Rescuing biologically relevant consensus regions across replicated samples.

ABSTRACT:

Background

Protein-DNA binding sites of ChIP-seq experiments are identified where the binding affinity is significant based on a given threshold. The choice of the threshold is a trade-off between conservative region identification and discarding weak, but true binding sites.

Results

We rescue weak binding sites using MSPC, which efficiently exploits replicates to lower the threshold required to identify a site while keeping a low false-positive rate, and we compare it to IDR, a widely used post-processing method for identifying highly reproducible peaks across replicates. We observe several master transcription regulators (e.g., SP1 and GATA3) and HDAC2-GATA1 regulatory networks on rescued regions in K562 cell line.

Conclusions

We argue the biological relevance of we

SUBMITTER: Jalili V 

PROVIDER: S-EPMC10246347 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature