Context effects on gene expression levels

In this tutorial we will show how to obtain figures 5B and 5E from the paper (REF) using the View page. Figures 5C and 5D can be obtained using the notebook from the Flapjack's Python package.

Figure 5B

Raw data

Click on the button and select the following filters for the Query tab:

• Studies: "Context effects".
• Assays: Leave the default (all studies).
• Vector: "pAAA".
• Strain: "MG1655z1".
• Media: "M9-glucose".
• Signal: "OD", "RFP", "YFP", "CFP".

Now for Plot Options tab select:

• Normalize: "Min/Max".
• Subplots: "Vector".
• Lines/Markers: "Signal".
• Plot: "Mean".

Hit the plot button and you will obtain the figure:

Expression rate

Next, keeping the same options for Query and Plot Options, we want to obtain the Expression rate for the pAAA plasmid (go to Supp Material LINK for more information about the plasmids). In the Analysis tab select:

• Analysis: Expression rate (direct)
• _Reporter Degradation: 0
• _Insignificant Value: 1e-7
• _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:

Figure 5E

The idea of this specific figure is to study the compositional effects in the expression rates for the different plasmids. All through this figure we used the following filters in Query:

• Studies: "Context effects".
• Assays: Leave the default (all studies).
• Strain: "MG1655z1".
• Media: "M9-glucose".

In order to observe the different effects, we varied Vector and Signal, considering the figures self-explanatory for these 2 variables.

RFP

Plasmids pBAA, pBCA, pBDA, pBFA

Select in Query

• Vector: "pBAA", "pBCA", "pBDA", "pBFA".
• Signal: "RFP".

Select in Analysis:

• Analysis: Expression rate (direct)
• _Reporter Degradation: 0
• _Insignificant Value: 1e-6
• _Std. Devs: 2
• Min. Biomass: 0.05
• Biomass Signal: "OD"

In Plot Options select:

• Normalize: "Mean/std".
• Subplots: "Signal".
• Lines/Markers: "Vector".
• Plot: "Mean".

Hit Plot and you will obtain the figure:

For the rest of the plasmids, for the field Vector in Query select the plasmids of each figure.

YFP

Same as for RFP, keep the same fields selected in Query, Analysis and Plot Options, just change the Signal for "YFP" and Vector when applies. You will obtain the figures:

For the rest of the plasmids, for the field Vector in Query select the plasmids of each figure.

CFP

As for RFP and YFP, we will obtain the expression rate (direct) but for all of this study plasmids. For Vector in Query select all the plasmids: pBAA, pBCA, pBDA, pBFA, pAAA, pGDA, pGAA, pEDA, pGFA, pGEA, pECA, pEAA, pEFA, pGCA. For Signal select "CFP".

Hit Plot and you will obtain the figure: