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Resource:GeneNetwork

Name: Resource:GeneNetwork
Description: A group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. It combines more than 25 years of legacy data generated by hundreds of scientists together with sequence data (SNPs) and massive transcriptome data sets (expression genetic or eQTL data sets). The quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. GeneNetwork can be used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Most of these population data sets are linked with dense genetic maps (genotypes) that can be used to locate the genetic modifiers that cause differences in expression and phenotypes, including disease susceptibility.

Users are welcome to enter their own private data directly into GeneNetwork to exploit the full range of analytic tools and to map modulators in a powerful environment. This combination of data and fast analytic functions enable users to study relations between sequence variants, molecular networks, and function.

What can be done with GeneNetwork?

  • QTL Mapping:
    • Interval Mapping
    • Simple interval mapping
    • Composite interval mapping
    • Pair-scan
  • Correlation Analysis
    • Correlation Matrix / Principal Components Analysis
    • QTL Heatmaps
    • Compare Correlates
    • Network Graph
  • Systems Genetics and Complex Trait Analysis
Source code is available and is written in Python, C, and JavaScript. The QTL Reaper module of GeneNetwork that is used by several mapping modules of GeneNetwork is also available.
Other Name(s): www.genenetwork.org, GeneNetwork / WebQTL, GeneNetwork WebQTL, GeneNetwork and WebQTL
Abbreviation: GeneNetwork, WebQTL
Parent Organization: University of Tennessee Health Science Center; Tennessee; USA
Supporting Agency: UT Center for Integrative and Translational Genomics, NIAAA, NIDA, NIMH, NCI, NCRR
Grant: U01AA13499, U24AA13513, U01AA014425, P20-DA 21131, U01CA105417, U24 RR021760
Resource Type(s): Database, Data repository
Resource: Resource
URL: http://www.genenetwork.org/
Id: nif-0000-00380
PMID: PMID 15043217, 15114364
Related to: Resource:NIF Data Federation, Resource:Monarch Initiative
Availability: Free, Public, Acknowledgement requested, GNU Affero General Public License, version 3, GNU General Public License, The community can contribute to this resource
Keywords: gene, genetic correlation, genome, abi panther, genome browser, genomic region, genotype, gnf expression atlas, mouse, network, phenotype, relational database, sequence, SNP, trait, transcriptome, transcript, webgestalt, molecular neuroanatomy resource, Source code, toxicity, cancer susceptibility, behavior, allelic variant, environmental factor, mRNA, expression, microarray, annotation, Data analysis service, mapping, Quantitative trait locus, phenotype, data sharing
Organism: Mouse, Rat, Human, Macaque, Drosophila, Barley, Arabidopsis thaliana, Soybean, Tomato
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

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Facts about Resource:GeneNetworkRDF feed
AbbrevGeneNetwork, WebQTL  +
AvailabilityFree  +, Public  +, Acknowledgement requested  +, GNU Affero General Public License  +, Version 3  +, GNU General Public License  +, and The community can contribute to this resource  +
CurationStatuscurated  +
DefiningCitationhttp://www.genenetwork.org/  +
DefinitionA group of linked data sets and tools used A group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. It combines more than 25 years of legacy data generated by hundreds of scientists together with sequence data (SNPs) and massive transcriptome data sets (expression genetic or eQTL data sets). The quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. GeneNetwork can be used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Most of these population data sets are linked with dense genetic maps (genotypes) that can be used to locate the genetic modifiers that cause differences in expression and phenotypes, including disease susceptibility.

Users are welcome to enter their own private data directly into GeneNetwork to exploit the full range of analytic tools and to map modulators in a powerful environment. This combination of data and fast analytic functions enable users to study relations between sequence variants, molecular networks, and function.

What can be done with GeneNetwork?

  • QTL Mapping:
    • Interval Mapping
    • Simple interval mapping
    • Composite interval mapping
    • Pair-scan
  • Correlation Analysis
    • Correlation Matrix / Principal Components Analysis
    • QTL Heatmaps
    • Compare Correlates
    • Network Graph
  • Systems Genetics and Complex Trait Analysis
Source code is available and is written in Python, C, and JavaScript. The QTL Reaper module of GeneNetwork that is used by several mapping modules of GeneNetwork is also available.
modules of GeneNetwork is also available.
ExampleImageGeneNetwork.png  +
GrantCategory:U01AA13499   +, Category:U24AA13513   +, Category:U01AA014425   +, Category:P20-DA 21131   +, Category:U01CA105417   +, and Category:U24 RR021760   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +, and Data repository  +
Idnif-0000-00380  +
Is part ofUniversity of Tennessee Health Science Center; Tennessee; USA  +
KeywordsGene  +, Genetic correlation  +, Genome  +, Abi panther  +, Genome browser  +, Genomic region  +, Genotype  +, Gnf expression atlas  +, Mouse  +, Network  +, Phenotype  +, Relational database  +, Sequence  +, SNP  +, Trait  +, Transcriptome  +, Transcript  +, Webgestalt  +, Molecular neuroanatomy resource  +, Source code  +, Toxicity  +, Cancer susceptibility  +, Behavior  +, Allelic variant  +, Environmental factor  +, MRNA  +, Expression  +, Microarray  +, Annotation  +, Data analysis service  +, Mapping  +, Quantitative trait locus  +, and Data sharing  +
LabelResource:GeneNetwork  +
ModifiedDate6 March 2014  +
PMID15043217, 15114364  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToResource:NIF Data Federation  +, and Resource:Monarch Initiative  +
SpeciesMouse  +, Rat  +, Human  +, Macaque  +, Drosophila  +, Barley  +, Arabidopsis thaliana  +, Soybean  +, and Tomato  +
SuperCategoryResource  +
Supporting AgencyUT Center for Integrative and Translational Genomics  +, NIAAA  +, NIDA  +, NIMH  +, NCI  +, and NCRR  +
Synonymwww.genenetwork.org  +, GeneNetwork / WebQTL  +, GeneNetwork WebQTL  +, and GeneNetwork and WebQTL  +