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EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions

Fig 1

Overview of the EAGLE pipeline.

Enhancers were obtained by integrating diverse high-throughput datasets and the expressed levels were estimated using RNA-seq data. We utilized six features based on the information of enhancers and gene expression. ChIA-PET or Hi-C datasets were used to define positive and negative EG pairs. Using the labeled pairs, we trained an ensemble classifier, EAGLE, which could predict enhancer-target interactions measured by prediction probabilities.

Fig 1

doi: https://doi.org/10.1371/journal.pcbi.1007436.g001