try GeneSCF, simple command line tool accepts gene list and perform enrichment analysis in real-time (directly extract information from selected database). You can also choose between different database GO, KEGG, REACTOME.
Use GSEA http://software.broadinstitute.org/gsea/index.jsp I am assuming the pathway and the list of genes is same. It will give enrichment results if your pathway is upregulated or down regulated with p-values. Also you can search for your own pathways,curate your own pathways to look for enrichments in your data.