What does "Fold change over controls" from Encode ChIP-Seq experiments mean?

Question

[marquimedes21]

Hello, everyone. I searched in ENCODE for ChIP-Seq experiments and visualized them in UCSC browser. For instance, I searched for TATA-box binding protein (TBP) assays and went to FOS' promoter to examine its TBP peaks.

I kind-of get the idea of optimal Irreproducible Discovery Rate (IDR) for the peaks, but I don't really understand the measure of "fold change over controls" that UCSC gives you along the optimal IDR. Correct me if I'm wrong, but in the ChIP-Seq experiments' metadata (from ENCODE) it was stated that there was no perturbation (no treatment, no illness, nothing) in the samples, which makes me think those are the controls. If that's the case, then what exactly do they mean with "FC over controls", if the peaks are comming from "control" samples?

Answer 1

[ATpoint]

Control most likely represents the chromatin input control that the peaks were called against, so the background levels of the assay. If this is new to you I suggest you read about ChIP-seq and what kind of controls are commonly included.

[marquimedes21]

I think it's clearer now, thank you. If I understood correctly, along with chromatine inmunoprecipitation another sample without the specific antibody is used as a control for inespecific binding and bias in the DNA sonication process. In that case I understand the FC over controls being the real representative peaks of the DNA binding protein. It was just that I thought they meant controls for induced contexts instead of the procedure controls.

For anyone who wondered the same I recomend this light introduction to ChIP-Seq experiments.