Analysis Examples

Activation of Kinases in Controlled Cell Lines

• EGF Stimulation of 184A1 Cells (Wolf Yadlin, 2007)
  • Agglomerative clustering of kinases
  • Agglomerative clustering of only significant kinases

• EGF and HRG Stimulation of ERBB2 Overexpressing HMEC Cells (Wolf Yadlin 2006)
  • Plot all samples and kinases
  • Plot just EGF HMEC data for comparison to MRM experiment
  • Reshape results and plot to compare kinase between conditions

• TCR Activation (Chylek, 2014)
  • Agglomerative clustering of kinases
  • Agglomerative clustering of all significant kinases

Inhibition of Kinases in Controlled Cell Lines

• BCR-ABL inhibition by dasatinib in K562 cells (Asmussen, 2014)
  • Plot kinases sorted by activity pre-treatment
  • Plot kinases sorted by activity pre-treatment, but with only significant kinases

• Inhibition of AKT by Five Different Inhibitors in Breast Cancer (Weichmann, 2021)
  • Plot and cluster kinase activities
  • Plot and cluster kinase activities, but with only significant kinases

• Paradoxical Activation of MAP-ERK pathway upon BRAF inhibition (Kubiniok, 2017)
  • Shared agglomerative clustering of kinases for both Colo205 and HCT116 cells
  • Shared agglomerative clustering of significant kinases for both Colo205 and HCT116 cells

Profiling HER2 therapy response in Breast Cancer

• Analysis of CPTAC Breast Cancer Patient Samples (Mertens 2016)
  • Plot using agglomerative clustering on both kinases and patients, and add context to each sample
  • Plot ERBB2 activities with each samples associated HER2 status
  • Measure the number of cross-predictions between HER2-status and HER2/ERBB2 activity

• Analysis of PDX Tumor Samples (Huang 2017)
  • Plot all samples and all kinases, with HER2 status context
  • Plot all samples and all significant kinases, with HER2 status context

• Analysis of HER2 Positive Patients using Microbiopsies (Satpathy 2021)
  • Agglomerative clustering of all patients and kinases, with context
  • Agglomerative clustering of all patients and all significant kinases, with context
  • Plot only pre-treatment samples and provide treatment response context
  • Plot specific kinases for each patient (all samples)