Tutorials

Visualizing RNA-seq data on human metabolic pathways

In this tutorial, we will grab a public RNA-seq dataset, format it for Escher, and visualize it on a number of human metabolic pathway maps.

First, the dataset we are interested in this paper:

Donohoe, D. R., Collins, L. B., Wali, A., Bigler, R., Sun, W., & Bultman, S. J. (2012). The Warburg Effect Dictates the Mechanism of Butyrate Mediated Histone Acetylation and Cell Proliferation. Molecular Cell, 48(4), 612–626. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3513569/

The raw data from this paper can be found on GEO, here. This R script will grab the raw data and run a quick normalization. You’ll need to install GEOquery, org.Hs.eg.db, and limma if you haven’t aleady.

If you like, you can skip the R script step and download my normalized data output.

Visualizing FBA fluxes for Escherichia coli

In this tutorial, we will generate a predicted flux state using COBRApy and FBA, and we will visualize the fluxes on the metabolic maps of Escherichia coli.

If you have never used the COBRA toolbox or COBRApy, this tutorial may be a little confusing. But you will still get to see the options for flux visualization in Escher, so don’t be perturbed. In fact, if you are totally uninterested in COBRA modeling, skip ahead to Visualizing flux on the Escher map.

Generate a flux vector using COBRApy

Visualizing flux on the Escher map

• discuss foward and reverse flux visualization, and the effect of absolute value
• show differential flux vs. options + mention the current bug

Visualizing yeast metabolomics data

Coming soon.