Supplementary Materials

Supplementary Materials for:

Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines

Mario Niepel,* Marc Hafner, Emily A. Pace, Mirra Chung, Diana H. Chai, Lili Zhou, Birgit Schoeberl, Peter K. Sorger*

*Corresponding author. E-mail: peter_sorger@hms.harvard.edu (P.K.S.); mario_niepel@hms.harvard.edu (M.N.)

This PDF file includes:

  • Text S1. Prediction algorithm and statistical tests.
  • Fig. S1. Experimental design and illustration of the collected data sets.
  • Fig. S2. Correlations of the basal amounts of phosphorylated RTKs and intracellular kinases.
  • Fig. S3. Loading and variance of the principal components of the PCA of the basal profiles.
  • Fig. S4. Correlation between the ligand responses measured by ELISA and high-throughput microscopy.
  • Fig. S5. Description of the leave-one-out PLSR algorithm used for prediction.
  • Fig. S6. Correlation between predictions made with ligand responses measured by ELISA or imaging.
  • Fig. S7. Coefficients of the models based on the signaling profiles for drugs targeting the PI3K/Akt pathway.
  • Fig. S8. Distribution of model variables in each cluster for the lapatinib network representation.
  • Table S1. Names, abbreviations, and UNIPROT IDs of the receptors and downstream signaling proteins mentioned in the main text.
  • Table S2. Cell lines and culture conditions.
  • Table S3. Description of the ELISA kits used for measuring the basal profiles.
  • Table S4. Description of ligands used for measuring the signaling profiles.
  • Table S5. Description of the antibodies used for the high-throughput microscopy imaging assays.
  • Table S6. Descriptions of the data sets used for the prediction of GI50 values.
  • Table S7. Enrichment analysis of the GI50 values by PTEN and PI3KCA mutational status.
  • Legends for data S1 to S5
  • References (63, 64)

[Download PDF]

Technical Details

Format: Adobe Acrobat PDF

Size: 4.02 MB

Other Supplementary Material for this manuscript includes the following:

  • Data S1 (Microsoft Excel format). Measures of the ligand response and basal levels grouped by data set as described in table S6 and raw values.
  • Data S2 (Microsoft Excel format). Signaling-targeted drugs used for drug sensitivity predictions and their corresponding reported GI50 in the cell lines.
  • Data S3 (Microsoft Excel format). Results of the predictions and coefficients for the significant models for the different data sets used (basal profiles and signaling profiles collected by microscopy).
  • Data S4 (Microsoft Excel format). Results of the predictions and coefficients for significant models using the ligand responses measured by ELISA.
  • Data S5 (Microsoft Excel format). Results of the stratified models using the basal levels and model coefficients.

[Download Data S1 to S5]


Citation: M. Niepel, M. Hafner, E. A. Pace, M. Chung, D. H. Chai, L. Zhou, B. Schoeberl, P. K. Sorger, Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines. Sci. Signal. 6, ra84 (2013).

© 2013 American Association for the Advancement of Science