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Figure 3 | BMC Bioinformatics

Figure 3

From: Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains

Figure 3

Comparison of QTL detection power. a) LOD scores on the original and the saturated map. QTL mapping was performed on all 10,801 tiling array probes showing differential expression between parents (p<0.01 Student t-test) using the original and saturated maps. 5,837 out of 10,801 probes show a QTL with a L O D>5 on the original map. Blue dots - represent 3,943 probes (67.6%) that show an increased LOD score on the new saturated map. Moreover, 210 new QTLs were detected on the saturated map. Red dots - probes showing a decrease in LOD score on the saturated map. Green circles - are probes used to saturate the map. b) Changing LOD scores. For each of the phenotypes the top QTL peak was selected. If the peaks measured on the original and saturated maps shared a location, then the difference between the LOD scores was calculated. Solid green line - shows median of differences between QTL peaks from chromosome 4, calculated inside a sliding 10 cM window stepped across the chromosome with a step of 1 cM. For each of the windows the value was plotted in the middle of the compartment (thus no value for the first and the last 5 cM). Ticks on the x-axis show the position of the markers: tall gray ticks - show original markers; short green ticks - show markers selected by Pheno2Geno. Only one region, in which no new markers were added (75-80 cM), does not show an increase in power.

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