how to filter the same GO present in both up- and down-regulated GO enrichment

[likebiology]

Hi all,

I compared two groups of transcriptomes, up- and down-regulated genes were isolated. GO enrichment was carried out on these differential expressed genes. But some GO terms are present in both groups, I think it is conflict, Could anybody explain to me is it reasonable? If not, how to filter it? Thank you!

Best regards,

[mbblack]

You mean the same GO terms in both the up-regulated and the down-regulated group? If so, sure that's highly possible. Remember that individual gene differential expression does not necessarily tell you the overall affect on a complete biochemical process or pathway. So it is very possible to have conflicting changes in separate genes in a given pathway.

All enrichment tells you is which pathways included gene products from your differentially expressed genes beyond what would be predicted by chance overlap alone. It does not tell you anything about the direction nor magnitude of change in the output of a pathway.

[likebiology]

Thank you Michael for your kind reply!

You are right. the same GO term is present in both up- and down- regulated group. I checked the genes in such GO terms and I found some of the genes are the same. So I think may be because of isoforms or bad assembly (de novo).If so, what do you suggest to do?

Thank you!

Best,