Upregulated and downregulated genes from ChIP-seq data

Question

[Sowmya Pulapet]

Hello everyone, I really want to know whether it's possible to perform DEG analysis (need upregulated and downregulated genes) with ChIP-seq data. All I could find was that it's possible to integrate RNAseq data and ChIPseq data.

What I want is to identify the upregulated and downregulated genes but I am not sure on accuracy of the concept. I have already performed peak calling and motif analysis with the ChIP-seq data.

Hope someone would help me. Thanks in advance !

[ATpoint]

ChIP-seq does not measure RNA levels, as such you cannot do expression analysis. What is your experimental setup? Do you have ChIP-seq in different conditions?

[Sowmya Pulapet]

Yes, I have control and treated samples in ChIP-seq data. My exact need is to get the downregulated and upregulated genes. But as I said I am not sure whether the concept is right.

[ATpoint]

No, you cannot directly investigate gene expression from ChIP-seq data. What you can do are predictions. If your factor is known to suppress transcription then you could predict that increased binding would enhance transcription of nearby genes and vice versa. Still, this is very unspecific and imprecise as it assumes that spatial proximity of a gene and a protein binding are actually causally related which is not necessarily the case, so it's a crude analysis without RNA-seq.

[Sowmya Pulapet]

Thank you for the clarification !

Answer 1

[Ian]

I am assuming that you are referring to DNA binding, as opposed to actual gene expression here. If so I would recommend DiffBind. This does assume you have replicates of samples in each group. Without replicates you could try MAnorm.

[Sowmya Pulapet]

Alright, Thank you.