Phenotype measure:   Paigen1   inflammation

ID, description, units MPD:2932   inflammation   liver inflammation (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 - liver inflammation (score: 0-4)



  MEASURE SUMMARY
Measure Summary FemaleMale
Number of strains tested43 strains40 strains
Mean of the strain means0.608   score 0.787   score
Median of the strain means0.333   score 0.333   score
SD of the strain means± 0.764 ± 1.03
Coefficient of variation (CV)1.26 1.30
Min–max range of strain means0   –   2.67   score 0   –   4.00   score
Mean sample size per strain3.0   mice 2.9   mice


  ANOVA, Q-Q NORMALITY ASSESSMENT
ANOVA summary      
FactorDFSum of squaresMean sum of squaresF valuep value (Pr>F)
sex 1 2.6356 2.6356 11.8047 0.0008
strain 39 170.6773 4.3763 19.6011 < 0.0001
sex:strain 39 21.4967 0.5512 2.4687 < 0.0001
Residuals 159 35.5 0.2233


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 0.0 0.0   3 0.0 0.0 -0.8
129S1/SvImJ m 0.333 0.577   3 0.333 1.73 -0.44
A/J f 2.33 0.577   3 0.333 0.247 2.0, 3.0 2.25
A/J m 3.0 0.0   3 0.0 0.0 3.0, 3.0 2.15
AKR/J f 0.333 0.577   3 0.333 1.73 -0.36
AKR/J m 0.333 0.577   3 0.333 1.73 -0.44
BALB/cJ f 0.667 0.577   3 0.333 0.866 0.08
BALB/cJ m 0.0 0.0   3 0.0 0.0 -0.77
BPH/2J f 0.333 0.577   3 0.333 1.73 -0.36
BPH/2J m 0.667 0.577   3 0.333 0.866 -0.12
BPL/1J f 0.0 0.0   3 0.0 0.0 -0.8
BPL/1J m 0.0 0.0   3 0.0 0.0 -0.77
BPN/3J f 0.0 0.0   3 0.0 0.0 -0.8
BPN/3J m 0.0 0.0   3 0.0 0.0 -0.77
BTBR T+ Itpr3tf/J f 0.667 0.577   3 0.333 0.866 0.08
BTBR T+ Itpr3tf/J m 0.0 0.0   3 0.0 0.0 -0.77
C3H/HeJ f 0.0 0.0   3 0.0 0.0 -0.8
C3H/HeJ m 0.0 0.0   3 0.0 0.0 -0.77
C57BL/10J f 0.0 0.0   3 0.0 0.0 -0.8
C57BL/10J m 1.33 0.577   3 0.333 0.433 1.0, 2.0 0.53
C57BL/6J f 1.0 0.0   3 0.0 0.0 1.0, 1.0 0.51
C57BL/6J m 1.33 1.53   3 0.882 1.15 0.53
C57BLKS/J f 2.0 0.0   3 0.0 0.0 2.0, 2.0 1.82
C57BLKS/J m 1.67 1.15   3 0.667 0.693 1.0, 3.0 0.86
C57BR/cdJ f 0.0 0.0   3 0.0 0.0 -0.8
C57BR/cdJ m 1.33 0.577   3 0.333 0.433 1.0, 2.0 0.53
C57L/J f 0.0 0.0   3 0.0 0.0 -0.8
C57L/J m 0.0 0.0   3 0.0 0.0 -0.77
C58/J f 2.0 0.0   3 0.0 0.0 2.0, 2.0 1.82
C58/J m 4.0 0.0   3 0.0 0.0 4.0, 4.0 3.13
CAST/EiJ f 0.0 0.0   5 0.0 0.0 -0.8
CAST/EiJ m 0.667 0.577   3 0.333 0.866 -0.12
CBA/J f 0.0 0.0   3 0.0 0.0 -0.8
CBA/J m 0.0 0.0   3 0.0 0.0 -0.77
CE/J f 1.0 0.0   3 0.0 0.0 1.0, 1.0 0.51
CE/J m 1.67 0.577   3 0.333 0.346 1.0, 2.0 0.86
CZECHII/EiJ f 0.0 0.0   3 0.0 0.0 -0.8
CZECHII/EiJ m 0.0 0.0   2   0.0 0.0 -0.77
DBA/1J f 0.333 0.577   3 0.333 1.73 -0.36
DBA/1J m 0.333 0.577   3 0.333 1.73 -0.44
DBA/2J f 0.0 0.0   3 0.0 0.0 -0.8
DBA/2J m 0.0 0.0   3 0.0 0.0 -0.77
FVB/NJ f 1.5 0.707   2   0.5 0.471 1.0, 2.0 1.17
FVB/NJ m 0.0 0.0   2   0.0 0.0 -0.77
I/LnJ f 0.0 0.0   3 0.0 0.0 -0.8
KK/HlJ f 1.0 0.0   3 0.0 0.0 1.0, 1.0 0.51
KK/HlJ m 0.5 0.577   4 0.289 1.15 -0.28
LP/J f 0.0 0.0   3 0.0 0.0 -0.8
LP/J m 0.0 0.0   3 0.0 0.0 -0.77
MOLF/EiJ f 0.333 0.577   3 0.333 1.73 -0.36
NOD/ShiLtJ f 0.333 0.577   3 0.333 1.73 -0.36
NOD/ShiLtJ m 0.667 0.577   3 0.333 0.866 -0.12
NON/ShiLtJ f 1.33 0.577   3 0.333 0.433 1.0, 2.0 0.94
NON/ShiLtJ m 2.33 0.577   3 0.333 0.247 2.0, 3.0 1.5
NZB/BlNJ f 2.33 0.577   3 0.333 0.247 2.0, 3.0 2.25
NZB/BlNJ m 3.0 0.0   3 0.0 0.0 3.0, 3.0 2.15
NZW/LacJ f 0.0 0.0   3 0.0 0.0 -0.8
NZW/LacJ m 0.333 0.577   3 0.333 1.73 -0.44
PERA/EiJ f 0.0 0.0   3 0.0 0.0 -0.8
PERA/EiJ m 0.0 0.0   2   0.0 0.0 -0.77
P/J f 0.0 0.0   3 0.0 0.0 -0.8
P/J m 0.0 0.0   3 0.0 0.0 -0.77
PL/J f 1.0 0.0   3 0.0 0.0 1.0, 1.0 0.51
PL/J m 0.667 0.577   3 0.333 0.866 -0.12
RBF/DnJ f 0.333 0.577   3 0.333 1.73 -0.36
RBF/DnJ m 0.0 0.0   3 0.0 0.0 -0.77
RF/J f 0.333 0.577   3 0.333 1.73 -0.36
RF/J m 0.333 0.577   3 0.333 1.73 -0.44
RIIIS/J f 1.33 0.577   3 0.333 0.433 1.0, 2.0 0.94
RIIIS/J m 1.0 0.0   3 0.0 0.0 1.0, 1.0 0.21
SEA/GnJ f 0.333 0.577   3 0.333 1.73 -0.36
SEA/GnJ m 0.0 0.0   3 0.0 0.0 -0.77
SJL/J f 0.0 0.0   3 0.0 0.0 -0.8
SJL/J m 0.667 1.15   3 0.667 1.73 -0.12
SM/J f 1.0 1.0   3 0.577 1.0 0.51
SM/J m 2.0 1.0   3 0.577 0.5 1.0, 3.0 1.18
SPRET/EiJ f 0.0 0.0   3 0.0 0.0 -0.8
SPRET/EiJ m 0.0 0.0   3 0.0 0.0 -0.77
SWR/J f 2.67 0.577   3 0.333 0.217 2.0, 3.0 2.7
SWR/J m 2.67 0.577   3 0.333 0.217 2.0, 3.0 1.83
WSB/EiJ f 0.333 0.577   3 0.333 1.73 -0.36
WSB/EiJ m 0.667 0.577   3 0.333 0.866 -0.12
YBR/EiJ f 1.33 1.53   3 0.882 1.15 0.94


  LEAST SQUARES MEANS (MODEL-ADJUSTED)
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ f 0.0 0.2728 0.5388 -0.5388
129S1/SvImJ m 0.3333 0.2728 0.8721 -0.2055
A/J f 2.3333 0.2728 2.8721 1.7945
A/J m 3.0 0.2728 3.5388 2.4612
AKR/J f 0.3333 0.2728 0.8721 -0.2055
AKR/J m 0.3333 0.2728 0.8721 -0.2055
BALB/cJ f 0.6667 0.2728 1.2055 0.1279
BALB/cJ m 0.0 0.2728 0.5388 -0.5388
BPH/2J f 0.3333 0.2728 0.8721 -0.2055
BPH/2J m 0.6667 0.2728 1.2055 0.1279
BPL/1J f 0.0 0.2728 0.5388 -0.5388
BPL/1J m 0.0 0.2728 0.5388 -0.5388
BPN/3J f 0.0 0.2728 0.5388 -0.5388
BPN/3J m 0.0 0.2728 0.5388 -0.5388
BTBR T+ Itpr3tf/J f 0.6667 0.2728 1.2055 0.1279
BTBR T+ Itpr3tf/J m 0.0 0.2728 0.5388 -0.5388
C3H/HeJ f 0.0 0.2728 0.5388 -0.5388
C3H/HeJ m 0.0 0.2728 0.5388 -0.5388
C57BL/10J f 0.0 0.2728 0.5388 -0.5388
C57BL/10J m 1.3333 0.2728 1.8721 0.7945
C57BL/6J f 1.0 0.2728 1.5388 0.4612
C57BL/6J m 1.3333 0.2728 1.8721 0.7945
C57BLKS/J f 2.0 0.2728 2.5388 1.4612
C57BLKS/J m 1.6667 0.2728 2.2055 1.1279
C57BR/cdJ f 0.0 0.2728 0.5388 -0.5388
C57BR/cdJ m 1.3333 0.2728 1.8721 0.7945
C57L/J f 0.0 0.2728 0.5388 -0.5388
C57L/J m 0.0 0.2728 0.5388 -0.5388
C58/J f 2.0 0.2728 2.5388 1.4612
C58/J m 4.0 0.2728 4.5388 3.4612
CAST/EiJ f 0.0 0.2113 0.4173 -0.4173
CAST/EiJ m 0.6667 0.2728 1.2055 0.1279
CBA/J f 0.0 0.2728 0.5388 -0.5388
CBA/J m 0.0 0.2728 0.5388 -0.5388
CE/J f 1.0 0.2728 1.5388 0.4612
CE/J m 1.6667 0.2728 2.2055 1.1279
CZECHII/EiJ f 0.0 0.2728 0.5388 -0.5388
CZECHII/EiJ m 0.0 0.3341 0.6599 -0.6599
DBA/1J f 0.3333 0.2728 0.8721 -0.2055
DBA/1J m 0.3333 0.2728 0.8721 -0.2055
DBA/2J f 0.0 0.2728 0.5388 -0.5388
DBA/2J m 0.0 0.2728 0.5388 -0.5388
FVB/NJ f 1.5 0.3341 2.1599 0.8401
FVB/NJ m 0.0 0.3341 0.6599 -0.6599
KK/HlJ f 1.0 0.2728 1.5388 0.4612
KK/HlJ m 0.5 0.2363 0.9666 0.0334
LP/J f 0.0 0.2728 0.5388 -0.5388
LP/J m 0.0 0.2728 0.5388 -0.5388
NOD/ShiLtJ f 0.3333 0.2728 0.8721 -0.2055
NOD/ShiLtJ m 0.6667 0.2728 1.2055 0.1279
NON/ShiLtJ f 1.3333 0.2728 1.8721 0.7945
NON/ShiLtJ m 2.3333 0.2728 2.8721 1.7945
NZB/BlNJ f 2.3333 0.2728 2.8721 1.7945
NZB/BlNJ m 3.0 0.2728 3.5388 2.4612
NZW/LacJ f 0.0 0.2728 0.5388 -0.5388
NZW/LacJ m 0.3333 0.2728 0.8721 -0.2055
PERA/EiJ f 0.0 0.2728 0.5388 -0.5388
PERA/EiJ m 0.0 0.3341 0.6599 -0.6599
P/J f 0.0 0.2728 0.5388 -0.5388
P/J m 0.0 0.2728 0.5388 -0.5388
PL/J f 1.0 0.2728 1.5388 0.4612
PL/J m 0.6667 0.2728 1.2055 0.1279
RBF/DnJ f 0.3333 0.2728 0.8721 -0.2055
RBF/DnJ m 0.0 0.2728 0.5388 -0.5388
RF/J f 0.3333 0.2728 0.8721 -0.2055
RF/J m 0.3333 0.2728 0.8721 -0.2055
RIIIS/J f 1.3333 0.2728 1.8721 0.7945
RIIIS/J m 1.0 0.2728 1.5388 0.4612
SEA/GnJ f 0.3333 0.2728 0.8721 -0.2055
SEA/GnJ m 0.0 0.2728 0.5388 -0.5388
SJL/J f 0.0 0.2728 0.5388 -0.5388
SJL/J m 0.6667 0.2728 1.2055 0.1279
SM/J f 1.0 0.2728 1.5388 0.4612
SM/J m 2.0 0.2728 2.5388 1.4612
SPRET/EiJ f 0.0 0.2728 0.5388 -0.5388
SPRET/EiJ m 0.0 0.2728 0.5388 -0.5388
SWR/J f 2.6667 0.2728 3.2055 2.1279
SWR/J m 2.6667 0.2728 3.2055 2.1279
WSB/EiJ f 0.3333 0.2728 0.8721 -0.2055
WSB/EiJ m 0.6667 0.2728 1.2055 0.1279


  LEAST SQUARES MEANS (MODEL-ADJUSTED), SEXES COMBINED
Strain Sex Mean SEM UpperCL LowerCL
129S1/SvImJ both 0.1667 0.1929 0.5477 -0.2143
A/J both 2.6667 0.1929 3.0477 2.2857
AKR/J both 0.3333 0.1929 0.7143 -0.0477
BALB/cJ both 0.3333 0.1929 0.7143 -0.0477
BPH/2J both 0.5 0.1929 0.881 0.119
BPL/1J both 0.0 0.1929 0.381 -0.381
BPN/3J both 0.0 0.1929 0.381 -0.381
BTBR T+ Itpr3tf/J both 0.3333 0.1929 0.7143 -0.0477
C3H/HeJ both 0.0 0.1929 0.381 -0.381
C57BL/10J both 0.6667 0.1929 1.0477 0.2857
C57BL/6J both 1.1667 0.1929 1.5477 0.7857
C57BLKS/J both 1.8333 0.1929 2.2143 1.4523
C57BR/cdJ both 0.6667 0.1929 1.0477 0.2857
C57L/J both 0.0 0.1929 0.381 -0.381
C58/J both 3.0 0.1929 3.381 2.619
CAST/EiJ both 0.3333 0.1725 0.6741 -0.0074
CBA/J both 0.0 0.1929 0.381 -0.381
CE/J both 1.3333 0.1929 1.7143 0.9523
CZECHII/EiJ both 0.0 0.2157 0.426 -0.426
DBA/1J both 0.3333 0.1929 0.7143 -0.0477
DBA/2J both 0.0 0.1929 0.381 -0.381
FVB/NJ both 0.75 0.2363 1.2166 0.2834
KK/HlJ both 0.75 0.1804 1.1064 0.3936
LP/J both 0.0 0.1929 0.381 -0.381
NOD/ShiLtJ both 0.5 0.1929 0.881 0.119
NON/ShiLtJ both 1.8333 0.1929 2.2143 1.4523
NZB/BlNJ both 2.6667 0.1929 3.0477 2.2857
NZW/LacJ both 0.1667 0.1929 0.5477 -0.2143
PERA/EiJ both 0.0 0.2157 0.426 -0.426
P/J both 0.0 0.1929 0.381 -0.381
PL/J both 0.8333 0.1929 1.2143 0.4523
RBF/DnJ both 0.1667 0.1929 0.5477 -0.2143
RF/J both 0.3333 0.1929 0.7143 -0.0477
RIIIS/J both 1.1667 0.1929 1.5477 0.7857
SEA/GnJ both 0.1667 0.1929 0.5477 -0.2143
SJL/J both 0.3333 0.1929 0.7143 -0.0477
SM/J both 1.5 0.1929 1.881 1.119
SPRET/EiJ both 0.0 0.1929 0.381 -0.381
SWR/J both 2.6667 0.1929 3.0477 2.2857
WSB/EiJ both 0.5 0.1929 0.881 0.119




  GWAS USING LINEAR MIXED MODELS