What’s New in e87:

Updated assemblies, gene sets and annotations

In Ensembl 87, there are a number of updates to the assemblies and gene sets for several species:

• Human: updated cDNA alignments and RefSeq import
• Mouse: updated gene set and assembly, see below
• Zebrafish: updated gene set
• Chicken: updated gene set

Updated gene models for mouse olfactory receptors

e87 includes an updated Ensembl-Havana mouse gene set, a merge of complete Ensembl gene models and the latest Havana gene annotation. All CCDS genes are included in this gene set.

This latest Havana gene annotation includes improved gene models for the mouse olfactory receptors. Over 2Mbp of additional sequence has been added to the mouse olfactory genes to create several hundred multi-exonic models. These new models are based on RNA-seq data from Ibarra-Soria X et. al.

The mouse assembly has been updated to GRCm38.p5. The patches for GRCm38.p5 were annotated using a combination of manual annotation, annotation projected from the primary assembly and annotation derived from cDNA and protein alignment evidence.

New lincRNA data

• lincRNA data is now available for Tilapia, Opossum and Spotted gar.

New regulation summary activity table

Other News

• DGVa structural variant study updates for Human, Cow and Macaque
• dbSNP updates for Sheep
• Cosmic version 78 imported for human
• Phenotype data updates for several species

A complete list of the changes can be found on the Ensembl website. 

Find out more about the new release and ask the team questions, in our free webinar: Wednesday 14th December, 4pm GMT. Register here.

As part of Ensembl 85, we are excited to introduce expression quantitative trait loci (eQTL) data, through our partnership with the Genotype-Tissue Expression (GTEx) project.

The GTEx project has the goal of identifying the influence of genetics on tissue-specific gene expression, i.e. to map correlations between genotype (SNPs) and gene expression levels (RNA-seq). eQTLs are variants which are found to be significantly correlated with differences in gene expression. Though still in its infancy, we hope that in time this type of data will allow us to conclusively determine the link between regulatory features and their gene targets.

Thanks to our use of HDF5 technology, we offer the only rapid look-up service across all GTEx SNP-gene association tests. We have included all of the correlated variants, including those that fall short of the significance threshold. The GTEx V6 dataset represents 7051 tissue samples from 44 tissues of 449 donors, and a total of 6 billion data points.

GTEx eQTLs in the Ensembl Browser

To view GTEx eQTL data for any gene, navigate to the gene tab and select ‘regulation’ in the left panel. The display will show one example track of GTEx data for a single tissue. Configuring the page allows you to add more GTEx tracks for each tissue type, by selecting ‘other regulatory regions’ and choosing the tissues you are interested in:

The SNPs are displayed in a Manhattan plot on these tracks, and are coloured according to their consequences on the transcript – as determined by the VEP. Clicking on any of the variants will display correlation statistics and a link to the variant tab. Where the SNPs are clustered, clicking will bring up a list of all variants nearby:

GTEx eQTLs via REST API

We have also provided Ensembl REST API endpoints to access these data. Currently, these methods allow you to quickly find the beta correlations and their p-values filtered by gene, SNP and/or tissue. You can also list all the tissue types that are currently available on our server.

What’s next?

Currently we are displaying the variants around a gene and their correlation to its expression level. In our next release (e86), on the Variant view, we will display all the genes whose expression levels are correlated to that variant. We will also display the beta effect sizes on the Manhattan plots.
If you have any feedback or questions relating to eQTLs in Ensembl, please contact the helpdesk.

What’s new?

Ensembl Plants now has an archive site, where we will keep selected previous releases of Ensembl Plants publicly available. The first release available on the archive site is release 31, and includes the previous assemblies for wheat and maize.

New assemblies in Ensembl Plants include:

• A new assembly of the bread wheat genome (TGACv1). The assembly has a scaffold N50 of 88 Kbp and a total length of 13.4 Gbp in contigs greater than 500 bp. Approximately 99,000 genes (99% of the total) annotated on the previous IWGSC Chromosome Survey Sequence Assembly have been mapped to the new assembly
• An updated assembly of the Zea mays genome (AGPv4)

• Genome assemblies for 5 new species, including Beta vulgaris (sugar beet), Brassica napus (rapeseed) and Trifolium pratense (red clover)

Ensembl Metazoa: Rfam covariance models have been applied to all metazoan genomes, and are shown in the ‘Rfam models’ track in the genome browser. Click on a model to see the description and the secondary structure.

Ensembl Bacteria now includes the latest versions of 41,610 genomes (41,198 bacteria and 412 archaea) from the INSDC archives. In this release we added 2269 new genomes, 15 genomes with updated assemblies, 212 genomes with updated annotation, 906 genomes where the assigned name has changed, and 243 genomes removed since the last release.

Ensembl Fungi has been updated with 47 newly available genomes and now includes 634 genomes from 388 species. PHI-base references have been added where available, as have non-coding RNA matches to Rfam.

25 new genomes have been added to Ensembl Protists, which now includes 178 genomes from 114 species.

You can find more details in the release notes.

What’s New in e85:

• 30 new human epigenomes from the Roadmap Epigenomics Project
• Human and mouse: Updated GENCODE set; including manually annotated HAVANA annotation, and all CCDS genes 
• Imported symbol names from the Vertebrate Gene Nomenclature Committee (VGNC) for Chimpanzee
• Improved highlighting options in the Location View for Userdata and Tracks
• Wasabi Tree viewer

30 New Epigenomes from the Roadmap Epigenomics Project

Roadmap Epigenomics is producing epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. In Ensembl 85, we have run our regulatory pipeline on Roadmap Epigenomics data for 30 cell/tissue types.

Additionally, the peak calling component of the Ensembl Regulation Sequencing Analysis pipeline has been improved. All of the existing ENCODE and BLUEPRINT data in Ensembl’s Regulation database have been reprocessed.

Human Gene Set Update and New Assembly Patches

The human gene set now corresponds to GENCODE 25 and the assembly has been updated to include new assembly patches for GRCH38.p7

VGNC Symbols for Chimpanzee

We now import symbol names from the Vertebrate Gene Nomenclature Committee (VGNC) for Chimpanzee. VGNC is an extension of HGNC for standardising naming across vertebrates lacking a nomenclature committee by transferring gene symbols from human to known orthologues. This replaces our own system for naming chimpanzee genes. This has improved our naming of chimpanzee genes as seen in POMGNT2, which was previously named GTDC2 in Ensembl 84.

Userdata and Track Highlighting

We have updated the highlighting functions in Location View:

• User data Highlighting – When you upload your own data to Ensembl the newly uploaded track will be automatically highlighted. This highlighting will disappear when you hover your cursor over the track
• Highlight track on hover – When placing the cursor over any track, the whole width of the track will be highlighted
• Track menu Highlight Icon –  Track menu now contains an icon that allows you to manually turn highlighting on/off

Wasabi Tree Viewer

Wasabi has replaced Jalview as a way to view gene trees and multiple alignments. Clicking on any node within the gene tree will give you the option to ‘View in Wasabi’. 

Clicking on ‘View in Wasabi’ will open a pop-up window with the tree and alignment:

Other News

• Updated Ensembl-Havana rat gene set; a merge of complete Ensembl gene models and the latest Havana gene annotation
• Human and mouse CRISPR sites, predicted by Wellcome Trust Sanger Institute Genome Editing (WGE) have been added
• Human and mouse databases have been updated to dbSNP147 and dbSNP146 respectively
• Phenotype data updated for several species, including human, mouse, pig and chicken
• GTEX eQTL data for 14 human tissues has been added to the Gene Regulation view
• The Allele Frequency Calculator has been migrated from the 1000Genomes website to our GRCh37 archive. This tool takes a VCF file and a matching sample panel file, and calculates allele frequencies for one or more 1000G populations for a defined chromosomal region

• New tool: File Chameleon customises files from the Ensembl FTP server. Current functions include; adding ‘chr’ to your chromosome names for use with UCSC’s genome browser and removing long genes

A complete list of the changes can be found on the Ensembl website. 

Find out more about the new release and ask the team questions, in our free webinar: Wednesday 27th July, 4pm BST. Register here.

Ensembl 85 is scheduled for July 2016, highlights include:

Updated gene sets and annotations

• Human: updated to GENCODE release 25, new CCDS import
• Mouse: updated to GENCODE release M10,
• Rat: updated Ensembl/HAVANA gene set
• Vega 65 annotation added for human, mouse and rat
• C. elegans gene set and other annotations updated from WormBase release WS250
• Zebrafish: new development and tissue-specific RNA-seq tracks

• Armadillo/Dog/Ferret: new lincRNA models

Variation data imports and updates

• dbSNP updates for human (v147) and mouse (v146)
• COSMIC v77 data update
• New and updated structural variant studies from DGVa for human and dog
• Updated phenotype data for several species, including; human, mouse, rat, zebrafish and cat

Regulation data

• 23 new human epigenomes from the Roadmap Epigenomics Project
• ENCODE and BLUEPRINT data reprocessed with improved peak-calling pipeline

New web features

• Track highlighting for newly displayed tracks and on hover-over
• Summary information from SNPedia is included on Variation Summary pages
• Wasabi will replace Jalview for gene trees and multiple sequence alignment visualisation
• Web code for session records will be migrated to use Rose ORM

For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.

We have scheduled the next releases of Ensembl (Release 85) and Ensembl Genomes (Release 32) for July 2016. Details of the declared intentions will be announced nearer the time.

Please contact the helpdesk if you have any questions or feedback.