Ensembl 2015

Abstract

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.

Environmental toxicant induced epigenetic transgenerational inheritance of ovarian pathology and granulosa cell epigenome and transcriptome alterations: ancestral origins of polycystic ovarian syndrome and primary ovarian insufficiency

“…DMRs were annotated using the biomaRt R package [67] to access the Ensembl database [68]. The genes that overlapped with DMR were then input into the KEGG pathway search [69,70] to identify associated pathways.…”

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans

“…The resulting trimmed paired‐end reads were combined prior to alignment. We originally planned to align reads to the available M. lucifugus genome (Myoluc2.0; http://www.ensembl.org/Myotis_lucifugus/Info/Index?db=core; Cunningham et al., 2015), but alignment of reads was low (~28%). We therefore used Trinity v2.2.0 (Grabherr et al., 2011) to generate a de novo transcript assembly in strand‐specific mode (RF) with silico read normalization.…”

“…To characterize the transcriptome of P. destructans growing on a tolerant species, we used TopHat v2.1.1 (Kim et al., 2013) to align trimmed fastq files to the annotated Ensembl M. lucifugus genome sequence assembly (Myoluc2.0; Cunningham et al., 2015). Approximately 28% of the reads from each library aligned to the M. lucifugus genome.…”

Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

“…The Kappa index is a measure of interrater agreement, between two or more methods: When the observed agreement exceeds chance agreement, kappa is positive, with its magnitude reflecting the strength of agreement. Gene annotations within candidate regions were obtained using the data provided by Ensembl (Cunningham et al., 2015) and NCBI (http://www.ncbi.nlm.nih.gov). To explore the linkage disequilibrium (LD) of selection signatures detected with other FST outliers and with nearby genes, we calculated the LD from these markers using Plink software (Purcell, 2014).…”