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The BioGRID Interaction Database: 2008 update

B.-J. Breitkreutz, C. Stark, T. Reguly, L. Boucher, A. Breitkreutz, M. Livstone, R. Oughtred, D. H. Lackner, J. Bahler, V. Wood, K. Dolinski, M. Tyers
2007 Nucleic Acids Research  
The BioGRID provides interaction data with monthly updates to Saccharomyces Genome Database, Flybase and Entrez Gene.  ...  The Biological General Repository for Interaction Datasets (BioGRID) database (http://www. thebiogrid.org) was developed to house and distribute collections of protein and genetic interactions from major  ...  The IMS instantly commits new interactions to the BioGRID update pipeline, unless specified otherwise; interactions are collated each month and released as updates to the primary BioGRID and mirror sites  ... 
doi:10.1093/nar/gkm1001 pmid:18000002 pmcid:PMC2238873 fatcat:cqmz56s4uje2tmjr5mejrvompy

Measuring pathway database coverage of the phosphoproteome

Hannah Huckstep, Liam G. Fearnley, Melissa J. Davis
2021 PeerJ  
We first determined the global coverage of each database at both the protein and phosphosite level.  ...  Finally, we looked in detail at the coverage of each database over six experimental datasets.  ...  ACKNOWLEDGEMENTS The authors thank Daniel Esposito, Samuel Lee and Dharmesh Bhuva for technical support. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.11298 pmid:34113485 pmcid:PMC8162239 fatcat:yx4zibz3cvcm7h344ie3g2ge5u

ConsensusPathDB—a database for integrating human functional interaction networks

Atanas Kamburov, Christoph Wierling, Hans Lehrach, Ralf Herwig
2008 Nucleic Acids Research  
ConsensusPathDB is a database system for the integration of human functional interactions.  ...  The ConsensusPathDB database is available at  ...  ACKNOWLEDGEMENTS We are grateful to the interaction database providers ( Table 1 ) that allowed automated access to their databases.  ... 
doi:10.1093/nar/gkn698 pmid:18940869 pmcid:PMC2686562 fatcat:xaeqf3acsjgalo6vb7fymcu3pm

The Molecule Pages Database

B. Saunders, S. Lyon, M. Day, B. Riley, E. Chenette, S. Subramaniam
2008 Nucleic Acids Research  
The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture.  ...  The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and  ...  Warren Hedley, Yuhong Ning and Ilango Vadivelu contributed to the business and presentation tiers of the Molecule Page application, and Joshua Li contributed to the Oracle database tier.  ... 
doi:10.1093/nar/gkn139 fatcat:zqvpnydhuncuxlmtwnrii6rloq

MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions

Emilie Chautard, Lionel Ballut, Nicolas Thierry-Mieg, Sylvie Ricard-Blum
2009 Computer applications in the biosciences : CABIOS  
MatrixDB (http://matrixdb.ibcp.fr) is a database reporting mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules.  ...  It takes into account the full interaction repertoire of the extracellular matrix involving full-length molecules, fragments and multimers.  ...  Blanchet for his strong support in building the web site. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp025 pmid:19147664 pmcid:PMC2647840 fatcat:drk4tkxkfnav5pinjujfnisc74

iRefIndex: A consolidated protein interaction database with provenance

Sabry Razick, George Magklaras, Ian M Donaldson
2008 BMC Bioinformatics  
Interaction data for a given protein may be spread across multiple databases.  ...  Conclusion: We have applied our method to protein interaction records from BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID.  ...  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

The Molecule Pages database

B. Saunders, S. Lyon, M. Day, B. Riley, E. Chenette, S. Subramaniam
2007 Nucleic Acids Research  
The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture.  ...  The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and  ...  Warren Hedley, Yuhong Ning and Ilango Vadivelu contributed to the business and presentation tiers of the Molecule Page application, and Joshua Li contributed to the Oracle database tier.  ... 
doi:10.1093/nar/gkm907 pmid:17965093 pmcid:PMC2238911 fatcat:4ok4pvg4azarrbzdgml6os5qeq

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

B. Turner, S. Razick, A. L. Turinsky, J. Vlasblom, E. K. Crowdy, E. Cho, K. Morrison, I. M. Donaldson, S. J. Wodak
2010 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors wish to thank Sandra Orchard for helpful suggestions regarding several iRefWeb features. Conflict of interest statement. None declared. Author Contribution  ...  PMID 11283351 (7) : Out of six databases, only BioGRID seems to annotate the core set, and the other databases annotated both the core and non-core interactions.  ...  BioGRID 2616 http://thebiogrid.org/77339/publication/18467557.html IntAct 10181 Experiment 'tarassov-2008-1' (http://www.ebi.ac.uk/intact/pages/details/ details.xhtml?  ... 
doi:10.1093/database/baq023 pmid:20940177 pmcid:PMC2963317 fatcat:2o7m36ql4vdbbbix7venxl3i6m

ENDEAVOUR update: a web resource for gene prioritization in multiple species

L.-C. Tranchevent, R. Barriot, S. Yu, S. Van Vooren, P. Van Loo, B. Coessens, B. De Moor, S. Aerts, Y. Moreau
2008 Nucleic Acids Research  
Third, ENDEAVOUR makes use of additional data sources and is now including numerous databases: ontologies and annotations, protein-protein interactions, cis-regulatory information, gene expression data  ...  candidate genes to rank those candidates against the profile of the known genes and (iii) merging the several rankings into a global ranking of the candidate genes.  ...  ACKNOWLEDGEMENTS This research was supported by the Research Council KUL (GOA AMBioRICS, CoE EF/05/007 SymBioSys, PROMETA, several PhD/postdoc & fellow grants), FWO  ... 
doi:10.1093/nar/gkn325 pmid:18508807 pmcid:PMC2447805 fatcat:37k5fwm6xzfx5lyimmnmsse44i

YCRD: Yeast Combinatorial Regulation Database

Wei-Sheng Wu, Yen-Chen Hsieh, Fu-Jou Lai, Robertus A M de Bruin
2016 PLoS ONE  
Because there is no such kind of databases in the public domain, this prompts us to construct a database, called Yeast Combinatorial Regulation Database (YCRD), which deposits 434,197 regulatory associations  ...  TF1-TF2) are defined as the common target genes of TF1 and TF2, where a TF's experimentally validated target genes were downloaded from YEASTRACT database.  ...  Acknowledgments The physical/genetic interaction data and a TF's experimentally validated target genes were retrieved from BioGRID and YEASTRACT in March 2016, respectively.  ... 
doi:10.1371/journal.pone.0159213 pmid:27392072 pmcid:PMC4938206 fatcat:ms2wntabaff77b7ynqsspyvapa

CoopTFD: a repository for predicted yeast cooperative transcription factor pairs

Wei-Sheng Wu, Fu-Jou Lai, Bor-Wen Tu, Darby Tien-Hao Chang
2016 Database: The Journal of Biological Databases and Curation  
or genetic interactions, (iii) the publications which experimentally study the biological roles of both TFs of this PCTFP, (iv) the common Gene Ontology (GO) terms of this PCTFP and (v) the common target  ...  However, until now, there is still no database which collects the predicted yeast cooperative TFs from existing algorithms.  ...  Acknowledgements The physical or genetic interaction data, co-citation papers, coannotated GO terms and the co-regulatory target genes were retrieved from BioGRID, SGD and YEASTRACT on 24 February 2016  ... 
doi:10.1093/database/baw092 pmid:27242036 pmcid:PMC4885606 fatcat:ptkyeq3iafh77fwwshiih6jyqu

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases

Tiago J. S. Lopes, Martin Schaefer, Jason Shoemaker, Yukiko Matsuoka, Jean−Fred Fontaine, Gabriele Neumann, Miguel A. Andrade-Navarro, Yoshihiro Kawaoka, Hiroaki Kitano
2011 Computer applications in the biosciences : CABIOS  
Results: We found that the evaluated databases are comparable in terms of node connectivity (i.e. proteins with few interaction partners also have few interaction partners in other databases), but may  ...  Here, we evaluated the characteristics of six interaction databases, incorporated tissue-specific gene expression information and finally, investigated if the most popular proteins of scientific literature  ...  ACKNOWLEDGEMENTS We are grateful to the skillful and critical reading of the manuscript by Amie Eisfeld-Fenney and fruitful discussions with Takeshi Hase. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btr414 pmid:21798963 fatcat:4bzihh5yi5e7rfmzwbornfamiy

Biocuration at theSaccharomycesgenome database

Marek S. Skrzypek, Robert S. Nash
2015 Genesis  
Saccharomyces Genome Database is an online resource dedicated to managing information about the biology and genetics of the model organism, yeast (Saccharomyces cerevisiae).  ...  In this review we will demonstrate how biocuration and biocurators add a key component, the biological context, to our understanding of how genes, proteins, genomes and cells function and interact.  ...  Michael Cherry for their helpful suggestions during the writing of this manuscript; the authors also acknowledge the tireless effort of all the system administrators, programmers and biocurators in building  ... 
doi:10.1002/dvg.22862 pmid:25997651 pmcid:PMC4545726 fatcat:krnxivky4fdvviye4bunx2dz7m

PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae

C. Stark, T.-C. Su, A. Breitkreutz, P. Lourenco, M. Dahabieh, B.-J. Breitkreutz, M. Tyers, I. Sadowski
2010 Database: The Journal of Biological Databases and Curation  
ACKNOWLEDGMENTS The authors thank LeAnn Howe and Francis Ouellette for helpful discussions.  ...  yeast BioGRID database (13) .  ...  All entries in PhosphoGRID are linked to other existing online yeast resources, including the BioGRID interaction database (13) and the Saccharomyces Genome Database (SGD) (23) .  ... 
doi:10.1093/database/bap026 pmid:20428315 pmcid:PMC2860897 fatcat:2lmv5x7r75dchmft7hwgugzky4

BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts

Beibei Wang, Huayi Yang, Jianan Sun, Chuhao Dou, Jian Huang, Feng-Biao Guo
2021 Frontiers in Microbiology  
Genetically Engineered Machine (iGEM) Registry with more comprehensive information integrated from 10 databases, providing corresponding information about functions, activities, interactions, and related  ...  Here, a database termed BioMaster http://www.biomaster-uestc.cn was developed to extensively complement information about BioBrick parts, which includes 47,934 items of BioBrick parts from the international  ...  ., 2008; Shetty et al., 2008) .  ... 
doi:10.3389/fmicb.2021.593979 pmid:33552037 pmcid:PMC7858672 fatcat:dthun62r75csbn4pzwaro5lgwu
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