Data navigation on the ENCODE Portal

Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data generated by the consortium is shared through a web-portal (https://www.encodeproject.org/) with no access restrictions. The fourth and final phase of the project added a diverse set of new samples (including few associated with human diseases), and a wide range of new assays aimed at detection, characterization and validation of functional genomic elements. The ENCODE data portal hosts results from over 23,000 functional genomics experiments, over 800 functional elements characterization experiments (including in vivo transgenic enhancer assays, reporter assays and CRISPR screens) along with over 60,000 results of computational and integrative analyses (including imputations, predictions and genome annotations). The ENCODE Data Coordination Center (DCC) is responsible for development and maintenance of the data portal, along with the implementation and utilisation of the ENCODE uniform processing pipelines to generate uniformly processed data. Here we report recent updates to the data portal. Specifically, we have completely redesigned the home page, improved search interface, added several new pages to highlight collections of biologically related data (deeply profiled cell lines, immune cells, Alzheimer’s Disease, RNA-Protein interactions, degron matrix and a matrix of experiments organised by human donors), added single-cell experiments, and enhanced the cart interface for visualisation and download of user-selected datasets. Along with this, we also provide a brief summary of data generated using the ENCODE uniform processing pipelines. Finally, we have added extensive help pages, tutorials and documentation to assist researchers from a variety of backgrounds in exploring the universe of ENCODE data.