Project measure / variable:   Paigen2   HDLC_chg

ID, description, units MPD:9910   HDLC_chg   HDL cholesterol (plasma)   [mg/dL]  fold change  
high-fat diet study
Data set, strains Paigen2   inbred w/CC7   41 strains     sex: both     age: 7-9wks
Procedure lipid profile
Ontology mappings

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  STRAIN COMPARISON PLOT
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Paigen2 - HDL cholesterol (plasma) fold change



  MEASURE SUMMARY
Measure Summary FemaleMale
Number of strains tested40 strains35 strains
Mean of the strain means1.50   mg/dL 1.30   mg/dL
Median of the strain means1.33   mg/dL 1.18   mg/dL
SD of the strain means± 0.616 ± 0.436
Coefficient of variation (CV)0.411 0.336
Min–max range of strain means0.830   –   3.67   mg/dL 0.187   –   2.63   mg/dL
Mean sample size per strain8.6   mice 8.4   mice


  ANOVA, Q-Q NORMALITY ASSESSMENT
ANOVA summary      
FactorDFSum of squaresMean sum of squaresF valuep value (Pr>F)
sex 1 5.7174 5.7174 12.7724 0.0004
strain 33 129.8155 3.9338 8.7879 < 0.0001
sex:strain 33 43.0114 1.3034 2.9117 < 0.0001
Residuals 511 228.7433 0.4476


Q-Q normality assessment based on residuals

  


  STRAIN MEANS (UNADJUSTED)
  
Select table page:
Strain Sex Mean SD N mice SEM CV Min, Max Z score
129S1/SvImJ f 1.82 0.318   10 0.101 0.175 1.42, 2.25 0.52
129S1/SvImJ m 1.53 0.119   9 0.0395 0.0775 1.35, 1.68 0.53
A/J f 2.1 1.06   10 0.334 0.502 0.238, 3.17 0.98
A/J m 1.52 0.742   9 0.247 0.49 0.1, 2.48 0.5
AKR/J f 2.07 0.748   12 0.216 0.361 0.262, 2.93 0.93
BALB/cByJ f 1.45 0.368   11 0.111 0.253 0.949, 2.02 -0.08
BALB/cByJ m 1.17 0.345   8 0.122 0.294 0.826, 1.72 -0.3
BTBR T+ Itpr3tf/J f 0.941 0.306   8 0.108 0.325 0.338, 1.34 -0.9
BTBR T+ Itpr3tf/J m 0.8 0.238   7 0.0901 0.298 0.532, 1.12 -1.15
BUB/BnJ f 1.14 0.572   10 0.181 0.5 0.412, 2.24 -0.58
BUB/BnJ m 1.02 0.154   5 0.069 0.152 0.861, 1.18 -0.64
C3H/HeJ f 0.886 0.113   10 0.0356 0.127 0.756, 1.12 -0.99
C3H/HeJ m 1.06 0.223   8 0.0787 0.21 0.663, 1.38 -0.55
C57BL/10J f 1.17 0.287   9 0.0957 0.245 0.776, 1.61 -0.53
C57BL/10J m 1.11 0.402   10 0.127 0.362 0.569, 2.0 -0.44
C57BL/6J f 0.952 0.128   10 0.0405 0.135 0.723, 1.15 -0.89
C57BL/6J m 0.769 0.191   10 0.0603 0.248 0.455, 1.09 -1.22
C57BLKS/J f 1.75 0.69   9 0.23 0.395 0.8, 2.61 0.41
C57BR/cdJ f 0.887 0.205   10 0.0647 0.231 0.631, 1.16 -0.99
C57BR/cdJ m 2.07 2.34   10 0.741 1.13 0.766, 8.62 1.76
C57L/J f 1.42 0.402   10 0.127 0.282 0.964, 2.14 -0.13
C57L/J m 1.17 0.246   10 0.0778 0.211 0.852, 1.48 -0.3
C58/J f 1.7 0.377   5 0.168 0.222 1.27, 2.13 0.33
C58/J m 1.66 1.28   7 0.484 0.77 0.503, 4.24 0.82
CAST/EiJ f 1.12 0.353   9 0.118 0.316 0.8, 1.85 -0.61
CAST/EiJ m 1.55 0.341   8 0.121 0.22 1.22, 2.19 0.57
CBA/J f 0.83 0.505   8 0.179 0.609 0.291, 1.82 -1.08
CBA/J m 1.11 0.126   8 0.0446 0.114 0.952, 1.27 -0.44
CZECHII/EiJ f 1.1 0.171   11 0.0517 0.156 0.836, 1.45 -0.65
CZECHII/EiJ m 1.01 0.234   9 0.0781 0.232 0.643, 1.38 -0.66
DBA/1J f 1.07 0.335   7 0.127 0.313 0.508, 1.44 -0.69
DBA/1J m 1.68 0.875   8 0.309 0.521 0.533, 2.76 0.87
DBA/2J f 1.5 0.389   9 0.13 0.259 1.04, 2.3 0.0
DBA/2J m 1.04 0.13   9 0.0432 0.124 1.0, 1.39 -0.6
FVB/NJ f 1.1 0.337   8 0.119 0.306 0.579, 1.71 -0.65
FVB/NJ m 0.681 0.142   5 0.0636 0.209 0.473, 0.852 -1.42
I/LnJ f 0.937 0.376   5 0.168 0.402 0.538, 1.55 -0.91
JF1/MsJ f 1.64 0.378   10 0.12 0.23 1.07, 2.15 0.23
JF1/MsJ m 1.32 0.445   7 0.168 0.338 0.544, 1.96 0.05
KK/HlJ f 1.11 0.249   5 0.111 0.224 0.926, 1.44 -0.63
LP/J f 3.67 2.77   10 0.877 0.755 1.0, 9.04 3.53
LP/J m 1.59 0.397   10 0.125 0.25 1.0, 2.27 0.66
MA/MyJ f 1.83 0.441   10 0.139 0.241 1.18, 2.57 0.54
MA/MyJ m 1.4 0.29   10 0.0918 0.208 0.895, 1.95 0.23
MOLF/EiJ f 1.2 0.494   7 0.187 0.413 0.333, 1.94 -0.48
MOLF/EiJ m 0.187 0.0689   9 0.023 0.368 0.114, 0.316 -2.55
MSM/MsJ f 1.38 0.427   5 0.191 0.309 0.947, 2.04 -0.19
MSM/MsJ m 1.18 0.231   11 0.0697 0.195 0.861, 1.54 -0.28
NOD/ShiLtJ f 2.55 0.425   6 0.173 0.167 1.95, 3.14 1.71
NOD/ShiLtJ m 1.73 0.945   4 0.473 0.545 1.01, 3.12 0.98
NON/ShiLtJ f 1.29 0.445   10 0.141 0.344 0.848, 2.1 -0.34
NON/ShiLtJ m 1.16 0.73   12 0.211 0.632 0.43, 3.35 -0.32
NZB/BlNJ f 1.66 0.333   11 0.1 0.2 1.08, 2.12 0.26
NZB/BlNJ m 1.16 0.265   9 0.0882 0.228 0.776, 1.58 -0.32
NZW/LacJ f 1.09 0.21   9 0.07 0.192 0.814, 1.53 -0.66
NZW/LacJ m 1.37 0.278   8 0.0984 0.202 1.05, 1.95 0.16
PERA/EiJ f 3.24 1.49   9 0.498 0.461 1.39, 5.61 2.83
PERA/EiJ m 2.63 0.652   8 0.23 0.247 1.65, 3.72 3.05
PL/J f 2.07 0.832   10 0.263 0.403 1.02, 3.81 0.93
PWK/PhJ m 1.89 0.368   8 0.13 0.195 1.27, 2.34 1.35
RF/J f 1.55 0.403   7 0.152 0.259 1.0, 2.02 0.09
RIIIS/J f 2.19 0.514   6 0.21 0.235 1.35, 2.73 1.12
RIIIS/J m 1.75 0.401   8 0.142 0.229 1.0, 2.39 1.03
SEA/GnJ f 0.951 0.233   9 0.0778 0.245 0.658, 1.41 -0.89
SEA/GnJ m 1.26 0.144   7 0.0545 0.114 1.06, 1.53 -0.09
SJL/J f 1.53 0.333   9 0.111 0.218 1.0, 2.04 0.05
SJL/J m 1.43 0.379   12 0.11 0.265 0.912, 2.1 0.3
SM/J f 1.29 0.267   8 0.0944 0.207 0.881, 1.65 -0.34
SM/J m 1.04 0.445   9 0.148 0.429 0.508, 1.7 -0.6
SPRET/EiJ f 1.22 1.02   4 0.511 0.837 0.211, 2.48 -0.45
SPRET/EiJ m 1.04 0.536   5 0.24 0.515 0.423, 1.45 -0.6
SWR/J f 1.07 0.516   8 0.182 0.481 0.766, 2.33 -0.69
SWR/J m 1.4 0.394   7 0.149 0.282 0.958, 2.1 0.23
WSB/EiJ f 1.42 0.417   8 0.147 0.293 0.921, 1.96 -0.13
WSB/EiJ m 1.02 0.187   9 0.0624 0.183 0.83, 1.38 -0.64


  LEAST SQUARES MEANS (MODEL-ADJUSTED)
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ f 1.8181 0.2116 2.2337 1.4024
129S1/SvImJ m 1.5304 0.223 1.9685 1.0922
A/J f 2.1044 0.2116 2.52 1.6887
A/J m 1.5151 0.223 1.9533 1.077
BALB/cByJ f 1.4511 0.2017 1.8474 1.0548
BALB/cByJ m 1.1728 0.2365 1.6375 0.708
BTBR T+ Itpr3tf/J f 0.9405 0.2365 1.4052 0.4758
BTBR T+ Itpr3tf/J m 0.8005 0.2529 1.2973 0.3037
BUB/BnJ f 1.1435 0.2116 1.5592 0.7279
BUB/BnJ m 1.0165 0.2992 1.6044 0.4287
C3H/HeJ f 0.8862 0.2116 1.3018 0.4705
C3H/HeJ m 1.0584 0.2365 1.5232 0.5937
C57BL/10J f 1.173 0.223 1.6112 0.7349
C57BL/10J m 1.1104 0.2116 1.5261 0.6948
C57BL/6J f 0.9518 0.2116 1.3674 0.5361
C57BL/6J m 0.7691 0.2116 1.1848 0.3534
C57BR/cdJ f 0.8874 0.2116 1.3031 0.4718
C57BR/cdJ m 2.0746 0.2116 2.4903 1.6589
C57L/J f 1.4245 0.2116 1.8402 1.0088
C57L/J m 1.1676 0.2116 1.5833 0.752
C58/J f 1.6999 0.2992 2.2877 1.112
C58/J m 1.6622 0.2529 2.159 1.1654
CAST/EiJ f 1.1169 0.223 1.5551 0.6788
CAST/EiJ m 1.5523 0.2365 2.017 1.0875
CBA/J f 0.8299 0.2365 1.2946 0.3652
CBA/J m 1.1067 0.2365 1.5714 0.642
CZECHII/EiJ f 1.0956 0.2017 1.4919 0.6993
CZECHII/EiJ m 1.0085 0.223 1.4467 0.5704
DBA/1J f 1.0684 0.2529 1.5652 0.5716
DBA/1J m 1.6785 0.2365 2.1432 1.2138
DBA/2J f 1.4979 0.223 1.9361 1.0598
DBA/2J m 1.0432 0.223 1.4814 0.6051
FVB/NJ f 1.0994 0.2365 1.5641 0.6347
FVB/NJ m 0.6808 0.2992 1.2686 0.0929
JF1/MsJ f 1.64 0.2116 2.0556 1.2243
JF1/MsJ m 1.3162 0.2529 1.813 0.8194
LP/J f 3.6731 0.2116 4.0888 3.2574
LP/J m 1.5893 0.2116 2.005 1.1737
MA/MyJ f 1.8267 0.2116 2.2424 1.4111
MA/MyJ m 1.3981 0.2116 1.8137 0.9824
MOLF/EiJ f 1.1956 0.2529 1.6924 0.6988
MOLF/EiJ m 0.187 0.223 0.6252 0.0
MSM/MsJ f 1.3839 0.2992 1.9717 0.796
MSM/MsJ m 1.1848 0.2017 1.5811 0.7885
NOD/ShiLtJ f 2.5472 0.2731 3.0838 2.0106
NOD/ShiLtJ m 1.7349 0.3345 2.3921 1.0776
NON/ShiLtJ f 1.2949 0.2116 1.7106 0.8793
NON/ShiLtJ m 1.1557 0.1931 1.5352 0.7763
NZB/BlNJ f 1.6624 0.2017 2.0587 1.2661
NZB/BlNJ m 1.1584 0.223 1.5966 0.7203
NZW/LacJ f 1.0935 0.223 1.5317 0.6554
NZW/LacJ m 1.3748 0.2365 1.8396 0.9101
PERA/EiJ f 3.2432 0.223 3.6813 2.805
PERA/EiJ m 2.6337 0.2365 3.0985 2.169
RIIIS/J f 2.19 0.2731 2.7267 1.6534
RIIIS/J m 1.7521 0.2365 2.2169 1.2874
SEA/GnJ f 0.9514 0.223 1.3896 0.5133
SEA/GnJ m 1.2607 0.2529 1.7575 0.7639
SJL/J f 1.5254 0.223 1.9636 1.0873
SJL/J m 1.4316 0.1931 1.8111 1.0522
SM/J f 1.2923 0.2365 1.757 0.8275
SM/J m 1.036 0.223 1.4742 0.5979
SPRET/EiJ f 1.2202 0.3345 1.8774 0.563
SPRET/EiJ m 1.0421 0.2992 1.6299 0.4543
SWR/J f 1.0716 0.2365 1.5363 0.6068
SWR/J m 1.3994 0.2529 1.8962 0.9026
WSB/EiJ f 1.4236 0.2365 1.8883 0.9589
WSB/EiJ m 1.0248 0.223 1.4629 0.5867


  LEAST SQUARES MEANS (MODEL-ADJUSTED), SEXES COMBINED
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ both 1.6742 0.1537 1.9762 1.3723
A/J both 1.8097 0.1537 2.1117 1.5078
BALB/cByJ both 1.3119 0.1554 1.6173 1.0065
BTBR T+ Itpr3tf/J both 0.8705 0.1731 1.2106 0.5303
BUB/BnJ both 1.08 0.1832 1.44 0.7201
C3H/HeJ both 0.9723 0.1587 1.2841 0.6606
C57BL/10J both 1.1417 0.1537 1.4437 0.8397
C57BL/6J both 0.8604 0.1496 1.1544 0.5665
C57BR/cdJ both 1.481 0.1496 1.7749 1.1871
C57L/J both 1.2961 0.1496 1.59 1.0022
C58/J both 1.681 0.1959 2.0658 1.2962
CAST/EiJ both 1.3346 0.1626 1.6539 1.0152
CBA/J both 0.9683 0.1673 1.2969 0.6397
CZECHII/EiJ both 1.0521 0.1504 1.3475 0.7567
DBA/1J both 1.3735 0.1731 1.7136 1.0333
DBA/2J both 1.2706 0.1577 1.5804 0.9608
FVB/NJ both 0.8901 0.1907 1.2648 0.5154
JF1/MsJ both 1.4781 0.1649 1.802 1.1542
LP/J both 2.6312 0.1496 2.9251 2.3373
MA/MyJ both 1.6124 0.1496 1.9063 1.3185
MOLF/EiJ both 0.6913 0.1686 1.0225 0.3601
MSM/MsJ both 1.2843 0.1804 1.6388 0.9298
NOD/ShiLtJ both 2.141 0.2159 2.5653 1.7168
NON/ShiLtJ both 1.2253 0.1432 1.5067 0.9439
NZB/BlNJ both 1.4104 0.1504 1.7058 1.115
NZW/LacJ both 1.2342 0.1626 1.5535 0.9148
PERA/EiJ both 2.9385 0.1626 3.2578 2.6191
RIIIS/J both 1.9711 0.1807 2.326 1.6161
SEA/GnJ both 1.1061 0.1686 1.4373 0.7748
SJL/J both 1.4785 0.1475 1.7683 1.1887
SM/J both 1.1641 0.1626 1.4835 0.8448
SPRET/EiJ both 1.1312 0.2244 1.572 0.6903
SWR/J both 1.2355 0.1731 1.5756 0.8953
WSB/EiJ both 1.2242 0.1626 1.5436 0.9049




  GWAS USING LINEAR MIXED MODELS