Data navigation on the ENCODE portal

Meenakshi S. Kagda(Stanford University), Bonita R. Lam(Stanford University), Casey Litton(Stanford University), Corinn Small(Stanford University), Cricket A. Sloan(Stanford University), Emma Spragins(Stanford University), Forrest Y. Tanaka(Stanford University), Ian Whaling(Stanford University), Idan Gabdank(Stanford University), Ingrid Youngworth(Stanford University), J. Seth Strattan(Stanford University), Jason Hilton(Stanford University), Jennifer Jou(Stanford University), Jessica Au(Stanford University), Jin‐Wook Lee(Stanford University), Kalina Andreeva(Stanford University), Keenan Graham(Stanford University), Khine Lin(Stanford University), Matt Simison(Stanford University), Otto Jolanki(Stanford University), Paul Sud(Stanford University), Pedro Assis(Stanford University), Philip Adenekan(Stanford University), Stuart R. Miyasato(Stanford University), Weiwei Zhong(Stanford University), Yunhai Luo(Stanford University), Zachary Myers(Stanford University), J. Michael Cherry(Stanford University), Benjamin C. Hitz(Stanford University)
Nature Communications
October 30, 2025
10.1038/s41467-025-64343-9
Cited by 22Open Access
Full Text

Abstract

Spanning two decades, the collaborative ENCODE project aims to identify all the functional elements within human and mouse genomes. To best serve the scientific community, the comprehensive ENCODE data including results from 23,000+ functional genomics experiments, 800+ functional elements characterization experiments and 60,000+ results from integrative computational analyses are available on an open-access data-portal ( https://www.encodeproject.org/ ). The final phase of the project includes data from several novel assays aimed at characterization and validation of genomic elements. In addition to developing and maintaining the data portal, the Data Coordination Center (DCC) implemented and utilised uniform processing pipelines to generate uniformly processed data. Here we report recent updates to the data portal including a redesigned home page, an improved search interface, new custom-designed pages highlighting biologically related datasets and an enhanced cart interface for data visualisation plus user-friendly data download options. A summary of data generated using uniform processing pipelines is also provided.

Related Papers

No related papers found

Powered by citation graph analysis