Skip to main content
SpringerLink
Log in

Integrating Multidimensional Data Sources to Identify Genes Regulating Complex Phenotypes

  • Protocol
  • First Online:
Systems Genetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1488))

Abstract

Phenotypes collected with a view to quantitative trait locus mapping can be augmented with compatible whole-transcriptome expression data and information from several other sources. These different data sources can be assembled into multidimensional network models which allow the identification of key genes potentially driving the phenotype of interest. The following chapter describes this approach using an example workflow. Several alternatives and potential limitations are discussed to aid the researcher when applying these techniques to their own work.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Overall RW, Williams RW, Heimel JA (2015) Collaborative mining of public data resources in neuroinformatics. Front Neurosci 9:90. doi:10.3389/fnins.2015.00090

    Article  PubMed  PubMed Central  Google Scholar 

  2. Team RC (2014) R: a language and environment for statistical computing

    Google Scholar 

  3. von Mering C, Huynen M, Jaeggi D et al (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 31:258–261. doi:10.1093/nar/gkg034

    Article  Google Scholar 

  4. Szklarczyk D, Franceschini A, Kuhn M et al (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39:D561–D568. doi:10.1093/nar/gkq973

    Article  CAS  PubMed  Google Scholar 

  5. Kempermann G, Chesler EJ, Lu L et al (2006) Natural variation and genetic covariance in adult hippocampal neurogenesis. Proc Natl Acad Sci 103:780–785. doi:10.1073/pnas.0510291103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Overall RW, Kempermann G, Peirce J et al (2009) Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource. Front Neurosci 3:55. doi:10.3389/neuro.15.003.2009

    PubMed  PubMed Central  Google Scholar 

  7. Overall RW, Paszkowski-Rogacz M, Kempermann G (2012) The mammalian adult neurogenesis gene ontology (MANGO) provides a structural framework for published information on genes regulating adult hippocampal neurogenesis. PLoS One 7:e48527. doi:10.1371/journal.pone.0048527

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Sone M, Hayashi T, Tarui H et al (2007) The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 120:2498–2506. doi:10.1242/jcs.009357

    Article  CAS  PubMed  Google Scholar 

  9. Mercer TR, Qureshi IA, Gokhan S et al (2010) Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 11:14. doi:10.1186/1471-2202-11-14

    Article  PubMed  PubMed Central  Google Scholar 

  10. Han Y-G, Spassky N, Romaguera-Ros M et al (2008) Hedgehog signaling and primary cilia are required for the formation of adult neural stem cells. Nat Neurosci 11:277–284. doi:10.1038/nn2059

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CRTD – DFG Research Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstrasse 105, 01307, Dresden, Germany

    Rupert W. Overall

Authors
  1. Rupert W. Overall
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rupert W. Overall .

Editor information

Editors and Affiliations

  1. Department of Infection Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine Hannover, Braunschweig, Niedersachsen, Germany

    Klaus Schughart

  2. Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA

    Robert W. Williams

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Overall, R.W. (2017). Integrating Multidimensional Data Sources to Identify Genes Regulating Complex Phenotypes. In: Schughart, K., Williams, R. (eds) Systems Genetics. Methods in Molecular Biology, vol 1488. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6427-7_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6427-7_10

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6425-3

  • Online ISBN: 978-1-4939-6427-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation