Phenotype measure:   Paigen1   freeHCC

ID, description, units MPD:2926   freeHCC   hepatic cholesterol concentration (free 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 (free per g liver)



  MEASURE SUMMARY
Measure Summary FemaleMale
Number of strains tested43 strains42 strains
Mean of the strain means5.19   mg 5.47   mg
Median of the strain means4.90   mg 5.41   mg
SD of the strain means± 1.36 ± 1.33
Coefficient of variation (CV)0.262 0.243
Min–max range of strain means2.72   –   7.95   mg 3.49   –   9.01   mg
Mean sample size per strain6.0   mice 5.8   mice


  ANOVA, Q-Q NORMALITY ASSESSMENT
ANOVA summary      
FactorDFSum of squaresMean sum of squaresF valuep value (Pr>F)
sex 1 20.6709 20.6709 15.1252 0.0001
strain 41 739.3175 18.0321 13.1943 < 0.0001
sex:strain 41 155.4166 3.7906 2.7737 < 0.0001
Residuals 414 565.7958 1.3667


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 3.0 1.45   6 0.592 0.483 1.09, 5.27 -1.61
129S1/SvImJ m 4.64 0.771   6 0.315 0.166 3.48, 5.65 -0.63
A/J f 6.7 0.226   6 0.0925 0.0338 6.54, 7.15 1.11
A/J m 8.23 0.78   6 0.318 0.0948 6.87, 9.26 2.07
AKR/J f 4.47 1.46   6 0.596 0.327 3.16, 6.68 -0.53
AKR/J m 4.79 0.809   6 0.33 0.169 3.66, 5.78 -0.51
BALB/cJ f 2.72 0.956   9 0.319 0.351 1.73, 4.58 -1.81
BALB/cJ m 6.0 1.42   6 0.58 0.236 4.71, 8.25 0.4
BPH/2J f 4.61 1.14   5 0.508 0.246 3.13, 6.1 -0.42
BPH/2J m 3.83 0.601   6 0.245 0.157 2.9, 4.45 -1.24
BPL/1J f 6.37 1.18   6 0.483 0.186 4.72, 8.4 0.87
BPL/1J m 6.81 4.92   5 2.2 0.722 4.52, 15.6 1.01
BPN/3J f 3.55 0.604   6 0.246 0.17 2.79, 4.5 -1.2
BPN/3J m 4.84 1.09   6 0.445 0.225 3.78, 6.28 -0.48
BTBR T+ Itpr3tf/J f 4.57 0.227   3 0.131 0.0498 4.38, 4.82 -0.45
BTBR T+ Itpr3tf/J m 4.11 0.762   7 0.288 0.186 2.78, 5.21 -1.03
C3H/HeJ f 5.13 0.754   6 0.308 0.147 4.32, 6.32 -0.04
C3H/HeJ m 7.51 1.95   8 0.691 0.26 4.47, 10.2 1.53
C57BL/10J f 5.48 0.261   4 0.131 0.0477 5.18, 5.8 0.22
C57BL/10J m 4.84 0.694   7 0.262 0.144 3.73, 5.65 -0.48
C57BL/6J f 4.8 0.863   7 0.326 0.18 3.53, 5.85 -0.28
C57BL/6J m 5.99 0.943   6 0.385 0.157 4.89, 7.54 0.39
C57BLKS/J f 3.87 0.821   6 0.335 0.212 2.66, 5.24 -0.97
C57BLKS/J m 4.46 0.845   6 0.345 0.189 3.15, 5.51 -0.76
C57BR/cdJ f 4.86 0.874   7 0.33 0.18 3.79, 5.92 -0.24
C57BR/cdJ m 3.58 0.577   5 0.258 0.161 3.03, 4.51 -1.42
C57L/J f 4.33 0.724   8 0.256 0.167 3.49, 5.31 -0.63
C57L/J m 3.54 0.295   6 0.12 0.0832 3.14, 4.02 -1.45
C58/J f 4.54 2.29   6 0.935 0.504 2.32, 8.8 -0.47
C58/J m 6.07 0.927   6 0.378 0.153 4.95, 7.5 0.45
CAST/EiJ f 4.9 1.87   6 0.765 0.383 2.96, 6.94 -0.21
CAST/EiJ m 7.09 2.11   5 0.942 0.297 4.2, 9.44 1.22
CBA/J f 4.72 0.684   6 0.279 0.145 3.74, 5.67 -0.34
CBA/J m 5.58 1.36   6 0.556 0.244 3.24, 7.07 0.08
CE/J f 7.74 0.965   5 0.431 0.125 6.72, 9.25 1.88
CE/J m 8.08 0.663   6 0.271 0.0821 7.38, 8.88 1.96
CZECHII/EiJ f 7.04 0.626   5 0.28 0.089 6.44, 7.93 1.36
CZECHII/EiJ m 6.09 0.569   6 0.232 0.0933 5.62, 6.93 0.46
DBA/1J f 4.3 0.616   7 0.233 0.143 3.29, 5.03 -0.65
DBA/1J m 5.43 1.35   6 0.549 0.248 3.98, 7.67 -0.03
DBA/2J f 4.01 0.494   6 0.202 0.123 3.31, 4.53 -0.86
DBA/2J m 3.49 0.621   6 0.254 0.178 2.75, 4.05 -1.49
FVB/NJ f 3.09 1.22   5 0.547 0.396 2.06, 4.88 -1.54
FVB/NJ m 5.74 1.59   3 0.92 0.277 4.54, 7.55 0.2
I/LnJ f 4.92 0.85   6 0.347 0.173 3.67, 5.94 -0.2
I/LnJ m 4.69 0.765   6 0.312 0.163 3.2, 5.25 -0.59
KK/HlJ f 5.06 0.94   6 0.384 0.186 3.81, 6.6 -0.09
KK/HlJ m 5.78 1.44   6 0.587 0.249 5.03, 8.71 0.23
LP/J f 2.97 0.722   7 0.273 0.243 1.67, 3.85 -1.63
LP/J m 3.66 0.665   6 0.272 0.182 2.7, 4.57 -1.36
MOLF/EiJ f 7.54 1.47   6 0.599 0.195 5.38, 9.36 1.73
MOLF/EiJ m 9.01 1.75   7 0.662 0.194 6.99, 12.5 2.66
NOD/ShiLtJ f 6.09 1.33   6 0.544 0.219 4.23, 7.59 0.66
NOD/ShiLtJ m 5.39 0.406   6 0.166 0.0753 4.97, 6.03 -0.06
NON/ShiLtJ f 6.06 1.55   6 0.632 0.255 4.27, 8.59 0.64
NON/ShiLtJ m 5.63 0.641   5 0.287 0.114 4.81, 6.56 0.12
NZB/BlNJ f 6.9 2.03   6 0.83 0.295 4.04, 8.89 1.26
NZB/BlNJ m 6.02 1.02   5 0.456 0.17 4.29, 6.74 0.41
NZW/LacJ f 4.44 0.587   6 0.24 0.132 3.78, 5.24 -0.55
NZW/LacJ m 4.76 0.538   6 0.22 0.113 4.0, 5.37 -0.54
PERA/EiJ f 7.9 0.952   5 0.426 0.121 6.36, 8.59 1.99
PERA/EiJ m 6.1 1.2   4 0.602 0.197 4.35, 7.1 0.47
P/J f 4.93 0.984   6 0.402 0.2 3.23, 6.02 -0.19
P/J m 4.25 0.773   6 0.316 0.182 3.19, 5.18 -0.92
PL/J f 4.29 0.968   6 0.395 0.225 2.41, 5.18 -0.66
PL/J m 4.55 0.241   3 0.139 0.053 4.3, 4.78 -0.69
RBF/DnJ f 5.17 0.836   8 0.295 0.161 4.12, 6.6 -0.01
RBF/DnJ m 5.92 1.59   5 0.713 0.269 4.2, 8.4 0.34
RF/J f 6.32 0.837   6 0.342 0.133 5.3, 7.2 0.83
RF/J m 5.67 1.08   6 0.442 0.191 4.11, 6.89 0.15
RIIIS/J f 5.71 1.26   8 0.445 0.221 3.29, 6.87 0.38
RIIIS/J m 5.03 1.24   7 0.47 0.247 3.06, 6.49 -0.33
SEA/GnJ f 6.47 1.27   6 0.52 0.197 4.48, 8.27 0.94
SEA/GnJ m 5.65 0.711   7 0.269 0.126 4.96, 7.04 0.13
SJL/J f 4.54 0.69   6 0.282 0.152 3.29, 5.17 -0.47
SJL/J m 4.01 0.262   6 0.107 0.0653 3.56, 4.32 -1.1
SM/J f 5.14 1.03   6 0.42 0.2 4.07, 6.97 -0.03
SM/J m 5.3 0.724   6 0.296 0.137 4.64, 6.26 -0.13
SPRET/EiJ f 4.67 0.325   6 0.133 0.0697 4.31, 5.14 -0.38
SPRET/EiJ m 4.98 0.753   4 0.376 0.151 4.35, 5.97 -0.37
SWR/J f 4.22 0.678   6 0.277 0.161 3.42, 5.28 -0.71
SWR/J m 4.84 1.06   6 0.434 0.219 3.49, 6.39 -0.48
WSB/EiJ f 7.95 1.41   6 0.578 0.178 5.79, 10.2 2.03
WSB/EiJ m 7.92 1.45   6 0.591 0.183 5.69, 9.35 1.84
YBR/EiJ f 6.91 2.12   5 0.948 0.307 4.89, 10.4 1.27


  LEAST SQUARES MEANS (MODEL-ADJUSTED)
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ f 3.005 0.4773 3.9432 2.0668
129S1/SvImJ m 4.6383 0.4773 5.5765 3.7002
A/J f 6.6983 0.4773 7.6365 5.7602
A/J m 8.2267 0.4773 9.1648 7.2885
AKR/J f 4.4717 0.4773 5.4098 3.5335
AKR/J m 4.7917 0.4773 5.7298 3.8535
BALB/cJ f 2.7211 0.3897 3.4871 1.9551
BALB/cJ m 6.005 0.4773 6.9432 5.0668
BPH/2J f 4.612 0.5228 5.6397 3.5843
BPH/2J m 3.8333 0.4773 4.7715 2.8952
BPL/1J f 6.365 0.4773 7.3032 5.4268
BPL/1J m 6.806 0.5228 7.8337 5.7783
BPN/3J f 3.55 0.4773 4.4882 2.6118
BPN/3J m 4.84 0.4773 5.7782 3.9018
BTBR T+ Itpr3tf/J f 4.5667 0.6749 5.8934 3.2399
BTBR T+ Itpr3tf/J m 4.1057 0.4419 4.9743 3.2372
C3H/HeJ f 5.1333 0.4773 6.0715 4.1952
C3H/HeJ m 7.5125 0.4133 8.325 6.7
C57BL/10J f 5.485 0.5845 6.634 4.336
C57BL/10J m 4.8371 0.4419 5.7057 3.9686
C57BL/6J f 4.7986 0.4419 5.6671 3.93
C57BL/6J m 5.9917 0.4773 6.9298 5.0535
C57BLKS/J f 3.8667 0.4773 4.8048 2.9285
C57BLKS/J m 4.4583 0.4773 5.3965 3.5202
C57BR/cdJ f 4.86 0.4419 5.7286 3.9914
C57BR/cdJ m 3.582 0.5228 4.6097 2.5543
C57L/J f 4.3262 0.4133 5.1387 3.5138
C57L/J m 3.5383 0.4773 4.4765 2.6002
C58/J f 4.545 0.4773 5.4832 3.6068
C58/J m 6.0667 0.4773 7.0048 5.1285
CAST/EiJ f 4.895 0.4773 5.8332 3.9568
CAST/EiJ m 7.094 0.5228 8.1217 6.0663
CBA/J f 4.7167 0.4773 5.6548 3.7785
CBA/J m 5.5817 0.4773 6.5198 4.6435
CE/J f 7.744 0.5228 8.7717 6.7163
CE/J m 8.0833 0.4773 9.0215 7.1452
CZECHII/EiJ f 7.036 0.5228 8.0637 6.0083
CZECHII/EiJ m 6.095 0.4773 7.0332 5.1568
DBA/1J f 4.3 0.4419 5.1686 3.4314
DBA/1J m 5.4283 0.4773 6.3665 4.4902
DBA/2J f 4.0133 0.4773 4.9515 3.0752
DBA/2J m 3.4933 0.4773 4.4315 2.5552
FVB/NJ f 3.09 0.5228 4.1177 2.0623
FVB/NJ m 5.7433 0.6749 7.0701 4.4166
I/LnJ f 4.9167 0.4773 5.8548 3.9785
I/LnJ m 4.69 0.4773 5.6282 3.7518
KK/HlJ f 5.0567 0.4773 5.9948 4.1185
KK/HlJ m 5.7833 0.4773 6.7215 4.8452
LP/J f 2.9671 0.4419 3.8357 2.0986
LP/J m 3.6583 0.4773 4.5965 2.7202
MOLF/EiJ f 7.5367 0.4773 8.4748 6.5985
MOLF/EiJ m 9.0129 0.4419 9.8814 8.1443
NOD/ShiLtJ f 6.0933 0.4773 7.0315 5.1552
NOD/ShiLtJ m 5.39 0.4773 6.3282 4.4518
NON/ShiLtJ f 6.06 0.4773 6.9982 5.1218
NON/ShiLtJ m 5.628 0.5228 6.6557 4.6003
NZB/BlNJ f 6.9033 0.4773 7.8415 5.9652
NZB/BlNJ m 6.018 0.5228 7.0457 4.9903
NZW/LacJ f 4.445 0.4773 5.3832 3.5068
NZW/LacJ m 4.7567 0.4773 5.6948 3.8185
PERA/EiJ f 7.898 0.5228 8.9257 6.8703
PERA/EiJ m 6.1 0.5845 7.249 4.951
P/J f 4.9317 0.4773 5.8698 3.9935
P/J m 4.245 0.4773 5.1832 3.3068
PL/J f 4.295 0.4773 5.2332 3.3568
PL/J m 4.5533 0.6749 5.8801 3.2266
RBF/DnJ f 5.1738 0.4133 5.9862 4.3613
RBF/DnJ m 5.918 0.5228 6.9457 4.8903
RF/J f 6.3167 0.4773 7.2548 5.3785
RF/J m 5.6667 0.4773 6.6048 4.7285
RIIIS/J f 5.7087 0.4133 6.5212 4.8963
RIIIS/J m 5.0271 0.4419 5.8957 4.1586
SEA/GnJ f 6.4717 0.4773 7.4098 5.5335
SEA/GnJ m 5.6514 0.4419 6.52 4.7829
SJL/J f 4.54 0.4773 5.4782 3.6018
SJL/J m 4.0083 0.4773 4.9465 3.0702
SM/J f 5.1417 0.4773 6.0798 4.2035
SM/J m 5.3 0.4773 6.2382 4.3618
SPRET/EiJ f 4.665 0.4773 5.6032 3.7268
SPRET/EiJ m 4.98 0.5845 6.129 3.831
SWR/J f 4.2167 0.4773 5.1548 3.2785
SWR/J m 4.845 0.4773 5.7832 3.9068
WSB/EiJ f 7.9483 0.4773 8.8865 7.0102
WSB/EiJ m 7.9183 0.4773 8.8565 6.9802


  LEAST SQUARES MEANS (MODEL-ADJUSTED), SEXES COMBINED
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ both 3.8217 0.3375 4.485 3.1583
A/J both 7.4625 0.3375 8.1259 6.7991
AKR/J both 4.6317 0.3375 5.295 3.9683
BALB/cJ both 4.3631 0.3081 4.9686 3.7575
BPH/2J both 4.2227 0.3539 4.9184 3.5269
BPL/1J both 6.5855 0.3539 7.2813 5.8897
BPN/3J both 4.195 0.3375 4.8584 3.5316
BTBR T+ Itpr3tf/J both 4.3362 0.4034 5.1291 3.5433
C3H/HeJ both 6.3229 0.3157 6.9434 5.7024
C57BL/10J both 5.1611 0.3664 5.8812 4.4409
C57BL/6J both 5.3951 0.3252 6.0344 4.7559
C57BLKS/J both 4.1625 0.3375 4.8259 3.4991
C57BR/cdJ both 4.221 0.3423 4.8938 3.5482
C57L/J both 3.9323 0.3157 4.5528 3.3118
C58/J both 5.3058 0.3375 5.9692 4.6425
CAST/EiJ both 5.9945 0.3539 6.6903 5.2987
CBA/J both 5.1492 0.3375 5.8125 4.4858
CE/J both 7.9137 0.3539 8.6094 7.2179
CZECHII/EiJ both 6.5655 0.3539 7.2613 5.8697
DBA/1J both 4.8642 0.3252 5.5034 4.2249
DBA/2J both 3.7533 0.3375 4.4167 3.09
FVB/NJ both 4.4167 0.4269 5.2558 3.5776
I/LnJ both 4.8033 0.3375 5.4667 4.14
KK/HlJ both 5.42 0.3375 6.0834 4.7566
LP/J both 3.3127 0.3252 3.952 2.6735
MOLF/EiJ both 8.2748 0.3252 8.914 7.6355
NOD/ShiLtJ both 5.7417 0.3375 6.405 5.0783
NON/ShiLtJ both 5.844 0.3539 6.5398 5.1482
NZB/BlNJ both 6.4607 0.3539 7.1564 5.7649
NZW/LacJ both 4.6008 0.3375 5.2642 3.9375
PERA/EiJ both 6.999 0.3921 7.7698 6.2282
P/J both 4.5883 0.3375 5.2517 3.925
PL/J both 4.4242 0.4133 5.2366 3.6117
RBF/DnJ both 5.5459 0.3332 6.2009 4.8908
RF/J both 5.9917 0.3375 6.655 5.3283
RIIIS/J both 5.3679 0.3025 5.9626 4.7733
SEA/GnJ both 6.0615 0.3252 6.7008 5.4223
SJL/J both 4.2742 0.3375 4.9375 3.6108
SM/J both 5.2208 0.3375 5.8842 4.5575
SPRET/EiJ both 4.8225 0.3773 5.5642 4.0808
SWR/J both 4.5308 0.3375 5.1942 3.8675
WSB/EiJ both 7.9333 0.3375 8.5967 7.27




  GWAS USING LINEAR MIXED MODELS