fourSynergy: ensemble-based interaction calling on 4C-seq data using gradient-free optimization

Abstract

Abstract Background Chromatin organization plays a crucial role in gene regulation and is associated with various severe diseases like cancer. Since chromatin changes are potentially reversible, a deeper understanding of the alterations could be harnessed for the development of new therapies. Circular Chromosome Conformation Capture Sequencing (4C-seq) is a sequencing technique enabling the identification of chromatin interactions between genes and regulatory elements. This work aims to develop an ensemble algorithm that utilizes synergies among available 4C-seq tools, which in turn allows to achieve improved 4C-seq chromatin interaction calling. We employed existing 4C-seq algorithms using a weighted-voting approach. By optimizing the tool weights according to various predictive performance metrics using gradient-free optimization strategies, we demonstrate the potential of combining multiple 4C-seq analysis tools for interaction calling. Results Our results demonstrate that a weighted-voting-based ensemble approach significantly improves predictive performance in chromatin interaction detection in a leave-one-group-out cross-validation setting, achieving a mean F1-score of 0.31 and a mean AUPRC of 0.34, compared to 0.13 and 0.16, respectively. To make this approach accessible, we integrated it into fourSynergy, a 4C-seq analysis framework focusing on near-bait 4C-seq interactions that includes a Snakemake pipeline, an R/Bioconductor package, and an interactive Shiny application. Conclusions This work provides not only a comprehensive curated collection of 4C-seq datasets, but also demonstrates that ensemble approaches can improve predictive performance in chromatin interaction detection compared to individual 4C-seq algorithms.