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Tsitsiridis G, Steinkamp R, Giurgiu M, Brauner B, Fobo G, Frishman G, Montrone C, Ruepp A. CORUM: the comprehensive resource of mammalian protein complexes-2022. Nucleic Acids Res 2022; 51:D539-D545. [PMID: 36382402 PMCID: PMC9825459 DOI: 10.1093/nar/gkac1015] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The CORUM database has been providing comprehensive reference information about experimentally characterized, mammalian protein complexes and their associated biological and biomedical properties since 2007. Given that most catalytic and regulatory functions of the cell are carried out by protein complexes, their composition and characterization is of greatest importance in basic and disease biology. The new CORUM 4.0 release encompasses 5204 protein complexes offering the largest and most comprehensive publicly available dataset of manually curated mammalian protein complexes. The CORUM dataset is built from 5299 different genes, representing 26% of the protein coding genes in humans. Complex information from 3354 scientific articles is mainly obtained from human (70%), mouse (16%) and rat (9%) cells and tissues. Recent curation work includes sets of protein complexes, Functional Complex Groups, that offer comprehensive collections of published data in specific biological processes and molecular functions. In addition, a new graphical analysis tool was implemented that displays co-expression data from the subunits of protein complexes. CORUM is freely accessible at http://mips.helmholtz-muenchen.de/corum/.
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Affiliation(s)
- George Tsitsiridis
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Ralph Steinkamp
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Madalina Giurgiu
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité Universitätsmedizin Berlin, Berlin 13125, Germany
| | - Barbara Brauner
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Gisela Fobo
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Goar Frishman
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Corinna Montrone
- Institute of Experimental Genetics, Helmholtz Center Munich (GmbH), German research Center for environmental Health, Neuherberg D-85764, Germany
| | - Andreas Ruepp
- To whom correspondence should be addressed. Tel: +49 89 3187 3189; Fax: +49 89 3187 3500;
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Maier H, Schütt C, Steinkamp R, Hurt A, Schneltzer E, Gormanns P, Lengger C, Griffiths M, Melvin D, Agrawal N, Alcantara R, Evans A, Gannon D, Holroyd S, Kipp C, Raj NP, Richardson D, LeBlanc S, Vasseur L, Masuya H, Kobayashi K, Suzuki T, Tanaka N, Wakana S, Walling A, Clary D, Gallegos J, Fuchs H, de Angelis MH, Gailus-Durner V. Principles and application of LIMS in mouse clinics. Mamm Genome 2015. [PMID: 26208973 PMCID: PMC4602070 DOI: 10.1007/s00335-015-9586-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 11/29/2022]
Abstract
Large-scale systemic mouse phenotyping, as performed by mouse clinics for more than a decade, requires thousands of mice from a multitude of different mutant lines to be bred, individually tracked and subjected to phenotyping procedures according to a standardised schedule. All these efforts are typically organised in overlapping projects, running in parallel. In terms of logistics, data capture, data analysis, result visualisation and reporting, new challenges have emerged from such projects. These challenges could hardly be met with traditional methods such as pen & paper colony management, spreadsheet-based data management and manual data analysis. Hence, different Laboratory Information Management Systems (LIMS) have been developed in mouse clinics to facilitate or even enable mouse and data management in the described order of magnitude. This review shows that general principles of LIMS can be empirically deduced from LIMS used by different mouse clinics, although these have evolved differently. Supported by LIMS descriptions and lessons learned from seven mouse clinics, this review also shows that the unique LIMS environment in a particular facility strongly influences strategic LIMS decisions and LIMS development. As a major conclusion, this review states that there is no universal LIMS for the mouse research domain that fits all requirements. Still, empirically deduced general LIMS principles can serve as a master decision support template, which is provided as a hands-on tool for mouse research facilities looking for a LIMS.
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Affiliation(s)
- Holger Maier
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Ralph Steinkamp
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anja Hurt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Elida Schneltzer
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Philipp Gormanns
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Christoph Lengger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Mark Griffiths
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Melvin
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Neha Agrawal
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Rafael Alcantara
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Arthur Evans
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Gannon
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Simon Holroyd
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Christian Kipp
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Navis Pretheeba Raj
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Richardson
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Sophie LeBlanc
- Institut Clinique de la Souris - ICS, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France
| | - Laurent Vasseur
- Institut Clinique de la Souris - ICS, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France
| | - Hiroshi Masuya
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Kimio Kobayashi
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Tomohiro Suzuki
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Nobuhiko Tanaka
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Shigeharu Wakana
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Alison Walling
- Mary Lyon Centre, Medical Research Council Harwell, Harwell Science and Innovation Campus, Harwell, Oxfordshire, OX11 0RD, UK
| | - David Clary
- Mouse Biology Program, University of California, Davis, 2795 2nd Street, Suite 400, Davis, CA, 95618, USA
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Chair for Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität Munich, Freising-Weihenstephan, 85354, Munich, Germany. .,Member of German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
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Fuchs H, Gailus-Durner V, Neschen S, Adler T, Afonso LC, Aguilar-Pimentel JA, Becker L, Bohla A, Calzada-Wack J, Cohrs C, Dewert A, Fridrich B, Garrett L, Glasl L, Götz A, Hans W, Hölter SM, Horsch M, Hurt A, Janas E, Janik D, Kahle M, Kistler M, Klein-Rodewald T, Lengger C, Ludwig T, Maier H, Marschall S, Micklich K, Möller G, Naton B, Prehn C, Puk O, Rácz I, Räss M, Rathkolb B, Rozman J, Scheerer M, Schiller E, Schrewe A, Steinkamp R, Stöger C, Sun M, Szymczak W, Treise I, Vargas Panesso IL, Vernaleken AM, Willershäuser M, Wolff-Muscate A, Zeh R, Adamski J, Beckers J, Bekeredjian R, Busch DH, Eickelberg O, Favor J, Graw J, Höfler H, Höschen C, Katus H, Klingenspor M, Klopstock T, Neff F, Ollert M, Schulz H, Stöger T, Wolf E, Wurst W, Yildirim AÖ, Zimmer A, Hrabě de Angelis M. Innovations in phenotyping of mouse models in the German Mouse Clinic. Mamm Genome 2012; 23:611-22. [PMID: 22926221 PMCID: PMC3463795 DOI: 10.1007/s00335-012-9415-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [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] [Received: 03/11/2012] [Accepted: 07/05/2012] [Indexed: 01/29/2023]
Abstract
Under the label of the German Mouse Clinic (GMC), a concept has been developed and implemented that allows the better understanding of human diseases on the pathophysiological and molecular level. This includes better understanding of the crosstalk between different organs, pleiotropy of genes, and the systemic impact of envirotypes and drugs. In the GMC, experts from various fields of mouse genetics and physiology, in close collaboration with clinicians, work side by side under one roof. The GMC is an open-access platform for the scientific community by providing phenotypic analysis in bilateral collaborations ("bottom-up projects") and as a partner and driver in international large-scale biology projects ("top-down projects"). Furthermore, technology development is a major topic in the GMC. Innovative techniques for primary and secondary screens are developed and implemented into the phenotyping pipelines (e.g., detection of volatile organic compounds, VOCs).
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Affiliation(s)
- Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg/Munich, Germany
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Fuchs H, Gailus-Durner V, Adler T, Aguilar Pimentel J, Becker L, Bolle I, Brielmeier M, Calzada- Wack J, Dalke C, Ehrhardt N, Fasnacht N, Ferwagner B, Frischmann U, Hans W, Holter S, Holzlwimmer G, Horsch M, Javaheri A, Kallnik M, Kling E, Lengger C, Maier H, Moβbrugger I, Morth C, Naton B, Noth U, Pasche B, Prehn C, Przemeck G, Puk O, Racz I, Rathkolb B, Rozman J, Schable K, Schreiner R, Schrewe A, Sina C, Steinkamp R, Thiele F, Willershauser M, Zeh R, Adamski J, Busch D, Beckers J, Behrendt H, Daniel H, Esposito I, Favor J, Graw J, Heldmaier G, Hofler H, Ivandic B, Katus H, Klingenspor M, Klopstock T, Lengeling A, Mempel M, Muller W, Neschen S, Ollert M, Quintanilla-Martinez L, Rosenstiel P, Schmidt J, Schreiber S, Schughart K, Schulz H, Wolf E, Wurst W, Zimmer A, de Angelis M. The German Mouse Clinic: A Platform for Systemic Phenotype Analysis of Mouse Models. Curr Pharm Biotechnol 2009; 10:236-43. [DOI: 10.2174/138920109787315051] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Gailus-Durner V, Fuchs H, Becker L, Bolle I, Brielmeier M, Calzada-Wack J, Elvert R, Ehrhardt N, Dalke C, Franz TJ, Grundner-Culemann E, Hammelbacher S, Hölter SM, Hölzlwimmer G, Horsch M, Javaheri A, Kalaydjiev SV, Klempt M, Kling E, Kunder S, Lengger C, Lisse T, Mijalski T, Naton B, Pedersen V, Prehn C, Przemeck G, Racz I, Reinhard C, Reitmeir P, Schneider I, Schrewe A, Steinkamp R, Zybill C, Adamski J, Beckers J, Behrendt H, Favor J, Graw J, Heldmaier G, Höfler H, Ivandic B, Katus H, Kirchhof P, Klingenspor M, Klopstock T, Lengeling A, Müller W, Ohl F, Ollert M, Quintanilla-Martinez L, Schmidt J, Schulz H, Wolf E, Wurst W, Zimmer A, Busch DH, de Angelis MH. Introducing the German Mouse Clinic: open access platform for standardized phenotyping. Nat Methods 2005; 2:403-4. [PMID: 15908916 DOI: 10.1038/nmeth0605-403] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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