elowitz_data: Expression of reporter genes in the D22 and M22 E. coli cells...

In noise: Estimation of Intrinsic and Extrinsic Noise from Single-Cell Data

Expression of reporter genes in the D22 and M22 E. coli cells from Elowitz et al (2002).

Description

Expression of reporter genes CFP and YFP in over 200 E. coli cells of two strains: D22 and M22. These values are displayed in a scatterplot in Elowitz et al (2002) Fig 3a.

Usage

data("elowitz_data")

Format

The format is: List of 2 $ D22:'data.frame': 284 obs. of 2 variables: ..$ CFP: num [1:284] 3080 3082 2893 3053 2891 ... ..$ YFP: num [1:284] 2309 2394 2145 2340 2245 ... $ M22:'data.frame': 250 obs. of 2 variables: ..$ CFP: num [1:250] 2438 2316 2521 2646 2830 ... ..$ YFP: num [1:250] 1409 1391 1511 1460 1638 ...

References

Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186.

Examples

data(elowitz_data)

# Normalize data such that they are 
# comparable to Fig 3a in Elowitz et al. (2002).
# Normalized data have mean 1.
D22.cfp.norm <- (elowitz_data$D22[,1]-mean (elowitz_data$D22[,1]))/sd(elowitz_data$D22[,1])/8+1
D22.yfp.norm <- (elowitz_data$D22[,2]-mean (elowitz_data$D22[,2]))/sd(elowitz_data$D22[,2])/8+1

M22.cfp.norm <- (elowitz_data$M22[,1]-mean (elowitz_data$M22[,1]))/sd(elowitz_data$M22[,1])/12+1
M22.yfp.norm <- (elowitz_data$M22[,2]-mean (elowitz_data$M22[,2]))/sd(elowitz_data$M22[,2])/12+1

# Compute noise estimates.
# Since the mean is 1, estimates with and without 
# the scaling are the same.
unlist (computeIntrinsicNoise (D22.cfp.norm, D22.yfp.norm))
unlist (computeExtrinsicNoise (D22.cfp.norm, D22.yfp.norm))

unlist (computeIntrinsicNoise (M22.cfp.norm, M22.yfp.norm))
unlist (computeExtrinsicNoise (M22.cfp.norm, M22.yfp.norm))

noise documentation built on May 29, 2024, 2:08 a.m.