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