How to deal with the clusterProfiler analysis result?

Question

[Tundup]

I have done enrichGO, enrichKEGG, gseGO, gseKEGG, reactomePA for my DESeq results.

# Run enrichGO
go_up <- enrichGO(
    gene = upregulated_merged$ENTREZID,
    OrgDb = org.Mm.eg.db, 
    ont = "BP",
    pAdjustMethod = "BH",
    minGSSize = 10,
    maxGSSize = 500,
    pvalueCutoff  = 0.01,
    qvalueCutoff = 0.05,
    readable = TRUE
)
go_down <- enrichGO(
    gene = downregulated_merged$ENTREZID,
    OrgDb = org.Mm.eg.db, 
    ont = "BP",
    pAdjustMethod = "BH",
    minGSSize = 10,
    maxGSSize = 500,
    pvalueCutoff  = 0.01,
    qvalueCutoff = 0.05,
    readable = TRUE
)

This gave me lots of terms: up- 5106, down - 4833

i further used filtering like this:

#Filter and Save the lists with p.adjust<0.0001
#Filter and save the significantly enriched GO Biological Processes (BP) - for upregulated genes
go_up@result[go_up@result$p.adjust<0.0001,]%>%arrange(desc(Count))%>%
write.csv("enrichGO_results_UP.csv",row.names=F)
#Filter and save the significantly enriched GO Biological Processes (BP) - for downregulated genes
go_down@result[go_up@result$p.adjust<0.0001,]%>%arrange(desc(Count))%>%
write.csv("enrichGO_results_DOWN.csv",row.names=F)

I can still see 300,400 terms in both up and downs.

1. Usually people dotplot or barplot the top 20 go terms. In my case my study relevant terms (metabolic) are not showing up in top 20. But i can see my terms in my significant results. I do see such terms but distributed in the entire list. How should I report my results? Also what filtering or adjustment in plot i can do?

2. when I did gseKEGG it returned as NULL error. Does it mean I am not getting significant terms or am I doing some wrong?

thanks for your inputs.