STRING
available at http://string-db.org/

Just try the Biocyc omics viewer (http://biocyc.org/ov-expr.shtml), but please be sure that the right ID was choosen, because Biocyc is not able to recognize all id’s. Under tool, cellular overview you can upload your experimental data. The output is is not the nicest, but it will help you to get an overview.

You might also want to consider DAVID, http://david.abcc.ncifcrf.gov/home.jsp, which is more a functional annotation tool than a strict pathway analysis tool. However, it does offer a visualization of the genes/proteins on BioCarta & KEGG pathway maps. We have used this tool quite successfully.
As always, you have to be a bit careful what your input is, but the documentation is pretty good.

oh yes DAVID is fine too!
Just some more free tools:
KEGG Atlas, iPath, Omix, ProMeTra, PathVisio, WikiPathways, Arena3D Secrier, yED and its algorithms implemented in Cytoscape.

Thank you for the answers. Really appreciate it.

Could you suggest the best software for the pathways analysis? because String underline the connection between the proteins but it doesn’t group the proteins in biological pathways, am I wrong?