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QUESTIONS AND ANSWERS

DR. JENSEN: I am interested in the motif-finding aspect. Usually, with these algorithms you find all frequently occurring patterns, and then at some point you go on threshold. You say, you know things about the threshold, those are unexpected things, but because of the nature of them it is often difficult to do good hypotheses tests and say where we should draw that threshold. So, what approach did you use for saying these are motifs that seem big and interesting?

DR. IYENGAR: Actually, I did not have a real initial statistical threshold, because I was going from a biological point of view. The protein that participated was known to have important biology.

REFERENCES

Bhalla, U.S., and R. Iyengar. 1999. “Emergent properties of networks of biological signaling pathways.” Science 283:5400.

Bhalla, U.S., P.T. Ram, and R. Iyengar. 2002. “MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network.” Science 297:5583.

Eungdamrong, N.J., and R. Iyengar. 2007. “Compartment specific feedback loop and regulated trafficking can result in sustained activation of ras at the golgi.” Journal of Biophysics 92:808-815.

Jordan J.D., E.M. Landau, and R. Iyengar. 2000. “Signaling Networks: Origins of Cellular Multitasking” Cell 103:193-200.

Ma’ayan, R., R.D. Blitzer, and R. Iyengar. 2005. “Toward Predictive Models of Mammalian Cells.” Annual Review of Biophysics and Biomolecular Structure 34:319-349.



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