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GeneNet in 2005

E. A. Ananko
2004 Nucleic Acids Research  
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

F. A. Kolpakov, E. A. Ananko
1999 Bioinformatics  
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

E. A. Ananko
2002 Nucleic Acids Research  
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

Jo Wixon
2001 Comparative and Functional Genomics  
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

Naoki Kiyosawa, Sunao Manabe, Atsushi Sanbuissho, Takashi Yamoto
2010 Genomics  
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

A. D. Baxevanis
2002 Nucleic Acids Research  
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

N. A. Kolchanov, M. P. Ponomarenko, A. S. Frolov, E. A. Ananko, F. A. Kolpakov, E. V. Ignatieva, O. A. Podkolodnaya, T. N. Goryachkovskaya, I. L. Stepanenko, T. I. Merkulova, V. V. Babenko, Y. V. Ponomarenko (+10 others)
1999 Bioinformatics  
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

Lacey-Anne Sanderson, Stephen P. Ficklin, Chun-Huai Cheng, Sook Jung, Frank A. Feltus, Kirstin E. Bett, Dorrie Main
2013 Database: The Journal of Biological Databases and Curation  
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

N A Kolchanov, M P Ponomarenko, A E Kel, Kondrakhin YuV, A S Frolov, F A Kolpakov, T N Goryachkovsky, O V Kel, E A Ananko, E V Ignatieva, O A Podkolodnaya, V N Babenko (+13 others)
1998 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
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  
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

Catharina Olsen, Kathleen Fleming, Niall Prendergast, Renee Rubio, Frank Emmert-Streib, Gianluca Bontempi, Benjamin Haibe-Kains, John Quackenbush
2014 Genomics  
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

Jeffrey D. Allen, Yang Xie, Min Chen, Luc Girard, Guanghua Xiao, Petter Holme
2012 PLoS ONE  
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

Jimmy Omony, Anne de Jong, Jan Kok, Sacha A. F. T. van Hijum, Arun K. Bhunia
2019 PLoS ONE  
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

Stephen J Goodswen, Cedric Gondro, Nathan S Watson-Haigh, Haja N Kadarmideen
2010 BMC Bioinformatics  
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

J. Donitz, B. Goemann, M. Lize, H. Michael, N. Sasse, E. Wingender, A. P. Potapov
2007 Nucleic Acids Research  
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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