Whole genome analysis for QTL/association enrichment

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Data:

Number of fatness traits:20
Number of QTL / associations found:162
Number of chromosomes where QTL / associations are found:24

Chi-squared (χ2) test: are fatness traits over-represented on some chromosomes?

Chromosomes Total χ2 df p-values FDR * Size of χ2
Chromosome X253.51860239.820166e-417.856133e-40
Chromosome 131.29620230.11568841.322153e-01
Chromosome 2986.85180238.326852e-1941.998444e-192
Chromosome 3201.66660231.652651e-309.915906e-30
Chromosome 40.18520230.9983293258231159.983293e-01
Chromosome 597.96300233.157256e-119.471768e-11
Chromosome 64335.00000239e-417.856133e-40
Chromosome 866.85180233.68741e-065.899856e-06
Chromosome 941.66660230.0099251121.191013e-02
Chromosome 101.66660230.9983293258231159.983293e-01
Chromosome 1166.85180233.68741e-065.899856e-06
Chromosome 1241.66660230.0099251121.191013e-02
Chromosome 1341.66660230.0099251121.191013e-02
Chromosome 1466.85180233.68741e-065.899856e-06
Chromosome 1566.85180233.68741e-065.899856e-06
Chromosome 169.07400230.99570179.983293e-01
Chromosome 1797.96300233.157256e-119.471768e-11
Chromosome 1841.66660230.0099251121.191013e-02
Chromosome 1966.85180233.68741e-065.899856e-06
Chromosome 2066.85180233.68741e-065.899856e-06
Chromosome 2297.96300233.157256e-119.471768e-11
Chromosome 2341.66660230.0099251121.191013e-02
Chromosome 2497.96300233.157256e-119.471768e-11
Chromosome 2566.85180233.68741e-065.899856e-06

Chi-squared (χ2) test: Which of the 20 fatness traits are over-represented in the QTLdb

Traits Total χ2 df p-values FDR * Size of χ2
Abdominal fat weight 15.20003 19 0.7098019 9.988997e-01
Backfat at 12th/13th ribs 76.71434 19 6.803957e-09 1.360791e-07
Backfat at third lumbar 16.76001 19 0.6061227 9.988997e-01
Carcass fat percentage 41.12005 19 0.002326141 6.646117e-03
Fat density 11.44003 19 0.9081482 9.988997e-01
Intermuscular fat weight 5.48003 19 0.9988997 9.988997e-01
Kidney fat weight 5.48003 19 0.9988997 9.988997e-01
Leg fat weight 5.48003 19 0.9988997 9.988997e-01
Loin fat thickness 10.96003 19 0.9251756 9.988997e-01
Loin fat weight 10.96003 19 0.9251756 9.988997e-01
Shoulder fat percentage 5.48003 19 0.9988997 9.988997e-01
Shoulder fat weight 5.48003 19 0.9988997 9.988997e-01
Subcutaneous fat area 62.80003 19 1.384337e-06 9.228913e-06
Subcutaneous fat thickness 47.63664 19 0.0002894174 9.647247e-04
Subcutaneous fat weight 5.48003 19 0.9988997 9.988997e-01
Tail fat deposition 53.94132 19 3.371341e-05 1.685671e-04
Total fat area 37.80002 19 0.006292139 1.573035e-02
fat weight in carcass 49.34543 19 0.000163501 6.540040e-04
internal fat amount 69.1143 19 1.290197e-07 1.290197e-06
intramuscular fat amount 5.48003 19 0.9988997 9.988997e-01

Correlations found between some of these traits for your reference

Backfat at 12th/13th ribsKidney fat weight
Loin fat weight
0.93(g)
0.52(p)
Subcutaneous fat thickness
0.12(g)
0.15(p)
Legend: Color gradients for degree of correlations
Correlation value range: -1.0~-0.8 -0.8~-0.6 -0.6~-0.4 -0.4~-0.2 -0.2~0 0~0.2 0.2~0.4 0.4~0.6 0.6~0.8 0.8~1.0
Genetic Correlations (g)                    
Phenotypic Correlations (p)                    
Environment Correlations (e)                    
Residual Correlations (r)                    

Overall Test

Data Chi'Square Test Fisher's Exact Test
Number of chrom.:24 χ2=6887.406600
Number of traits:20 df=437
Number of QTLs:162 p-value=0

FOOT NOTE: * : FDR is short for "false discovery rate", representing the expected proportion of type I errors. A type I error is where you incorrectly reject the null hypothesis, i.e. you get a false positive. It's statistical definition is FDR = E(V/R | R > 0) P(R > 0), where V = Number of Type I errors (false positives); R = Number of rejected hypotheses. Benjamini–Hochberg procedure is a practical way to estimate FDR.


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