Expression noise as a function of the mean.

<p>The standard deviation of the protein concentration <i>σ_g</i>/<i>g</i>₀ is plotted against the mean protein concentration <i>g̅</i> = 〈<i>g</i>〉/<i>g</i>₀, from Eq (16) with <i>h</i> = 5. In all cases the output noise term has a strength <i>α</i> = 0.01, and the different curves are indexed by the ratio of input noise to output noise <i>β</i>/<i>α</i> = 0,10,20,30. In the inset, we show the same results plotted as a fractional noise variance vs the mean [Eq (17)], on a logarithmic scale.</p

A simple model for transcriptional regulation.

<p>Transcription factor is present at an average concentration <i>c</i>, diffusing freely with diffusion constant <i>D</i>; it can bind to the binding site of linear dimension <i>a</i> and the fractional occupancy of this site is <i>n</i>∈[0,1]. Binding occurs with a second order rate constant <i>k</i>₊, and unbinding occurs with a first order rate constant <i>k</i>₋. When the site is bound, the mRNA are transcribed at rate <i>R_e</i> and degraded with rate , resulting in a number of transcripts <i>e</i>. Proteins are translated from each mRNA molecule with rate <i>R_g</i> and degraded with rate , resulting in a copy number <i>g</i>.</p

Liu et al. - BcdGFP_embryos_raw_data

High-resolution images of 28 embryos acquired by live two-photon microscopy; dorsal view, coronal plane (linear pixel dimension 0.46 micrometer). Embryos express Bcd-GFP fusion protein in a bcdE1 null mutant background (flyline 2XA). For 23 embryos two time points are provided: 16+/-2 min after mitosis 13 (for Bicoid gradient measurement) and 67+/-2 min after mitosis 13 (for cephalic furrow position measurement). Two additional embryos are provided for early time point (09 and 12); three additional embryos are provided for late time point (15, 24 and 28). Embryo 05 is missing from dataset. This dataset reproduces gradients in Figure 1C of main text

Liu et al. - LiveImaging_data_structure

LiveImaging_data_structure.mat contains a data structure named "FlyLines" with Bicoid-GFP intensity gradient and cephalic furrow (CF) position measurements of fly embryos from live two-photon imaging for 29 fly lines

Standard deviation of Hunchback expression as a function of the mean (points with error bars), replotted from Ref [32].

<p>The black line is a fit of combined output and diffusion noise contributions, from Eq (16) with <i>h</i> = 5, and the dashed red line is with <i>h</i>→∞, from Eq (18). In contrast, the dashed blue line is the best fit of combined output and switching noise contributions, i.e. (<i>σ_g</i>/<i>g</i>₀)² = <i>αg̅</i>+<i>γ</i>(1−<i>g̅</i>)²<i>g̅</i>. Although both diffusion and switching noise produce a peak at intermediate expression levels, the shapes of the peaks are distinguishable, and the data favor the diffusion noise model.</p

Logarithmic plot of fractional variance vs the mean expression level for Hunchback, replotted from Ref [32].

<p>Each black point represents the noise level measured across nuclei that experience the same Bcd concentration within one embryo, and results are collected from nine embryos. The solid line shows a fit to in the region below half maximal mean expression; we find a good fit, with <i>ζ</i> = 1.04, despite the fact that these data show a clear signature of input noise when plotted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002774#pone-0002774-g004" target="_blank">Fig. 4</a>. Dashed line indicates the global noise floor suggested in Ref <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002774#pone.0002774-BarEven1" target="_blank">[9]</a>, and red points show the raw data with this variance added. Although the input noise still appears as a drop in fractional noise level near maximal mean expression, this now is quite subtle and easily obscured by experimental errors.</p

Dubuis et al. - Processed_Profiles

Each file contains the source data for gap gene (Hb, Kr, Gt, Kni) processed dorsal gene expression levels measured using immunofluorescence techniques in 23 Drosophila embryos with FC depth comprised between 10 and 20 microns. We only selected embryos that were imaged close to their midsagittal plane (Orientation '1'). Column 1 contains the embryo number referring to its position on the slide (see Images.zip). Column 2 contains an information about the azimuthal orientation of the embryo on the slide ('1' if the confocal plane is closer to midsagittal plane, '2' if it is closer to the coronal plane). Column 3 contains the furrow canal depth (delta_FC) measured in micrometers. Column 4 contains the corresponding estimated age in minutes. Columns 5 to 1004 contain a 1x1000 vector representing the dorsal time-corrected gene expression level of the gap gene (Hb, Kr, Gt, Kni) in the embryo. The 1000 points are equally spaced along the AP axis. Thus, g345 represents the gene expression level at 34.5%EL. NaN means that we coudn't reliably detect the profile intensity at that position (usually near the edges). Columns 1-4 are identical in the four files

Dubuis et al. - Raw_Profiles

Each file contains the source data for raw gap gene (Hb, Kr, Gt, Kni) dorsal intensity profiles measured using immunofluorescence techniques in 163 Drosophila embryos during n.c. 14. Column 1 contains the embryo number referring to its position on the slide (see Images.zip). Column 2 contains an information about the azimuthal orientation of the embryo on the slide ('1' if the confocal plane is closer to midsagittal plane, '2' if it is closer to the coronal plane). Column 3 contains the furrow canal depth (delta_FC) measured in micrometers. Column 4 contains the corresponding estimated age in minutes. Columns 5 to 1004 contain a 1x1000 vector representing the dorsal intensity profile of the gap gene (Hb, Kr, Gt, Kni) in the embryo. The 1000 points are equally spaced along the AP axis. Thus, Intensity345 represents the intensity at 34.5%EL. NaN means that we couldn't reliably detect the profile intensity at that position (usually near the edges). Columns 1-4 are identical in the four files

The input–output relation for Bicoid regulation of Hunchback expression, redrawn from Ref [32] (cf. Fig. 4 of the reference).

<p>Dashed curves show mean expression levels in different embryos, thick black line is the mean across all embryos, and points with error bars show the mean and standard deviation of Hb expression at a given Bcd concentration in one embryo.</p

Liu et al. - Immunofluorescence_data_structure

ImmunoFluorescence_data_structure.mat contains a data structure named "Sessions" that contains raw gap ( Hb, Kr, Gt and Kni) and pair rule (Eve) gene expression (protein) intensity profiles measured using immunofluorescence imaging for fly embryos during n.c. 14 for 6 fly lines from our Bicoid-GFP fly line library