Combining RNA-Seq and ChIP-Seq

Question

[benjyrolls]

Hi,

I have a list of differentially expressed genes in Cuffdiff from a mouse RNA-Seq experiment involving POU1F1 Knock Out and Wild Type mouse. Secondly, I have a list of genes from a ChIP-Seq experiment involving POU1F1 - enriched (ChIP) and WildType mouse (input DNA).

For example in the ChIP-Seq experiment I have this gene(Sbspon) which is targeted by POU1F1 and this gene is also upregulated in the RNA-Seq data.

1. Could I say in the RNA-Seq data POU1F1 is up-regulating this gene in the RNA-Seq data ?

2. Is there a way to intersect the genes in my Cuffdiff output with the gene list targeted by POU1F1 to produce a Venn diagram showing a list of the intersecting genes?

thanks

Benjy

[Ben]

About the first question, you need to do qRT-PCR and ChIP-qPCR to validate the results you analyzed. Second question, you need to annotate the peaks, then you can obtain a Venn diagram.

Answer 1

[Kristoffer Vitting-Seerup]

1: That is a good hypothesis - but you cannot be sure that is the way it happens (the difference between correlation and causation). To really show that you would need to go into the lab and do some experiments that affected the POU1F1's ability to bind to your gene and then observe the gene was not upregulated anymore. Currently state-of-the-art would probably be to do CRISPRi against the POU1F1 binding site.

2: Not competely sure what you are asking - a webtool such as this?