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WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior

Nature Neuroscience volume 7, pages 485–486 (2004)Cite this article

Brain mRNA expression is modulated by numerous genetic factors and often varies substantially between strains of mice that have been reared in a standard laboratory environment. Examples include members of the NMDA receptor family that are critical in learning and memory, and genes involved in synaptic vesicle trafficking. Molecular variation of this type is often heritable and is produced by genetic polymorphisms at many locations across the genome. Differences in both alleles and mRNA levels will often produce significant behavioral, pharmacological and neuroanatomical variants1. Over the past several years, with support from the NIH Human Brain Project, we have assembled a suite of databases and web-based analysis software called WebQTL (www.webqtl.org). WebQTL is a freely accessible system that exploits sophisticated gene mapping methods2,3 to rapidly perform whole-genome analysis at many levels—from differences in NR2B mRNA levels to differences in open-field activity levels.

WebQTL has three major applications: exploring variation in gene expression using a panel of more than 30 recombinant inbred strains and several different tissues (for example, forebrain, cerebellum, hematopoietic stem cells); mapping upstream gene loci that modulate transcript levels; and studying networks of genetic correlations among ∼100,000 transcript assays and 650 published phenotypes. Additional features include tools for the simultaneous analysis of groups of traits, custom annotation of Affymetrix probes and probe sets, and external links to the Gene Ontology Machine (http://genereg.ornl.gov/gotm), the Gene Expression Atlas (http://expression.gnf.org), NCBI (www.ncbi.nlm.nih.gov) and the Genome Browser (http://genome.ucsc.edu). The integration of diverse data types provides a powerful resource for exploratory systems biology.

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Figure 1: A map of quantitative trait loci on chromosomes 6 and 8 regulating the expression of the ionotropic glutamate receptor gene Grin2b.

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Authors and Affiliations

  1. Center for Genomics and Bioinformatics, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, 38163, Tennessee, USA

    Elissa J Chesler, Lu Lu, Jintao Wang, Robert W Williams & Kenneth F Manly

  2. Department of Anatomy and Neurobiology,

    Elissa J Chesler, Lu Lu, Jintao Wang, Robert W Williams & Kenneth F Manly

  3. Department of Pathology and Laboratory Medicine,

    Elissa J Chesler, Lu Lu, Jintao Wang, Robert W Williams & Kenneth F Manly

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  1. Elissa J Chesler
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  2. Lu Lu
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  3. Jintao Wang
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  4. Robert W Williams
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  5. Kenneth F Manly
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Correspondence to Elissa J Chesler.

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Chesler, E., Lu, L., Wang, J. et al. WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nat Neurosci 7, 485–486 (2004). https://doi.org/10.1038/nn0504-485

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