A Bioinformatic Framework for Enhancer RNAs Identification in Cancer Based on RNA-Seq and ChIP-Seq

Enhancer RNAs (eRNAs) are noncoding RNAs transcribed from the genomic regions of enhancers. eRNAs are increasingly recognized to play an important role in gene regulation, and they can associate with various traits in humans. Here, we provide a bioinformatic pipeline to identify eRNA expression profiles using either an in-house dataset or public datasets from large-scale samples. We also summarized approaches for the identification of eRNAs' putative regulatory network, and eRNA-correlated traits and clinical features. This workflow provides guidance for readers to use bioinformatic tools for analyzing eRNA expression and eRNA-associated traits.