User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/11/04

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Noise
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Noise in protein abundance
Today I am reading the paper:

A. Bar-Even, J. Paulsson, N. Maheshri, M. Carmi, E. O'Shea, Y. Pilpel, N. Barkai: Noise in protein expressions scales with natural protein abundance. Nature Genetics, doi:10.1038/ng1807.

Summarizing:


 * 1) Noise versus mean protein abundance: at intermediate protein abundances the noise is strongly correlated with the mean.
 * 2) Is noise driven by global or pathway-specific factors? Noise in global or pathway specific factors may plausible explain the region of high abundance, in which noise is inversely proportional to the mean protein abundance.
 * 3) is noise driven by mRNA fluctuations? It seems that low-copy mRNA fluctuations, coupled with differential transcription rates as a major source of protein copy number variation, could explain the scaling behavior observed in the reported data.
 * 4) Is noise driven  by promoter fluctuation? If the genes are mostly off, and the average level of gene activity is modulated by tuning the 'on rate', one would obtain a dependency of the noise on the mean protein abundance as observed in the reported data (one some constraining conditions are satisfied). This result concerns steady-state behavior. In the transient case things are slightly different. the proportionality factor decreases with time as the system approaches steady state.
 * 5) The dependence of noise residuals on module affiliation. It is suggested the possibility of the existence of noise buffering devices (occurring at the higher level of cellular processing). It seems that stress genes are very noisy.

Neural networks for data matching
With the data provided by David I want to buil a neural network.


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