Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Oct;4(10):e1000232.
doi: 10.1371/journal.pgen.1000232. Epub 2008 Oct 24.

Genetical genomics: spotlight on QTL hotspots

Rainer Breitling  1 , Yang Li, Bruno M Tesson, Jingyuan Fu, Chunlei Wu, Tim Wiltshire, Alice Gerrits, Leonid V Bystrykh, Gerald de Haan, Andrew I Su, Ritsert C Jansen
Affiliations

Genetical genomics: spotlight on QTL hotspots

Rainer Breitling et al. PLoS Genet. 2008 Oct.
No abstract available

PubMed Disclaimer

Figures

Figure 1
Figure 1. Alternative Permutation Strategies for Determining the Significance of eQTL Hotspots in Linkage and Association Studies.
(A) The top panel shows the original data. The genotype matrix contains information about the genotype of each strain (S1…Sn) at each marker position along the genome (M1…Mn). For each strain, the expression of genes G1…Gn is measured. Linkage or association mapping combines these two sources of information to yield the eQTL matrix, where each purple entry indicates a significant linkage or association for a gene at a particular locus. The bottom panel illustrates the permutation strategy advocated here, where the strain labels are permuted, so that each strain is assigned the genotype vector of another random strain, while the expression matrix is unchanged. When the mapping is repeated on these permuted data, the correlation structure of gene expression is maintained, leading to an accurate estimate of the clustered distribution of false eQTLs along the genome. (B) shows the permutation strategy used in , where the original eQTL matrix is permuted by assigning the same number of eQTLs to genes randomly. The correlation of gene expression is lost, leading to an underestimate of the clustered pattern of spurious eQTLs.
See this image and copyright information in PMC

Comment on

  • PLoS Genet. 4:e070.

References

    1. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. Genetics of gene expression surveyed in maize, mouse and man. Nature. 2003;422:297–302. - PubMed
    1. de Koning DJ, Haley CS. Genetical genomics in humans and model organisms. Trends Genet. 2005;21:377–381. - PubMed
    1. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, et al. Genetics of gene expression and its effect on disease. Nature. 2008;452:423–428. - PubMed
    1. Keurentjes JJ, Fu J, Terpstra IR, Garcia JM, van den Ackerveken G, et al. Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci U S A. 2007;104:1708–1713. - PMC - PubMed
    1. Wu C, Delano DL, Mitro N, Su SV, Janes J, et al. Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet. 2008;4(5):e1000070. doi:10.1371/journal.pgen.1000070. - PMC - PubMed