QTLdb: entrichment tests

Release 56
(Apr 24, 2025)

Whole genome analysis for QTL/association enrichment

Running...

Version: Enrich S: beta v0.8

Data:

Number of reproductive organs traits:	21
Number of QTL / associations found:	2,915
Number of chromosomes where QTL / associations are found:	19

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

Chromosomes	Total χ²	df	p-values	FDR ^*	Size of χ²
Chromosome X	2364.09117	18	9e-41	2.442857e-40
Chromosome 1	519.03768	18	1.032225e-98	9.806137e-98
Chromosome 2	0.34125	18	0.998329325823115	9.983293e-01
Chromosome 3	5.64354	18	0.9974406	9.983293e-01
Chromosome 4	135.13752	18	5.514319e-20	1.164134e-19
Chromosome 5	1924.64013	18	9e-41	2.442857e-40
Chromosome 6	0.04578	18	0.998329325823115	9.983293e-01
Chromosome 7	6781.13688	18	9e-41	2.442857e-40
Chromosome 8	203.72058	18	1.804241e-33	4.285072e-33
Chromosome 9	0.34125	18	0.998329325823115	9.983293e-01
Chromosome 10	9.70662	18	0.9410623	9.983293e-01
Chromosome 11	102.92058	18	6.441295e-14	1.223846e-13
Chromosome 12	95.55084	18	1.435601e-12	2.479674e-12
Chromosome 13	32.55084	18	0.01890408	2.993146e-02
Chromosome 14	0.80241	18	0.998329325823115	9.983293e-01
Chromosome 15	28.46613	18	0.05530691	8.083318e-02
Chromosome 16	467.16810	18	8.18141e-88	3.886170e-87
Chromosome 17	483.29799	18	3.370484e-91	2.134640e-90
Chromosome 18	550.55574	18	2.364558e-105	4.492660e-104

Chi-squared (χ²) test: Which of the 21 reproductive organs traits are over-represented in the QTLdb

Traits	Total χ²	df	p-values	FDR ^*	Size of χ²
Cryptorchidism	24.54936	20	0.219218	2.557543e-01
Epididymis weight	35.4294	20	0.017933	3.423573e-02
Functional teat number	90.03918	20	7.2969e-11	3.064698e-10
Nonfunctional nipples	32.38573	20	0.03935762	6.357769e-02
Ovary weight	33.87391	20	0.02699039	4.723318e-02
Reproductive tract weight	35.57845	20	0.01723122	3.423573e-02
Seminiferous tubule diameter	31.56531	20	0.04815615	7.223422e-02
Teat number	10.86103	20	0.949747	9.497470e-01
Teat number symmetry	137.40347	20	1.570678e-19	3.298424e-18
Teat number, difference between sides	58.9164	20	1.046411e-05	3.139233e-05
Teat number, maximum per side	26.29718	20	0.1562198	2.050385e-01
Testicular length	19.02424	20	0.5202509	5.750142e-01
Testicular parenchyma color	131.49999	20	2.037994e-18	2.139894e-17
Testicular percentage	45.71662	20	0.000881389	2.056574e-03
Testicular weight	101.57185	20	6.58384e-13	4.608688e-12
Testicular width	74.65873	20	3.105378e-08	1.086882e-07
Uterine capacity	11.72968	20	0.925066	9.497470e-01
Vulva height	53.35151	20	7.214048e-05	1.893688e-04
Vulva width	25.81986	20	0.1718441	2.122780e-01
uterine horn length	26.82971	20	0.1401233	1.961726e-01
uterine horn weight	100.78152	20	9.12557e-13	4.790924e-12

Correlations found between some of these traits for your reference

No correlation data found on these traits

Overall Test

Data		Chi'Square Test			Fisher's Exact Test
Number of chrom.:	19	χ²	=	13705.155030
Number of traits:	21	df	=	360
Number of QTLs:	2,915	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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