Transcription profiles from FANTOM5 and ENCODE, captured across cell lines, primary cells, and tissues. Coverage spans adult, embryonic, and fetal samples across brain, blood, lung, and skin tissues.
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://fantom.gsc.riken.jp/5/
Publication: Gateways to the FANTOM5 promoter level mammalian expression atlas
Citation: Lizio M, Harshbarger J, Shimoji H, et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015;16(1):22. Published 2015 Jan 5. doi:10.1186/s13059-014-0560-6
Funding: Research Grant for RIKEN Omics Science Center from MEXT to Yoshihide Hayashizaki; Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Yoshihide Hayashizaki; Research Grant from MEXT to the RIKEN Center for Life Science Technologies; Research Grant to RIKEN Preventive Medicine and Diagnosis Innovation Program from MEXT to Yoshihide Hayashizaki. This publication was also supported by a grant from the John Templeton Foundation, EU’s Innovative Medicine Joint Undertaking under grant agreement number 115191 (Open PHACTS), the Novo Nordisk and Lundbeck Foundations, the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement number 305444 (RD-Connect), the Center for Medical Systems Biology within the framework of The Netherlands Genomics Initiative (NGI)/Netherlands Organisation for Scientific Research (NWO), an Institute Strategic Grant from the Biotechnology and Biological Sciences Research Council (BBSRC; grant number BB/JO1446X/1, BB/I001107/1), and the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under contract number DE-AC02-05CH11231.