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. 2018 Jul 31;8(8):2559-2562.
doi: 10.1534/g3.118.200230.

gQTL: A Web Application for QTL Analysis Using the Collaborative Cross Mouse Genetic Reference Population

Kranti Konganti  1 , Andre Ehrlich  1 , Ivan Rusyn  2 , David W Threadgill  3   4
Affiliations

gQTL: A Web Application for QTL Analysis Using the Collaborative Cross Mouse Genetic Reference Population

Kranti Konganti et al. G3 (Bethesda). .

Abstract

Multi-parental recombinant inbred populations, such as the Collaborative Cross (CC) mouse genetic reference population, are increasingly being used for analysis of quantitative trait loci (QTL). However specialized analytic software for these complex populations is typically built in R that works only on command-line, which limits the utility of these powerful resources for many users. To overcome analytic limitations, we developed gQTL, a web accessible, simple graphical user interface application based on the DOQTL platform in R to perform QTL mapping using data from CC mice.

Keywords: collaborative cross; qtl; software.

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Figures

Figure 1
Figure 1
Screen shots of data entry and initial processing. (A) Data loading and file type selection. (B) Uploaded data visualization, outlier selection, and normalization options.
Figure 2
Figure 2
Screen shots of QTL analysis results. (A) Options for data visualization with normalized histogram. (B) QQ plot. (C) QTL plot with threshold levels and locations of significant markers. (D) Allele effect and genotype-phenotype plots. (E) A zoomed version of the significant QTL interval.
See this image and copyright information in PMC

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References

    1. Aylor D. L., Valdar W., Foulds-Mathes W., Buus R. J., Verdugo R. A., et al. , 2011. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res. 21: 1213–1222. 10.1101/gr.111310.110 - DOI - PMC - PubMed
    1. Chang, W., J. Cheng, J. Allaire, Y. Xie and J. McPherson, 2016 shiny: Web application framework for R, http://shiny.rstudio.com.
    1. Churchill G. A., Airey D. C., Allayee H., Angel J. M., Attie A. D., et al. , 2004. The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat. Genet. 36: 1133–1137. 10.1038/ng1104-1133 - DOI - PubMed
    1. Churchill G. A., Doerge R. W., 1994. Empirical threshold values for quantitative trait mapping. Genetics 138: 963–971. - PMC - PubMed
    1. Dorman A., Baer D., Tomlinson I., Mott R., Iraqi F. A., 2016. Genetic analysis of intestinal polyp development in Collaborative Cross mice carrying the Apc (Min/+) mutation. BMC Genet. 17: 46 (erratum: BMC Genet. 17: 147) 10.1186/s12863-016-0349-6 - DOI - PMC - PubMed

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