eRNA-IDO

eRNA-IDO integrates computational modules for the identification, interactome discovery, and functional annotation of human enhancer RNAs.

Key Features:

• eRNA-ID module: Identifies eRNAs from de novo assembled transcriptomes using eight kinds of enhancer markers for customizable enhancer region definition.
• eRNA-Anno module: Provides cell- and tissue-specific functional annotation for new and known eRNAs by analyzing the eRNA interactome from prebuilt or user-defined networks between eRNAs and protein-coding genes.
• Prebuilt networks: Includes Genotype-Tissue Expression (GTEx)-based co-expression networks in normal tissues, The Cancer Genome Atlas (TCGA)-based co-expression networks in cancer tissues, and omics-based eRNA-centric regulatory networks.

Scientific Applications:

• eRNA identification: Enables discovery of eRNAs from de novo assembled transcriptomes with flexible enhancer marker selection.
• Interactome analysis: Supports investigation of eRNA interactions with protein-coding genes through co-expression and regulatory networks.
• Functional annotation: Facilitates research on eRNA biogenesis and functions through cell- and tissue-specific functional characterization.

Methodology:

eRNA-IDO comprises two modules: eRNA-ID for eRNA identification from de novo assembled transcriptomes using eight enhancer markers, and eRNA-Anno for functional annotation via analysis of eRNA interactome networks.