Is there a tool that can identify both upregulated and downregulated genes from RNA-seq data that are specifically involved in the apoptosis pathway? I am interested in filtering for genes linked to apoptosis only. Any suggestions?
So, in short the first thing you should do is getting to a list that includes all apoptosis-related genes. (Using KEGG, Reactome and GO). Next, you would want to run a GSEA analysis on your gene list (It's important to set the right parameters). You will then have enrichment scores and p-values which allow you to identify ones with significant up- or down-regulated expression values (Visualization and looking for literature support are necessary steps).