We would like you to have a look at the website http://pcxn.org/ and provide a brief critique of no more than 200 words.
To guide you, we've written out a suggestion to get you started (below). Please try this and spend about 10 minutes having a poke about. Write up your thoughts, paying particular attention to what you would do to improve things.
Please e-mail your written critique (200 words max) to david.r.jones@sheffield.ac.uk; Any questions or clarifications to the same e-mail address.
pcxn.org is a tool that allows you to explore co-activity relationships between pathways.
To start with you will need to paste a list of pathways into the first text box, labelled "Find correlation among gene sets up-regulated in phenotype 0". Use the gene list below as an example:
Pentose and glucuronate interconversions (KEGG)
Fructose and mannose metabolism (KEGG)
Lysine degradation (KEGG)
Starch and sucrose metabolism (KEGG)
Pantothenate and CoA biosynthesis (KEGG)
Nitrogen metabolism (KEGG)
Phase I, non P450 (Wikipathways)
Ganglio Sphingolipid Metabolism (Wikipathways)
Urea cycle and metabolism of amino groups (Wikipathways)
Biogenic Amine Synthesis (Wikipathways)
{POR,15} (Static Module)
{SREBF1,11} (Static Module)
Prion diseases (KEGG)
These are genes from the pathprint database, so you will need to select Pathprint from the dropdown labelled "The gene sets are from".
Then press GO.
You should see a screen with a heatmap on the left and a network graph on the right.
Please explore and write up your thoughts and send them (200 words max) to david.r.jones@sheffield.ac.uk.