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Performing Integrative Functional Genomics Analysis in GeneWeaver.org

  • Jeremy J. Jay
  • Elissa J. Chesler
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1101)

Abstract

Functional genomics experiments and analyses give rise to large sets of results, each typically quantifying the relation of molecular entities including genes, gene products, polymorphisms, and other genomic features with biological characteristics or processes. There is tremendous utility and value in using these data in an integrative fashion to find convergent evidence for the role of genes in various processes, to identify functionally similar molecular entities, or to compare processes based on their genomic correlates. However, these gene-centered data are often deposited in diverse and non-interoperable stores. Therefore, integration requires biologists to implement computational algorithms and harmonization of gene identifiers both within and across species. The GeneWeaver web-based software system brings together a large data archive from diverse functional genomics data with a suite of combinatorial tools in an interactive environment. Account management features allow data and results to be shared among user-defined groups. Users can retrieve curated gene set data, upload, store, and share their own experimental results and perform integrative analyses including novel algorithmic approaches for set–set integration of genes and functions.

Key words

Gene function Data integration Gene annotation Web-enabled analysis 

References

  1. 1.
    Baker EJ, Jay JJ, Philip VM, Zhang Y, Li Z, Kirova R, Langston MA, Chesler EJ (2009) Ontological discovery environment: a system for integrating gene-phenotype associations. Genomics 94:377–387. doi: 10.1016/j.ygeno.2009.08.016 PubMedCrossRefGoogle Scholar
  2. 2.
    Baker EJ, Jay JJ, Bubier JA, Langston MA, Chesler EJ (2011) GeneWeaver: a web-based system for integrative functional genomics. Nucleic Acids Res. doi:  10.1093/nar/gkr968. Available at: http://nar.oxfordjournals.org/content/early/2011/11/12/nar.gkr968.abstract. Accessed 7 Dec 2011
  3. 3.
    Wang J, Yuan W, Li MD (2011) Genes and pathways co-associated with the exposure to multiple drugs of abuse, including alcohol, amphetamine/methamphetamine, cocaine, marijuana, morphine, and/or nicotine: a review of proteomics analyses. Mol Neurobiol 44:269–286. doi: 10.1007/s12035-011-8202-4 PubMedCrossRefGoogle Scholar
  4. 4.
    Uhl GR, Liu Q-R, Drgon T, Johnson C, Walther D, Rose JE, David SP, Niaura R, Lerman C (2008) Molecular genetics of successful smoking cessation: convergent genome-wide association study results. Arch Gen Psychiatry 65:683–693. doi: 10.1001/archpsyc.65.6.683 PubMedCrossRefGoogle Scholar
  5. 5.
    Drgon T, Montoya I, Johnson C, Liu Q-R, Walther D, Hamer D, Uhl GR (2009) Genome-wide association for nicotine dependence and smoking cessation success in NIH research volunteers. Mol Med 15:21–27. doi: 10.2119/molmed.2008.00096 PubMedCrossRefGoogle Scholar
  6. 6.
    Kuntz-Melcavage K, Brucklacher R, Grigson P, Freeman W, Vrana K (2009) Gene expression changes following extinction testing in a heroin behavioral incubation model. BMC Neurosci 10:95. doi: 10.1186/1471-2202-10-95 PubMedCrossRefGoogle Scholar
  7. 7.
    Jay JJ (2012) Cross species integration of functional genomics experiments. In International Review of Neurobiology. Bioinformatics of Behavior 104:1–24. doi:  10.1016/B978-0-12-398323-7.00001-X
  8. 8.
    Bell RL, Kimpel MW, McClintick JN, Strother WN, Carr LG, Liang T, Rodd ZA, Mayfield RD, Edenberg HJ, McBride WJ (2009) Gene expression changes in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption. Pharmacol Biochem Behav 94:131–147. doi: 10.1016/j.pbb.2009.07.019 PubMedCrossRefGoogle Scholar
  9. 9.
    Tabakoff B, Bhave SV, Hoffman PL (2003) Selective breeding, quantitative trait locus analysis, and gene arrays identify candidate genes for complex drug-related behaviors. J Neurosci 23:4491–4498PubMedGoogle Scholar
  10. 10.
    Kily LJM, Cowe YCM, Hussain O, Patel S, McElwaine S, Cotter FE, Brennan CH (2008) Gene expression changes in a zebrafish model of drug dependency suggest conservation of neuro-adaptation pathways. J Exp Biol 211:1623–1634. doi: 10.1242/jeb.014399 PubMedCrossRefGoogle Scholar
  11. 11.
    Kawai T, Morita K, Masuda K, Nishida K, Shikishima M, Ohta M, Saito T, Rokutan K (2007) Gene expression signature in peripheral blood cells from medical students exposed to chronic psychological stress. Biol Psychol 76:147–155. doi: 10.1016/j.biopsycho.2007.07.008 PubMedCrossRefGoogle Scholar
  12. 12.
    Andrus BM, Blizinsky K, Vedell PT, Dennis K, Shukla PK, Schaffer DJ, Radulovic J, Churchill GA, Redei EE (2012) Gene expression patterns in the hippocampus and amygdala of endogenous depression and chronic stress models. Mol Psychiatry 17:49–61. doi: 10.1038/mp.2010.119 PubMedCrossRefGoogle Scholar
  13. 13.
    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25:25–29. doi: 10.1038/75556 PubMedCrossRefGoogle Scholar
  14. 14.
    Smith CL, Goldsmith C-AW, Eppig JT (2005) The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6. doi:  10.1186/gb-2004-6-1-r7. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=549068. Accessed 1 July 2008
  15. 15.
    Bachmanov AA, Reed DR, Li X, Li S, Beauchamp GK, Tordoff MG (2002) Voluntary ethanol consumption by mice: genome-wide analysis of quantitative trait loci and their interactions in a C57BL/6ByJ × 129P3/J F2 intercross. Genome Res 12:1257–1268. doi: 10.1101/gr.129702 PubMedCrossRefGoogle Scholar
  16. 16.
    Kimpel MW, Strother WN, McClintick JN, Carr LG, Liang T, Edenberg HJ, McBride WJ (2007) Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions. Alcohol 41:95–132. doi:10.1016/j.alcohol.2007.03.003 10.1016/j.alcohol.2007.03.003 Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2014

Authors and Affiliations

  • Jeremy J. Jay
    • 1
  • Elissa J. Chesler
    • 1
  1. 1.The Jackson LaboratoryBar HarborUSA

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