Context effects on gene expression dynamics
In this tutorial we will show how to obtain figures 6A and 6B from the paper (REF) using the View page. This figure aims to compare the expression rate profiles of two plasmids for which 2 transcriptional units (TUs) have been flipped, named pAAA and pAAAF. The TUs' architectures are, respectively:
Click on the 
button and select the following filters for the Query tab:
- Studies: "Context effects".
- Assays: Leave the default (all studies).
- Vector: "pAAA", "pAAAF".
- Strain: "MG1655z1".
- Media: "M9-glucose".
- Signal: "OD", "RFP", "YFP", "CFP".
In the Analysis tab select:
- Analysis: Expression rate (direct)
- Reporter Degradation: 0
- Insignificant Value: 1e-6
- _Std. Devs: 2
- Min. Biomass: 0.05
- Biomass Signal: "OD"
Now for Plot Options tab select:
- Normalize: "Mean/std".
- Subplots: "Vector".
- Lines/Markers: "Signal".
- Plot: "Mean".
Hit the plot button and you will obtain the figure:
