Supplementary regulatory annotations from ENCODE and DASHR2, including candidate cis-regulatory elements and small RNA gene loci.
Data in this track hub were uniformly downloaded, processed, and harmonized by FILER2. Raw files were obtained from each source repository, converted to BED/bigBed format, lifted to the target genome assembly where necessary, and annotated with standardized metadata including cell type, tissue category, and assay type.
Source: https://www.encodeproject.org
Publication: An integrated encyclopedia of DNA elements in the human genome
Citation: ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74. doi:10.1038/nature11247
Funding: The Consortium is funded by grants from the NHGRI as follows: Production Grants: U54HG004570 (Bernstein); U01HG004695 (Birney); U54HG004563 (Crawford); U54HG004557 (Gingeras); U54HG004555 (Hubbard); U41HG004568 (Kent); U54HG004576 (Myers); U54HG004558 (Snyder); U54HG004592 (Stamatoyannopoulos). Pilot Grants: R01HG003143 (Dekker); RC2HG005591 and R01HG003700 (Giddings); R01HG004456-03 (Ruan); U01HG004571 (Tenenbaum); U01HG004561 (Weng); RC2HG005679 (White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541, U01HG004561, RC2HG005679 and R01HG003988 (PI: Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (Elnitski, ZIAHG200323; Margulies, ZIAHG200341). Research in the Pennachio lab was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.
Publication: Data navigation on the ENCODE portal
Citation: Kagda MS, Lam B, Litton C, et al. Data navigation on the ENCODE portal. Nat Commun. 2025;16(1):9592. Published 2025 Oct 30. doi:10.1038/s41467-025-64343-9
Funding: All the figures in the manuscript are prepared using the free academic licence version of Tableau Desktop 2023.1. The authors would like to thank Salesforce for providing us with a free academic version. In addition, we would like to thank all the past and present members of the ENCODE and affiliated consortia. National Human Genome Research Institute, National Institutes of Health [U24 HG009397].
Publication: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
Citation: Luo Y, Hitz BC, Gabdank I, et al. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 2020;48(D1):D882-D889. doi:10.1093/nar/gkz1062
Funding: National Human Genome Research Institute, National Institutes of Health [U24 HG009397]. The content is solely theresponsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. The funders had no role in design, data processing, implementation, decision to publish, or preparation of the manuscript. Funding for open access charge: National Human Genome Research Institute, National Institutes of Health [U24 HG009397].
Source: http://dashr2.lisanwanglab.org/index.php
Publication: DASHR 2.0: integrated database of human small non-coding RNA genes and mature products
Citation: Kuksa PP, Amlie-Wolf A, Katanić Ž, Valladares O, Wang LS, Leung YY. DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. Bioinformatics. 2019;35(6):1033-1039. doi:10.1093/bioinformatics/bty709
Funding: This work is supported by the National Institute of General Medical Sciences (R01-GM099962 to all co-authors); National Institute on Aging (U54-AG052427, U01-AG032984, U24-AG041689, UF1-AG047133 to P.P.K., Z.K., O.V., L.S.W. and Y.Y.L.), National Institute on Aging (T32-AG00255 to A.A.W.). Funding for open access charge: National Institute on Aging (U24-AG041689).