Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Sci. Signal., 7 December 2010
[DOI: 10.1126/scisignal.2001034]

Supplementary Materials for:

ATM-Dependent and -Independent Dynamics of the Nuclear
Phosphoproteome After DNA Damage

Ariel Bensimon, Alexander Schmidt, Yael Ziv, Ran Elkon, Shih-Ya Wang, David J. Chen, Ruedi Aebersold,* Yosef Shiloh*

*To whom correspondence should be addressed. E-mail: yossih{at}post.tau.ac.il (Y.S.); rudolf.aebersold{at}imsb.biol.ethz.ch (R.A.)

This PDF file includes:

  • Fig. S1. Schematic workflow and estimation of signal-to-noise criteria for fold-change filtering.
  • Fig. S2. Time course data set analyzed for overrepresented sequence motifs, as well as known kinase-substrate relationships.
  • Fig. S3. PPI network of the DDR phosphoproteome obtained with STRING.
  • Fig. S4. Full network view of the protein complexes associated with DDR phosphoproteome identified by CORUM analysis.
  • Fig. S5. Full network view of the PPI network of the DDR phosphoproteome identified by PPI Spider analysis.
  • Fig. S6. Properties of the PPI Spider protein-protein interaction network of the DDR phosphoproteome.
  • Fig. S7. pSer2996 on ATM, identified by MS/MS and a phosphorylation-specific antibody, is DNA-PK–independent.
  • Fig. S8. The S2996A mutation in ATM does not affect ATM-dependent phosphorylations after DNA damage induction.
  • Table S1. List of samples (biological replicates) used for the two MasterMaps.
  • Table S3. Significant GO terms extracted from DAVID.
  • Table S4. DNA damage–responsive phosphorylation sites with a known kinase identified in databases.
  • Table S5. Kinase prediction enrichment analysis of phosphorylation sites and the association with Motif-X motifs.
  • Table S6. Kinase prediction enrichment analysis coupled to DAVID GO analysis.
  • Table S7. Kinase prediction enrichment analysis coupled to CLICK clustering analysis.
  • Table S8. DAVID GO analysis of CLICK clusters.
  • Table S9. Protein complexes depicted by CORUM in the protein lists obtained in this study.
  • Table S10. Effect of the PPI Spider network generation procedure on the analysis of GO term enrichment.
  • Table S12. Kinase prediction enrichment analysis of the ATM dependence data set.

[Download PDF]

Technical Details

Format: Adobe Acrobat PDF

Size: 9,045 KB

Other Supplementary Material for this manuscript includes the following:

  • Table S2. DNA damage–responsive phosphorylation events in the time course data set.
  • Table S11. DNA damage–responsive phosphorylation events in the ATM dependence data set.
  • Table S13. Complete list of phosphorylation sites identified in this study.
  • Table S14. Complete list of phosphopeptides identified in this study.

[Download Tables]

Technical Details

Format: Microsoft Excel

Size: 922 KB


Citation: A. Bensimon, A. Schmidt, Y. Ziv, R. Elkon, S.-Y. Wang, D. J. Chen, R. Aebersold, Y. Shiloh, ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage. Sci. Signal. 3, rs3 (2010).

© 2010 American Association for the Advancement of Science


To Advertise     Find Products


Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882