Question: Plot of up and down regulated metabolic pathways in this way
gravatar for khhgng
2.7 years ago by
khhgng60 wrote:

Dear all,

Can anyone help me with this kind of plot ?

How can I plot biochemical pathways in terms of fraction of samples that are either up or down regulated from transcriptomic data.

I guess if a similar approach can be used for plotting data from single (in terms of genes up or down in a pathway) or multiple experiments data in terms of samples ?

Reference :


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plot kegg R • 967 views
ADD COMMENTlink modified 2.7 years ago by Lluís R.890 • written 2.7 years ago by khhgng60
gravatar for Lluís R.
2.7 years ago by
Lluís R.890
Spain, Barcelona
Lluís R.890 wrote:

The relevant section of the methods is "Identification of metabolic pathways with significant expression changes." and "Statistical significance of the observed metabolic pathway expression patterns.".

  • You need to calculate if a pathway in up or down regulated for each of sample (tumor, condition, strain,...).

    You can calculate this with GSVA package to calculate the enrichment score of each pathway per sample plus limma to find if the pathway is differentially expressed in Bioconductor.

  • Then calculate the fraction of samples that a pathway is significantly differently expressed both up and down-regulated, that is your n and m.
  • With this information for each pathway you can draw this plot.
ADD COMMENTlink written 2.7 years ago by Lluís R.890

Thanks. I am new to such analysis and R so its difficult to follow the methods section exactly. Two things:

Just to clarify, this n would be a simple fraction i.e. No. of samples where pathway is upregulated/ Total samples used in analysis ?

And, Can the scatterplot function be used to draw the plot with this dashed line indicating the cut off (20% in this case) ?

ADD REPLYlink written 2.7 years ago by khhgng60

Yes, n and m are simple fractions. The scatterplot will only plot the points for each pathway but then you can add the dashed lines with abline. Check the help of the functions about how do they work.

ADD REPLYlink written 2.7 years ago by Lluís R.890
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