Sat, 26 Jul 2008 06:37:49 BST CiteULike: jyuh's Mewes http://www.citeulike.org/user/jyuh/author/Mewes CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/jyuh/article/2782605 <i>Nucleic acids research, Vol. 36, No. Database issue. (January 2008)</i><br /><br />The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). MIPS: analysis and annotation of genome information in 2007. HW Mewes S Dietmann D Frishman R Gregory G Mannhaupt KF Mayer M Münsterkötter A Ruepp M Spannagl V Stümpflen T Rattei Nucleic acids research, Vol. 36, No. Database issue. (January 2008) 2008-05-10T08:57:38-00:00 2008 Nucleic acids research 1362-4962 36 Database issue no-tag http://www.citeulike.org/user/jyuh/article/2782593 <i>Nucleic acids research (6 May 2008)</i><br /><br />ProfCom is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of 'complex functions'. A 'Complex function' is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes. ProfCom provides a user friendly dialog-driven web page submission available for several model organisms and supports most available gene identifiers. In addition, the web service interface allows the submission of any kind of annotation data. ProfCom is freely available at http://webclu.bio.wzw.tum.de/profcom/. ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data. Alexey V Antonov Thorsten Schmidt Yu Wang Hans W Mewes Nucleic acids research (6 May 2008) 2008-05-10T08:46:46-00:00 2008 Nucleic acids research 1362-4962 no-tag http://www.citeulike.org/user/jyuh/article/2622747 <i>Endocrinology (27 March 2008)</i><br /><br />Metabolomics is a powerful tool for identifying both known and new disease-related perturbations in metabolic pathways. In preclinical drug testing, it has a high potential for early identification of drug off-target effects. Recent advances in high-precision high-throughput mass spectrometry have brought the Metabolomics field to a point where quantitative, targeted, metabolomic measurements with ready-to-use kits allow for the automated in-house screening for hundreds of different metabolites in large sets of biological samples. Today, the field of metabolomics is, arguably, at a point where transcriptomics was about five years ago. This being so, the field has a strong need for adapted bioinformatics tools and methods. In this paper, we describe a systematic analysis of a targeted quantitative characterization of more than 800 metabolites in blood plasma samples from healthy and diabetic mice under rosiglitazone treatment. We show that known and new metabolic phenotypes of diabetes and medication can be recovered in a statistically objective manner. We find that concentrations of methylglutarylcarnitine are oppositely impacted by rosiglitazone treatment of both healthy and diabetic mice. Analyzing ratios between metabolite concentrations dramatically reduces the noise in the dataset, allowing for the discovery of new potential biomarkers of diabetes, such as the N-hydroxyacyloylsphingosyl-phosphocholines SM(OH)28:0 and SM(OH)26:0. Using a hierarchical clustering technique on partial eta-squared values, we identify functionally related groups of metabolites, indicating a diabetes-related shift from lysophosphatidylcholine to phosphatidylcholine levels. The bioinformatics data analysis approach introduced here can be readily generalized to other drug-testing scenarios and to other medical disorders. Bioinformatics analysis of targeted metabolomics - uncovering old and new tales of diabetic mice under medication. Elisabeth Altmaier Steven L Ramsay Armin Graber Hans-Werner Mewes Klaus M Weinberger Karsten Suhre doi:10.1210/en.2007-1747 Endocrinology (27 March 2008) 2008-04-02T09:09:41-00:00 2008 Endocrinology 0013-7227 no-tag http://www.citeulike.org/user/jyuh/article/2249143 <i>Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)</i><br /><br />Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes. For functional annotation, we use the FunCat catalogue that enables to organize the protein complex space into biologically meaningful subsets. The database contains more than 1750 protein complexes that are built from 2400 different genes, thus representing 12% of the protein-coding genes in human. A web-based system is available to query, view and download the data. CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases. Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes. CORUM: the comprehensive resource of mammalian protein complexes. A Ruepp B Brauner I Dunger-Kaltenbach G Frishman C Montrone M Stransky B Waegele T Schmidt ON Doudieu V Stümpflen HW Mewes Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008) 2008-01-18T03:50:41-00:00 2008 Nucleic Acids Res 1362-4962 36 Database issue no-tag http://www.citeulike.org/user/jyuh/article/1544639 <i>Nature Biotechnology, Vol. 25, No. 8. (08 August 2007), pp. 894-898.</i> The minimum information required for reporting a molecular interaction experiment (MIMIx) Sandra Orchard Lukasz Salwinski Samuel Kerrien Luisa Montecchi-Palazzi Matthias Oesterheld Volker Stümpflen Arnaud Ceol Andrew Chatr-Aryamontri John Armstrong Peter Woollard John Salama Susan Moore Jérôme Wojcik Gary Bader Marc Vidal Michael Cusick Mark Gerstein Anne-Claude Gavin Giulio Superti-Furga Jack Greenblatt Joel Bader Peter Uetz Mike Tyers Pierre Legrain Stan Fields Nicola Mulder Michael Gilson Michael Niepmann Lyle Burgoon Javier Carlos Prieto Victoria Perreau Chris Hogue Hans-Werner Mewes Rolf Apweiler Ioannis Xenarios David Eisenberg Gianni Cesareni Henning Hermjakob doi:10.1038/nbt1324 Nature Biotechnology, Vol. 25, No. 8. (08 August 2007), pp. 894-898. 2007-08-09T00:39:24-00:00 2007 Nature Biotechnology 1087-0156 25 8 894 898 Nature Publishing Group no-tag