Supplementary Materials

Supplementary Materials for:

Using Functional Signature Ontology (FUSION) to Identify Mechanisms of Action for Natural Products

Malia B. Potts, Hyun Seok Kim, Kurt W. Fisher, Youcai Hu, Yazmin P. Carrasco, Gamze Betul Bulut, Yi-Hung Ou, Mireya L. Herrera-Herrera, Federico Cubillos, Saurabh Mendiratta, Guanghua Xiao, Matan Hofree, Trey Ideker, Yang Xie, Lily Jun-shen Huang, Robert E. Lewis,* John B. MacMillan,* Michael A. White*

*Corresponding author. E-mail: (M.A.W.); (J.B.M.); (R.E.L.)

This PDF file includes:

  • Materials and Methods: Natural Products and Producing Organisms
  • Fig. S1. Characteristics of the reporter genes used for FUSION mapping.
  • Fig. S2. Mapping functional similarity among miRNAs.
  • Fig. S3. Mapping functional similarity among kinases and kinase accessory proteins.
  • Fig. S4. Using FUSION mapping to identify miRNAs and kinases that regulate autophagy.
  • Fig. S5. Representative flow cytometry data and characterization of the role of BMP2K in autophagy and erythrocyte development.
  • Fig. S6. SRMS as an inhibitor of autophagy.
  • Fig. S7. Using FUSION mapping to identify natural product inhibitors of autophagy and migration.
  • Fig. S8. Using FUSION mapping to identify inhibitors of AKT signaling.
  • Fig. S9. Natural product structure determination.
  • Fig. S10. Profiles of reporter gene expression changes in response to each of 1124 genetic perturbations.
  • Fig. S11. Analysis of correlation among reporter gene expression and between distance metrics.
  • Fig. S12. Estimation of FDR from P value density distribution, rank sum as an example.
  • Legends for tables S1 to S5

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Reporter gene expression in response to individual genetic and chemical perturbations in HCT116 cells.
  • Table S2 (Microsoft Excel format). Endogenous miRNA expression.
  • Table S3 (Microsoft Excel format). MiRNA-siRNA oligonucleotide seed identities.
  • Table S4 (Microsoft Excel format). Kinase inhibition screen (KinaseProfiler).
  • Table S5 (Microsoft Excel format). Maintenance and transfection conditions for cell lines used in this study.

[Download Tables S1 to S5]

Citation: M. B. Potts, H. S. Kim, K. W. Fisher, Y. Hu, Y. P. Carrasco, G. B. Bulut, Y.-H. Ou, M. L. Herrera-Herrera, F. Cubillos, S. Mendiratta, G. Xiao, M. Hofree, T. Ideker, Y. Xie, L. J.-s. Huang, R. E. Lewis, J. B. MacMillan, M. A. White, Using Functional Signature Ontology (FUSION) to Identify Mechanisms of Action for Natural Products. Sci. Signal. 6, ra90 (2013).

© 2013 American Association for the Advancement of Science