I have been stuck on this one for a while as it seems available tools are more concentrated on enrichment and differential expression at pathway level.
I am however interested in understanding if my gene-level expression data say something regarding the direction of known pathways (e.g. those available on KEGG).
With the methods I am aware of I can only say that a gene set (e.g. upregulated significant genes) is enriched in genes from a particular subset of pathways. The next logical step should be to see if such genes are enriched in enhancers of inhibitors of each pathway in order to understand if my gene set has a predominant role (and what this role is) in a biological function as a whole.
I hope in a small help from scientists more experienced than me before embarking in the development of a tool that may already exist.
Thank you in advance
Hello Matteo,
IPA software allows you to make inferences of activation of biological functions and also pathways based on the gene expression data you have. It gives you scores based on the up- downregulation of the different mollecules in your dataset that belong to the same pathway or function. But this is not a free software. I dont know if a free one exists for this purpose
Hello Mateo
Iam agree with Cristina. IPA is a good option, besides you can search whether there are miRNAs involved in your candidate pathways.
Regards
Hiya Matteo,
you may find
a) SPIA (R/Bioconductor)
b) viper (R/Bioconductor)
helpful for gene expression profiles measured via microarrays.
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