Ensembl 2015
Open accessAbstract
Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license.
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Transcript-based co-expression networks increase quadratically in size with the number of genes included, and for human transcripts versus protein-coding genes the resulting network increases 100-fold in size.
“As co-expression networks are square matrixes, the size of the network increases quadratically (n2) with the number of genes included. As there are ∼200 000 annotated transcripts in the human genome (according to Ensembl GRCh38.p5 (human) annotation [53]) and only ∼20 000 protein-coding genes, the resulting network increases 100-fold in size”
From Gene co-expression analysis for functional classification and gene–disease predictions (2017) · cites this paper as [53]
The “NEW HUMAN ASSEMBLY - GRCh38” section describes Ensembl’s human gene and transcript annotation on GRCh38. It does not give the cited figures of approximately 200,000 transcripts and 20,000 protein-coding genes, identify the annotation as GRCh38.p5, or discuss co-expression network size. Thus it supports the annotation context, but not the numerical basis attributed to it. (LLM, conf=0.82)
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Sinha, S., Eisenhaber, B., Jensen, L. J., Kalbuaji, B., & Eisenhaber, F. (2018) · PROTEOMICS · doi:10.1002/pmic.201800093 · Cited by 60 · see citing works
The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content
Pett, W., Adamski, M., Adamska, M., Francis, W. R., Eitel, M., Pisani, D., & Wörheide, G. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz013 · Cited by 57 · see citing works
Pandey, R. S., Graham, L., Uyar, A., Preuss, C., Howell, G. R., & Carter, G. W. (2019) · Molecular Neurodegeneration · doi:10.1186/s13024-019-0351-3 · Cited by 37 · see citing works
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Chintalapati, M., Dannemann, M., & Prüfer, K. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-1018-8 · Cited by 13 · see citing works
- Authors
- Cunningham, F., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., Gil, L., Girón, C. G., Gordon, L., Hourlier, T., Hunt, S. E., Janacek, S. H., Johnson, N., Juettemann, T., Kähäri, A. K., Keenan, S., Martin, F. J., Maurel, T., McLaren, W., Murphy, D. N., Nag, R., Overduin, B., Parker, A., Patricio, M., Perry, E., Pignatelli, M., Riat, H. S., Sheppard, D., Taylor, K., Thormann, A., Vullo, A., Wilder, S. P., Zadissa, A., Aken, B. L., Birney, E., Harrow, J., Kinsella, R., Muffato, M., Ruffier, M., Searle, S. M. J., Spudich, G., Trevanion, S. J., Yates, A., Zerbino, D. R., & Flicek, P.
- Affiliations
- European Bioinformatics Institute (GB)
- Wellcome Sanger Institute (GB)
- Corresponding author
- Flicek, Paul
- ORCID
- Cunningham, Fiona
- Barrell, Daniel
- Beal, Kathryn
- Billis, Konstantinos
- Brent, Simon
- Coates, Guy
- Fitzgerald, Stephen
- Gil, Laurent
- Girón, Carlos García
- Hourlier, Thibaut
- Hunt, Sarah E.
- Janacek, Sophie H.
- Johnson, Nathan
- Juettemann, Thomas
- Kähäri, Andreas K.
- Keenan, Stephen
- Martin, Fergal J.
- Maurel, Thomas
- McLaren, William
- Murphy, Daniel N.
- Nag, Rishi
- Perry, Emily
- Pignatelli, Miguel
- Taylor, Kieron
- Thormann, Anja
- Vullo, Alessandro
- Wilder, Steven P.
- Zadissa, Amonida
- Aken, Bronwen L.
- Birney, Ewan
- Harrow, Jennifer
- Muffato, Matthieu
- Ruffier, Magali
- Trevanion, Stephen J.
- Zerbino, Daniel R.
- Flicek, Paul
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-10-28
- Volume
- 43
- Issue
- D1
- Pages
- D662-D669
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4383879
- OpenAlex
- W4230266413
- Cited by
- 1,115
- References
- 43
- Citations by year
- 2026: 12 · 2025: 14 · 2024: 17 · 2023: 15 · 2022: 24 · 2021: 44 · 2020: 54 · 2019: 81 · 2018: 107 · 2017: 212 · 2016: 332 · 2015: 202 · 2014: 1
- FWCI
- 102.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (FP7/2007–2013, 095908, WT095908, WT 098051)
- European Bioinformatics Institute
- European Commission (282510, 2007–2013, FP7 2007-2013, FP7/2007, 312301, 241504)
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (BB/I025328/1, BB/I025506/1, BB/I025360/2, BB/K009524/1, BB/L024225/1)
- National Human Genome Research Institute (U41HG007234)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD074078)
- 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 annotation, GRCh38, human genome assembly, regulatory elements, epigenetic information, comparative genomics, gene models, variant effect prediction, model organisms, open source software
- MeSH terms
- Animals, Humans, Regulatory Sequences, Nucleic Acid, Software, Genetic Variation, Genome, Human, Internet, Genomics, Databases, Nucleic Acid, Epigenesis, Genetic, Mice, Molecular Sequence Annotation
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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