Attractor Landscape Analysis Reveals Feedback Loops in the p53 Network That Control the Cellular Response to DNA Damage

Minsoo Choi, Jue Shi, Sung Hoon Jung, Xi Chen, Kwang-Hyun Cho*

*To whom correspondence should be addressed. E-mail: ckh{at}kaist.ac.kr

This PDF file includes:

• Text (sections 1 to 4)
• Fig. S1. The attractor landscapes of the p53 regulatory network in normal cells under different conditions.
• Fig. S2. The attractor landscapes of the p53 regulatory network in MCF7 cells in the absence and presence of DNA damage and with different inhibitory treatments.
• Fig. S3. Robustness of the cyclic attractor against µ and c.
• Fig. S4. Knockdown of Wip1 by RNAi in MCF7 cells.
• Fig. S5. Transformation of a state transition logic into a linear function with the weight of each link and the base level (the basal activity) of each node.
• Table S1. Positive and negative feedbacks interlinked through p53 in the p53 network.
• Table S2. The stable states of the p53 network in response to each of the single node deletions.
• Table S3. The stable states of the p53 network in response to each of the single link deletions.
• Table S4. Boolean rules specifying the state transition logic.
• Tables S5 and S6 legends
• References (53–107)
• Movies S1 to S5 legend
  

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Other Supplementary Material for this manuscript includes the following:

• Table S5 (Microsoft Excel format). All the state transition logics and the range of possible parameter sets for each node that satisfy the same state transition logic.
• Table S6 (Microsoft Excel format). A list of all states in the deterministic Boolean network together with the corresponding potential energy in the probabilistic Boolean network.
• Movie S1 (.avi format). Supporting movie of p53 dynamics under etoposide alone.
• Movie S2 (.avi format). Supporting movie of p53 dynamics under etoposide + nutlin-3.
• Movie S3 (.avi format). Supporting movie of p53 dynamics under etoposide + Wip1 knockdown.
• Movie S4 (.avi format). Supporting movie of p53 dynamics under etoposide + nutlin-3 + Wip1 knockdown.
• Movie S5 (.avi format). Supporting movie of p53 dynamics under nutlin-3 + Wip1 knockdown.

[Download Movies S1 to S5 (Compressed)]

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© 2012 American Association for the Advancement of Science