Hi, I am setting up and automating some RNA-seq downstream analysis steps for a lab that works mostly with mouse and have lots of samples and wants to explore with different cutoffs (thus multiplying the lists of genes that one would upload in an online tool). I adapted and automated successfully a in jupyter notebook a process that reads the different .csv files from a folder (the different results from DESeq2 based on different cutoffs for padj and FC) and, by relying on the the EnrichR API, I can obtain the needed enrichment files and plot them via seaborn as desired.
Now, I wanted to double check the same lists on ShinyGO v0.75, another tool that should perform pretty much the same (I was expecting the same results). ShinyGO offers the possibility to select your species, while enrichR should be adapted for human/mouse. What I have noticed is that ShinyGO result for mouse is very different from enrichR result for the same terms requested (eg, GO biological process. One scores mostly for ubiquitination while the other goes with some metabolic processes). By changing the ShinyGO species to human (even if my dataset is mouse), the analysis now shows the same for 90% (just arranged slightly different/some differences in the bottom but top results are the same and the context is now the same).
I think ShinyGO is more reliable since it compares with GO lists specifically for mouse, but this tools lack an API or integration to work in an automated way (as far as I know or can understand). I did some research but I cannot find any consensus or suggested tool for an automated analysis for mouse GO terms enrichment. Doing this manually, by uploading, arranging, and downloading the graphs and files for every cutoff would be painful and time consuming.
Is there any tool, package or way that you could suggest or think of to perform GO enrichment analysis specifically for mouse in an automated way (ie, having dozens of different list at a time)?
Thanks!
PS: by some additional research I have noticed which are the pathways utilized by ShinyGO here for mouse. It is not super informative, but I think they refer to http://www.informatics.jax.org/downloads/reports/index.html#go the international database resource for laboratory mouse. I would love to be able to upload or use custom libraries with EnrichR, but this does not seem possible.
