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GeneNet in 2005
2004
Nucleic Acids Research
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The current SRS release of the GeneNet database contains 37 graphical maps of gene networks, as well as descriptions of 1766 proteins, 1006 genes, 241 small molecules and 3254 relationships between gene ...
SRS release of the GeneNet database, the graphical viewer and the modeling section are available at http://wwwmgs.bionet.nsc.ru/mgs/ gnw/genenet/. ...
data and also to establish a database of gene network computer models. ...
doi:10.1093/nar/gki077
pmid:15608230
pmcid:PMC540031
fatcat:togpnb7e3zaona5mmu6nsio7wq
Interactive data input into the GeneNet database
1999
Bioinformatics
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The GeneNet database has been developed for a formalized hierarchical description of the gene networks. ...
To provide rapid data accumulation in the database, the Java graphical interface for data input through the Internet by independent experts equipped with convenient visual tools is developed. ...
Ignatieva and O. A. Podkolodnaya for helpful advice and comments, S. L. Kivileva for technical assistance and G. V. Orlova for translating the manuscript into English. ...
doi:10.1093/bioinformatics/15.7.713
pmid:10487877
fatcat:dzhm6haemzcoxh4jo33fe5rpjq
GeneNet: a database on structure and functional organisation of gene networks
2002
Nucleic Acids Research
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Current release 3.0 of GeneNet database contains descriptions of 25 gene networks, 945 proteins, 567 genes, 151 other substances and 1364 relationships between components of gene networks. ...
The GeneNet database is designed for accumulation of information on gene networks. ...
); MD, GeneNet Dynamic Model link; DE, gene network description; OS, species; EN, link to the list of entities included in the gene network; RE, link to the list of regulatory events in the gene network ...
doi:10.1093/nar/30.1.398
pmid:11752348
pmcid:PMC99151
fatcat:itv5ka4nlrb43a3f77cemou4dy
Pathway Databases
2001
Comparative and Functional Genomics
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descriptions for a number of basic metabolic pathways. ...
The 'NetModel' pages have detailed information on three approaches for building models of genetic networks. ...
doi:10.1002/cfg.123
pmid:18628870
pmcid:PMC2447229
fatcat:3mcklutvcfaq7csir42rjq7vsu
Gene set-level network analysis using a toxicogenomics database
2010
Genomics
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Expression changing levels for 58 gene sets was used for network inference with a Gaussian graphical model algorithm. ...
The established network contained reasonable relationships, such as ones between the blood glucose level and glycolysis-related genes or the blood transaminase level and cellular injury-related genes, ...
Taku Nagao, Yasuo Ohno, Tetsuro Urushidani, Toshikazu Miyagishima, Atsushi Ono, Hiroshi Yamada, and all the TGP members for their devotion to the development of the TG-GATEs database system. ...
doi:10.1016/j.ygeno.2010.03.014
pmid:20363313
fatcat:ku6ih56u7nee7glwm2queknmuy
The Molecular Biology Database Collection: 2002 update
2002
Nucleic Acids Research
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Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http:// nar.oupjournals.org. ...
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. ...
/EpoDB/
Genes expressed during human erythropoiesis
GeneNet
http://wwwmgs.bionet.nsc.ru/mgs/systems/genenet/ Formalized descriptions of the structure and
functional organization of gene networks ...
doi:10.1093/nar/30.1.1
pmid:11752241
pmcid:PMC99169
fatcat:n46iu5l6oreapd5yxswe7pmg5m
Integrated databases and computer systems for studying eukaryotic gene expression
1999
Bioinformatics
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Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the ...
Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the ...
the Russian Human Genome Program, the Ministry of Science and Technology of Russian Federation, Integrated Program of Siberian Department of Russian Academy of Sciences. ...
doi:10.1093/bioinformatics/15.7.669
pmid:10487874
fatcat:v53hphh7v5cjhctnlixpxingyy
Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases
2013
Database: The Journal of Biological Databases and Curation
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Conflict of interest. None declared.
Page 17 of 18 ...
Acknowledgements Appreciation is extended to the funding agencies and organizations mentioned previously for supporting this work and to Scott Cain and the GMOD project team for logistical support, consultation ...
Tripal has also been used for construction of network biology databases such as the GeneNet Engine (http://sysbio.genome.clemson. edu/) for cereal grasses (20) . ...
doi:10.1093/database/bat075
pmid:24163125
pmcid:PMC3808541
fatcat:khwlk7dc6zadpntbze5xskz7um
GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome
1998
Proceedings. International Conference on Intelligent Systems for Molecular Biology
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The system includes 5 basic units: (1) GeneNet contains an object-oriented database for accumulation of data on gene networks and signal transduction pathways and a Java-based viewer that allows an exploration ...
and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor ...
Acknowledgments This work was supported partially by grants of Russian National Human Genome Project, Russian Ministry of Science and Technical Politics, Siberian Department of Russian Academy of Sciences ...
pmid:9783214
fatcat:dgjqc755gve2ljpxqpn45hfc74
Gramene (rice and other grasses database)
[chapter]
2008
Encyclopedia of Genetics, Genomics, Proteomics and Informatics
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▶gene, ▶gene number in quantitative traits, ▶transcriptome, ▶genetic network, ▶proteome, ▶duplications, ▶knockout, ▶mtDNA; An improved model of Zeng, considered linkage and variation in their effect where ...
(See separate entries mentioned, ▶small-world networks, ▶networks, ▶cell model, ▶hub, ▶microarray, ▶protein complexes, ▶protein interactions, Yeast The SGI network. (From Byme AB et al 2007 J. ...
The cause of the dysgenesis may reside either in autosomal recessive genes or in the sex chromosomes. ...
doi:10.1007/978-1-4020-6754-9_7111
fatcat:dsqojxeco5gwhgpgdcm22jb33y
Inference and validation of predictive gene networks from biomedical literature and gene expression data
2014
Genomics
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Although many methods have been developed for inference of biological networks, the validation of the resulting models has largely remained an unsolved problem. ...
Here we present a framework for quantitative assessment of inferred gene interaction networks using knock-down data from cell line experiments. ...
Most published network inference methods attempt to validate their models through comparison with biological databases, calculating the proportion of interactions found both in the inferred networks and ...
doi:10.1016/j.ygeno.2014.03.004
pmid:24691108
pmcid:PMC4119824
fatcat:2hxpxfeswbcapgjawjtva22mji
Comparing Statistical Methods for Constructing Large Scale Gene Networks
2012
PLoS ONE
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The gene regulatory network (GRN) reveals the regulatory relationships among genes and can provide a systematic understanding of molecular mechanisms underlying biological processes. ...
of Accurate Cellular Networks) performed well in constructing the global network structure; (2) GeneNet and SPACE (Sparse PArtial Correlation Estimation) performed well in identifying a few connections ...
network for E. coli derived from the RegulonDB database. ...
doi:10.1371/journal.pone.0029348
pmid:22272232
pmcid:PMC3260142
fatcat:gopllfz6czaerlnvio2k7jy23y
Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network
2019
PLoS ONE
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Gene networks enable predicting gene behavior and function in the context of transcriptionally linked processes. ...
We compared the structural properties of the MG1363 GCNs generated by five methods, namely Pearson correlation, Spearman correlation, GeneNet, Weighted Gene Co-expression Network Analysis (WGCNA), and ...
B: Example network of L. lactis MG1363 generated using GeneNet (ω = 0.90; 2235 genes and 70386 edges). ...
doi:10.1371/journal.pone.0214868
pmid:31116749
pmcid:PMC6530827
fatcat:e5lcpawhuveidohenggmhmm4oi
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases
2010
BMC Bioinformatics
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Finding the potential biological functions of such SNPs can be an important step towards further use in human and agricultural populations (e.g., for identifying genes related to susceptibility to complex ...
., genes, pathways, ontologies). We also introduce dbAutoMaker, a suite of Perl scripts, which can be scheduled to run periodically to automatically create/update the customised SNP databases. ...
Special thanks to Professor Julius van der Werf (University of New England) who provided helpful guidance and manuscript editing.
Author Details ...
doi:10.1186/1471-2105-11-311
pmid:20534127
pmcid:PMC2901372
fatcat:ehj7pcnyyjfaxbgfaoo7ayvpwy
EndoNet: an information resource about regulatory networks of cell-to-cell communication
2007
Nucleic Acids Research
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Therefore, the database covers the hierarchy of cellular organization of tissues and organs as it has been modeled in the Cytomer ontology, which has now been directly embedded into EndoNet. ...
Whenever expression, synthesis and/or secretion of another hormone are part of this response, it renders the corresponding cell an internal node of the resulting network. ...
Altogether, they form the necessary basis for modeling and simulation of large intracellular networks. ...
doi:10.1093/nar/gkm940
pmid:18045786
pmcid:PMC2238947
fatcat:icpv6in4mzbylelzygo2j64uka
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