i have RNA transcriptomic data and i would like to select a pathway for further analysis, but in transcriptomic ,have many pathways, so on which basis, and how to select a specific path way?
In the BIOCONDUCTOR, you will get GEO packages. Those packages are well descriptive and easy to use, will help you to analyse Gene-to-pathway data.
Saurabh Mandal Dear can you share with me the link about BIOCONDUCTOR, , GEO packages , as i will use step by step,
as its my first time to do these analysis, and have no such experience in it
You can do a quick ontology enrichment with gene lists using the web tools for reactome, panther, GO or other public ontologies (just search for any of those, upload your gene lists and run the analysis). An over-representation analysis will tell you how many and what elements in your gene list overlap with the defined elements in an ontology pathway as well as a p-value (or FDR) of the significance of that overlap. An established best practice for picking gene lists for over-representation analysis is to pick those that are both statistically significantly differentially expressed (typically with an FDR
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