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Ensembl 2015.

Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P - Nucleic Acids Res. (2014)

Bottom Line: 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.Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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Ensembl ‘Region in Detail’ view showing the improved annotation of SLC38A3 in GRCh38, regulatory region information, default variation track and Age of Base track. (a) The GRCh38 assembly has resulted in an improved annotation of many genes compared to GRCh37.p13. Here we show the SLC38A3 gene as an example, where updates to the genome sequence now allow an open reading frame to be annotated. SLC38A3 is viewable in the GENCODE Basic track which shows only selected transcripts per gene. (b) The following regulatory tracks are shown from our new Ensembl Regulatory Build: MultiCell regulatory features (regions that are assigned a function that is independent of the cell type); cell type-specific regulatory data (for 4 selected cell types, out of 18 available - a regulatory feature is shaded in grey if it is inactive in the corresponding cell type, below each cell type is the cell type-specific segmentation track); H1ESC cell line Whole Genome Bisulphite Sequencing; Fantom5 (enhancers and promoters defined by the FANTOM5 project). (c) A track for variants genotyped by the 1000 Genomes project (phase 1) with frequency of at least 1% across any population is now on by default. The variants are colour coded by most severe consequence type (see Variation Legend in the lower part of the image). (d) Age of Base track: Each base pair that differs by a substitution in the human genome is classified as an event according to when it occurred: before the primate evolutionary branch (grey), in the primate-specific branch (blue), in the human-specific branch and is now fixed (red) or in the human-specific branch as a segregating variant (yellow).
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Figure 1: Ensembl ‘Region in Detail’ view showing the improved annotation of SLC38A3 in GRCh38, regulatory region information, default variation track and Age of Base track. (a) The GRCh38 assembly has resulted in an improved annotation of many genes compared to GRCh37.p13. Here we show the SLC38A3 gene as an example, where updates to the genome sequence now allow an open reading frame to be annotated. SLC38A3 is viewable in the GENCODE Basic track which shows only selected transcripts per gene. (b) The following regulatory tracks are shown from our new Ensembl Regulatory Build: MultiCell regulatory features (regions that are assigned a function that is independent of the cell type); cell type-specific regulatory data (for 4 selected cell types, out of 18 available - a regulatory feature is shaded in grey if it is inactive in the corresponding cell type, below each cell type is the cell type-specific segmentation track); H1ESC cell line Whole Genome Bisulphite Sequencing; Fantom5 (enhancers and promoters defined by the FANTOM5 project). (c) A track for variants genotyped by the 1000 Genomes project (phase 1) with frequency of at least 1% across any population is now on by default. The variants are colour coded by most severe consequence type (see Variation Legend in the lower part of the image). (d) Age of Base track: Each base pair that differs by a substitution in the human genome is classified as an event according to when it occurred: before the primate evolutionary branch (grey), in the primate-specific branch (blue), in the human-specific branch and is now fixed (red) or in the human-specific branch as a segregating variant (yellow).

Mentions: The benefits of refreshing the gene set include removing gene models built from data that have since been discarded from the public databases, adding new isoforms that are supported by new data and annotation of new or improved genomic regions. In some cases genes that were annotated as non-coding in GRCh37.p13 are now coding in the new assembly (Figure 1a). A full Ensembl Gene set was produced on GRCh38, then merged with manual annotation from HAVANA to produce the GENCODE 20 gene set (4) and made available in Ensembl release 76 (August 2014). Regular updates of this manual annotation are planned in the coming year. For large consortia working on human data, we recommend using the GENCODE 21 gene set, made available in Ensembl release 77 (October 2014). In addition to updating the gene set, we recalculated pairwise whole-genome alignments from human to all other species in Ensembl and also our cross-species genome-wide multiple sequence alignments. The Regulation team regenerated regulatory annotation based on ENCODE (5) and Roadmap Epigenomics (6) data for the new assembly using a new Regulatory Build process, described below.


Ensembl 2015.

Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P - Nucleic Acids Res. (2014)

Ensembl ‘Region in Detail’ view showing the improved annotation of SLC38A3 in GRCh38, regulatory region information, default variation track and Age of Base track. (a) The GRCh38 assembly has resulted in an improved annotation of many genes compared to GRCh37.p13. Here we show the SLC38A3 gene as an example, where updates to the genome sequence now allow an open reading frame to be annotated. SLC38A3 is viewable in the GENCODE Basic track which shows only selected transcripts per gene. (b) The following regulatory tracks are shown from our new Ensembl Regulatory Build: MultiCell regulatory features (regions that are assigned a function that is independent of the cell type); cell type-specific regulatory data (for 4 selected cell types, out of 18 available - a regulatory feature is shaded in grey if it is inactive in the corresponding cell type, below each cell type is the cell type-specific segmentation track); H1ESC cell line Whole Genome Bisulphite Sequencing; Fantom5 (enhancers and promoters defined by the FANTOM5 project). (c) A track for variants genotyped by the 1000 Genomes project (phase 1) with frequency of at least 1% across any population is now on by default. The variants are colour coded by most severe consequence type (see Variation Legend in the lower part of the image). (d) Age of Base track: Each base pair that differs by a substitution in the human genome is classified as an event according to when it occurred: before the primate evolutionary branch (grey), in the primate-specific branch (blue), in the human-specific branch and is now fixed (red) or in the human-specific branch as a segregating variant (yellow).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383879&req=5

Figure 1: Ensembl ‘Region in Detail’ view showing the improved annotation of SLC38A3 in GRCh38, regulatory region information, default variation track and Age of Base track. (a) The GRCh38 assembly has resulted in an improved annotation of many genes compared to GRCh37.p13. Here we show the SLC38A3 gene as an example, where updates to the genome sequence now allow an open reading frame to be annotated. SLC38A3 is viewable in the GENCODE Basic track which shows only selected transcripts per gene. (b) The following regulatory tracks are shown from our new Ensembl Regulatory Build: MultiCell regulatory features (regions that are assigned a function that is independent of the cell type); cell type-specific regulatory data (for 4 selected cell types, out of 18 available - a regulatory feature is shaded in grey if it is inactive in the corresponding cell type, below each cell type is the cell type-specific segmentation track); H1ESC cell line Whole Genome Bisulphite Sequencing; Fantom5 (enhancers and promoters defined by the FANTOM5 project). (c) A track for variants genotyped by the 1000 Genomes project (phase 1) with frequency of at least 1% across any population is now on by default. The variants are colour coded by most severe consequence type (see Variation Legend in the lower part of the image). (d) Age of Base track: Each base pair that differs by a substitution in the human genome is classified as an event according to when it occurred: before the primate evolutionary branch (grey), in the primate-specific branch (blue), in the human-specific branch and is now fixed (red) or in the human-specific branch as a segregating variant (yellow).
Mentions: The benefits of refreshing the gene set include removing gene models built from data that have since been discarded from the public databases, adding new isoforms that are supported by new data and annotation of new or improved genomic regions. In some cases genes that were annotated as non-coding in GRCh37.p13 are now coding in the new assembly (Figure 1a). A full Ensembl Gene set was produced on GRCh38, then merged with manual annotation from HAVANA to produce the GENCODE 20 gene set (4) and made available in Ensembl release 76 (August 2014). Regular updates of this manual annotation are planned in the coming year. For large consortia working on human data, we recommend using the GENCODE 21 gene set, made available in Ensembl release 77 (October 2014). In addition to updating the gene set, we recalculated pairwise whole-genome alignments from human to all other species in Ensembl and also our cross-species genome-wide multiple sequence alignments. The Regulation team regenerated regulatory annotation based on ENCODE (5) and Roadmap Epigenomics (6) data for the new assembly using a new Regulatory Build process, described below.

Bottom Line: 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.Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Show MeSH