Interpreting Chip Seq Results

Question

[benjyrolls]

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

[venu]

It is really difficult/ not possible to give suggestions based on the information you provided. Would be helpful if you give more details like which histone mark / TF ChIP data you are analysing, which disease context the analysis based on, because PTEN, WNT pathway may not be useful for some diseases. Do you have RNA-seq data or microarray gene expression data?

btw, what is you aim/hypothesis behind analysis?

Answer 1

[Devon Ryan]

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