Differentiall analysis of chip-deq data

Question

[atsalaki]

I am new to genetics study , i dont completely understand what differentialy analysis of chip-seq data means .Whats the meaning of differentially binding sites in simple words, whats the meaning of word differentiall in biology?Can someone help?Thanks in advance!

Answer 1

[Satyajeet Khare]

Different in two conditions.

1. Protein A binds to promoter A but not promoter B
2. Protein A binds to promoter A in condition 1 but not in condition 2
3. Protein A binds but Protein B doesn't to promoter A

These are examples of differential binding.

[Chris Fields]

To add to this, the differential part is important; it's not as simple as a binary 'bound/not bound' state, since you are normally assessing DNA isolated from a population of cells which can be in various states depending on the experimental design. So, in effect you are assessing whether there is a significant switch from one state or the other based on the experimental conditions, and what you are measuring is an averaging of the states in that condition. This also underscores the need for experimental replicates.

[GouthamAtla]

And also, its not only in "promoters", it could be anywhere in the genome, especially enhancers.