Help understanding the data for the basic visualization tutorial

[jim.hu...@gmail.com]

I'm going through the visualization tutorial

https://cytoscape.github.io/cytoscape-tutorials/protocols/modules/basic-data-visualization/#/0/8

and I'm trying to reconstruct the biology of what is being used in the example. I've figured out that the expression data is the same as in the galExpData.csv file provided in the sampleData directory in the distribution and the README refers to

Ideker, T., Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R,
Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of
a systematically perturbed metabolic network. Science, 292, 929-34 (2001).

However, when I download the supp data excel spreadsheet from the Science website, it is not clear how the conditions and values map onto what is provided in the paper.

I have guessed that gal80RExp is the relative expression of the gal80 knockout in raffinose media. But the actual numerical values don't match so I'm guessing that some transformation has been done. Unfortunately I can't figure out what was done to generate the tutorial data from the Ideker dataset.

[Scooter Morris]

Hi Jim,
   That's a great question, but unfortunately not one that any of us know that answer to.  The galFiltered data set (and corresponding xls data) predates all of us, unfortunately, so we really don't know what the detailed history of it is.  There are a number of alternate tutorials coming out that use more recent data, including some recent TCGA data.

-- scooter