Boom!

Due to a somewhat catastrophic hardware failure during our production cycle for Ensembl release 79, we have only been able to release human dbSNP 142 incorporating 1000 Genomes phase 3 data on our GRCh37-based services (Web: grch37.ensembl.org, REST API: grch37.rest.ensembl.org, MySQL: anonymous@ensembldb.ensembl.org:3337, VEP: grch37.ensembl.org/vep). We hope to have these data on GRCh38 for Ensembl release 80; our GRCh38 database is based on dbSNP 138 until then.

VEP and GRCh38

For users of the Variant Effect Predictor (VEP) living in the brave new GRCh38 world, we have made available a VCF file which can be used to incorporate IDs and allele frequencies from the 1000 Genomes phase 3 data into your results. See this handy guide for details.

Viewing phase 3 data on the web

Using the same VCF as above, you can attach this as a custom data file to your Ensembl browser; this will allow you to see the genomic locations of the variants and their consequence types on our Region in Detail view.

Attach the following URL as a VCF (indexed): ftp://ftp.ensembl.org/pub/release-79/variation/VEP/1KG.phase3.GRCh38.vcf.gz

You can then see the data alongside the tracks from our database:

After running our brand new Ensembl Regulatory Build on the human GRCh38 and GRCh37 assemblies, we spent some time revamping our current Regulation mart to make it faster, easier to use and pack it with brand new features. A complete re-design of the mart has been done in the background to make sure our mart can provide improved performance and deal with the data increase. The new Regulation mart can still be found on the Ensembl website under the BioMart tab.

The first thing that you will notice is that you can now access each regulation data type separately, this allows you to get the data quickly and make the filter and attribute sections neater.

Each Regulation section holds its own type of data, for example you can get the following data for human GRCh38:

• Binding Motifs (TFBS Annotation)
  • Binding Matrix ID (e.g: MA0003.1)
  • Feature type data (e.g: BHLHE40,CTCFL,…)
• Other Regulatory Regions
  • Feature type data (e.g: FANTOM predictions, VISTA Enhancers)
  • Identifiers (e.g: hs1, 1:922877-923268,…)
• Regulatory Evidence (Regulatory Build Information)
  • Feature type data (e.g: ATF3, DNase1,…)
  • Cell type (e.g: A549, H1ESC,..)
  • Feature Type class (e.g: Histone, Polymerase, Transcription Factor, Open Chromatin)
  • Project name (e.g: ENCODE and Roadmap Epigenomics)
  • SRA Experiment Accession (e.g: SRX018823, SRX056730,…)
• Regulatory Features (Regulatory Build Information)
  • Ensembl Regulatory Stable ID (e.g: ENSR00001516677)
  • Feature type (e.g: CTCF Binding Site, Enhancer, Open chromatin, Promoter, Promoter Flanking Region, TF binding site)
  • Cell type (e.g: A549, DND-41, GM12878, H1ESC,…)
• Regulatory Segments (Segmentation Information)
  • Feature type (e.g: CTCF enriched, Predicted Enhancer, Predicted heterochromatin, Predicted low activity, Predicted Promoter flank, Predicted Promoter with TSS, Predicted Repressed, Predicted Transcribed Region)
  • Cell type (e.g: HeLa-S3, HepG2)
• miRNA Target Regions (TarBase miRNA target predictions)
  • miRNA Identifier ID (e.g: hsa-miR-124-3p, hsa-miR-122-5p,…)
  • miRNA Accession ID (e.g: MIMAT0000069, MIMAT0000646,…)

We also have Binding motifs, Regulatory evidence, Regulatory Features, miRNA Target Regions data available for mouse and Other Regulatory Regions available for both mouse and fruit fly.

In addition of the above, we have added the following brand new information:

• Band Start/End, Marker Start/End and ENCODE Pilot Regions filters to the six Regulation data sections
• SO name and accession to the six Regulation data sections
• EFO Term accession to the Regulatory evidence, Regulatory features and Regulatory segments.
• “Has evidence”, which denotes whether Regulatory features have supporting evidence on a particular cell type or not.
• Chromosome Strand and Evidence to miRNA Target Regions.

Working with R?

Did you know that you can access all our marts using the BiomaRt Bioconductor R package?

To do this, first install the Bioconductor BiomaRt package: http://bioconductor.org/packages/release/bioc/html/biomaRt.html.

The following R code will then give you the chromosome location and scores for the human GRCh38 Binding matrix ID MA0005.2:

> library(biomaRt)

> ensembl_regulation = useMart(biomart="ENSEMBL_MART_FUNCGEN",host="www.ensembl.org",dataset="hsapiens_motif_feature")

> binding_matrix = getBM(attributes=c('binding_matrix_id','chromosome_name', 'chromosome_start', 'chromosome_end','chromosome_strand', 'score'), filters='motif_binding_matrix_id',values="MA0005.2", mart=ensembl_regulation)

The new Regulation mart is available for human, mouse and fruit fly on both www.ensembl.org and www.grch37.ensembl.org.

Annotation of the recent human assembly, GRCh38, was released in e76 in August 2014. Since then we have been maintaining a dedicated site to the GRCh37 assembly. The reason for updating annotations on the previous human assembly is to support those users who may still have data annotated on the old assembly, and who can not yet run their analyses on the new assembly. The Genome Reference Consortium (GRC) keeps a blog on the assemblies that they maintain which may be a good source of information if you are still contemplating a move to GRCh38. If you are wondering about the migration from GRCh37 to GRCh38 within Ensembl, we published a blog series which may be of interest.

We are now pleased to announce that the GRCh37 archive site has been updated with new human data sets. In addition to data imports, we have also utilised the improved regulatory build pipeline for mapping all available human regulatory features to the GRCh37 assembly. We have also re-built the GRCh37 Ensembl, Regulation and Variation BioMarts to integrate the updated data sets.

Highlights from some of the data imports for this release are:

• Genotypes from 1000 Genomes Phase 3
• dbSNP142 human data
• Latest release of public HGMD data (version 2014.4)
• COSMIC version 71
• RefSeq GFF3 annotation

A complete list of the changes can be found on the Ensembl GRCh37 website.

Highlights

• Updated names and descriptions for Strigamia maritima genes
• 777 new bacterial genomes (Ensembl Bacteria now contains 21,767genomes)
• Assemblies 2.40 and 2.50 of tomato available in Assembly Converter (to transfer genomic coordinates between assemblies)
• New variation data for the plant pathogens Verticillium dahliae (JR2 strain) and Zymoseptoria tritici

Explore the new variation data in the plant pathogen Z. tritici. This variation database was constructed based on as study SRP017760 downloaded from ENA.

Genome comparisons for Triticeae and related species

Whole genome alignments between seven pairs of Triticeae genomes, including the bread wheat A, B and D component genomes, Triticum urartu (the A genome progenitor), Aegilops tauschii (the D genome progenitor), and barley are now available. The alignments were obtained using ATAC and the statistics on genome and coding exon coverages can be found on our website. See the ATAC results for the comparison between T. urartu versus A. tauschii genomes.

MAF files on our FTP sites

In response to several requests from our users we now provide the pairwise alignments as MAF files. These can be found on the FTP download site of all Ensembl Genomes divisions. See an example of this data in Ensembl Metazoa.

Other news

• Fungi and Protists: Updated PHIbase annotation and protein domain information based on InterProScan
• Latest assemblies and gene sets for Medicago truncatula and Oryza meridionalis
• New RNASeq data in barley, Oryza sp and Leersia perrieri

A complete list of both new and updated date can be found on our website.

Get in touch if you have any questions or comments.

The Ensembl Genomes team

What’s new in e79:

• Human: genes updated to GENCODE 22, and new assembly patches (GRCh38.p2)
• Comparison of imported human RefSeq transcript set to Ensembl models
• New interactive gene gain/loss tree view
• Global Alliance REST endpoints
• NextGen project genotype sheep data from Iranian and Moroccan populations

Human update

The human gene set now corresponds to GENCODE 22 while the assembly has been updated to include new assembly patches for GRCh38.p2.

The HG-126 patch (KN538364.1) in GRCh38.p2 corrects a misassembly in this region which affects the RYBP gene.

Comparison of human RefSeq transcripts to Ensembl models

In this release we provide comparisons between the imported RefSeq transcripts in human to all overlapping Ensembl models. The comparison is done at the transcript level where all exons are compared in terms of genomic coordinates and the transcript sequences of the two models are also compared. Additionally, we have also compared the genomic sequences of the RefSeq transcripts to the Ensembl models. Both of these data sets are available via our API.

Gene gain/loss tree view

It is now possible to view the Gene gain/loss tree with our new interactive view (which uses the same engine as the species tree view introduced last release). Click on the toolbar to change the layout of the tree or on a node to get its details and expand, collapse, or focus on it.

Global Alliance REST Endpoints

Our REST server now implements the Global Alliance for Genomics and Health (GA4GH) Genomics API. The aim of the GA4GH API is to allow the interoperable exchange of genomic information across multiple organisations and on multiple platforms – see http://ga4gh.org/#/api for further details. Phase 3 genotype data from the 1000 Genomes project is now available from Ensembl via three new GA4GH endpoints.

Import of NextGen project sheep genotype data

Genotype data for three sheep species have been imported from the NextGen project. The project aims to preserve the biodiversity of farm animals. The imported populations are Iranian Ovis aries and Ovis orientalis and Moroccan Ovis aries. You can read more about other NextGen data set on the Ensembl projects.

Other news

• Updated human HAVANA annotation in Vega
• Import of phenotype and disease data from the Rat Genome Database (RGD)
• RefSeq GFF3 annotations for majority of Ensembl species
• Addition of non-coding genes to the vervet-AGM gene set
• Updated APPRIS flags for human, mouse, rat, zebrafish with addition of pig
• Assembly and gene set update for Drosophila to BDGP6 (FB2014_05)

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

Find out more at the Ensembl Release Webinar e79 (16.00 GMT, Thursday 26th March). Register here (for free!).

Ensembl 79 is scheduled for March 2015. Highlights include:

Updated gene sets and annotations

• Human GENCODE release 22 (GRCh38.p2): An updated version of the GENCODE gene set, which combines Havana’s manual annotation and Ensembl’s evidence-based automatic annotation, will be released
• Assembly patches will be added and annotated for the new human assembly GRCh38.p2
• RefSeq to Ensembl model comparison attributes will be added for human
• Fruitfly assembly will be updated to BDGP6

Variation data imports and updates

• 1000 Genomes phase 3 studies will be imported for human
• The latest sequence variants from dbSNP build 142 for human will be imported
• New Global Alliance standards REST endpoints will be available for sets of Variation data
• NextGen Project genotype data will be added from 3 sheep populations (Iranian Ovis aries, Iranian Ovis orientalis, Moroccan Ovis aries)
• New rat strain-specific variants and genotypes, and QTLs and phenotypes from the Rat Genome Database (RGD)

New web features

• Updated Gene gain/loss tree view
• New summary statistics of the homologs predicted between each pair of species

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.