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  1. Article ; Online: Expression data analysis with Reactome.

    Jupe, Steve / Fabregat, Antonio / Hermjakob, Henning

    Current protocols in bioinformatics

    2015  Volume 49, Page(s) 8.20.1–8.20.9

    Abstract: The Reactome database of curated biological pathways provides a tool for visualizing user-supplied expression data as an overlay on pathway diagrams, thereby affording an effective means to examine expression of the constituents of the pathway and ... ...

    Abstract The Reactome database of curated biological pathways provides a tool for visualizing user-supplied expression data as an overlay on pathway diagrams, thereby affording an effective means to examine expression of the constituents of the pathway and determine whether all that are necessary are present. Several experiments can be visualized in succession, to determine whether expression changes with experimental conditions, a useful feature for examining a time-course, dose-response, or disease progression.
    MeSH term(s) Gene Expression Regulation ; Humans ; Oligonucleotide Array Sequence Analysis ; Signal Transduction/genetics ; Statistics as Topic ; User-Computer Interface
    Language English
    Publishing date 2015-03-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2179022-X
    ISSN 1934-340X ; 1934-3396
    ISSN (online) 1934-340X
    ISSN 1934-3396
    DOI 10.1002/0471250953.bi0820s49
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A controlled vocabulary for pathway entities and events.

    Jupe, Steve / Jassal, Bijay / Williams, Mark / Wu, Guanming

    Database : the journal of biological databases and curation

    2014  Volume 2014

    Abstract: Entities involved in pathways and the events they participate in require descriptive and unambiguous names that are often not available in the literature or elsewhere. Reactome is a manually curated open-source resource of human pathways. It is ... ...

    Abstract Entities involved in pathways and the events they participate in require descriptive and unambiguous names that are often not available in the literature or elsewhere. Reactome is a manually curated open-source resource of human pathways. It is accessible via a website, available as downloads in standard reusable formats and via Representational State Transfer (REST)-ful and Simple Object Access Protocol (SOAP) application programming interfaces (APIs). We have devised a controlled vocabulary (CV) that creates concise, unambiguous and unique names for reactions (pathway events) and all the molecular entities they involve. The CV could be reapplied in any situation where names are used for pathway entities and events. Adoption of this CV would significantly improve naming consistency and readability, with consequent benefits for searching and data mining within and between databases. Database URL: http://www.reactome.org.
    MeSH term(s) Humans ; Peptides/chemistry ; Signal Transduction ; Small Molecule Libraries/chemistry ; Vocabulary, Controlled
    Chemical Substances Peptides ; Small Molecule Libraries
    Language English
    Publishing date 2014-06-20
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2496706-3
    ISSN 1758-0463 ; 1758-0463
    ISSN (online) 1758-0463
    ISSN 1758-0463
    DOI 10.1093/database/bau060
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Interleukins and their signaling pathways in the Reactome biological pathway database.

    Jupe, Steve / Ray, Keith / Roca, Corina Duenas / Varusai, Thawfeek / Shamovsky, Veronica / Stein, Lincoln / D'Eustachio, Peter / Hermjakob, Henning

    The Journal of allergy and clinical immunology

    2018  Volume 141, Issue 4, Page(s) 1411–1416

    Abstract: Background: There is a wealth of biological pathway information available in the scientific literature, but it is spread across many thousands of publications. Alongside publications that contain definitive experimental discoveries are many others that ... ...

    Abstract Background: There is a wealth of biological pathway information available in the scientific literature, but it is spread across many thousands of publications. Alongside publications that contain definitive experimental discoveries are many others that have been dismissed as spurious, found to be irreproducible, or are contradicted by later results and consequently now considered controversial. Many descriptions and images of pathways are incomplete stylized representations that assume the reader is an expert and familiar with the established details of the process, which are consequently not fully explained. Pathway representations in publications frequently do not represent a complete, detailed, and unambiguous description of the molecules involved; their precise posttranslational state; or a full account of the molecular events they undergo while participating in a process. Although this might be sufficient to be interpreted by an expert reader, the lack of detail makes such pathways less useful and difficult to understand for anyone unfamiliar with the area and of limited use as the basis for computational models.
    Objective: Reactome was established as a freely accessible knowledge base of human biological pathways. It is manually populated with interconnected molecular events that fully detail the molecular participants linked to published experimental data and background material by using a formal and open data structure that facilitates computational reuse. These data are accessible on a Web site in the form of pathway diagrams that have descriptive summaries and annotations and as downloadable data sets in several formats that can be reused with other computational tools. The entire database and all supporting software can be downloaded and reused under a Creative Commons license.
    Methods: Pathways are authored by expert biologists who work with Reactome curators and editorial staff to represent the consensus in the field. Pathways are represented as interactive diagrams that include as much molecular detail as possible and are linked to literature citations that contain supporting experimental details. All newly created events undergo a peer-review process before they are added to the database and made available on the associated Web site. New content is added quarterly.
    Results: The 63rd release of Reactome in December 2017 contains 10,996 human proteins participating in 11,426 events in 2,179 pathways. In addition, analytic tools allow data set submission for the identification and visualization of pathway enrichment and representation of expression profiles as an overlay on Reactome pathways. Protein-protein and compound-protein interactions from several sources, including custom user data sets, can be added to extend pathways. Pathway diagrams and analytic result displays can be downloaded as editable images, human-readable reports, and files in several standard formats that are suitable for computational reuse. Reactome content is available programmatically through a REpresentational State Transfer (REST)-based content service and as a Neo4J graph database. Signaling pathways for IL-1 to IL-38 are hierarchically classified within the pathway "signaling by interleukins." The classification used is largely derived from Akdis et al.
    Conclusion: The addition to Reactome of a complete set of the known human interleukins, their receptors, and established signaling pathways linked to annotations of relevant aspects of immune function provides a significant computationally accessible resource of information about this important family. This information can be extended easily as new discoveries become accepted as the consensus in the field. A key aim for the future is to increase coverage of gene expression changes induced by interleukin signaling.
    MeSH term(s) Databases, Factual ; Humans ; Interleukins/immunology ; Internet ; Protein Interaction Maps/immunology ; Proteins/immunology ; Signal Transduction/immunology ; Software
    Chemical Substances Interleukins ; Proteins
    Language English
    Publishing date 2018-02-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 121011-7
    ISSN 1097-6825 ; 1085-8725 ; 0091-6749
    ISSN (online) 1097-6825 ; 1085-8725
    ISSN 0091-6749
    DOI 10.1016/j.jaci.2017.12.992
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Reactome enhanced pathway visualization.

    Sidiropoulos, Konstantinos / Viteri, Guilherme / Sevilla, Cristoffer / Jupe, Steve / Webber, Marissa / Orlic-Milacic, Marija / Jassal, Bijay / May, Bruce / Shamovsky, Veronica / Duenas, Corina / Rothfels, Karen / Matthews, Lisa / Song, Heeyeon / Stein, Lincoln / Haw, Robin / D'Eustachio, Peter / Ping, Peipei / Hermjakob, Henning / Fabregat, Antonio

    Bioinformatics (Oxford, England)

    2017  Volume 33, Issue 21, Page(s) 3461–3467

    Abstract: Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the ... ...

    Abstract Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications.
    Results: For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like 'mitochondrion' or 'receptor' are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects.
    Availability and implementation: http://reactome.org.
    Contact: fabregat@ebi.ac.uk or hhe@ebi.ac.uk.
    MeSH term(s) Biological Phenomena ; Computer Graphics ; Gene Ontology ; Internet ; Knowledge Bases ; Libraries ; Signal Transduction ; User-Computer Interface
    Language English
    Publishing date 2017-10-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btx441
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A synthesis approach of mouse studies to identify genes and proteins in arterial thrombosis and bleeding.

    Baaten, Constance C F M J / Meacham, Stuart / de Witt, Susanne M / Feijge, Marion A H / Adams, David J / Akkerman, Jan-Willem N / Cosemans, Judith M E M / Grassi, Luigi / Jupe, Steve / Kostadima, Myrto / Mattheij, Nadine J A / Prins, Martin H / Ramirez-Solis, Ramiro / Soehnlein, Oliver / Swieringa, Frauke / Weber, Christian / White, Jacqueline K / Ouwehand, Willem H / Heemskerk, Johan W M

    Blood

    2018  Volume 132, Issue 24, Page(s) e35–e46

    Abstract: Antithrombotic therapies reduce cardiovascular diseases by preventing arterial thrombosis and thromboembolism, but at expense of increased bleeding risks. Arterial thrombosis studies using genetically modified mice have been invaluable for identification ...

    Abstract Antithrombotic therapies reduce cardiovascular diseases by preventing arterial thrombosis and thromboembolism, but at expense of increased bleeding risks. Arterial thrombosis studies using genetically modified mice have been invaluable for identification of new molecular targets. Because of low sample sizes and heterogeneity in approaches or methodologies, a formal meta-analysis to compare studies of mice with single-gene defects encountered major limitations. To overcome these, we developed a novel synthesis approach to quantitatively scale 1514 published studies of arterial thrombus formation (in vivo and in vitro), thromboembolism, and tail-bleeding of genetically modified mice. Using a newly defined consistency parameter (CP), indicating the strength of published data, comparisons were made of 431 mouse genes, of which 17 consistently contributed to thrombus formation without affecting hemostasis. Ranking analysis indicated high correlations between collagen-dependent thrombosis models in vivo (FeCl
    MeSH term(s) Animals ; Disease Models, Animal ; Hemorrhage/genetics ; Hemorrhage/metabolism ; Hemorrhage/pathology ; Humans ; Mice ; Mice, Knockout ; Thrombosis/genetics ; Thrombosis/metabolism ; Thrombosis/pathology
    Language English
    Publishing date 2018-10-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 80069-7
    ISSN 1528-0020 ; 0006-4971
    ISSN (online) 1528-0020
    ISSN 0006-4971
    DOI 10.1182/blood-2018-02-831982
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: COSMIC: the Catalogue Of Somatic Mutations In Cancer.

    Tate, John G / Bamford, Sally / Jubb, Harry C / Sondka, Zbyslaw / Beare, David M / Bindal, Nidhi / Boutselakis, Harry / Cole, Charlotte G / Creatore, Celestino / Dawson, Elisabeth / Fish, Peter / Harsha, Bhavana / Hathaway, Charlie / Jupe, Steve C / Kok, Chai Yin / Noble, Kate / Ponting, Laura / Ramshaw, Christopher C / Rye, Claire E /
    Speedy, Helen E / Stefancsik, Ray / Thompson, Sam L / Wang, Shicai / Ward, Sari / Campbell, Peter J / Forbes, Simon A

    Nucleic acids research

    2018  Volume 47, Issue D1, Page(s) D941–D947

    Abstract: COSMIC, the Catalogue Of Somatic Mutations In Cancer (https://cancer.sanger.ac.uk) is the most detailed and comprehensive resource for exploring the effect of somatic mutations in human cancer. The latest release, COSMIC v86 (August 2018), includes ... ...

    Abstract COSMIC, the Catalogue Of Somatic Mutations In Cancer (https://cancer.sanger.ac.uk) is the most detailed and comprehensive resource for exploring the effect of somatic mutations in human cancer. The latest release, COSMIC v86 (August 2018), includes almost 6 million coding mutations across 1.4 million tumour samples, curated from over 26 000 publications. In addition to coding mutations, COSMIC covers all the genetic mechanisms by which somatic mutations promote cancer, including non-coding mutations, gene fusions, copy-number variants and drug-resistance mutations. COSMIC is primarily hand-curated, ensuring quality, accuracy and descriptive data capture. Building on our manual curation processes, we are introducing new initiatives that allow us to prioritize key genes and diseases, and to react more quickly and comprehensively to new findings in the literature. Alongside improvements to the public website and data-download systems, new functionality in COSMIC-3D allows exploration of mutations within three-dimensional protein structures, their protein structural and functional impacts, and implications for druggability. In parallel with COSMIC's deep and broad variant coverage, the Cancer Gene Census (CGC) describes a curated catalogue of genes driving every form of human cancer. Currently describing 719 genes, the CGC has recently introduced functional descriptions of how each gene drives disease, summarized into the 10 cancer Hallmarks.
    MeSH term(s) Databases, Nucleic Acid ; Genes ; Humans ; Mutation ; Neoplasms/genetics ; Protein Conformation
    Language English
    Publishing date 2018-10-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gky1015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Reactome enhanced pathway visualization

    Sidiropoulos, Konstantinos / Viteri, Guilherme / Sevilla, Cristoffer / Jupe, Steve / Webber, Marissa / Orlic-Milacic, Marija / Jassal, Bijay / May, Bruce / Shamovsky, Veronica / Duenas, Corina / Rothfels, Karen / Matthews, Lisa / Song, Heeyeon / Stein, Lincoln / Haw, Robin / D’Eustachio, Peter / Ping, Peipei / Hermjakob, Henning / Fabregat, Antonio

    Bioinformatics. 2017 Nov. 01, v. 33, no. 21

    2017  

    Abstract: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to ... ...

    Abstract Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users’ own research presentations and publications. For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like ‘mitochondrion’ or ‘receptor’ are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects. http://reactome.org fabregat@ebi.ac.uk or hhe@ebi.ac.uk
    Keywords bioinformatics ; immune system ; phosphorylation
    Language English
    Dates of publication 2017-1101
    Size p. 3461-3467.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1468345-3
    ISSN 1460-2059 ; 1367-4811 ; 1367-4803
    ISSN (online) 1460-2059 ; 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btx441
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: New gene functions in megakaryopoiesis and platelet formation.

    Gieger, Christian / Radhakrishnan, Aparna / Cvejic, Ana / Tang, Weihong / Porcu, Eleonora / Pistis, Giorgio / Serbanovic-Canic, Jovana / Elling, Ulrich / Goodall, Alison H / Labrune, Yann / Lopez, Lorna M / Mägi, Reedik / Meacham, Stuart / Okada, Yukinori / Pirastu, Nicola / Sorice, Rossella / Teumer, Alexander / Voss, Katrin / Zhang, Weihua /
    Ramirez-Solis, Ramiro / Bis, Joshua C / Ellinghaus, David / Gögele, Martin / Hottenga, Jouke-Jan / Langenberg, Claudia / Kovacs, Peter / O'Reilly, Paul F / Shin, So-Youn / Esko, Tõnu / Hartiala, Jaana / Kanoni, Stavroula / Murgia, Federico / Parsa, Afshin / Stephens, Jonathan / van der Harst, Pim / Ellen van der Schoot, C / Allayee, Hooman / Attwood, Antony / Balkau, Beverley / Bastardot, François / Basu, Saonli / Baumeister, Sebastian E / Biino, Ginevra / Bomba, Lorenzo / Bonnefond, Amélie / Cambien, François / Chambers, John C / Cucca, Francesco / D'Adamo, Pio / Davies, Gail / de Boer, Rudolf A / de Geus, Eco J C / Döring, Angela / Elliott, Paul / Erdmann, Jeanette / Evans, David M / Falchi, Mario / Feng, Wei / Folsom, Aaron R / Frazer, Ian H / Gibson, Quince D / Glazer, Nicole L / Hammond, Chris / Hartikainen, Anna-Liisa / Heckbert, Susan R / Hengstenberg, Christian / Hersch, Micha / Illig, Thomas / Loos, Ruth J F / Jolley, Jennifer / Khaw, Kay Tee / Kühnel, Brigitte / Kyrtsonis, Marie-Christine / Lagou, Vasiliki / Lloyd-Jones, Heather / Lumley, Thomas / Mangino, Massimo / Maschio, Andrea / Mateo Leach, Irene / McKnight, Barbara / Memari, Yasin / Mitchell, Braxton D / Montgomery, Grant W / Nakamura, Yusuke / Nauck, Matthias / Navis, Gerjan / Nöthlings, Ute / Nolte, Ilja M / Porteous, David J / Pouta, Anneli / Pramstaller, Peter P / Pullat, Janne / Ring, Susan M / Rotter, Jerome I / Ruggiero, Daniela / Ruokonen, Aimo / Sala, Cinzia / Samani, Nilesh J / Sambrook, Jennifer / Schlessinger, David / Schreiber, Stefan / Schunkert, Heribert / Scott, James / Smith, Nicholas L / Snieder, Harold / Starr, John M / Stumvoll, Michael / Takahashi, Atsushi / Tang, W H Wilson / Taylor, Kent / Tenesa, Albert / Lay Thein, Swee / Tönjes, Anke / Uda, Manuela / Ulivi, Sheila / van Veldhuisen, Dirk J / Visscher, Peter M / Völker, Uwe / Wichmann, H-Erich / Wiggins, Kerri L / Willemsen, Gonneke / Yang, Tsun-Po / Hua Zhao, Jing / Zitting, Paavo / Bradley, John R / Dedoussis, George V / Gasparini, Paolo / Hazen, Stanley L / Metspalu, Andres / Pirastu, Mario / Shuldiner, Alan R / Joost van Pelt, L / Zwaginga, Jaap-Jan / Boomsma, Dorret I / Deary, Ian J / Franke, Andre / Froguel, Philippe / Ganesh, Santhi K / Jarvelin, Marjo-Riitta / Martin, Nicholas G / Meisinger, Christa / Psaty, Bruce M / Spector, Timothy D / Wareham, Nicholas J / Akkerman, Jan-Willem N / Ciullo, Marina / Deloukas, Panos / Greinacher, Andreas / Jupe, Steve / Kamatani, Naoyuki / Khadake, Jyoti / Kooner, Jaspal S / Penninger, Josef / Prokopenko, Inga / Stemple, Derek / Toniolo, Daniela / Wernisch, Lorenz / Sanna, Serena / Hicks, Andrew A / Rendon, Augusto / Ferreira, Manuel A / Ouwehand, Willem H / Soranzo, Nicole

    Nature

    2011  Volume 480, Issue 7376, Page(s) 201–208

    Abstract: Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes ... ...

    Abstract Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes controlling both traits. Here we carried out a high-powered meta-analysis of genome-wide association studies (GWAS) in up to 66,867 individuals of European ancestry, followed by extensive biological and functional assessment. We identified 68 genomic loci reliably associated with platelet count and volume mapping to established and putative novel regulators of megakaryopoiesis and platelet formation. These genes show megakaryocyte-specific gene expression patterns and extensive network connectivity. Using gene silencing in Danio rerio and Drosophila melanogaster, we identified 11 of the genes as novel regulators of blood cell formation. Taken together, our findings advance understanding of novel gene functions controlling fate-determining events during megakaryopoiesis and platelet formation, providing a new example of successful translation of GWAS to function.
    MeSH term(s) Animals ; Blood Platelets/cytology ; Blood Platelets/metabolism ; Cell Size ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Europe ; Gene Expression Profiling ; Gene Silencing ; Genome, Human/genetics ; Genome-Wide Association Study ; Hematopoiesis/genetics ; Humans ; Megakaryocytes/cytology ; Megakaryocytes/metabolism ; Platelet Count ; Protein Interaction Maps ; Transcription, Genetic/genetics ; Zebrafish/genetics ; Zebrafish Proteins/genetics
    Chemical Substances Drosophila Proteins ; Zebrafish Proteins
    Language English
    Publishing date 2011-11-30
    Publishing country England
    Document type Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature10659
    Database MEDical Literature Analysis and Retrieval System OnLINE

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