Whole genome enrichment analysis of the number of QTL/association found
on user selected chromosomes / chromosomal sub-regions

Running...
The design of this trait enrichment analysis tool aims at allowing evaluation of all reported QTL/associations of selected traits throughout a genome, to determine if a trait or traits are over-represented in one or more regions of the genome. The setup of the analysis is based on an underlining assumption, that the selected traits are related. For example the traits may belong to a given trait type, or are from a given trait ontology path.

In this implementation we used Chi-squared analysis of the frequencies of reported QTL/associations classified by traits and their chromosome locations. The contingency p-values (p) are estimated to indicate the degree of over-representations (enrichments) of QTL/associations. The false discovery rates (FDR) is also estimated with Benjamini–Hochberg procedure. The size of Chi-squares in each contingency class are graphically indicated with bars of varying lengthes drawn with transformed Chi-square values.

In addition, some available trait correlation data are appended when available, to provide additional support information for users to evaluate the results.

Step 1: Select at least 1 trait
305-DAY MILK YIELD (486)
ABOMASUM DISPLACEMENT (470)
AGE AT FIRST CALVING (458)
AGE AT PUBERTY (549)
AVERAGE DAILY GAIN (519)
BODY DEPTH (549)
BODY WEIGHT (549)
BODY WEIGHT (BIRTH) (549)
BODY WEIGHT (MATURE) (540)
BODY WEIGHT (WEANING) (549)
BODY WEIGHT (YEARLING) (549)
BODY WEIGHT GAIN (549)
BOVINE RESPIRATORY DISEASE SUSCEPTIBILITY (549)
BOVINE TUBERCULOSIS SUSCEPTIBILITY (519)
CALVING EASE (549)
CALVING EASE (MATERNAL) (549)
CARCASS WEIGHT (549)
CLINICAL MASTITIS (549)
CONCEPTION RATE (519)
DAIRY FORM (549)
DAUGHTER PREGNANCY RATE (549)
DRY MATTER INTAKE (549)
FAT THICKNESS AT THE 12TH RIB (549)
FECAL LARVA COUNT (233)
FEET AND LEG CONFORMATION (549)
FERTILITY INDEX (473)
FOOT ANGLE (549)
GESTATION LENGTH (355)
IMMUNOGLOBULIN G LEVEL (446)
INHIBIN LEVEL (152)
INSEMINATIONS PER CONCEPTION (486)
INSULIN-LIKE GROWTH FACTOR 1 LEVEL (318)
INTERVAL FROM FIRST TO LAST INSEMINATION (502)
INTERVAL TO FIRST ESTRUS AFTER CALVING (549)
INTRAMUSCULAR FAT (539)
LACTATION PERSISTENCY (497)
LEAN MEAT YIELD (519)
LENGTH OF PRODUCTIVE LIFE (549)
LONGISSIMUS MUSCLE AREA (549)
LUTEAL ACTIVITY (193)
M. PARATUBERCULOSIS SUSCEPTIBILITY (519)
MARBLING SCORE (549)
MATURITY RATE (515)
METABOLIC BODY WEIGHT (538)
MILK ALPHA-S2-CASEIN PERCENTAGE (388)
MILK BETA-LACTOGLOBULIN PERCENTAGE (347)
MILK BETA-LACTOGLOBULIN PROTEIN CONTENT (22)
MILK BUTYRIC ACID CONTENT (514)
MILK C14 INDEX (302)
MILK CAPRIC ACID CONTENT (450)
MILK CAPROIC ACID CONTENT (509)
MILK CAPRYLIC ACID CONTENT (478)
MILK CASEIN PERCENTAGE (395)
MILK FAT PERCENTAGE (549)
MILK FAT YIELD (549)
MILK GLYCOSYLATED KAPPA-CASEIN PERCENTAGE (503)
MILK IRON CONTENT (435)
MILK KAPPA-CASEIN PERCENTAGE (519)
MILK LAURIC ACID CONTENT (376)
MILK LINOLEIC ACID CONTENT (438)
MILK MYRISTIC ACID CONTENT (518)
MILK MYRISTOLEIC ACID CONTENT (413)
MILK PALMITOLEIC ACID CONTENT (421)
MILK PHOSPHORUS CONTENT (148)
MILK PHOSPHORYLATED ALPHA-S2-CASEIN PERCENTAGE (211)
MILK POTASSIUM CONTENT (355)
MILK PROTEIN PERCENTAGE (549)
MILK PROTEIN YIELD (549)
MILK RIBOFLAVIN CONTENT (497)
MILK STEARIC ACID CONTENT (400)
MILK TRIDECYLIC ACID CONTENT (549)
MILK UNGLYCOSYLATED KAPPA-CASEIN PERCENTAGE (519)
MILK YIELD (549)
MILK ZINC CONTENT (382)
MILKING SPEED (531)
MONOUNSATURATED FATTY ACID CONTENT (498)
MUSCLE ANSERINE CONTENT (392)
MYRISTIC ACID CONTENT (348)
MYRISTOLEIC ACID CONTENT (229)
NET MERIT (549)
NON-RETURN RATE (513)
OLEIC ACID CONTENT (378)
PERCENTAGE NORMAL SPERM (47)
PTA TYPE (549)
REAR LEG PLACEMENT - REAR VIEW (549)
REAR LEG PLACEMENT - SIDE VIEW (549)
RESIDUAL FEED INTAKE (519)
RUMP ANGLE (549)
RUMP WIDTH (549)
SATURATED FATTY ACID CONTENT (372)
SCROTAL CIRCUMFERENCE (508)
SEXUAL PRECOCITY (374)
SHEAR FORCE (549)
SOMATIC CELL COUNT (525)
SOMATIC CELL SCORE (549)
STATURE (549)
STILLBIRTH (549)
STILLBIRTH (MATERNAL) (549)
STRENGTH (549)
SUBCUTANEOUS FAT (519)
TEAT LENGTH (539)
TEAT PLACEMENT - FRONT (549)
TEAT PLACEMENT - REAR (549)
TENDERNESS SCORE (492)
TICK RESISTANCE (469)
TWINNING (481)
UDDER ATTACHMENT (549)
UDDER CLEFT (549)
UDDER DEPTH (549)
UDDER HEIGHT (549)
UDDER SWELLING SCORE (492)
Step 2: Input at least 1 targeted chromosome segments for analysis.

Format: "chr#:coordA-coordB" (Mbp)

Reference: Genome build UMD info:
Chromosomes QTL/associations Chr. Sizes (Mbp)
X25,699148.82
12,884158.34
23,403137.06
33,283121.43
44,742120.83
56,295121.19
612,859119.46
73,019112.64
81,595113.38
91,660105.71
102,528104.31
113,905107.31
121,27891.16
132,95984.24
1410,23484.65
151,42085.30
161,74181.72
175,36475.16
182,35366.00
192,65864.06
203,67972.04
213,83471.60
221,28861.44
231,35952.53
2491562.71
253,19342.90
264,70151.68
271,51945.41
2882146.31
291,70451.51
3010.00

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Contact: NAGRP Bioinformatics Team
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