MIPS: analysis and annotation of genome information in 2007
Hans-Werner Mewes,Sabine Dietmann,Dmitrij Frishman,Richard Gregory,Gertrud Mannhaupt,Klaus F. X. Mayer,Martin Münsterkötter,Andreas Ruepp,Manuel Spannagl,Volker Stümpflen,Thomas Rattei +10 more
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TLDR
The Munich Information Center for Protein Sequences combines automatic processing of large amounts of sequences with manual annotation of selected model genomes with the compilation of manually curated databases for protein interactions based on scrutinized information from the literature.Abstract:
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).read more
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Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
Elizabeth J. Rossin,Kasper Lage,Soumya Raychaudhuri,Soumya Raychaudhuri,Soumya Raychaudhuri,Ramnik J. Xavier,Ramnik J. Xavier,Diana Tatar,Yair Benita,Chris Cotsapas,Chris Cotsapas,Mark J. Daly +11 more
TL;DR: Results constitute evidence that, for many of the complex diseases studied here, common genetic associations implicate regions encoding proteins that physically interact in a preferential manner, in line with observations in Mendelian disease.
Journal ArticleDOI
Overview of the protein-protein interaction annotation extraction task of BioCreative II
TL;DR: The BioCreative II PPI task is the first attempt to compare the performance of text-mining tools specific for each of the basic steps of the PPI extraction pipeline, and challenges identified range from problems in full-text format conversion of articles to difficulties in detecting interactor protein pairs and then linking them to their database records.
Journal ArticleDOI
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.
TL;DR: The functional-linkage network is used to prioritize candidate genes for 110 diseases, and to reliably disclose hidden associations between disease pairs having dissimilar phenotypes, such as hypercholesterolemia and Alzheimer's disease.
Journal ArticleDOI
Network-based methods for human disease gene prediction
TL;DR: Recent, state of the art, network-based methods used for prioritizing disease genes as well as unraveling the molecular basis of human diseases are reviewed.
Journal ArticleDOI
PIPs: human protein–protein interaction prediction database
TL;DR: The PIPs database provides a new resource on protein–protein interactions in human that is straightforward to browse, or can be exploited completely, for interaction network modelling.
References
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TL;DR: The Generic Genome Browser (GBrowse) is described, a Web-based application for displaying genomic annotations and other features and easy integration with other components of a model organism system Web site.
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