Should edge scores or topology be included Knockout Experiments Reverse

Should edge scores or topology be included knockout

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Should edge scores or topology be included?
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Knockout Experiments & Reverse Engineering Input : Signal Output : Gene expression. Given input-output relationship for normal (“wild type”) and mutant (“knockout”) cells, what can one infer about the network? Topology (hard or impossible de novo ) New interactions or signs of existing interactions.
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Sources Shen-Orr, S.S., Milo, R., Mangan, S., et al. 2002. Network motifs in the transcriptional regulation network of Escherichia coli . Nature Genetics 31, 64–68. Newman, M.E.J., Strogatz, S.H., and Watts, D.J. 2001. Random graphs with arbitrary degree distributions and their applications. Phys. Rev. E 64, 026118– 026134. Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics . 2002;18 Suppl 1:S233- 40. Chuang HY, Lee E, Liu YT, Lee D, Ideker T. 2007. Network-based classification of breast cancer metastasis. Mol Syst Biol . 2007;3:140.
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