There are a number of advantages to using iPathwayGuide beyond it being 100% free to use, but the key difference is that we use Impact Analysis to score the pathways. With these data we provide a free platform to look at your data in the context of Genes, GO Tems, Predicted miRNAs, Pathways, or Diseases.

custom *.txt file (must have gene symbol, FC, p-value).The application now accepts a wide variety of gene-expression data including: It made me realize it's time for an update about iPathwayGuide. Thanks to Kissaj for bringing this back to the top. At the PathVisio download page we also offer converted KEGG pathways for many species that you could also analyze using PathVisio. You might also want to try our own WikiPathways and the accompanying pathway analysis tool PathVisio. Check out Pathwaycommons for a kind of integrated approach (that includes Reactome a.o). That being said there are a lot of freely available pathway analysis tools and pathways. Although all the content they offer is based on knowledge freely available in other pathway databases (Ingenuity started with a lot of KEGG pathways) and the literature.

So if you did something specifically in Ingenuity or want to reproduce that you might not easily find an alternative. Ingenuity is quite good in the cardiovascular field and GeneGo's Metacore is good Toxicology for instance (and more metabolite directed research in general). The thing is that all those commercial pathway providers like Ingenuity and GeneGO offer a lot of content that they developed in house for specific fields.

Pathway download