



The logic of EGFR/ErbB signaling: Theoretical properties and analysis of high-throughput data (EN)
Samaga, R (EN)
Sorger, PK (EN)
Saez-Rodriguez, J (EN)
Alexopoulos, LG (EN)
Klamt, S (EN)
journalArticle (EN)
2014-03-01T01:32:10Z
2009 (EN)
The epidermal growth factor receptor (EGFR) signaling pathway is probably the best-studied receptor system in mammalian cells, and it also has become a popular example for employing mathematical modeling to cellular signaling networks. Dynamic models have the highest explanatory and predictive potential; however, the lack of kinetic information restricts current models of EGFR signaling to smaller sub-networks. This work aims to provide a large-scale qualitative model that comprises the main and also the side routes of EGFR/ErbB signaling and that still enables one to derive important functional properties and predictions. Using a recently introduced logical modeling framework, we first examined general topological properties and the qualitative stimulus-response behavior of the network. With species equivalence classes, we introduce a new technique for logical networks that reveals sets of nodes strongly coupled in their behavior. We also analyzed a model variant which explicitly accounts for uncertainties regarding the logical combination of signals in the model. The predictive power of this model is still high, indicating highly redundant sub-structures in the network. Finally, one key advance of this work is the introduction of new techniques for assessing high-throughput data with logical models (and their underlying interaction graph). By employing these techniques for phospho-proteomic data from primary hepatocytes and the HepG2 cell line, we demonstrate that our approach enables one to uncover inconsistencies between experimental results and our current qualitative knowledge and to generate new hypotheses and conclusions. Our results strongly suggest that the Rac/Cdc42 induced p38 and JNK cascades are independent of PI3K in both primary hepatocytes and HepG2. Furthermore, we detected that the activation of JNK in response to neuregulin follows a PI3K-dependent signaling pathway. © 2009 Samaga et al. (EN)
Biochemical Research Methods (EN)
Mathematical & Computational Biology (EN)
stoichiometry (EN)
High Throughput (EN)
mitogen activated protein kinase p38 (EN)
data analysis (EN)
proteomics (EN)
signal transduction (EN)
epidermal growth factor receptor (EN)
predictive validity (EN)
mitogen activated protein kinase (EN)
analysis (EN)
article (EN)
mammal cell (EN)
Mammalia (EN)
high throughput screening (EN)
qualitative analysis (EN)
stimulus response (EN)
mathematical model (EN)
liver cell (EN)
logic (EN)
stress activated protein kinase (EN)
cell line (EN)
information science (EN)
PLoS Computational Biology (EN)
English
PUBLIC LIBRARY SCIENCE (EN)
National Technical University of Athens
Digital Library of National Technical University of Athens | Dspace@NTUA
Κεντρική Βιβλιοθήκη Ε.Μ.Π.
Ιδρυματικό Αποθετήριο
Δημοσιεύσεις μελών Δ.Ε.Π. σε περιοδικά



*Institutions are responsible for keeping their URLs functional (digital file, item page in repository site)