GENCODE reference annotation for the human and mouse genomes

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D766 - D773

Published: Oct. 8, 2018

The accurate identification and description of the genes in human mouse genomes is a fundamental requirement for high quality analysis data informing both genome biology clinical genomics. Over last 15 years, GENCODE consortium has been producing reference gene annotations to provide this foundational resource. includes experimental computational groups who work together improve extend annotation. Specifically, we generate primary data, create bioinformatics tools support expert manual annotators automated annotation pipelines. In addition, workflows use any all publicly available analysis, along with research literature identify characterise loci highest standard. are accessible via Ensembl UCSC Genome Browsers, FTP site, Biomart, Perl REST APIs as well https://www.gencodegenes.org.

Language: Английский

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Ensembl 2018

Nucleic Acids Research, Journal Year: 2017, Volume and Issue: 46(D1), P. D754 - D761

Published: Oct. 21, 2017

The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of draft human genome, with aim accelerating genomics research through rapid open distribution public data. Large amounts raw data are thus transformed into knowledge, which is made available via a multitude channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded multiple directions. First, resources describe fields genomics, gene annotation, comparative genetics epigenomics. Second, cover growing number genome assemblies; Release 90 contains exactly 100. Third, databases feed simultaneously an array services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here latest developments project, focus on managing increasing assemblies, supporting efforts interpretation improving browser.

Language: Английский

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Ensembl 2021

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 49(D1), P. D884 - D891

Published: Oct. 7, 2020

Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed comprehensive annotation of gene structures, regulatory elements variants, enable comparative genomics by inferring the evolutionary history genes genomes. Our integrated are made available in a variety ways, including genome browsers, search interfaces, specialist tools such as Variant Effect Predictor, download files programmatic interfaces. Here, we present recent developments two new website portals. Rapid Release (http://rapid.ensembl.org) is designed to provide core services soon possible has been deployed support large biodiversity sequencing projects. SARS-CoV-2 browser (https://covid-19.ensembl.org) integrates our own with publicly from numerous sources facilitate use international scientific response COVID-19 pandemic. also report on other updates resources, services. All software freely without restriction.

Language: Английский

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InterPro in 2017—beyond protein family and domain annotations

Nucleic Acids Research, Journal Year: 2016, Volume and Issue: 45(D1), P. D190 - D199

Published: Oct. 27, 2016

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and predict the presence of important domains sites. InterProScan underlying software that allows both nucleic acid be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with associated software, including addition two new databases (SFLD CDD), functionality include residue-level annotation prediction intrinsic disorder. These enrich annotations InterPro, increase overall number residues annotated allow more specific functional inferences.

Language: Английский

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InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D351 - D360

Published: Oct. 22, 2018

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains sites. Here, we report recent developments with (version 70.0) its associated software, including an 18% growth in size terms on new entries, updates to content, inclusion additional entry type, refined modelling discontinuous domains, development a programmatic interface website. These extend enrich information provided by InterPro, provide greater flexibility data access. We also show that InterPro's sequence coverage has kept pace UniProtKB, discuss how our evaluation residue may help guide future curation activities.

Language: Английский

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iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

BMC Bioinformatics, Journal Year: 2018, Volume and Issue: 19(1)

Published: Dec. 1, 2018

RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially biologists. We aim to streamline bioinformatic analyses gene-level by developing a user-friendly, interactive web application exploratory analysis, differential expression, pathway analysis.iDEP (integrated Differential Expression Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 2 services, comprehensive annotation databases 220 plant animal species. The workflow reproduced downloading customized R code related files. As an example, we analyzed RNA-Seq dataset lung fibroblasts with Hoxa1 knockdown revealed possible roles SP1 E2F1 their target genes, including microRNAs, in blocking G1/S transition. In another our shows that mouse B cells without functional p53, ionizing radiation activates MYC its downstream genes involved cell proliferation, ribosome biogenesis, non-coding RNA metabolism. wildtype cells, induces p53-mediated apoptosis DNA repair while suppressing E2F1, leads growth cycle arrest. iDEP helps unveil multifaceted functions p53 involvement several microRNAs such as miR-92a, miR-504, miR-30a. both examples, validated known molecular pathways generated novel, testable hypotheses.Combining analytic functionalities massive databases, ( http://ge-lab.org/idep/ ) enables biologists easily translate proteomic into actionable insights.

Language: Английский

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Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function

Science, Journal Year: 2017, Volume and Issue: 357(6357)

Published: Aug. 11, 2017

Hundreds of circular RNAs (circRNAs) are highly abundant in the mammalian brain, often with conserved expression. Here we show that circRNA Cdr1as is massively bound by microRNAs (miRNAs) miR-7 and miR-671 human mouse brains. When locus was removed from genome, knockout animals displayed impaired sensorimotor gating-a deficit ability to filter out unnecessary information-which associated neuropsychiatric disorders. Electrophysiological recordings revealed dysfunctional synaptic transmission. Expression specifically posttranscriptionally misregulated all brain regions analyzed. immediate early genes such as Fos, a direct target, enhanced Cdr1as-deficient brains, providing possible molecular link behavioral phenotype. Our data indicate an vivo loss-of-function phenotype suggest interactions between miRNAs important for normal function.

Language: Английский

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Ensembl 2020

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: unknown

Published: Oct. 11, 2019

The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation comparative genomics across the vertebrate subphylum key model organisms. pipeline capable of integrating experimental reference data from multiple providers into single integrated resource. Here, we present 94 newly annotated re-annotated genomes, bringing total number genomes offered by to 227. This represents largest expansion resource since its inception. We also detail our continued efforts improve human annotation, developments in epigenome analysis display, new tool imputing causal genes genome-wide association studies visualisation variation within 3D protein model. Finally, information on website. Both software are made available without restriction via website, online tools platform programmatic interfaces (available under an Apache 2.0 license) updates four times year.

Language: Английский

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GENCODE 2021

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 49(D1), P. D916 - D923

Published: Oct. 25, 2020

Abstract The GENCODE project annotates human and mouse genes transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology clinical genomics. annotation processes make use of primary bioinformatic tools analysis generated both within the consortium externally to support creation transcript structures determination their function. Here, we present improvements our infrastructure, bioinformatics tools, analysis, advances they in genomes including: completion first pass manual for reference genome; targeted associated SARS-CoV-2 infection; collaborative projects achieve convergence across databases protein-coding genes; manually supervised automated lncRNAs. Our is accessible via Ensembl, UCSC Genome Browser https://www.gencodegenes.org.

Language: Английский

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Ensembl 2019

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D745 - D751

Published: Oct. 23, 2018

The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. seeks be a fundamental resource driving progress by creating, maintaining and updating reference genome annotation comparative genomics resources. This year we describe our new expanded gene, variant capabilities, which led 50% increase in number of vertebrate genomes support. We have also doubled human variants added regulatory regions for many mouse cell types developmental stages. Our tools are via website as well through RESTful webservice, Perl application programming interface files download.

Language: Английский

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