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Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, Cunningham F, Hindorff LA, MacArthur JAL. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biol 2018; 19:21. [PMID: 29448949 PMCID: PMC5815218 DOI: 10.1186/s13059-018-1396-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022] Open
Abstract
The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog. We confirm known biases and gaps in diversity, and find that African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations. It is our hope that widespread adoption of this framework will lead to improved analysis, interpretation, and integration of human genomics data.
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Affiliation(s)
- Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Danielle Welter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Emily H Bowler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892-9305, USA
| | - Heather A Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892-9305, USA
| | - Annalisa Milano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Emma Hastings
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Cinzia Malangone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892-9305, USA
| | - Jacqueline A L MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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2
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MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Res 2016; 45:D896-D901. [PMID: 27899670 PMCID: PMC5210590 DOI: 10.1093/nar/gkw1133] [Citation(s) in RCA: 1388] [Impact Index Per Article: 173.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/02/2016] [Indexed: 02/02/2023] Open
Abstract
The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies. The infrastructure improvements also support scaling for larger arrays, exome and sequencing studies, allowing the Catalog to adapt to the needs of evolving study design, genotyping technologies and user needs in the future.
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Affiliation(s)
- Jacqueline MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Emily Bowler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emma Hastings
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Heather Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Annalisa Milano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Zoe May Pendlington
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Danielle Welter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lucia Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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3
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Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AMP, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A. Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res 2016; 44:D746-52. [PMID: 26481351 PMCID: PMC4702781 DOI: 10.1093/nar/gkv1045] [Citation(s) in RCA: 396] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 09/25/2015] [Accepted: 09/29/2015] [Indexed: 11/12/2022] Open
Abstract
Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons-estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: 'enrichment' in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.
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Affiliation(s)
- Robert Petryszak
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Maria Keays
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Y Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Nuno A Fonseca
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Elisabet Barrera
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | - Simon Jupp
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Satu Koskinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Oliver Mannion
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Laura Huerta
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Karine Megy
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Catherine Snow
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Eleanor Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Mitra Barzine
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Emma Hastings
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | | | | | - Wolfgang Huber
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | - Helen E Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
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4
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Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A. ArrayExpress update--simplifying data submissions. Nucleic Acids Res 2014; 43:D1113-6. [PMID: 25361974 PMCID: PMC4383899 DOI: 10.1093/nar/gku1057] [Citation(s) in RCA: 499] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository for data supporting peer-reviewed publications. It contains data from over 7000 public sequencing and 42 000 array-based studies comprising over 1.5 million assays in total. The proportion of sequencing-based submissions has grown significantly over the last few years and has doubled in the last 18 months, whilst the rate of microarray submissions is growing slightly. All data in ArrayExpress are available in the MAGE-TAB format, which allows robust linking to data analysis and visualization tools and standardized analysis. The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold. In the near future, Annotare will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines. ArrayExpress is a stable and highly accessed resource. Our future tasks include automation of data flows and further integration with other EMBL-EBI resources for the representation of multi-omics data.
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Affiliation(s)
- Nikolay Kolesnikov
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Emma Hastings
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Maria Keays
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Olga Melnichuk
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Y Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Eleanor Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Miroslaw Dylag
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Natalja Kurbatova
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Marco Brandizi
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Karyn Megy
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Ekaterina Pilicheva
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Gabriella Rustici
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK School of Biological Sciences, Cambridge Systems Biology Centre, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Andrew Tikhonov
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Robert Petryszak
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
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5
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Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A. Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res 2013; 42:D926-32. [PMID: 24304889 PMCID: PMC3964963 DOI: 10.1093/nar/gkt1270] [Citation(s) in RCA: 251] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell types, organism parts, developmental stages, diseases and other biological and experimental conditions. The database consists of selected high-quality microarray and RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms and processed using standardized microarray and RNA-sequencing analysis methods. The new version of Expression Atlas introduces the concept of 'baseline' expression, i.e. gene and splice variant abundance levels in healthy or untreated conditions, such as tissues or cell types. Differential gene expression data benefit from an in-depth curation of experimental intent, resulting in biologically meaningful 'contrasts', i.e. instances of differential pairwise comparisons between two sets of biological replicates. Other novel aspects of Expression Atlas are its strict quality control of raw experimental data, up-to-date RNA-sequencing analysis methods, expression data at the level of gene sets, as well as genes and a more powerful search interface designed to maximize the biological value provided to the user.
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Affiliation(s)
- Robert Petryszak
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
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6
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Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U. ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res 2012. [PMID: 23193272 PMCID: PMC3531147 DOI: 10.1093/nar/gks1174] [Citation(s) in RCA: 299] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.
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Affiliation(s)
- Gabriella Rustici
- Functional Genomics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.
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7
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Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A. ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 2010; 39:D1002-4. [PMID: 21071405 PMCID: PMC3013660 DOI: 10.1093/nar/gkq1040] [Citation(s) in RCA: 271] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The ArrayExpress Archive (http://www.ebi.ac.uk/arrayexpress) is one of the three international public repositories of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.
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Affiliation(s)
- Helen Parkinson
- Functional Genomics Team, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.
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8
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Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ, Ball CA. Annotare--a tool for annotating high-throughput biomedical investigations and resulting data. Bioinformatics 2010; 26:2470-1. [PMID: 20733062 PMCID: PMC2944206 DOI: 10.1093/bioinformatics/btq462] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Summary: Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis. Availability and Implementation: Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows. Contact:rshankar@stanford.edu
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Affiliation(s)
- Ravi Shankar
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
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9
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Tandon L, Hastings E, Banar J, Barnes J, Beddingfield D, Decker D, Dyke J, Farr D, FitzPatrick J, Gallimore D, Garner S, Gritzo R, Hahn T, Havrilla G, Johnson B, Kuhn K, LaMont S, Langner D, Lewis C, Majidi V, Martinez P, McCabe R, Mecklenburg S, Mercer D, Meyers S, Montoya V, Patterson B, Pereyra RA, Porterfield D, Poths J, Rademacher D, Ruggiero C, Schwartz D, Scott M, Spencer K, Steiner R, Villarreal R, Volz H, Walker L, Wong A, Worley C. Nuclear, chemical, and physical characterization of nuclear materials. J Radioanal Nucl Chem 2008. [DOI: 10.1007/s10967-008-0528-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Weist MD, Myers CP, Hastings E, Ghuman H, Han YL. Psychosocial functioning of youth receiving mental health services in the schools versus community mental health centers. Community Ment Health J 1999; 35:69-81. [PMID: 10094511 DOI: 10.1023/a:1018700126364] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Evaluated psychosocial differences between youth receiving mental health services in Community Mental Health Centers (CMHCs; n = 79) as compared to youth receiving services from a program operating in 10 Baltimore schools (n = 186). Racial and gender differences were shown, with more African American youth and females in the School than CMHC sample. Multivariate analyses that controlled for these racial and gender differences failed to reveal significant effects, indicating comparable functioning on measures of life stress, violence exposure, family support, self-concept, and emotional/behavioral problems for youth from the two samples. However, particularly for those with internalizing disturbances, youth in the School sample were less likely to have received prior mental health services than youth from the CMHCs. Findings support the conclusion that school-based mental health programs are reaching youth who need mental health services, who otherwise may not receive them.
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Affiliation(s)
- M D Weist
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore 21201-1549, USA.
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11
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Richert JR, Robinson ED, Camphausen K, Hastings E, Martin R, Voskuhl R, McFarland HF. T-cell receptor alpha and beta CDR3 expression by myelin basic protein-specific human T-cell clones. Ann N Y Acad Sci 1995; 756:317-8. [PMID: 7544080 DOI: 10.1111/j.1749-6632.1995.tb44531.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- J R Richert
- Georgetown University Medical Center, Washington, D.C. 20007, USA
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12
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Hastings E. Open letter from the Disability Discrimination Commissioner. Lamp 1995; 52:41-2. [PMID: 7500727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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13
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Hastings E. On being 'disabled'--six needless burdens and four better ways. Aust Nurses J 1981; 10:58-9. [PMID: 6455984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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14
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Hastings E. Achieving rehabilitation. Australas Nurses J 1981; 10:18. [PMID: 6455988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Benton C, Hastings E. Intravenous cholangiography--excretion hepatography. Radiology 1972; 104:61-2. [PMID: 5033600 DOI: 10.1148/104.1.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Shaw G, Groden B, Hastings E. Coronary care in a General Hospital. Results and observations on the first year's work in the unit in the Southern General Hospital, Glasgow. Scott Med J 1971; 16:173-82. [PMID: 5557056 DOI: 10.1177/003693307101600302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The establishment, staffing and structure and observations made in the first year of the existence of coronary care in an intensive care unit in a general hospital are recorded. Two hundred and twenty eight patients were admitted during the year in whom the diagnosis of myocardial infarction was confirmed. There were 29 deaths in the unit and 14 deaths occurred in the wards of the hospital after discharge from the unit. 49.1 per cent of the patients were admitted within 4 hours of the onset of symptoms and the mean duration of stay in the unit was 86.5 hours. The type of arrhythmia detected in the unit, and the treatment given to the patients both before and after admission to the intensive care unit are described.
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