Popular tools for pathway analysis from proteomic/phosphoproteomics results

Question

[martingarridorc]

Hi!

I want to reproduce the results obtained in a paper where the authors generate a group of phosphoproteomics results under different conditions. They used the peak intensities based quantification and a software called MetaCore (not free) to make a pathway analysis.

I have heard about IPA (not free) and IPathwayGuide and I'm looking for a similar (and if its possible, free) tool. I would like to know which ones are the most popular softwares used in pathway analysis from proteomic/phosphoproteomic results and what databases do they use for it (KEGG, for example).

Thank you for your answers!!

[Jean-Karim Heriche]

It is unlikely you're going to be able to exactly reproduce results from a non-free platform using different tools because they are black boxes and, for one thing, they curate their own data sources so you usually have no idea how a result has been obtained. If you want to use other tools, it would be better if you identified more precisely what question you're trying to address or what feature you need.

[martingarridorc]

Hi again!!

I'm trying to obtain the overrepresented pathways within the data set and how do they change under the different conditions. I wonder if exists a tool similar to IPathwayGuide (but freely avaliable) in the pathway analysis field. Sorry if my question was not well oriented!

Thanks JK!

[Jean-Karim Heriche]

I am not familiar with iPathwayGuide but you can do pathway analysis on the Reactome website or on Panther's site.