{
  "titles": [
    "2020 - Gene network a completely updated tool for systems genetics analyses.pdf",
    "2020 -Highlights from the Era of Open Source Web-Based Tools.pdf",
    "2021 -Highlights from the Era of Open Source Web-Based Tools.pdf",
    "2008 - Systems_genetics_can_provide_new_insight.pdf",
    "2007 - Systems genetics the next generation.pdf",
    "2010 - Systems genetics analyses predict a transcription role for P2P-R Molecular confirmation that P2P-R is a transcriptional co-repressor.pdf",
    "2012 - Genetic and Molecular Network Analysis of Behavior.pdf",
    "2008 - Towards systems genetic analyses in barley Integration of phenotypic, expression and genotype data into GeneNetwork.pdf",
    "2012 - Genetic and Genomic Web Resources for Research on Alcohol Use and Abuse.pdf",
    "2009 - Herding cats the sociology of data integration.pdf"
  ],
  "extraction_id": [
    "858f630f-9443-5f13-ac40-8e16eadd9ba1",
    "14530ed7-e49e-5a1a-9df6-820c7495a8ce",
    "ffafdd06-808c-58be-bcb5-bd74d7ffa89a",
    "bfd98d6d-b026-5bbd-896f-b70045a032c8",
    "d7d6d0a8-db35-5be6-a3fc-82f347e5d37b",
    "ec624ebb-489a-5437-a721-f01cf981d0a7",
    "833f822f-9080-5434-b9a1-2473531becfe",
    "b3c1f52a-f5be-586f-a3c9-04bed83fb12e",
    "83ae495f-31a2-5977-a63a-57e704c394e2",
    "c5e5623c-2373-535c-978d-3af1cec77f1a"
  ],
  "document_id": [
    "128224f1-3545-52c3-93cb-77c3cf4ec70a",
    "f2f0dc2f-eaf5-57f6-9ffa-816d3fab6640",
    "0a6f3d2e-70c3-5db7-bfc0-93ad04806104",
    "0bc5b1ee-f7fe-5d12-9ebf-ab7363119424",
    "a6202d00-514d-5b48-89cd-5fc9649c0ee4",
    "e4d1e2e9-f267-5814-8c7b-dc11d7eec9bf",
    "4b6759f8-fdaf-59a1-94bd-5a7cf184e1f9",
    "8513abbe-65ed-5f35-9f86-ba93cfc5a194",
    "08b12d72-9776-5acb-b1ef-7ee402781897",
    "15e14cfc-dbeb-5998-b42a-9fbfb7464bf2"
  ],
  "id": [
    "chatcmpl-AIGn3AbKULjVBzRjcrJYXxi0av0dH",
    "c63cfaee-749e-547b-9c0a-086266f10670",
    "7beda13b-1ea5-53c0-9380-72eee2df79fe",
    "a1124460-ae34-57fb-846b-e033f4bbf49c",
    "55461d7c-995b-5f5a-be38-a64acd4a904a",
    "f3821133-e965-535b-88d0-f43b14d311b6",
    "a9508122-3b14-5365-979c-ba580bdcb78f",
    "27eda296-b0b7-5ae4-881e-31987ba63dec",
    "b82c0ee6-9e1b-595d-95b3-1cc9d7aff44d",
    "db6bfa4e-9612-5f7e-8b7f-162f60b91c9d",
    "dc06eebe-4d67-5bd0-9ed8-3dd9d5a588bd"
  ],
  "contexts": [
    "GeneNetwork have reinvigorated it, including the addition  of data from  10 species, multi -omics  analysis, updated code, and new tools. The new GeneNetwork is now an exciting resource for  predictive 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 common  functions on GeneNetwork, as a gateway to deeper analyses , demonstrating how a small",
    "GeneNetwork.org is also a valuable teaching tool. While mainly designed for researchers interested in testing gene-to- phenotype relationships, GeneNetwork. orghas been adapted for dry-lab teaching in neuroscience and genetics ( Grisham et al., 2017 ). A useful approach is to assign sets of vetted questions, such as the exam- ples discussed above, and to help students work toward answers, solutions, or novelquestions. Several examples relating to the",
    "GeneNetwork.org is also a valuable teaching tool. While mainly designed for researchers interested in testing gene-to- phenotype relationships, GeneNetwork. orghas been adapted for dry-lab teaching in neuroscience and genetics ( Grisham et al., 2017 ). A useful approach is to assign sets of vetted questions, such as the exam- ples discussed above, and to help students work toward answers, solutions, or novelquestions. Several examples relating to the",
    "Its use is centred upon user-specied genes and can identify novel potential master regulatory genes for further investigation. We are working to increase the functionality and power of the GeneNet- work and systems genetics further in a number of areas. In partic- ular, increasing the number of strains studied can increase the mapping resolution. By increasing the genetic diversity of the founders of an RI set, the potential for observing regulatory poly-",
    "and can identify novel potential master regulatory genes for further investigation. We are working to increase the functionality and power of GeneNetwork and systems genetics in a number of areas. In particular, the mapping resolution can be increased by increasing the number of strains studied. By increasing the genetic diversity of the founders of an RI set, the potential for observing regulatory poly-morphisms increases dramatically. In this context, the availability of 1000 RI strains from The Gene",
    "GeneNetwork http://www.genenetwork.org is anexample of a bioinformatics tool that can be used to explore systems genetics data. The importance of defining biological networks and predicting molecular interactions has been emphasized by several reports [1,2]. Such studies emphasize that when knowledge about DNA variation within popula- tions is interfaced with data on gene expression, protein interactions and DNA-protein binding, biological networks can be constructed that are predictive of the",
    "files on GeneNetwork) will also reduce the energy barrier of adopting powerful systems  genetics and systems behavioral approaches. Web services such as GeneNetwork and its  companionsGeneWeaver ( Baker et al., 2012 ), WebGestalt ( Zhang et al., 2005 ), DAVID  (Huang et al., 2009a ; Huang et al., 2009b ), and the Allen Brain Atlas ( Lein et al., 2007 ) can now be used as virtual and free laboratories to test specific biological hypothesis, or they  can be used to generate new ideas ab initio .",
    "within GeneNetwork's analytical en vironment we provide simple we b access to the data for the research community. In this envi ronment, a combination of correl ation analysis and linkage mapping provides the potential to identify and substant iate gene targets for saturation mapping and positional cloning. By integratin g datasets from an unsequenced cr op plant (barley) in a database that has been designed for an  animal model species (mouse) with a well established genome",
    "need to read the help files, FAQs, or one of the references(Chesler et al., 2003; Grisham et al., 2010, www.lifescied.org/content/9/2/98.full.pdf). GeneNetwork is one ofan interlinked trio of sites built up by NIAAA (GeneWeaverand WebGestalt are the other two) to house extensivedata for human, monkey, rat, mouse, and fruit fly. Itincludes hundreds of data sets on responsesto alcohol,particularly in a family of mice called the BXDs. Dataare linked with powerful gene analysis and mappingtools. Think of it as",
    "will be convincing both the community and its leaders that it is  doable today. acKnoWledgmenTs Thanks to Glenn D. Rosen and Kathryn Graehl for comments and editorial improvements. Thanks also to the NIH for support of many  data sets for GRPs now being incorporated into GeneNetwork, a  pilot project in systems genetics. references Carneiro, A. M., Airey, D. C., Thompson,  B.,  Zhu, C. B., Lu, L., Chesler, E. J.,  Erikson,  K. M., and Blakely, R. D.  (2009). Functional coding variation"
  ],
  "answer": "GeneNetwork.org can contribute to advancements in genetic engineering in several ways:  1. **Predictive Medicine and Systems Genetics**: GeneNetwork.org is an exciting resource for predictive medicine and systems genetics, providing a platform for multi-omics analysis and data from multiple species [1]. This can help in understanding complex genetic interactions and predicting phenotypic outcomes, which are crucial for genetic engineering.  2. **Identification of Master Regulatory Genes**: The platform allows users to identify novel potential master regulatory genes for further investigation [4]. This capability is essential for genetic engineering as it can help in pinpointing key genes that control important traits or pathways.  3. **Increased Mapping Resolution**: By increasing the number of strains studied and the genetic diversity of the founders of a recombinant inbred (RI) set, GeneNetwork.org enhances the mapping resolution [5]. This improvement can lead to more precise genetic modifications and better understanding of genetic variations.  4. **Construction of Biological Networks**: GeneNetwork.org facilitates the construction of biological networks by integrating data on DNA variation, gene expression, protein interactions, and DNA-protein binding [6]. These networks are predictive of molecular interactions, which can guide genetic engineering efforts.  5. **Virtual Laboratory for Hypothesis Testing**: GeneNetwork.org, along with its companion tools, can be used as a virtual and free laboratory to test specific biological hypotheses or generate new ideas [7]. This feature supports experimental design and innovation in genetic engineering.  Overall, GeneNetwork.org provides a comprehensive analytical environment and a wealth of data that can significantly aid in the advancement of genetic engineering by enabling detailed genetic analysis, hypothesis testing, and the discovery of key genetic regulators.",
  "question": "How can GeneNetwork.org contribute to advancements in genetic engineering?"
}