Visualisation Of Multiple Gene Expression Profiles

Question

[David Westergaard]

Hello,

I have identified Gene Expression Profiles for 15 different vegetables, and I now wish to visualise the results. Normally, one could use a variety of tools to do this. E.g. iPath (http://pathways.embl.de/), BiNGO for Cytoscape (http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html), Reactome (http://www.reactome.org/ReactomeGWT/entrypoint.html) or DAVID (http://david.abcc.ncifcrf.gov/) or any of the other methods suggested in http://www.nature.com/nmeth/journal/v7/n3s/full/nmeth.1436.html - This seems to only deal with situations where you have 1-2 particular Gene Expression Profiles

I cannot make 15 individual plots to be included in a report. I have made a heatmap to compare Expression Profiles on Genesymbols alone. This does not, however, indicate if any particular pathway is enriched, so to speak.

In all honesty, I am not quite sure what kind of visualition I am looking for, but I am open for ideas. I have the data in a format so I know by how great a factor some gene is up or downregulated.

Answer 1

[Michael Kuhn]

You could try to get (for each species) the median expression across all the genes in the different pathways. So basically you convert your heatmap of gene symbols to a heatmap of pathways.

[David Westergaard]

I'm not quite sure that would present very good results. The experiments are done on various arrays, which means that expression levels between experiments are not really comparable, and that the sets of genes measured in each experiment are not necessarily the same.