{
  "question": [
    "What are the practical applications of the research done through GeneNetwork.org?",
    "How can I access and use the data available on GeneNetwork.org?",
    "What are some recent discoveries made using GeneNetwork.org?",
    "How do scientists ensure the accuracy of the data on GeneNetwork.org?",
    "What\u2019s the difference between looking at one gene and studying a whole gene network?"
  ],
  "answer": [
    "GeneNetwork.org is used for exploratory and statistical analysis of large published phenotype and genome datasets. It allows researchers to model causal networks linking DNA differences to traits such as differences in expression, cell number, volumes, and behavior. It can also be used to identify plausible candidate genes for specific phenotypes, predict the behavior of a system following perturbations, and identify genes directly interacting with a compound of interest. Furthermore, it can be used to investigate the co-expression of genes with distinct functional sets, and generate networks of genes based on their connectivity.",
    "Please try to rephrase your question to receive feedback",
    "Please try to rephrase your question to receive feedback",
    "Please try to rephrase your question to receive feedback",
    "Please try to rephrase your question to receive feedback"
  ],
  "contexts": [
    [
      "Nonetheless,influence networks do have practical utility for (1) identifyingfunctional modules, that is, identify the subset of genes thatregulate each other with multiple (indirect) interactions, buthave few regulations to other genes outside the subset;(2) predicting the behaviour of the system following perturbations, that is, gene network models can be used to predictthe response of a network to an external perturbation andto identify the genes directly hit by the perturbation (diBernardo et al, 2005), a situation often encountered in the drugdiscovery process, where one needs to identify the genes thatare directly interacting with a compound of interest; (3)identifying real physical interactions by integrating the genenetwork with additional information from sequence data andother experimental data (i.e.",
      "These programs have the capability to integrate large datasets ofgenetic and expression data from humans and animalstudies. Notably, the GeneNetwork program (www.genenetwork.org) can combine expression data gathered fromdifferent brain regions and tissues and map these withdescribed traits as a way to build gene networks [65]. Evolving developments in bioinformatics promise muchmore; it is now feasible to adopt a new modular approach,known as systems biology. Systems biology is a mathematical modeling technique applied to complex biologicalorganizations or processes for the purposes of generatingpredictive models that are more representative of biological situations [66,67].",
      "This approach requires the accumulation and integration of many types of data,and also requires the use of many types of statistical tools to extract relevant patterns ofcovariation and causal relations as a function of genetics, environment, stage, and treatment. Inthis protocol we explain how to use the GeneNetwork web service, a powerful and free onlineresource for systems genetics. We provide workflows and methods to navigate massive multiscalardata sets and we explain how to use an extensive systems genetics toolkit for analysis andsynthesis.",
      "GeneNetwork is one ofeither generate or test ideas by reusing data that oftenan interlinked trio of sites built up by NIAAA (GeneWeaverhave been rescued from the classic literature. Below is a short list of both well-known and more esoteric and WebGestalt are the other two) to house extensiveresources, many of which have been supported by NIAAA, data for human, monkey, rat, mouse, and fruit fly.",
      "Thus, a simple WebQTL session generates hypotheses that caninitiate investigations into genes previously unsuspected of havingany functional involvement with the original reference gene, letalone with thymocyte development. These examples give an indication of only some of the functionsavailable within GeneNetwork. Currently, systems genetics isa powerful technology for dening clusters of co-regulated genes. Its use is centred upon user-specied genes and can identify novelpotential master regulatory genes for further investigation. We areworking to increase the functionality and power of the GeneNetwork and systems genetics further in a number of areas.",
      "Each data set containing gene identifierswas uploaded into the online application, and each gene was overlaid onto a molecularnetwork developed from information contained in the ingenuity pathways database. Networks of genes were then generated based on their connectivity, and we chose the top50 significant networks.",
      "Exploring genes, molecules, and phenotypes is easily accomplished using GeneNetwork. In thismanuscript we will outline some simple use cases, and show how a small number of plausiblecandidate genes can be identified for an immune phenotype. 1. DataOnce you have navigated to genenetwork.org, there are two ways to search for data in GN. Thefirst is to use the global search bar located at the top of the page (Figure 1). This is a newfeature in GN that allows researchers to search for genes, mRNAs, or proteins across all of thedatasets.Recent improvements toGeneNetwork have reinvigorated it, including the addition of data from 10 species, multi-omicsanalysis, updated code, and new tools. The new GeneNetwork is now an exciting resource forpredictive medicine and systems genetics, which is constantly being maintained and improved. Here, we give a brief overview of the process for carrying out some of the most commonfunctions on GeneNetwork, as a gateway to deeper analyses, demonstrating how a smallnumber of plausible candidate genes can be found for a typical immune phenotype.",
      "This approach requires the accumulation and integration of many types of data,and also requires the use of many types of statistical tools to extract relevant patterns ofcovariation and causal relations as a function of genetics, environment, stage, and treatment. Inthis protocol we explain how to use the GeneNetwork web service, a powerful and free onlineresource for systems genetics. We provide workflows and methods to navigate massive multiscalardata sets and we explain how to use an extensive systems genetics toolkit for analysis andsynthesis.",
      ", (Chesler et al. , 2005; Galperin and Cochrane,2009; Gentleman et al. , 2004; Mailman et al. , 2007; Saal et al. , 2002; Swertz et al. , 2010)). One relatively well-known database is GeneNetwork (www.genenetwork.org) (Chesler etal. , 2005). GeneNetwork is designed primarily as a web service for exploratory andstatistical analysis of large published phenotype and genome datasets, and includes datafrom several species (see Supplementary Discussion). GeneNetwork includes extensivephenotype data extracted from the literature and submitted by users, which makes itpractical to compare data on drug responses with gene expression patterns.",
      "In the currentstudies, the online GeneNetwork system was employed to further probe P2P-R biological functions. Molecularstudies were then performed to confirm the GeneNetwork evaluations. Results: GeneNetwork and associated gene ontology links were used to investigate the coexpression of P2P-R withdistinct functional sets of genes in an adipocyte genetic reference panel of HXB/BXH recombinant strains of ratsand an eye genetic reference panel of BXD recombinant inbred strains of mice.",
      "Exploring genes, molecules, and phenotypes is easily accomplished using GeneNetwork. In thismanuscript we will outline some simple use cases, and show how a small number of plausiblecandidate genes can be identified for an immune phenotype. 1. DataOnce you have navigated to genenetwork.org, there are two ways to search for data in GN. Thefirst is to use the global search bar located at the top of the page (Figure 1). This is a newfeature in GN that allows researchers to search for genes, mRNAs, or proteins across all of thedatasets.Recent improvements toGeneNetwork have reinvigorated it, including the addition of data from 10 species, multi-omicsanalysis, updated code, and new tools. The new GeneNetwork is now an exciting resource forpredictive medicine and systems genetics, which is constantly being maintained and improved. Here, we give a brief overview of the process for carrying out some of the most commonfunctions on GeneNetwork, as a gateway to deeper analyses, demonstrating how a smallnumber of plausible candidate genes can be found for a typical immune phenotype.",
      "Taking this approach a step further, GeneNetwork[99] is constructedfrom co-regulation patterns found within tens of thousands of samplesfor which gene expression was measured. GeneNetwork provides unprecedented resolution and predictive power across multiple cell typesand tissues. Analogous to discovering patterns in expression data, thenetwork of protein-protein interactions can also be computationally predicted using various methods[381]. The combined current knowledge of how cells control functionssuch as growth, movement, dierentiation, metabolism, communication, and response to stress or pathogens is captured in high-level pathway databases such as WikiPathways[188], Reactome[97] or KEGG[180].",
      "However, the accurate derivation of such high-throughput data andtheir analysis in terms of biological function has been critical to truly leveraging the postgenomicrevolution. This chapter will describe an approach that focuses on the use of gene networks to bothorganize and interpret genomic expression data. Such networks, derived from statistical analysisof large genomic datasets and the application of multiple bioinformatics data resources, potentially allow the identification of key control elements for networks associated with human disease,and thus may lead to derivation of novel therapeutic approaches.",
      "To test this hypothesis, we used the Web-basedGeneNetwork databases that have been recently introducedto the scientific community and proved to be a powerful toolfor hypothesis-driven investigations (Chesler et al. 2003,2004; Wang et al. 2003). Researchers can take advantageof genetic diversity in panels of recombinant inbred mousestrains to use these databases for studies of the regulation ofgene expression and genetic mechanisms of complex traits. Our in silico investigation provided evidence for potentialfunctional relationships among the 21 DAT-associated proteins detected by mass spectrometry in this study.",
      "As mentioned previously, GeneNetwork(www.genenetwork.org) is a collaborative Web-based resource equipped with tools andfeatures for studying gene/gene and exploring genetic correlates to neurobehavioralphenotypes (Chesler et al. , 2003, 2004). The Web site is home to a growing collection ofgene expression and phenotypic data from a variety of species and brain regions, with a hostof links to external resources for tracing the interrelationships of a gene among multipleWeb-based resources. GeneNetwork also offers a number of correlation and mappingstrategies for assessing associations among multiple genes and QTLs.",
      "Here we provide open access and availability tothese data by integrating them into the GeneNetwork, aweb-based analytical tool that has been designed for multiscale integration of networks of genes, transcripts andtraits and optimized for on-line analysis of traits controlled by a combination of allelic variants and environmental factors. GeneNetwork with its central module WebQTLfacilitates the exploitation of permanent genetic referencepopulations that are accompanied by genotypic, phenotypic and mRNA abundance datasets.",
      "GeneNetwork.org also offers a powerful statistical platform foronline network analyses and mapping, enabling numerous molecular questions to be probed in one centralized location(Chesler et al. , 2003, 2005; Li et al. , 2010; Mulligan et al. , 2012,2017, 2019). Most data are from groups of animals or humanswho have been fully genotyped or even sequenced. As a result, itcan be used to model causal networks that link DNA differencesto traits such as differences in expression, cell number, volumes,and behavior using real-time computation and graphing.",
      "While the improvement of gene rankings upon application of GeneRank is already significant in the examplespresented, it may become even more so once comprehensive high-quality biological network informationbecomes available. Of particular interest in that respectwill be transcriptional regulatory networks, such as arenow being generated by technologies like ChIP-chip (see[19-21] for early examples using yeast as a model organism). As discussed above, the information encoded insuch regulatory networks will be intuitively amenable toGeneRank analysis. It will also re-introduce an element ofdirectedness into the network, moving it even closer to theoriginal PageRank application."
    ],
    [],
    [],
    [],
    []
  ],
  "task_id": [
    {
      "task_id": "1AE8A08B2F0E63DC504738485B576741"
    },
    {
      "task_id": "BB02D281C914C63292C0AE91D32CE476"
    },
    {
      "task_id": "852E48D775CF521A5BA7FFF4F42E87C2"
    },
    {
      "task_id": "FC617AC44D108DA97F5988E63DF6C0E6"
    },
    {
      "task_id": "D40628404D48DA90F3E2B0F93FB6640E"
    }
  ]
}