Academic
Publications
Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes

Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed He

Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes   (Citations: 5)
BibTex | RIS | RefWorks Download
Journal: Molecular & Cellular Proteomics - MOL CELL PROTEOMICS , vol. 9, no. 9, pp. 1849-1865, 2010
Cumulative Annual
View Publication
The following links allow you to view full publications. These links are maintained by other sources not affiliated with Microsoft Academic Search.
    • ...Their main conceptual difference is their methodology for identifying intracellular connectivity: data-driven models are highly abstract and can identify molecular dependencies within experimental data based on regression analysis, i.e., principal component analysis-(PCA), Partial Least Square Regression (PLSR), Multi-Linear Regression (MLR), Bayesian or other probabilistic models [11-14]...
    • ...As pro-growth stimuli, Tumor Growth Factor alpha (TGFa), Hepatocyte Growth Factor (HGF) and Heregulin (HER) have been chosen based on the response yielded on liver cells in previous experiments [13]...
    • ...Construction of a 2-step Multiple Linear Regression (MLR) model and comparison to our approach (Additional File 3, S2) The performance of our hybrid ILP-MLR approach is compared against a data-driven 2-step MLR approach [13] that correlates i) stimuli and inhibitors to the measured phosphoproteins and ii) phosphoprotein activities to cytokine releases...
    • ...2-step MLR is a data driven approach [13,15] aiming at correlating inputs to outputs ignoring any a-priori knowledge of protein connectivity...
    • ...These findings are in agreement with recently published data that shows HCC cell types are less responsive to Toll Like Receptor (TLR) stimuli than primary hepatocytes [13], presumably to avoid detection and clearance by the innate immune system [44-46]...
    • ...Kinase inhibitors were used at concentrations sufficient to inhibit at least 95% of the phosphorylation of the nominal target as determined by dose-response assays in previous work [13]...
    • ...The selection of these two time points was based on preliminary results published in [13], that identified 5 and 25 minutes as the optimal reporters of early phosphorylation activities...
    • ...At the end of the treatment cell lysates were collected using standard lysate procedure [13]...
    • ...The noise level of the assay has been estimated in [13] at the range of 166 fluorescent units, by considering the standard deviation of repeated measurements of unstimulated controls...

    Ioannis N Melaset al. Combined logical and data-driven models for linking signalling pathway...

    • ...). We demonstrate the value of the CellNOpt-cFL method by elucidating new information from a recently published experimental dataset describing phospho-protein signaling in HepG2 cells exposed to a set of inflammatory cytokines ...

    Melody K. Morriset al. Training Signaling Pathway Maps to Biochemical Data with Constrained F...

Sort by: