Expanding the Functional Atlas of human Enhancer RNAs Beyond the Nucleus
eRNAkit is the first comprehensive resource specifically designed to investigate the cytoplasmic functions of enhancer RNAs (eRNAs). It integrates a suite of analytical workflows for processing and analysing eRNA-related data, facilitating tasks such as data manipulation, statistical analysis, and visualisation.
To assist users, eRNAkit provides a transcriptome-wide map of:
- eRNA subcellular localisation
- eRNA-mRNA interactions
- Expression speificity across major tissues and primary cell types
- eRNA-ribosome associations
These insights help elucidate the functional roles of eRNAs beyond the nucleus. We are currently working on expanding the analytics workflows and database to include - additional utility functions and profiles of eRNA under various stress conditions "STRESS eRNA".
The recommended way to install eRNAkit and its associated database is by running:
devtools::install_github("username/eRNAkit")
Most dependencies should install automatically. If not, install them manually using:
install.packages(c("tidyr", "dplyr", "ggplot2", "igraph", "data.table", "rintrojs", "shiny"))BiocManager::install("GenomicRanges")
The first run of the eRNAkitApp should also install any missing packages automatically.
Standard bioinformatics files such as .bed, .gtf and .fa are available in the downloads folder in the root directory.
Combinations of files needed for integration into other workflows are also provided.
The emi.rds database file includes a core table that can be used to recreate key resources.
For windowed analysis, 100bp windows of sufficiently long eRNAs are included in the donwloads folder.
To generate windows of custom lengths, use the make_window() function in eRNAkit.
Description of the implemented functions are described in eRNAkit_0.2.1.pdf file in the root directory.
eRNAkit: Expanding the Functional Atlas of human Enhancer RNAs Beyond the Nucleus Natalia Benova, Rene Kuklinkova, Mahmoud Eldahshoury, Chinedu A. Anene