Hello everyone I am doing RNA seq analyses, I am studying genes pathway. I am using IPA ingenuity and ipathway Guide. My problem I got lost and I do not know how to choose the most precise and accurate pathway. Are there any specific points to follow to finish the analyses?.
Best Shaima
I believe you have IPA pathway guide with you. For IPA if you are doing pathway analysis with the differential analysis I believe and you did the core tox analysis. The most detailed way to do is to put both up and down regulated list of genes in the first column and then in the second column of the input file should be your log transformed fold-changes with sign. This will enable you to see for specific pathways which gene from your list are up/down regulated in the pathway of interest. One thing which I suggest is to use the species and the stringency filters before running the analysis. It should correspond to what species your data is from. Once you have the results you should be able to look into the tab of canonical pathways. You can customize for your target pathways as well or you can just filter for FDR and then select and download the pathway list. Then the tab delimited file you are using will show list of pathways with the enrichment and the p-value and the qvalue and you can sort the list according to your highest significance calls.
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Those commercial programs cost a pretty penny! You should get in touch with the tech support at Ingenuity and have them guide you.
The title of your post appears to be misleading since you must have completed your RNAseq analysis before trying Ingenuity pathway mapping. Or are you trying to use Ingenuity as your RNAseq analysis program?