Data navigation on the ENCODE portal

Meenakshi S. Kagda; Bonita Lam; Casey Litton; Corinn Small; Cricket A. Sloan; Emma Spragins; Forrest Tanaka; Ian Whaling; Idan Gabdank; Ingrid Youngworth; J. Seth Strattan; Jason Hilton; Jennifer Jou; Jessica Au; Jin Wook Lee; Kalina Andreeva; Keenan Graham; Khine Lin; Matt Simison; Otto Jolanki; Paul Sud; Pedro Assis; Philip Adenekan; Stuart Miyasato; Weiwei Zhong; Yunhai Luo; Zachary Myers; J. Michael Cherry; Benjamin C. Hitz

doi:10.1038/s41467-025-64343-9

Data navigation on the ENCODE portal

Meenakshi S. Kagda
, Bonita Lam
, Casey Litton
, Corinn Small
, Cricket A. Sloan
, Emma Spragins
, Forrest Tanaka
, Ian Whaling
, Idan Gabdank
, Ingrid Youngworth
, J. Seth Strattan
, Jason Hilton
, Jennifer Jou
, Jessica Au
, Jin Wook Lee
, Kalina Andreeva
, Keenan Graham
, Khine Lin
, Matt Simison
, Otto Jolanki

Paul Sud, Pedro Assis, Philip Adenekan, Stuart Miyasato, Weiwei Zhong, Yunhai Luo, Zachary Myers, J. Michael Cherry, Benjamin C. Hitz

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

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.

Original language	English
Article number	9592
Journal	Nature Communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-025-64343-9
State	Published - 1 Dec 2025
Externally published	Yes

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General
General Physics and Astronomy

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Kagda, M. S., Lam, B., Litton, C., Small, C., Sloan, C. A., Spragins, E., Tanaka, F., Whaling, I., Gabdank, I., Youngworth, I., Strattan, J. S., Hilton, J., Jou, J., Au, J., Lee, J. W., Andreeva, K., Graham, K., Lin, K., Simison, M., ... Hitz, B. C. (2025). Data navigation on the ENCODE portal. Nature Communications, 16(1), Article 9592. https://doi.org/10.1038/s41467-025-64343-9

@article{aad63963c1f4446eb7f21cb7580a61a2,

title = "Data navigation on the ENCODE portal",

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.",

author = "Kagda, \{Meenakshi S.\} and Bonita Lam and Casey Litton and Corinn Small and Sloan, \{Cricket A.\} and Emma Spragins and Forrest Tanaka and Ian Whaling and Idan Gabdank and Ingrid Youngworth and Strattan, \{J. Seth\} and Jason Hilton and Jennifer Jou and Jessica Au and Lee, \{Jin Wook\} and Kalina Andreeva and Keenan Graham and Khine Lin and Matt Simison and Otto Jolanki and Paul Sud and Pedro Assis and Philip Adenekan and Stuart Miyasato and Weiwei Zhong and Yunhai Luo and Zachary Myers and Cherry, \{J. Michael\} and Hitz, \{Benjamin C.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

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doi = "10.1038/s41467-025-64343-9",

language = "English",

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journal = "Nature Communications",

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Kagda, MS, Lam, B, Litton, C, Small, C, Sloan, CA, Spragins, E, Tanaka, F, Whaling, I, Gabdank, I, Youngworth, I, Strattan, JS, Hilton, J, Jou, J, Au, J, Lee, JW, Andreeva, K, Graham, K, Lin, K, Simison, M, Jolanki, O, Sud, P, Assis, P, Adenekan, P, Miyasato, S, Zhong, W, Luo, Y, Myers, Z, Cherry, JM & Hitz, BC 2025, 'Data navigation on the ENCODE portal', Nature Communications, vol. 16, no. 1, 9592. https://doi.org/10.1038/s41467-025-64343-9

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AU - Kagda, Meenakshi S.

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AU - Litton, Casey

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AU - Sloan, Cricket A.

AU - Spragins, Emma

AU - Tanaka, Forrest

AU - Whaling, Ian

AU - Gabdank, Idan

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AU - Strattan, J. Seth

AU - Hilton, Jason

AU - Jou, Jennifer

AU - Au, Jessica

AU - Lee, Jin Wook

AU - Andreeva, Kalina

AU - Graham, Keenan

AU - Lin, Khine

AU - Simison, Matt

AU - Jolanki, Otto

AU - Sud, Paul

AU - Assis, Pedro

AU - Adenekan, Philip

AU - Miyasato, Stuart

AU - Zhong, Weiwei

AU - Luo, Yunhai

AU - Myers, Zachary

AU - Cherry, J. Michael

AU - Hitz, Benjamin C.

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AB - 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.

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SN - 2041-1723

VL - 16

JO - Nature Communications

JF - Nature Communications

IS - 1

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Data navigation on the ENCODE portal

Abstract

ASJC Scopus subject areas

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