I'm a newbie to bioinformatics so apologies for the naivety of my question. I'm doing RNASeq analysis on a list of genes (bacterial genome) under one condition vs another. After using the DESeq2 package in R, I have a list of up+downregulated DE genes. I did gene enrichment analysis on them using PANTHER GO and got back a list of significant pathways (p<0.05 with no correction method).
Next, I've inputted the genes under each pathway that PANTHER outputted into KEGG search&color mapper and have now have a set of several pathway maps, colored based on the genes I inputted. Just to clarify I've a set of maps that color the genes that are downregulated and another set of maps that color the genes that are upregulated.(Some of the these maps cross over i.e I have one map with 1 gene upregulated under the TCA cycle and another with 3 genes downregulated under the TCA cycle). The pathways fall under metabolic pathways, amino acid biosynthesis and nucleotide biosynthesis etc.
I'm a bit stuck on where to go from here. Ideally I'd like to have the significant pathways belonging to say amino acid biosynthesis all together on the one map with upregulated genes colored in one color and downregulated genes in another. Any suggestions on websites/apps to use? Or is there a method in KEGG to do this? Thanks in advanced for your help!