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MPact: the MIPS protein interaction resource on yeast

U. Guldener
2006 Nucleic Acids Research  
In recent years, the Munich Information Center for Protein Sequences (MIPS) yeast protein-protein interaction (PPI) dataset has been used in numerous analyses of protein networks and has been called a  ...  This work was supported by a grant of the German Federal Ministry of Education and Research (BMBF) within the BFAM framework (031U112C/212C), the European Commission (QLRI-CT 1999-01333) and the Impuls-und  ...  Funding to pay the Open Access publication charges for this article was provided by the GSF National Research Center for Environment and Health. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkj003 pmid:16381906 pmcid:PMC1347366 fatcat:h7wgsv5ba5bmzgpx2lfyor7igm

MIPS: analysis and annotation of proteins from whole genomes

H. W. Mewes
2004 Nucleic Acids Research  
The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information.  ...  The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework.  ...  Funding to pay the Open Access publication charges for this article was provided by the GSF-National Research Center for Environment and Health.  ... 
doi:10.1093/nar/gkh092 pmid:14681354 pmcid:PMC308826 fatcat:btjnepsiuzdptenlftjde5v4lq

MIPS: curated databases and comprehensive secondary data resources in 2010

H. Werner Mewes, Andreas Ruepp, Fabian Theis, Thomas Rattei, Mathias Walter, Dmitrij Frishman, Karsten Suhre, Manuel Spannagl, Klaus F.X. Mayer, Volker Stümpflen, Alexey Antonov
2010 Nucleic Acids Research  
interaction data sets (MPACT, MPPI and CORUM).  ...  More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research.  ...  : representation of interaction data at MIPS PlantsDB PhenomiR: miRNA-phenotype relations  ... 
doi:10.1093/nar/gkq1157 pmid:21109531 pmcid:PMC3013725 fatcat:ovrbatthcnb7vbb7bgntbu2mha

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

Javier De Las Rivas, Celia Fontanillo, Fran Lewitter
2010 PLoS Computational Biology  
, Ssc & Lsc published studies (literature-curated) MIPS-MPact MIPS protein interaction resource on yeast, genre/proj/mpact/ Meta-Databases: PPI experimental  ...  usually obtained from curation of research articles (8 resources included: BIND, BioGRID, DIP, HPRD, IntAct, MINT, MIPS-MPACT, MIPS-MPPI); meta-databases, which include PPIs derived from integration and  ... 
doi:10.1371/journal.pcbi.1000807 pmid:20589078 pmcid:PMC2891586 fatcat:5ciyxdoxpvhqzgwpcwcwo4aqou

MIPS: analysis and annotation of genome information in 2007

H. W. Mewes, S. Dietmann, D. Frishman, R. Gregory, G. Mannhaupt, K. F. X. Mayer, M. Munsterkotter, A. Ruepp, M. Spannagl, V. Stumpflen, T. Rattei
2007 Nucleic Acids Research  
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).  ...  (Bioinformatics Munich, BIM), and the Max-Planck-Society (MUMDB).  ... 
doi:10.1093/nar/gkm980 pmid:18158298 pmcid:PMC2238900 fatcat:3xeojdnfnngg7nd3lelf6tieke

Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases

Benjamin A. Shoemaker, Anna R. Panchenko
2007 PLoS Computational Biology  
This work was supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health of the US Department of Health and Human Services.  ...  BAS and ARP analyzed the data and wrote the paper. Funding. The authors received no specific funding for this article. Competing interests. The authors have declared that no competing interests exist.  ...  MPact is a resource to access MIPS, which contains a manually curated yeast protein interaction dataset [97] collected by curators from the literature.  ... 
doi:10.1371/journal.pcbi.0030042 pmid:17397251 pmcid:PMC1847991 fatcat:ymo5mofnrfesroxasv7d57ahga

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality

G Traver Hart, Insuk Lee, Edward R Marcotte
2007 BMC Bioinformatics  
Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V: MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res 2006, 34(Database issue):D436-441. 16 24.  ...  Results: Using an unsupervised probabilistic scoring scheme, we assigned a confidence score to each interaction in the matrix-model interpretation of the large-scale yeast massspectrometry data sets.  ...  Munich Information center on Protein Sequences (MIPS) [23].  ... 
doi:10.1186/1471-2105-8-236 pmid:17605818 pmcid:PMC1940025 fatcat:n5dxs4itb5cuzptnwcmjagposi

CYGD: the Comprehensive Yeast Genome Database

U. Guldener
2004 Nucleic Acids Research  
In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements.  ...  The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the  ...  (MNCDB) and the Government of the Brussels Region, Belgium, for the aMAZE project.  ... 
doi:10.1093/nar/gki053 pmid:15608217 pmcid:PMC540007 fatcat:nxst4ximuzau7gbukjpntb6d7u

POINeT: protein interactome with sub-network analysis and hub prioritization

Sheng-An Lee, Chen-Hsiung Chan, Tzu-Chi Chen, Chia-Ying Yang, Kuo-Chuan Huang, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, Chi-Ying F Huang
2009 BMC Bioinformatics  
Protein-protein interactions (PPIs) are critical to every aspect of biological processes.  ...  Moreover, the reliability of available PPI resources, which consist of low-and high-throughput data, for network construction remains a significant challenge.  ...  MPact 2005/12/22 12,955 Ulrich G. et al. (2006) Güldener U, Münsterkötter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stümpflen V(2006). MPact: the MIPS protein interaction resource on yeast.  ... 
doi:10.1186/1471-2105-10-114 pmid:19379523 pmcid:PMC2683814 fatcat:bna36ahvsnatbapmp6qkn3vn5y

Identification of mitochondrial disease genes through integrative analysis of multiple datasets

Raeka S. Aiyar, Julien Gagneur, Lars M. Steinmetz
2008 Methods  
Determining the genetic factors in a disease is crucial to elucidating its molecular basis. This task is challenging due to a lack of information on gene function.  ...  Relevant public data resources are indicated. This report highlights the success and potential of data integration as well as its applicability to the search for mitochondrial disease genes.  ...  Acknowledgments The authors would like to acknowledge Amoolya Singh, Michael DiBernardo, Christine Panagiotidis, Stéphanie Blandin, Eugenio Mancera, Fabiana Perocchi, Himanshu Sinha, and Sebastian Kühner  ... 
doi:10.1016/j.ymeth.2008.10.002 pmid:18930150 pmcid:PMC2774125 fatcat:qmextxwyzfckbadqx7rwuryviy

An evolutionary and structural characterization of mammalian protein complex organization

Philip Wong, Sonja Althammer, Andrea Hildebrand, Andreas Kirschner, Philipp Pagel, Bernd Geissler, Pawel Smialowski, Florian Blöchl, Matthias Oesterheld, Thorsten Schmidt, Normann Strack, Fabian J Theis (+2 others)
2008 BMC Genomics  
A large proportion of the protein content and interactions in the complexes could be predicted from known binary protein-protein and domain-domain interactions.  ...  In particular, we found that large proteins interact preferentially with much smaller proteins.  ...  Conclusion: We observed similar trends in yeast and other data. Our results support the existence of conserved relations associated with the mammalian protein complexes.  ... 
doi:10.1186/1471-2164-9-629 pmid:19108706 pmcid:PMC2645396 fatcat:h2pqnjqdqfgyzjfqrpi2sbzqjy

Finding the "Dark Matter" in Human and Yeast Protein Network Prediction and Modelling

Juan A. G. Ranea, Ian Morilla, Jon G. Lees, Adam J. Reid, Corin Yeats, Andrew B. Clegg, Francisca Sanchez-Jimenez, Christine Orengo, Andrey Rzhetsky
2010 PLoS Computational Biology  
A clear signal between microarray data and interacting proteins has previously been observed with the yeast dataset and the MIPS (MPACT) PPI dataset [55] .  ...  Because virtually all yeast ORFS are present on the microarray, the combination of all pairwise correlation coefficients represents a near total population of ORF pairs.  ...  The interaction dataset is formed from a merger of the PPI resources from MIPS, IntAct, HPRD and MINT protein-protein interaction datasets, obtained from the Gene3D database [59] .  ... 
doi:10.1371/journal.pcbi.1000945 pmid:20885791 pmcid:PMC2944794 fatcat:nksrjpjjfbexxkhalcqlba7bxa

iRefIndex: A consolidated protein interaction database with provenance

Sabry Razick, George Magklaras, Ian M Donaldson
2008 BMC Bioinformatics  
Conclusion: We have applied our method to protein interaction records from BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID.  ...  Keys for protein participants allow for retrieval of interaction information independent of the protein references used in the original records.  ...  Acknowledgements We would like to thank the following for useful feedback and discussions: Andrew Winter, Mike Tyers, Ulrich Gueldener, Sandra Orchard, Luisa Montecchi, Henning Hermjakob, Tony Chiang,  ... 
doi:10.1186/1471-2105-9-405 pmid:18823568 pmcid:PMC2573892 fatcat:vsv6fbiizbaf7n6x3z6fsxvbcm

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

Samuel Kerrien, Sandra Orchard, Luisa Montecchi-Palazzi, Bruno Aranda, Antony F Quinn, Nisha Vinod, Gary D Bader, Ioannis Xenarios, Jérôme Wojcik, David Sherman, Mike Tyers, John J Salama (+18 others)
2007 BMC Biology  
of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions.  ...  Molecular interaction Information is a key resource in modern biomedical research.  ...  In addition, this work has been supported by the  ... 
doi:10.1186/1741-7007-5-44 pmid:17925023 pmcid:PMC2189715 fatcat:mihxus5nn5asfll7hsugdsqw4m

Proteomics-Based Methods for Discovery, Quantification, and Validation of Protein–Protein Interactions

Yana V. Miteva, Hanna G. Budayeva, Ileana M. Cristea
2012 Analytical Chemistry  
Thus, the protein of interest gets captured on the resin together with its interaction partners and, after different washing steps aimed at eliminating non-specific interactions, the isolated protein complex  ...  proteins include the dependence on availability, specificity, and affinity of antibodies recognizing the Miteva et al.  ...  learning algorithms trained on the curated MIPS database 108 of protein complexes, probabilities were assigned to each pairwise interaction.  ... 
doi:10.1021/ac3033257 pmid:23157382 pmcid:PMC3666915 fatcat:le3dkitowval5j3xddsdluiwxq
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