Supplementary Materials

Supplementary Materials for:

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

Tujin Shi, Mario Niepel, Jason E. McDermott, Yuqian Gao, Carrie D. Nicora, William B. Chrisler, Lye M. Markillie, Vladislav A. Petyuk, Richard D. Smith, Karin D. Rodland, Peter K. Sorger, Wei-Jun Qian, H. Steven Wiley*

*Corresponding author. Email: steven.wiley{at}pnnl.gov

This PDF file includes:

  • Fig. S1. Relative abundance of proteins of the EGFR-MAPK signaling pathway as assessed by deep proteomics surveys.
  • Fig. S2. Comparison of log2 variance distribution of conserved versus nonconserved proteins and mRNA.
  • Fig. S3. Relationship between mRNA expression and protein abundances of EGFRMAPK pathway components across all cell lines.
  • Fig. S4. Kinetic response of cells to EGF as a function of ligand dose.
  • Fig. S5. Comparison between simulated and measured EGF binding to cells.
  • Fig. S6. Two-component mixture model of the copy number gain frequencies for breast and all cancers.
  • Legends for tables S1 to S7

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). EGFR-MAPK pathway–associated genes regulated by pathway perturbation.
  • Table S2 (Microsoft Excel format). RNA expression and protein abundance of HMECs ranked by RNA-Seq reads.
  • Table S3 (Microsoft Excel format). iTRAQ and transcriptome analysis of proteins with conserved abundances.
  • Table S4 (Microsoft Excel format). Transcriptomics analysis of EGFR-MAPK pathway components across seven cell lines.
  • Table S5 (Microsoft Excel format). SRM analysis of all of the EGFR-MAPK pathway proteins.
  • Table S6 (Microsoft Excel format). Variance analysis of signaling proteins in the EGFR-MAPK pathway.
  • Table S7 (Microsoft Excel format). Copy number gain or loss frequency for genes in the EGFR pathway.

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Citation: T. Shi, M. Niepel, J.E. McDermott, Y. Gao, C. D. Nicora, W. B. Chrisler, L. M. Markillie, V. A. Petyuk, R. D. Smith, K. D. Rodland, P. K. Sorger, W.-J. Qian, H. S. Wiley, Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway. Sci. Signal. 9, rs6 (2016).

© 2016 American Association for the Advancement of Science