Ensembl 2018
Open accessAbstract
The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded in multiple directions. First, our resources describe multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics. Second, we cover a growing number of genome assemblies; Ensembl Release 90 contains exactly 100. Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser.
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Mitochondrial mRNA is enriched among genes more abundant in cells.
“as was mitochondrial mRNA (NES = −1.69, padj = 2.7e-04, gene set extracted from Ensembl’s BioMart; Zerbino et al., 2018).”
From Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans (2020) · cites this paper as Zerbino et al., 2018
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“In fact, our 5′ UTR–associated examples include three cases in which protein existence has been confirmed by others through laboratory work: within the 5′ UTRs of MIEF1 (Rathore et al. 2018), MKKS (Akimoto et al. 2013), and RAB34 (Zougman et al. 2011).”
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- Authors
- Zerbino, D. R., Achuthan, P., Akanni, W., Amode, M. R., Barrell, D., Bhai, J., Billis, K., Cummins, C., Gall, A., Girón, C. G., Gil, L., Gordon, L., Haggerty, L., Haskell, E., Hourlier, T., Izuogu, O. G., Janacek, S. H., Juettemann, T., To, J. K., Laird, M. R., Lavidas, I., Liu, Z., Loveland, J. E., Maurel, T., McLaren, W., Moore, B., Mudge, J., Murphy, D. N., Newman, V., Nuhn, M., Ogeh, D., Ong, C. K., Parker, A., Patricio, M., Riat, H. S., Schuilenburg, H., Sheppard, D., Sparrow, H., Taylor, K., Thormann, A., Vullo, A., Walts, B., Zadissa, A., Frankish, A., Hunt, S. E., Kostadima, M., Langridge, N., Martin, F. J., Muffato, M., Perry, E., Ruffier, M., Staines, D. M., Trevanion, S. J., Aken, B. L., Cunningham, F., Yates, A., & Flicek, P.
- Affiliations
- European Bioinformatics Institute (GB)
- Corresponding author
- Flicek, Paul
- ORCID
- Zerbino, Daniel R
- Achuthan, Premanand
- Akanni, Wasiu
- Barrell, Daniel
- Bhai, Jyothish
- Billis, Konstantinos
- Cummins, Carla
- Gall, Astrid
- Girón, Carlos García
- Gil, Laurent
- Haggerty, Leanne
- Haskell, Erin
- Hourlier, Thibaut
- Izuogu, Osagie G
- Janacek, Sophie H
- Juettemann, Thomas
- Laird, Matthew R
- Lavidas, Ilias
- Loveland, Jane E
- Maurel, Thomas
- McLaren, William
- Moore, Benjamin
- Mudge, Jonathan
- Murphy, Daniel N
- Nuhn, Michael
- Ogeh, Denye
- Ong, Chuang Kee
- Schuilenburg, Helen
- Sheppard, Dan
- Taylor, Kieron
- Thormann, Anja
- Vullo, Alessandro
- Walts, Brandon
- Zadissa, Amonida
- Frankish, Adam
- Hunt, Sarah E
- Kostadima, Myrto
- Langridge, Nicholas
- Martin, Fergal J
- Muffato, Matthieu
- Perry, Emily
- Ruffier, Magali
- Trevanion, Stephen J
- Aken, Bronwen L
- Cunningham, Fiona
- Yates, Andrew
- Flicek, Paul
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-11-16
- Volume
- 46
- Issue
- D1
- Pages
- D754-D761
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5753206
- OpenAlex
- W4250359879
- Cited by
- 2,605
- References
- 5
- Citations by year
- 2026: 55 · 2025: 86 · 2024: 124 · 2023: 166 · 2022: 241 · 2021: 357 · 2020: 635 · 2019: 658 · 2018: 274 · 2017: 6 · 2012: 1
- FWCI
- 178.13
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (WT201535/Z/16/Z, FP7/2007–2013, WT104947, WT104947/Z/14/Z, WT201535, WT108749, 201535/Z/16/Z, WT200990/Z/16/Z, /Z/15/Z, WT108749/Z/15/Z)
- European Bioinformatics Institute
- European Molecular Biology Laboratory
- European Federation of Pharmaceutical Industries and Associations (FP7/20072013)
- European Commission (733161, 2007–2013, FP7 2007-2013, HORIZON2020, 115582, FP7/2007, 634143)
- Innovative Medicines Initiative (FP7/2007‐2013, 115582)
- National Institutes of Health (WT108749/Z/15/Z, FP7/2007-2013)
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (BB/M020398/1, BB/M011615/1, BB/L024225/1)
- National Human Genome Research Institute (U41HG007823, U41HG007234, U41HG007823-S1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- Ensembl, genome assembly, genome annotation, comparative genomics, epigenomics, genome browser, genome interpretation
- MeSH terms
- Animals, Humans, Vertebrates, Genome, Human, Genome, Genomics, Databases, Genetic, Information Dissemination, Genome-Wide Association Study, Epigenomics, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing, Web Browser, Datasets as Topic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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