Phenotype measure:   Paigen1   estHCC

ID, description, units MPD:2927   estHCC   hepatic cholesterol concentration (esterified per g liver)   [mg]
high-fat diet study
Data set, strains Paigen1   inbred   43 strains     sex: both     age: 15-19wks
Procedure lipid profile
Ontology mappings

  STRAIN COMPARISON PLOT
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Paigen1 - hepatic cholesterol concentration (esterified per g liver)



  MEASURE SUMMARY
Measure Summary FemaleMale
Number of strains tested43 strains42 strains
Mean of the strain means34.3   mg 28.8   mg
Median of the strain means31.6   mg 25.6   mg
SD of the strain means± 14.7 ± 13.7
Coefficient of variation (CV)0.430 0.475
Min–max range of strain means3.61   –   75.9   mg 2.60   –   61.7   mg
Mean sample size per strain5.8   mice 5.7   mice


  ANOVA, Q-Q NORMALITY ASSESSMENT
ANOVA summary      
FactorDFSum of squaresMean sum of squaresF valuep value (Pr>F)
sex 1 2549.352 2549.352 25.9446 < 0.0001
strain 41 73353.9657 1789.1211 18.2078 < 0.0001
sex:strain 41 18611.0517 453.9281 4.6196 < 0.0001
Residuals 399 39206.2195 98.2612


Q-Q normality assessment based on residuals

  


  STRAIN MEANS (UNADJUSTED)
Strain Sex Mean SD N mice SEM CV Min, Max Z score
129S1/SvImJ f 25.0 7.07   6 2.88 0.283 16.4, 34.1 -0.63
129S1/SvImJ m 31.6 9.85   6 4.02 0.312 13.8, 44.0 0.2
A/J f 48.3 27.0   6 11.0 0.559 13.2, 71.3 0.95
A/J m 18.0 7.62   5 3.41 0.422 10.3, 30.1 -0.79
AKR/J f 25.8 3.48   6 1.42 0.135 21.8, 31.5 -0.58
AKR/J m 13.9 2.37   6 0.968 0.17 11.1, 17.6 -1.09
BALB/cJ f 28.1 11.6   9 3.87 0.414 16.9, 49.2 -0.42
BALB/cJ m 25.7 13.1   6 5.36 0.511 14.4, 51.5 -0.23
BPH/2J f 29.9 2.2   5 0.983 0.0735 26.6, 32.7 -0.3
BPH/2J m 22.1 4.88   5 2.18 0.221 15.9, 28.9 -0.49
BPL/1J f 34.3 8.09   6 3.3 0.236 26.3, 44.2 0.0
BPL/1J m 24.6 5.72   5 2.56 0.233 16.8, 31.9 -0.31
BPN/3J f 24.0 2.36   5 1.05 0.0984 21.9, 27.0 -0.7
BPN/3J m 13.3 3.05   6 1.25 0.23 9.39, 17.4 -1.13
BTBR T+ Itpr3tf/J f 25.6 6.49   3 3.75 0.254 18.3, 30.8 -0.59
BTBR T+ Itpr3tf/J m 21.9 7.61   7 2.88 0.348 10.7, 32.1 -0.51
C3H/HeJ f 30.0 6.58   6 2.68 0.22 20.6, 37.7 -0.29
C3H/HeJ m 36.1 7.65   8 2.7 0.212 27.3, 48.5 0.53
C57BL/10J f 20.3 10.3   6 4.22 0.51 8.82, 37.9 -0.95
C57BL/10J m 37.6 10.3   7 3.91 0.275 24.7, 51.0 0.64
C57BL/6J f 37.2 10.4   7 3.93 0.28 23.5, 54.0 0.2
C57BL/6J m 39.5 6.68   6 2.73 0.169 31.9, 50.4 0.78
C57BLKS/J f 34.5 4.79   5 2.14 0.139 27.2, 39.9 0.01
C57BLKS/J m 25.5 10.1   7 3.81 0.395 14.1, 44.5 -0.24
C57BR/cdJ f 28.9 16.4   7 6.19 0.566 11.4, 49.6 -0.37
C57BR/cdJ m 16.7 2.01   5 0.898 0.12 14.9, 20.1 -0.89
C57L/J f 27.9 3.39   7 1.28 0.121 23.9, 32.9 -0.43
C57L/J m 12.0 1.51   6 0.615 0.125 10.4, 14.0 -1.23
C58/J f 31.6 9.02   5 4.03 0.286 23.1, 46.6 -0.18
C58/J m 37.7 12.8   6 5.22 0.339 25.6, 59.7 0.65
CAST/EiJ f 31.2 12.4   6 5.08 0.399 20.7, 52.1 -0.21
CAST/EiJ m 29.1 17.1   5 7.66 0.589 14.8, 58.3 0.02
CBA/J f 17.3 5.35   6 2.18 0.309 13.1, 27.4 -1.15
CBA/J m 17.1 3.06   6 1.25 0.179 13.8, 22.1 -0.86
CE/J f 75.9 8.32   4 4.16 0.11 67.6, 86.0 2.82
CE/J m 17.9 10.2   6 4.17 0.572 8.11, 32.3 -0.8
CZECHII/EiJ f 28.4 8.88   4 4.44 0.313 18.2, 39.7 -0.4
CZECHII/EiJ m 33.0 4.21   5 1.88 0.128 28.6, 39.9 0.3
DBA/1J f 17.5 4.72   7 1.79 0.27 11.0, 22.6 -1.14
DBA/1J m 15.2 3.92   5 1.75 0.258 11.1, 20.9 -1.0
DBA/2J f 11.7 1.35   6 0.552 0.115 9.59, 13.2 -1.53
DBA/2J m 13.1 2.74   6 1.12 0.209 9.6, 16.4 -1.15
FVB/NJ f 32.6 13.5   5 6.03 0.413 20.6, 55.6 -0.11
FVB/NJ m 36.6 13.7   3 7.89 0.373 24.6, 51.5 0.57
I/LnJ f 22.5 8.96   6 3.66 0.398 13.7, 37.2 -0.8
I/LnJ m 20.7 12.2   6 4.96 0.588 12.6, 44.0 -0.59
KK/HlJ f 42.0 4.58   6 1.87 0.109 35.3, 48.1 0.52
KK/HlJ m 29.3 3.85   6 1.57 0.132 24.8, 35.1 0.03
LP/J f 20.6 2.97   6 1.21 0.144 17.3, 25.4 -0.93
LP/J m 20.9 5.47   6 2.24 0.262 14.7, 26.8 -0.58
MOLF/EiJ f 39.3 17.1   6 6.98 0.435 22.6, 59.2 0.34
MOLF/EiJ m 55.5 7.56   7 2.86 0.136 43.5, 64.8 1.95
NOD/ShiLtJ f 31.7 14.2   5 6.34 0.447 16.9, 55.2 -0.18
NOD/ShiLtJ m 19.4 6.65   5 2.97 0.343 13.5, 30.4 -0.69
NON/ShiLtJ f 19.9 1.31   5 0.588 0.0662 18.0, 21.4 -0.98
NON/ShiLtJ m 36.2 6.17   5 2.76 0.17 30.5, 45.8 0.54
NZB/BlNJ f 48.5 8.29   6 3.38 0.171 38.9, 58.7 0.96
NZB/BlNJ m 20.1 3.0   5 1.34 0.149 16.3, 24.6 -0.64
NZW/LacJ f 55.6 16.5   6 6.74 0.297 24.1, 69.1 1.45
NZW/LacJ m 61.7 7.89   6 3.22 0.128 51.5, 72.2 2.4
PERA/EiJ f 32.8 13.6   5 6.09 0.415 22.4, 48.7 -0.1
PERA/EiJ m 37.9 14.8   4 7.41 0.391 26.9, 58.9 0.66
P/J f 64.5 24.0   6 9.8 0.372 31.5, 99.3 2.05
P/J m 55.0 15.7   6 6.41 0.285 24.9, 69.9 1.91
PL/J f 40.7 4.32   5 1.93 0.106 37.5, 48.0 0.44
PL/J m 35.8 14.8   3 8.55 0.414 18.7, 44.5 0.51
RBF/DnJ f 48.5 6.9   7 2.61 0.142 37.0, 59.2 0.96
RBF/DnJ m 46.2 4.76   5 2.13 0.103 39.8, 52.6 1.27
RF/J f 47.2 8.0   6 3.26 0.169 37.3, 58.8 0.88
RF/J m 34.6 3.98   6 1.62 0.115 29.1, 40.3 0.42
RIIIS/J f 34.9 17.1   8 6.04 0.49 12.6, 65.3 0.04
RIIIS/J m 33.2 12.5   7 4.74 0.378 11.3, 47.1 0.32
SEA/GnJ f 55.2 20.6   6 8.39 0.372 23.1, 83.3 1.42
SEA/GnJ m 44.3 9.74   6 3.98 0.22 26.1, 52.6 1.13
SJL/J f 21.0 3.72   6 1.52 0.177 17.2, 26.1 -0.9
SJL/J m 15.0 4.83   6 1.97 0.321 8.57, 22.8 -1.01
SM/J f 35.5 6.82   6 2.78 0.192 27.7, 45.7 0.08
SM/J m 25.3 5.31   6 2.17 0.21 17.6, 34.0 -0.26
SPRET/EiJ f 3.61 0.763   5 0.341 0.211 2.43, 4.52 -2.08
SPRET/EiJ m 2.6 1.14   4 0.568 0.436 1.68, 4.12 -1.92
SWR/J f 27.6 9.3   6 3.8 0.337 15.1, 37.7 -0.45
SWR/J m 19.8 3.13   6 1.28 0.159 15.1, 23.1 -0.66
WSB/EiJ f 61.7 10.2   6 4.17 0.166 50.4, 76.3 1.86
WSB/EiJ m 59.3 7.68   6 3.14 0.129 51.1, 71.6 2.22
YBR/EiJ f 54.9 11.1   5 4.98 0.203 41.3, 69.0 1.4


  LEAST SQUARES MEANS (MODEL-ADJUSTED)
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ f 24.9833 4.0468 32.9391 17.0276
129S1/SvImJ m 31.5667 4.0468 39.5224 23.6109
A/J f 48.2667 4.0468 56.2224 40.3109
A/J m 18.04 4.4331 26.7551 9.3249
AKR/J f 25.7667 4.0468 33.7224 17.8109
AKR/J m 13.9333 4.0468 21.8891 5.9776
BALB/cJ f 28.0556 3.3042 34.5514 21.5597
BALB/cJ m 25.7 4.0468 33.6558 17.7442
BPH/2J f 29.88 4.4331 38.5951 21.1649
BPH/2J m 22.12 4.4331 30.8351 13.4049
BPL/1J f 34.3 4.0468 42.2558 26.3442
BPL/1J m 24.58 4.4331 33.2951 15.8649
BPN/3J f 23.96 4.4331 32.6751 15.2449
BPN/3J m 13.265 4.0468 21.2208 5.3092
BTBR T+ Itpr3tf/J f 25.5667 5.7231 36.8178 14.3155
BTBR T+ Itpr3tf/J m 21.9 3.7466 29.2656 14.5344
C3H/HeJ f 29.95 4.0468 37.9058 21.9942
C3H/HeJ m 36.075 3.5047 42.9649 29.1851
C57BL/10J f 20.27 4.0468 28.2258 12.3142
C57BL/10J m 37.6 3.7466 44.9656 30.2344
C57BL/6J f 37.2143 3.7466 44.5799 29.8487
C57BL/6J m 39.4667 4.0468 47.4224 31.5109
C57BLKS/J f 34.54 4.4331 43.2551 25.8249
C57BLKS/J m 25.5429 3.7466 32.9085 18.1772
C57BR/cdJ f 28.9429 3.7466 36.3085 21.5772
C57BR/cdJ m 16.7 4.4331 25.4151 7.9849
C57L/J f 27.9429 3.7466 35.3085 20.5772
C57L/J m 12.0333 4.0468 19.9891 4.0776
C58/J f 31.56 4.4331 40.2751 22.8449
C58/J m 37.6833 4.0468 45.6391 29.7276
CAST/EiJ f 31.2167 4.0468 39.1724 23.2609
CAST/EiJ m 29.08 4.4331 37.7951 20.3649
CBA/J f 17.3 4.0468 25.2558 9.3442
CBA/J m 17.0833 4.0468 25.0391 9.1276
CE/J f 75.9 4.9563 85.6438 66.1562
CE/J m 17.8683 4.0468 25.8241 9.9126
CZECHII/EiJ f 28.35 4.9563 38.0938 18.6062
CZECHII/EiJ m 33.02 4.4331 41.7351 24.3049
DBA/1J f 17.4714 3.7466 24.8371 10.1058
DBA/1J m 15.18 4.4331 23.8951 6.4649
DBA/2J f 11.7317 4.0468 19.6874 3.7759
DBA/2J m 13.0917 4.0468 21.0474 5.1359
FVB/NJ f 32.64 4.4331 41.3551 23.9249
FVB/NJ m 36.6333 5.7231 47.8845 25.3822
I/LnJ f 22.5167 4.0468 30.4724 14.5609
I/LnJ m 20.6833 4.0468 28.6391 12.7276
KK/HlJ f 42.0 4.0468 49.9558 34.0442
KK/HlJ m 29.2667 4.0468 37.2224 21.3109
LP/J f 20.55 4.0468 28.5058 12.5942
LP/J m 20.8833 4.0468 28.8391 12.9276
MOLF/EiJ f 39.2833 4.0468 47.2391 31.3276
MOLF/EiJ m 55.4714 3.7466 62.8371 48.1058
NOD/ShiLtJ f 31.72 4.4331 40.4351 23.0049
NOD/ShiLtJ m 19.36 4.4331 28.0751 10.6449
NON/ShiLtJ f 19.86 4.4331 28.5751 11.1449
NON/ShiLtJ m 36.24 4.4331 44.9551 27.5249
NZB/BlNJ f 48.4833 4.0468 56.4391 40.5276
NZB/BlNJ m 20.14 4.4331 28.8551 11.4249
NZW/LacJ f 55.55 4.0468 63.5058 47.5942
NZW/LacJ m 61.6667 4.0468 69.6224 53.7109
PERA/EiJ f 32.8 4.4331 41.5151 24.0849
PERA/EiJ m 37.9 4.9563 47.6438 28.1562
P/J f 64.5167 4.0468 72.4724 56.5609
P/J m 54.9833 4.0468 62.9391 47.0276
PL/J f 40.66 4.4331 49.3751 31.9449
PL/J m 35.8 5.7231 47.0512 24.5488
RBF/DnJ f 48.5 3.7466 55.8656 41.1344
RBF/DnJ m 46.2 4.4331 54.9151 37.4849
RF/J f 47.25 4.0468 55.2058 39.2942
RF/J m 34.6 4.0468 42.5558 26.6442
RIIIS/J f 34.8625 3.5047 41.7524 27.9726
RIIIS/J m 33.1571 3.7466 40.5228 25.7915
SEA/GnJ f 55.2 4.0468 63.1558 47.2442
SEA/GnJ m 44.2833 4.0468 52.2391 36.3276
SJL/J f 21.0167 4.0468 28.9724 13.0609
SJL/J m 15.0283 4.0468 22.9841 7.0726
SM/J f 35.5 4.0468 43.4558 27.5442
SM/J m 25.3167 4.0468 33.2724 17.3609
SPRET/EiJ f 3.614 4.4331 12.3291 0.0
SPRET/EiJ m 2.605 4.9563 12.3488 0.0
SWR/J f 27.6167 4.0468 35.5724 19.6609
SWR/J m 19.7667 4.0468 27.7224 11.8109
WSB/EiJ f 61.7333 4.0468 69.6891 53.7776
WSB/EiJ m 59.35 4.0468 67.3058 51.3942


  LEAST SQUARES MEANS (MODEL-ADJUSTED), SEXES COMBINED
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ both 28.275 2.8615 33.9006 22.6494
A/J both 33.1533 3.0012 39.0535 27.2532
AKR/J both 19.85 2.8615 25.4756 14.2244
BALB/cJ both 26.8778 2.6122 32.0132 21.7423
BPH/2J both 26.0 3.1347 32.1625 19.8375
BPL/1J both 29.44 3.0012 35.3402 23.5398
BPN/3J both 18.6125 3.0012 24.5127 12.7123
BTBR T+ Itpr3tf/J both 23.7333 3.4202 30.4572 17.0095
C3H/HeJ both 33.0125 2.6767 38.2748 27.7502
C57BL/10J both 28.935 2.7575 34.356 23.514
C57BL/6J both 38.3405 2.7575 43.7614 32.9195
C57BLKS/J both 30.0414 2.9021 35.7468 24.336
C57BR/cdJ both 22.8214 2.9021 28.5268 17.116
C57L/J both 19.9881 2.7575 25.409 14.5671
C58/J both 34.6217 3.0012 40.5218 28.7215
CAST/EiJ both 30.1483 3.0012 36.0485 24.2482
CBA/J both 17.1917 2.8615 22.8173 11.5661
CE/J both 46.8842 3.1993 53.1738 40.5946
CZECHII/EiJ both 30.685 3.3248 37.2213 24.1487
DBA/1J both 16.3257 2.9021 22.0311 10.6203
DBA/2J both 12.4117 2.8615 18.0373 6.7861
FVB/NJ both 34.6367 3.6196 41.7525 27.5208
I/LnJ both 21.6 2.8615 27.2256 15.9744
KK/HlJ both 35.6333 2.8615 41.2589 30.0077
LP/J both 20.7167 2.8615 26.3423 15.0911
MOLF/EiJ both 47.3774 2.7575 52.7983 41.9564
NOD/ShiLtJ both 25.54 3.1347 31.7025 19.3775
NON/ShiLtJ both 28.05 3.1347 34.2125 21.8875
NZB/BlNJ both 34.3117 3.0012 40.2118 28.4115
NZW/LacJ both 58.6083 2.8615 64.2339 52.9827
PERA/EiJ both 35.35 3.3248 41.8863 28.8137
P/J both 59.75 2.8615 65.3756 54.1244
PL/J both 38.23 3.6196 45.3459 31.1141
RBF/DnJ both 47.35 2.9021 53.0554 41.6446
RF/J both 40.925 2.8615 46.5506 35.2994
RIIIS/J both 34.0098 2.5651 39.0527 28.9669
SEA/GnJ both 49.7417 2.8615 55.3673 44.1161
SJL/J both 18.0225 2.8615 23.6481 12.3969
SM/J both 30.4083 2.8615 36.0339 24.7827
SPRET/EiJ both 3.1095 3.3248 9.6458 0.0
SWR/J both 23.6917 2.8615 29.3173 18.0661
WSB/EiJ both 60.5417 2.8615 66.1673 54.9161




  GWAS USING LINEAR MIXED MODELS