Supplementary Materials

Supplementary Materials for:

Cross-Species Protein Interactome Mapping Reveals Species-Specific Wiring of Stress Response Pathways

Jishnu Das, Tommy V. Vo, Xiaomu Wei, Joseph C. Mellor, Virginia Tong, Andrew G. Degatano, Xiujuan Wang, Lihua Wang, Nicolas A. Cordero, Nathan Kruer-Zerhusen, Akihisa Matsuyama, Jeffrey A. Pleiss, Steven M. Lipkin, Minoru Yoshida, Frederick P. Roth, Haiyuan Yu*

*Corresponding author. E-mail: haiyuan.yu@cornell.edu

This PDF file includes:

  • Fig. S1. Detection of PRS interactions and RRS pairs by three orthogonal assays.
  • Fig. S2. Confirmation of the reliability of weights of the interactions.
  • Fig. S3. Evolutionary rate of essential and nonessential genes using S. cryophilus or S. octosporus for comparison.
  • Fig. S4. Evolutionary rate of stress response genes and all genes comparing S. cryophilus or S. octosporus to S. pombe.
  • Fig. S5. Measurement of evolutionary divergence of S. pombe from S. cryophilus and S. octosporus.
  • Fig. S6. Conservation as a function of sequence identity of the entire protein or sequence identity of the interacting domains.
  • Fig. S7. Graphical representation of global and local coexpression of genes that express interacting proteins.
  • Fig. S8. Functional analysis of conserved and rewired (by definition) interactions in S. cerevisiae.
  • Fig. S9. Fractions of globally and locally coexpressed pairs for interacting proteins with interactions of different confidence levels.
  • Fig. S10. Fractions of functionally similar pairs for interacting proteins with interactions of different confidence levels.
  • Fig. S11. Interactions in the fission and budding yeast MAPK pathways.
  • Fig. S12. Sensitivity assays for deletion strains of S. pombe KGY553 (ATCC) under various stress conditions (n = 3 experiments).
  • Table S1. Interactome sizes.
  • Table S8. Primers used.
  • Legends for tables S2 to S7

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Technical Details

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Other Supplementary Material for this manuscript includes the following:

  • Table S2 (Microsoft Excel format). S. pombe ORFs screened.
  • Table S3 (Microsoft Excel format). StressNet and interaction confidence scores.
  • Table S4 (Microsoft Excel format). Positive reference set.
  • Table S5 (Microsoft Excel format). Random reference set.
  • Table S6 (Microsoft Excel format). StressNet genes and number of interactions.
  • Table S7 (Microsoft Excel format). StressNet—Conservation and rewiring.

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Citation: J. Das, T. V. Vo, X. Wei, J. C. Mellor, V. Tong, A. G. Degatano, X. Wang, L. Wang, N. A. Cordero, N. Kruer-Zerhusen, A. Matsuyama, J. A. Pleiss, S. M. Lipkin, M. Yoshida, F. P. Roth, H. Yu, Cross-Species Protein Interactome Mapping Reveals Species-Specific Wiring of Stress Response Pathways. Sci. Signal. 6, ra38 (2013).

© 2013 American Association for the Advancement of Science