Hello,
I have some metatranscriptomics data that was processed by MG-RAST. A recent tool added to the MG-RAST analysis line-up, called KEGG Mapper, extrapolates the RNA-Seq annotation data onto KEGG pathways in a graphical, interactive map of all biological systems within a cell. This is great for comparing different treatments and inspecting the map for treatment-specific missing pathways, but it doesn't provide any direct means for seeing which pathways have the largest statistically significant fold change.
So, does anyone know of any software that can input any of the MG-RAST flavors of output, and conduct such pathway differential expression? Ideally, I would like to be able to specify some level of hierarchy (general metabolism, TCA cycle, protein degradation for input into TCA, etc) and then determine the statistically significant fold change of the pathway's expression between several treatments.
If you have multiple suggestions, please include them in your answers/comment, and I'll consolidate the results.
Thanks!
If anyone has a suggestion, please let me know and I'll make a list with each software's attributes!
Hi JacobS,
I am also interested doing things in same line. Have you got any reply or have found out the solution?