Systems analysis of EGF receptor signaling dynamics with microwestern arrays.
We describe microwestern arrays, which enable quantitative, sensitive and high-throughput assessment of protein abundance and modifications after electrophoretic separation of microarrayed cell lysates. This method allowed us to measure 91 phosphosites on 67 proteins at six time points after stimulation with five epidermal growth factor (EGF) concentrations in A431 human carcinoma cells. We inferred the connectivities among 15 phosphorylation sites in 10 receptor tyrosine kinases (RTKs) and two sites from Src kinase using Bayesian network modeling and two mutual information-based methods; the three inference methods yielded substantial agreement on the network topology. These results imply multiple distinct RTK coactivation mechanisms and support the notion that small amounts of experimental data collected from phenotypically diverse network states may enable network inference.
Ciaccio
Mark F
MF
The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA.
Wagner
Joel P
JP
Chuu
Chih-Pin
CP
Lauffenburger
Douglas A
DA
Jones
Richard B
RB
D015153:Blotting, Western / Q000295:instrumentation* / Q000379:methods; D004867:Equipment Design; D019544:Equipment Failure Analysis; D066246:ErbB Receptors / Q000378:metabolism*; D040081:Protein Array Analysis / Q000295:instrumentation* / Q000379:methods; D020543:Proteome / Q000378:metabolism*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology
D020543:Proteome; C512478:EGFR protein, human; D066246:ErbB Receptors