Hello

I performed a ChIP Seq experiment and performed these steps MACS, CEAS, Gene Ontology Enrichment with GREAT .

I have some enriched terms as well as enriched pathways such as PTEN Signalling pathway, WNT pathway etc.

From my information how can I find the genes which are up or down regulated and the effects they are having on these pathways?

How far can I go with my ChIP-Seq analysis after Gene Ontology Analysis to find the meaning of my enriched terms and pathways?

Thanks
Benjy



You can find the up/down regulated genes by performing RNAseq. You're done analysing the ChIPseq data, do the wetlab experiment.