I was wondering if it does exist a similar tool, but free... I' trying to reproduce some results I found on a recent paper, and I would rather prefer to try with a different tool. Otherwise, I think I'll go with the 2 free weeks that they offer...
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. Ingenuity is quite good in the cardiovascular field and GeneGo's Metacore is good Toxicology for instance (and more metabolite directed research in general). So if you did something specifically in Ingenuity or want to reproduce that you might not easily find an alternative. 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.
That being said there are a lot of freely available pathway analysis tools and pathways. Check out Pathwaycommons for a kind of integrated approach (that includes Reactome a.o). You might also want to try our own WikiPathways and the accompanying pathway analysis tool PathVisio. At the PathVisio download page we also offer converted KEGG pathways for many species that you could also analyze using PathVisio.
QuaternaryProd is an open-source alternative to IPA. It is an R package which can be used to predict upstream regulators given gene expression data. The R package uses StringDB and the "Quaternary Statistic" for performing causal inference.
The R package can be downloaded from Bioconductor (link) and the latest version is on github (link)
Ingenuity's pathways and networks are available for free in Sigma's Your Favorite Gene powered by Ingenuity tool. There are also several other datasets consolidated in one location, as well as a tag cloud view of PubMed literature.
HumanCyc plus Pathway Tools provides another set of options. HumanCyc has well
curated content on human metabolic pathways. The associated Pathway Tools software
will let you paint gene expression, proteomics, or metabolomics data onto the
HumanCyc pathway map, and Pathway Tools will also perform enrichment analysis.
See BioCyc.org. The pathway painting is available through the web site,
but to perform enrichment analysis you must download and install the software.
Thanks to Kissaj for bringing this back to the top. It made me realize it's time for an update about iPathwayGuide.
The application now accepts a wide variety of gene-expression data including:
Affy CEL files
custom *.txt file (must have gene symbol, FC, p-value)
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. 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. This approach uses two forms of evidence to score pathways, enrichment and perturbation.
Some of the new features since my last post in this thread include:
Predicted miRNA Analysis - We offer evidence of possible active miRNAs based on gene-expression signatures
Meta-Analysis - Quickly compare unique or common significant elements between experiments.
Affy CEL file support - Upload your CEL files directly and find your DEGenes in a couple minutes
I would also recommend GATHER for a quick-function enrichment tool (for KEGG pathways) along with several other categories.
I also developed a tool called BD-Func, which includes some categories that people would probably consider "pathways" (such as transcriptional regulators and some signatures for signaling pathways), although it tends to be most useful for custom signatures.
Of course, there are also tools like GSEA, FuncAssociate, DAVID, etc. (if you are more broad in what you define as a "pathway")
Moksiskaan is an integrative pathway analysis tookit, which supports data sources such as Ensembl, KEGG, PINA, PathwayCommons, DrugBank, GO, SNPs3D, COSMIC, WikiPathways, Tumourscape, and TSGene. Using the provided tools (http://csbi.ltdk.helsinki.fi/moksiskaan/anduril/index.html?q=Moksiskaan%20project), you can prepare all sorts of graph models representing genes, proteins, drugs, pathways, diseases, biological functions, etc. related to your data. Moksiskaan is an Anduril (anduril.org) based open source project, which means that it can be used easily with other Anduril components to carry out complete analyses. Here's one example output: http://csbi.ltdk.helsinki.fi/moksiskaan/archive/ProcessStudy.pdf, but you can find more from the web site and from the supplements of the articles.
IPA looks the best tool to view enriched pathways using P value and FC value. Do you guys know any other platform that could provide enriched pathways from differentially expressed genes? All the platforms that requires gene lists are not so informative because they lack FC values.
As far as I know the only tool that actually uses the FC in the calculation to assess significance of a pathway is iPathwayGuide. IPA uses FC to select for DEGs and to perform its upstream regulator analysis, but still relies on an enrichment model to score pathways.