Phenotype measure:   Paigen1   agLC

ID, description, units MPD:2913   agLC   gallbladder, aggregated liquid crystals (score: 0-4)   [score]
high-fat diet study
Data set, strains Paigen1   inbred   43 strains     sex: both     age: 15-19wks
Procedure histopathology
Ontology mappings

  STRAIN COMPARISON PLOT
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Paigen1 - gallbladder, aggregated liquid crystals (score: 0-4)



  MEASURE SUMMARY
Measure Summary FemaleMale
Number of strains tested43 strains42 strains
Mean of the strain means0.842   score 0.700   score
Median of the strain means0.750   score 0.667   score
SD of the strain means± 0.460 ± 0.362
Coefficient of variation (CV)0.547 0.517
Min–max range of strain means0   –   2.00   score 0   –   1.80   score
Mean sample size per strain8.8   mice 8.1   mice


  ANOVA, Q-Q NORMALITY ASSESSMENT
ANOVA summary      
FactorDFSum of squaresMean sum of squaresF valuep value (Pr>F)
sex 1 2.4564 2.4564 6.908 0.0088
strain 41 101.3122 2.471 6.9492 < 0.0001
sex:strain 41 23.1806 0.5654 1.59 0.0125
Residuals 623 221.5303 0.3556


Q-Q normality assessment based on residuals

  


  STRAIN MEANS (UNADJUSTED)
  
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Strain Sex Mean SD N mice SEM CV Min, Max Z score
129S1/SvImJ f 0.45 0.284   10 0.0898 0.631 -0.85
129S1/SvImJ m 0.4 0.394   10 0.125 0.986 -0.83
A/J f 1.35 0.747   10 0.236 0.553 0.5, 3.0 1.1
A/J m 0.6 0.394   10 0.125 0.657 -0.28
AKR/J f 1.11 0.697   9 0.232 0.627 0.5, 2.0 0.58
AKR/J m 0.944 0.726   9 0.242 0.769 0.67
BALB/cJ f 0.35 0.412   10 0.13 1.18 -1.07
BALB/cJ m 0.35 0.412   10 0.13 1.18 -0.97
BPH/2J f 0.65 0.474   10 0.15 0.73 -0.42
BPH/2J m 0.556 0.3   9 0.1 0.541 -0.4
BPL/1J f 0.9 0.658   10 0.208 0.731 0.13
BPL/1J m 0.85 0.337   10 0.107 0.397 0.41
BPN/3J f 0.45 0.643   10 0.203 1.43 -0.85
BPN/3J m 0.611 0.333   9 0.111 0.545 -0.25
BTBR T+ Itpr3tf/J f 0.833 0.289   3 0.167 0.346 0.5, 1.0 -0.02
BTBR T+ Itpr3tf/J m 0.9 0.876   10 0.277 0.973 0.55
C3H/HeJ f 1.44 0.882   9 0.294 0.611 1.3
C3H/HeJ m 0.6 0.548   5 0.245 0.913 -0.28
C57BL/10J f 0.35 0.337   10 0.107 0.964 -1.07
C57BL/10J m 1.25 0.825   10 0.261 0.66 0.5, 3.0 1.52
C57BL/6J f 1.3 0.789   10 0.249 0.607 0.5, 3.0 0.99
C57BL/6J m 1.0 0.0   6 0.0 0.0 1.0, 1.0 0.83
C57BLKS/J f 0.75 0.689   6 0.281 0.919 -0.2
C57BLKS/J m 0.9 0.742   5 0.332 0.824 0.55
C57BR/cdJ f 1.33 0.707   9 0.236 0.53 1.06
C57BR/cdJ m 0.45 0.438   10 0.138 0.973 -0.69
C57L/J f 2.0 0.0   10 0.0 0.0 2.0, 2.0 2.52
C57L/J m 1.8 0.422   10 0.133 0.234 1.0, 2.0 3.04
C58/J f 1.65 0.973   10 0.308 0.59 0.5, 3.0 1.76
C58/J m 1.35 0.973   10 0.308 0.721 0.5, 3.0 1.8
CAST/EiJ f 0.5 0.5   5 0.224 1.0 -0.74
CAST/EiJ m 0.333 0.5   9 0.167 1.5 -1.01
CBA/J f 1.39 0.782   9 0.261 0.563 0.5, 3.0 1.19
CBA/J m 0.75 0.589   10 0.186 0.786 0.14
CE/J f 0.333 0.707   9 0.236 2.12 -1.11
CE/J m 0.25 0.418   6 0.171 1.67 -1.24
CZECHII/EiJ f 1.07 0.673   7 0.254 0.628 0.5, 2.0 0.5
CZECHII/EiJ m 1.14 0.378   7 0.143 0.331 1.0, 2.0 1.22
DBA/1J f 0.75 0.791   10 0.25 1.05 -0.2
DBA/1J m 0.438 0.729   8 0.258 1.67 -0.72
DBA/2J f 0.0 0.0   10 0.0 0.0 -1.83
DBA/2J m 0.278 0.441   9 0.147 1.59 -1.17
FVB/NJ f 1.17 0.968   9 0.323 0.83 0.71
FVB/NJ m 0.5 0.5   3 0.289 1.0 -0.55
I/LnJ f 0.5 0.707   9 0.236 1.41 -0.74
I/LnJ m 0.944 0.464   9 0.155 0.491 0.5, 2.0 0.67
KK/HlJ f 0.25 0.463   8 0.164 1.85 -1.29
KK/HlJ m 0.389 0.333   9 0.111 0.857 -0.86
LP/J f 0.944 0.167   9 0.0556 0.176 0.5, 1.0 0.22
LP/J m 0.889 0.782   9 0.261 0.879 0.52
MOLF/EiJ f 0.611 0.486   9 0.162 0.795 -0.5
MOLF/EiJ m 0.667 0.5   9 0.167 0.75 -0.09
NOD/ShiLtJ f 0.625 0.694   8 0.245 1.11 -0.47
NOD/ShiLtJ m 0.667 0.516   6 0.211 0.775 -0.09
NON/ShiLtJ f 0.833 0.25   9 0.0833 0.3 0.5, 1.0 -0.02
NON/ShiLtJ m 0.667 0.433   9 0.144 0.65 -0.09
NZB/BlNJ f 1.17 0.707   9 0.236 0.606 0.71
NZB/BlNJ m 0.944 0.846   9 0.282 0.895 0.67
NZW/LacJ f 1.25 1.04   8 0.366 0.828 0.89
NZW/LacJ m 1.25 0.717   10 0.227 0.573 1.52
PERA/EiJ f 0.125 0.231   8 0.0818 1.85 -1.56
PERA/EiJ m 0.0 0.0   4 0.0 0.0 -1.94
P/J f 0.889 0.486   9 0.162 0.547 0.5, 2.0 0.1
P/J m 0.667 0.612   9 0.204 0.919 -0.09
PL/J f 0.55 0.643   10 0.203 1.17 -0.63
PL/J m 0.167 0.289   3 0.167 1.73 -1.47
RBF/DnJ f 0.889 0.601   9 0.2 0.676 0.1
RBF/DnJ m 0.333 0.433   9 0.144 1.3 -1.01
RF/J f 0.65 0.818   10 0.259 1.26 -0.42
RF/J m 0.5 0.0   5 0.0 0.0 0.5, 0.5 -0.55
RIIIS/J f 1.5 0.707   10 0.224 0.471 1.0, 3.0 1.43
RIIIS/J m 0.833 0.829   9 0.276 0.995 0.5, 3.0 0.37
SEA/GnJ f 1.75 0.463   8 0.164 0.265 1.0, 2.0 1.97
SEA/GnJ m 1.05 0.762   10 0.241 0.726 0.97
SJL/J f 0.45 0.497   10 0.157 1.1 -0.85
SJL/J m 0.556 0.464   9 0.155 0.835 -0.4
SM/J f 0.286 0.393   7 0.149 1.38 -1.21
SM/J m 0.6 0.224   5 0.1 0.373 0.5, 1.0 -0.28
SPRET/EiJ f 0.571 0.535   7 0.202 0.935 -0.59
SPRET/EiJ m 0.2 0.274   5 0.122 1.37 -1.38
SWR/J f 0.95 0.158   10 0.05 0.166 0.5, 1.0 0.23
SWR/J m 1.0 0.535   8 0.189 0.535 0.83
WSB/EiJ f 0.625 0.354   8 0.125 0.566 -0.47
WSB/EiJ m 0.833 0.753   6 0.307 0.903 0.37
YBR/EiJ f 0.667 0.577   3 0.333 0.866 -0.38


  LEAST SQUARES MEANS (MODEL-ADJUSTED)
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ f 0.45 0.1886 0.8203 0.0797
129S1/SvImJ m 0.4 0.1886 0.7703 0.0297
A/J f 1.35 0.1886 1.7203 0.9797
A/J m 0.6 0.1886 0.9703 0.2297
AKR/J f 1.1111 0.1988 1.5015 0.7208
AKR/J m 0.9444 0.1988 1.3348 0.5541
BALB/cJ f 0.35 0.1886 0.7203 -0.0203
BALB/cJ m 0.35 0.1886 0.7203 -0.0203
BPH/2J f 0.65 0.1886 1.0203 0.2797
BPH/2J m 0.5556 0.1988 0.9459 0.1652
BPL/1J f 0.9 0.1886 1.2703 0.5297
BPL/1J m 0.85 0.1886 1.2203 0.4797
BPN/3J f 0.45 0.1886 0.8203 0.0797
BPN/3J m 0.6111 0.1988 1.0015 0.2208
BTBR T+ Itpr3tf/J f 0.8333 0.3443 1.5094 0.1572
BTBR T+ Itpr3tf/J m 0.9 0.1886 1.2703 0.5297
C3H/HeJ f 1.4444 0.1988 1.8348 1.0541
C3H/HeJ m 0.6 0.2667 1.1237 0.0763
C57BL/10J f 0.35 0.1886 0.7203 -0.0203
C57BL/10J m 1.25 0.1886 1.6203 0.8797
C57BL/6J f 1.3 0.1886 1.6703 0.9297
C57BL/6J m 1.0 0.2434 1.4781 0.5219
C57BLKS/J f 0.75 0.2434 1.2281 0.2719
C57BLKS/J m 0.9 0.2667 1.4237 0.3763
C57BR/cdJ f 1.3333 0.1988 1.7237 0.943
C57BR/cdJ m 0.45 0.1886 0.8203 0.0797
C57L/J f 2.0 0.1886 2.3703 1.6297
C57L/J m 1.8 0.1886 2.1703 1.4297
C58/J f 1.65 0.1886 2.0203 1.2797
C58/J m 1.35 0.1886 1.7203 0.9797
CAST/EiJ f 0.5 0.2667 1.0237 -0.0237
CAST/EiJ m 0.3333 0.1988 0.7237 -0.057
CBA/J f 1.3889 0.1988 1.7792 0.9985
CBA/J m 0.75 0.1886 1.1203 0.3797
CE/J f 0.3333 0.1988 0.7237 -0.057
CE/J m 0.25 0.2434 0.7281 -0.2281
CZECHII/EiJ f 1.0714 0.2254 1.514 0.6288
CZECHII/EiJ m 1.1429 0.2254 1.5855 0.7003
DBA/1J f 0.75 0.1886 1.1203 0.3797
DBA/1J m 0.4375 0.2108 0.8515 0.0235
DBA/2J f 0.0 0.1886 0.3703 -0.3703
DBA/2J m 0.2778 0.1988 0.6681 -0.1126
FVB/NJ f 1.1667 0.1988 1.557 0.7763
FVB/NJ m 0.5 0.3443 1.1761 -0.1761
I/LnJ f 0.5 0.1988 0.8903 0.1097
I/LnJ m 0.9444 0.1988 1.3348 0.5541
KK/HlJ f 0.25 0.2108 0.664 -0.164
KK/HlJ m 0.3889 0.1988 0.7792 -0.0015
LP/J f 0.9444 0.1988 1.3348 0.5541
LP/J m 0.8889 0.1988 1.2792 0.4985
MOLF/EiJ f 0.6111 0.1988 1.0015 0.2208
MOLF/EiJ m 0.6667 0.1988 1.057 0.2763
NOD/ShiLtJ f 0.625 0.2108 1.039 0.211
NOD/ShiLtJ m 0.6667 0.2434 1.1447 0.1886
NON/ShiLtJ f 0.8333 0.1988 1.2237 0.443
NON/ShiLtJ m 0.6667 0.1988 1.057 0.2763
NZB/BlNJ f 1.1667 0.1988 1.557 0.7763
NZB/BlNJ m 0.9444 0.1988 1.3348 0.5541
NZW/LacJ f 1.25 0.2108 1.664 0.836
NZW/LacJ m 1.25 0.1886 1.6203 0.8797
PERA/EiJ f 0.125 0.2108 0.539 -0.289
PERA/EiJ m 0.0 0.2982 0.5855 -0.5855
P/J f 0.8889 0.1988 1.2792 0.4985
P/J m 0.6667 0.1988 1.057 0.2763
PL/J f 0.55 0.1886 0.9203 0.1797
PL/J m 0.1667 0.3443 0.8428 -0.5094
RBF/DnJ f 0.8889 0.1988 1.2792 0.4985
RBF/DnJ m 0.3333 0.1988 0.7237 -0.057
RF/J f 0.65 0.1886 1.0203 0.2797
RF/J m 0.5 0.2667 1.0237 -0.0237
RIIIS/J f 1.5 0.1886 1.8703 1.1297
RIIIS/J m 0.8333 0.1988 1.2237 0.443
SEA/GnJ f 1.75 0.2108 2.164 1.336
SEA/GnJ m 1.05 0.1886 1.4203 0.6797
SJL/J f 0.45 0.1886 0.8203 0.0797
SJL/J m 0.5556 0.1988 0.9459 0.1652
SM/J f 0.2857 0.2254 0.7283 -0.1569
SM/J m 0.6 0.2667 1.1237 0.0763
SPRET/EiJ f 0.5714 0.2254 1.014 0.1288
SPRET/EiJ m 0.2 0.2667 0.7237 -0.3237
SWR/J f 0.95 0.1886 1.3203 0.5797
SWR/J m 1.0 0.2108 1.414 0.586
WSB/EiJ f 0.625 0.2108 1.039 0.211
WSB/EiJ m 0.8333 0.2434 1.3114 0.3553


  LEAST SQUARES MEANS (MODEL-ADJUSTED), SEXES COMBINED
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ both 0.425 0.1333 0.6868 0.1632
A/J both 0.975 0.1333 1.2368 0.7132
AKR/J both 1.0278 0.1406 1.3038 0.7518
BALB/cJ both 0.35 0.1333 0.6118 0.0882
BPH/2J both 0.6028 0.137 0.8718 0.3338
BPL/1J both 0.875 0.1333 1.1368 0.6132
BPN/3J both 0.5306 0.137 0.7996 0.2615
BTBR T+ Itpr3tf/J both 0.8667 0.1963 1.2521 0.4812
C3H/HeJ both 1.0222 0.1663 1.3488 0.6956
C57BL/10J both 0.8 0.1333 1.0618 0.5382
C57BL/6J both 1.15 0.154 1.4524 0.8476
C57BLKS/J both 0.825 0.1805 1.1795 0.4705
C57BR/cdJ both 0.8917 0.137 1.1607 0.6226
C57L/J both 1.9 0.1333 2.1618 1.6382
C58/J both 1.5 0.1333 1.7618 1.2382
CAST/EiJ both 0.4167 0.1663 0.7432 0.0901
CBA/J both 1.0694 0.137 1.3385 0.8004
CE/J both 0.2917 0.1571 0.6003 -0.0169
CZECHII/EiJ both 1.1071 0.1594 1.4201 0.7942
DBA/1J both 0.5937 0.1414 0.8715 0.316
DBA/2J both 0.1389 0.137 0.4079 -0.1301
FVB/NJ both 0.8333 0.1988 1.2237 0.443
I/LnJ both 0.7222 0.1406 0.9982 0.4462
KK/HlJ both 0.3194 0.1449 0.604 0.0349
LP/J both 0.9167 0.1406 1.1927 0.6407
MOLF/EiJ both 0.6389 0.1406 0.9149 0.3629
NOD/ShiLtJ both 0.6458 0.161 0.962 0.3296
NON/ShiLtJ both 0.75 0.1406 1.026 0.474
NZB/BlNJ both 1.0556 0.1406 1.3316 0.7795
NZW/LacJ both 1.25 0.1414 1.5277 0.9723
PERA/EiJ both 0.0625 0.1826 0.4211 -0.2961
P/J both 0.7778 0.1406 1.0538 0.5018
PL/J both 0.3583 0.1963 0.7438 -0.0271
RBF/DnJ both 0.6111 0.1406 0.8871 0.3351
RF/J both 0.575 0.1633 0.8957 0.2543
RIIIS/J both 1.1667 0.137 1.4357 0.8976
SEA/GnJ both 1.4 0.1414 1.6777 1.1223
SJL/J both 0.5028 0.137 0.7718 0.2338
SM/J both 0.4429 0.1746 0.7857 0.1
SPRET/EiJ both 0.3857 0.1746 0.7286 0.0429
SWR/J both 0.975 0.1414 1.2527 0.6973
WSB/EiJ both 0.7292 0.161 1.0454 0.413




  GWAS USING LINEAR MIXED MODELS