Krt4

Models

All models for this gene with cis-heritability P-value <0.01 were tested and are shown here. In each tissue, a gene can have zero, one, or multiple RNA phenotypes for each RNA modality. After the heritability statistics, subsequent columns show cross-validation performance (R2 and P-value) of each modeling method. The best-performing method for each models is used for TWAS.

# Tissue Modality RNA phenotype h2 h2 SE h2 P xQTL R2 BLUP R2 ENET R2 LASSO R2 xQTL P BLUP P ENET P LASSO P
1 Eye gene expression Krt4 0.49 0.31 2.5e-03 0.09 0.09 0.1 0.12 1.7e-02 1.7e-02 1.5e-02 6.5e-03
2 Eye isoform ratio NM_001008806.2 0.5 0.18 5.1e-05 0.08 0.08 0.08 0.1 2.7e-02 2.1e-02 2.7e-02 1.2e-02
3 Liver gene expression Krt4 0.08 0.05 5.2e-07 0.06 0.06 0.08 0.06 1.2e-07 6.3e-07 5.1e-09 4.1e-07
4 Eye isoform ratio XM_006242395.5 0.48 0.2 2.1e-04 0.09 0.07 0.08 0.08 2.1e-02 3.1e-02 2.6e-02 2.2e-02

Trait associations

The numbered columns correspond to the numbered models in the table above. They contain the TWAS Z-score for each trait-model pair. Colors indicate strength of Z-scores: cells with lower negative Z-scores are darker blue, cells with higher positive Z-scores are darker red. Significant associations have white and bolded text.

Trait Avg chi2 ratio Avg chi2 Max chi2 1 2 3 4
Bone: apparent density0.81.33.3-1.81.1-0.7-0.4
Area under the delay curve0.30.30.7-0.80.70.1-0.3
BMI with tail2.06.811.7-3.43.00.1-2.4
BMI without tail0.82.54.3-1.62.10.8-1.5
Body weight0.52.23.2-1.81.8-0.3-1.5
Weight adjusted by age0.40.61.50.9-0.2-0.3-1.2
Bone surface1.52.66.6-2.61.9-0.0-0.6
Bone volume1.52.76.4-2.51.90.0-0.8
Breakpoint value in progressive ratio session1.11.33.5-1.91.10.60.0
Number of licking bursts0.50.83.00.60.21.70.0
Context. condit. distance diff. score0.20.20.5-0.70.20.40.3
Locomotion velocity, session 15.86.211.43.4-2.8-0.62.3
Locomotion distance, session 12.43.18.22.9-1.80.30.9
Locomotion velocity, session 23.23.76.12.5-2.0-1.21.8
Locomotion distance, session 22.02.86.62.6-1.8-0.11.1
Locomotion velocity, session 34.24.86.92.4-2.4-1.12.6
Locomotion distance, session 33.63.96.22.0-2.1-1.02.5
Stereotopy head waving bouts, day 31.82.12.9-1.51.71.1-1.4
Stereotopy head waving duration, day 30.20.20.3-0.60.60.3-0.2
Locomotion velocity, session 70.70.81.30.8-1.00.41.1
Locomotion distance, session 72.93.76.42.5-2.0-0.22.1
Stereotopy head waving bouts, day 73.23.64.4-1.82.01.7-2.1
Stereotopy head waving duration, day 72.22.73.2-1.81.81.4-1.5
Locomotion velocity, session 80.10.20.40.2-0.20.50.6
Locomotion distance, session 81.82.74.32.1-1.9-0.21.7
Degree of sensitization distance0.30.30.6-0.00.50.7-0.8
Degree of sensitization stereotypy2.02.22.5-1.41.51.4-1.6
Conditioned locomotion0.40.50.80.9-0.9-0.40.4
Cocaine response after cond. corrected0.50.61.81.4-0.50.4-0.5
Cocaine response after cond. not corrected0.40.51.21.1-0.8-0.2-0.1
Cocaine response before conditioning0.80.91.7-0.1-0.9-1.01.3
Saline control response0.00.10.2-0.1-0.4-0.20.0
Bone: connectivity density0.30.51.2-0.8-0.1-1.10.3
Bone: cortical apparent density1.11.53.41.00.31.3-1.8
Bone: cortical area1.01.63.6-1.91.4-0.3-0.9
Bone: cortical porosity1.11.21.70.5-1.1-1.31.3
Bone: cortical porosity1.31.42.10.5-1.3-1.51.3
Bone: cortical thickness0.20.30.5-0.60.6-0.2-0.7
Bone: cortical thickness1.72.03.21.3-1.5-1.80.8
Bone: cortical tissue density1.11.53.11.10.21.2-1.8
Condit. Reinf. active minus inactive responses0.50.51.00.8-1.0-0.50.5
Condit. Reinf. active-inactive response ratio0.50.50.90.6-1.0-0.80.6
Condit. Reinf. active responses1.21.42.31.5-1.5-0.80.8
Condit. Reinf. inactive responses1.21.42.91.7-1.4-0.60.7
Incentive salience index mean0.10.10.30.4-0.5-0.10.1
Condit. Reinf. lever presses0.40.51.1-0.20.61.1-0.8
Condit. Reinf. active minus inactive responses0.71.01.4-0.91.00.8-1.2
Condit. Reinf. active-inactive response ratio0.30.40.5-0.70.60.3-0.6
Condit. Reinf. active responses0.91.31.7-0.91.11.3-1.2
Condit. Reinf. inactive responses0.10.20.50.20.10.7-0.3
Condit. Reinf. lever presses0.30.40.80.3-0.9-0.60.7
Condit. Reinf. lever reinforcers received0.30.40.7-0.40.50.8-0.6
Conditioned reinforcement - actives0.50.92.90.7-0.11.70.3
Conditioned reinforcement - inactives0.40.61.30.9-1.1-0.20.4
Conditioned locomotion0.40.51.70.10.11.30.6
Patch foraging indifference point 0 sec0.71.43.21.8-1.10.80.6
Patch foraging indifference point AUC0.60.91.41.2-0.21.1-1.0
Delay disc. indifference point, 0s delay0.00.00.10.20.1-0.3-0.2
Delay disc. indifference point, 16s delay0.20.30.7-0.80.4-0.3-0.4
Delay disc. indifference point, 2s delay5.05.57.3-1.82.72.3-2.5
Delay disc. indifference point, 24s delay0.10.20.3-0.50.40.4-0.2
Delay disc. indifference point, 4s delay0.60.61.2-1.10.90.3-0.4
Delay disc. indifference point, 8s delay0.10.20.4-0.40.1-0.40.6
Indifference point function ln k0.71.23.2-1.81.0-0.80.4
Indifference point function log k0.71.23.2-1.81.0-0.80.4
Patch foraging total patch changes 0 sec1.02.04.32.1-1.50.51.1
Patch foraging total patch changes 12 sec1.11.53.92.0-1.10.8-0.2
Patch foraging total patch changes 18 sec1.52.45.52.3-1.41.30.5
Patch foraging total patch changes 24 sec0.61.02.71.1-0.31.6-0.1
Patch foraging total patch changes 6 sec1.72.66.22.5-0.52.0-0.2
Patch foraging time to switch 0 sec0.10.20.30.20.30.5-0.6
Patch foraging water rate 0 sec0.00.10.2-0.40.1-0.20.1
Patch foraging water rate 12 sec0.40.92.2-0.0-0.8-0.91.5
Patch foraging water rate 18 sec0.00.00.0-0.1-0.10.00.2
Patch foraging water rate 24 sec0.40.50.8-0.90.90.6-0.3
Patch foraging water rate 6 sec0.91.32.6-1.6-0.1-1.30.8
Seeking ratio, delayed vs. immediate footshock0.00.00.0-0.0-0.1-0.00.1
Distance traveled before self-admin0.00.00.1-0.30.1-0.1-0.0
Distance traveled after self-admin1.11.32.5-0.7-0.9-1.21.6
Extensor digitorum longus weight7.027.542.4-4.76.53.8-5.6
Bone: elastic displacement2.83.25.71.9-1.9-0.42.4
Bone: elastic work1.62.03.41.4-1.3-1.01.8
Bone: endosteal estimation1.32.87.2-2.71.90.0-0.4
Bone: endosteal perimeter1.53.37.7-2.82.1-0.0-1.0
Epididymis fat weight2.48.315.61.0-2.8-3.93.0
Delta time in closed arm before/after self-admin0.50.51.7-1.30.40.1-0.1
Delta time in open arm before/after self-admin4.74.65.92.0-2.4-2.12.1
Diff in mean of infusions in LGA sessions0.30.41.1-0.20.5-0.3-1.0
Delay discount exponential model param0.50.61.11.1-0.9-0.20.4
Extinction: sum of active levers before priming2.02.24.2-1.72.10.8-1.1
Active lever presses in extinction session 60.40.40.8-0.90.70.70.1
Bone: final force1.22.04.5-2.11.7-0.5-0.6
Bone: final moment1.42.35.4-2.31.8-0.5-0.5
Food consumed during 24 hour testing period0.50.61.1-0.4-0.5-1.01.0
Glucose0.40.61.41.2-0.60.40.8
Heart weight0.71.12.8-1.1-0.3-1.70.5
Delay discount hyperbolic model param0.70.81.31.1-1.1-0.40.6
Intermittent access intake day 1-15 change0.10.20.7-0.1-0.30.20.8
Intermittent access intake escalation0.00.00.1-0.0-0.10.10.4
Intermittent access intake escalation 20.20.20.40.1-0.4-0.60.6
Intermitt. access day 1 inactive lever presses0.20.71.2-1.10.50.3-1.1
Intermitt. access day 15 inactive lever presses0.10.20.4-0.3-0.4-0.60.3
Intermitt. access escalation Index2.02.85.7-0.51.72.4-1.5
Intermittent access day 1 total infusions0.30.41.30.5-0.51.10.1
Intermittent access day 15 total infusions0.81.13.41.0-0.41.80.2
Intermittent access terminal intake (last 3 days)0.91.24.50.5-0.12.10.1
Intermittent access total infusions1.21.45.50.30.12.4-0.1
Intermittent access day 1 locomotion0.70.83.30.2-0.11.80.2
Intermittent access day 15 total locomotion0.40.72.1-0.2-0.7-0.41.5
Intermittent access total locomotion0.30.41.0-0.2-0.31.00.7
Intermittent access standard deviation0.30.71.30.8-1.1-0.40.9
Left kidney weight0.10.51.30.00.2-1.2-0.9
Right kidney weight0.21.11.5-0.70.9-1.2-1.2
Cocaine induced anxiety0.40.50.6-0.80.80.80.6
Post-drug Anxiety0.70.71.9-1.40.3-0.20.9
Baseline Anxiety0.80.93.1-0.1-0.7-1.8-0.1
Tail length0.31.12.71.6-1.00.20.8
Length with tail0.10.40.60.7-0.6-0.70.3
Length without tail0.20.51.0-0.90.4-1.0-0.2
Times rat made contact with spout0.50.51.1-0.4-0.4-0.81.1
Lifetime Intake0.81.03.90.1-0.02.00.1
Liver weight, left2.03.28.7-2.92.0-0.5-0.3
Liver weight, right0.40.72.2-0.80.3-1.5-0.2
Locomotor activity0.10.10.20.5-0.2-0.00.3
Locomotor testing distance0.30.50.90.9-0.50.50.9
Locomotor testing rearing0.10.30.60.7-0.3-0.10.7
Locomotion in novel chamber2.93.76.6-2.32.61.0-1.4
Locomotion in novel chamber post-restriction0.71.23.2-0.71.01.8-0.4
Fecal boli incidents, locomotor time 11.82.63.61.7-1.9-0.91.7
Change in fecal boli incidents, locomotor task0.50.50.8-0.70.90.7-0.5
Time >=10cm from walls, locomotor time 10.60.71.60.3-0.9-0.41.3
Bouts of movement, locomotor time 10.60.71.41.2-1.1-0.30.5
Total resting periods, locomotor time 11.51.73.01.7-1.6-0.60.9
Rest time, locomotor task time 10.70.81.61.3-0.70.80.8
Distance moved, locomotor task time 10.40.60.9-0.80.90.5-0.9
Vertical activity count, locomotor time 10.81.83.2-1.31.40.7-1.8
Time >=10cm from walls, locomotor time 20.10.20.50.3-0.30.10.7
Bouts of movement, locomotor time 21.21.93.0-1.41.71.1-1.3
Total resting periods, locomotor time 21.32.33.4-1.41.81.2-1.6
Rest time, locomotor task time 20.30.40.80.9-0.60.60.2
Distance moved, locomotor task time 20.10.10.40.1-0.0-0.7-0.2
Vertical activity count, locomotor time 20.30.40.7-0.40.80.4-0.8
Light reinforcement 10.40.92.21.5-0.71.0-0.1
Light reinforcement 20.71.23.21.8-1.20.10.1
Bone: marrow area1.22.77.0-2.61.90.0-0.4
Bone: maximum diameter0.81.53.4-1.81.40.5-0.7
Bone: maximum force1.42.54.6-2.02.10.5-1.1
Bone: maximum moment1.52.75.1-2.12.30.5-1.0
Mean time between licks in bursts0.51.32.41.6-0.90.71.2
Mean num. licks in bursts1.21.85.5-0.6-0.7-2.30.9
Cd content in liver0.30.30.60.5-0.50.30.8
Co content in liver0.50.51.1-0.40.91.1-0.3
Cu content in liver3.23.811.4-3.41.90.4-0.1
Fe content in liver0.30.31.10.10.41.00.4
K content in liver0.30.30.6-0.60.80.5-0.1
Mg content in liver0.30.30.4-0.50.40.50.7
Mn content in liver0.20.20.40.70.00.5-0.2
Na content in liver0.60.61.4-1.21.00.50.2
Rb content in liver1.01.11.6-1.31.01.30.6
Se content in liver0.40.50.60.8-0.7-0.20.8
Sr content in liver0.40.30.70.4-0.6-0.80.4
Zn content in liver0.80.91.40.4-1.2-0.91.2
Bone: minimum diameter1.42.66.2-2.51.8-0.3-1.1
Time in familiar zone, hab. session 10.70.71.60.4-0.7-1.30.6
Time in novel zone, hab. session 11.71.73.1-0.81.21.7-1.4
Total zone transitions, hab. session 10.40.60.80.8-0.10.9-0.9
Total locomotion distance, hab. session 11.21.62.81.7-1.6-0.90.5
Locomotion velocity, hab. session 11.11.52.71.7-1.5-0.80.6
Time in familiar zone, hab. session 20.30.30.6-0.80.6-0.20.5
Time in novel zone, hab. session 20.50.50.90.20.31.0-0.9
Total zone transitions, hab. session 20.60.71.71.3-0.9-0.10.5
Total locomotion distance, hab. session 21.31.82.41.6-1.6-1.40.5
Locomotion velocity, hab. session 21.62.12.81.6-1.7-1.60.7
Novel to familiar place preference ratio0.50.51.3-0.60.5-0.3-1.2
Novelty place preference0.30.30.9-0.40.4-0.1-0.9
Time in novel zone, NPP test0.40.41.1-0.60.5-0.0-1.1
Total zone transitions, NPP test2.13.07.22.7-2.1-0.10.8
Total locomotion distance, NPP test4.05.59.33.0-2.8-1.81.3
Locomotion velocity, NPP test4.46.29.73.1-3.0-2.01.4
Intraocular pressure0.70.91.80.5-0.61.21.3
Delta distance traveled before/after self-admin3.94.16.10.0-2.1-2.52.5
Delta ambulatory time before/after self-admin3.24.07.6-0.5-1.8-2.82.2
Parametrial fat weight0.61.53.10.7-1.5-0.31.8
Pavlov. Cond. lever latency1.92.44.81.0-1.5-2.21.1
Pavlov. Cond. magazine entry latency2.83.55.5-1.22.12.3-1.7
Pavlov. Cond. change in total contacts3.53.74.6-1.82.11.9-1.8
Pavlov. Cond. index score4.75.98.4-1.82.72.9-2.1
Pavlov. Cond. latency score4.65.98.6-1.92.72.9-2.0
Pavlov. Cond. lever contacts2.22.75.4-1.01.72.3-1.2
Pavlov. Cond. magazine entry number2.12.64.61.0-1.7-2.11.4
Pavlov. Cond. intertrial magazine entries2.53.05.01.8-2.2-1.31.4
Pavlov. Cond. lever-magazine prob. diff.4.75.98.9-1.82.73.0-2.0
Pavlov. Cond. response bias1.51.94.0-0.71.42.0-1.0
Pavlov. Cond. lever latency1.52.13.4-1.21.81.0-1.6
Pavlov. Cond. magazine entry latency3.54.35.82.2-2.4-1.81.8
Pavlov. Cond. change in total contacts0.20.30.8-0.60.40.3-0.9
Pavlov. Cond. index score2.23.04.61.7-2.2-1.41.5
Pavlov. Cond. latency score2.22.94.61.8-2.1-1.41.4
Pavlov. Cond. lever contacts2.23.14.91.4-2.2-1.41.8
Pavlov. Cond. magazine entry number1.31.62.4-1.21.51.3-1.0
Pavlov. Cond. intertrial magazine entries0.30.51.30.3-0.6-0.41.1
Pavlov. Cond. lever-magazine prob. diff.1.72.33.61.5-1.9-1.41.3
Pavlov. Cond. response bias1.82.53.81.2-1.9-1.31.7
Time in closed arm before self-admin0.81.02.50.20.80.8-1.6
Time in closed arm after self-admin2.93.14.0-1.21.82.0-2.0
Time in open arm before self-admin1.92.13.1-1.41.61.8-0.9
Time in open arm after self-admin1.11.21.60.6-1.2-1.31.2
Bone: periosteal estimation1.94.010.1-3.22.3-0.1-0.8
Bone: periosteal perimeter2.34.07.9-2.82.40.3-1.5
Bone: post-yield work0.81.22.1-1.41.50.5-0.6
Progressive ratio test 1 active lever presses1.62.04.11.5-0.92.00.7
Progressive ratio test 1 breakpoint1.62.03.71.5-1.01.90.9
Progressive ratio test 1 inactive lever presses0.40.51.20.00.11.1-0.9
Progressive ratio test 2 active lever presses0.70.82.4-0.70.51.6-0.1
Progressive ratio test 2 breakpoint0.91.02.8-0.80.71.7-0.3
Progressive ratio test 2 inactive lever presses0.10.20.5-0.7-0.00.60.4
Incentive Sensitization - Responses0.91.22.7-1.61.20.6-0.6
Incentive Sensitization - Breakpoint1.21.53.0-1.71.40.7-0.8
Sum of active levers in priming session hrs 5-60.20.20.4-0.10.30.4-0.6
Progressive ratio0.10.10.50.20.10.7-0.0
Food seeking constrained by brief footshock0.10.20.4-0.5-0.10.6-0.1
Seeking ratio, punishment vs. effort0.10.10.2-0.5-0.3-0.4-0.1
Retroperitoneal fat weight2.08.712.42.5-3.5-2.13.4
Reaction time number correct0.30.62.30.4-0.4-0.11.5
Reaction time mean minus median0.10.20.40.5-0.2-0.0-0.7
Reaction time mean minus median AUC0.10.30.80.30.10.7-0.9
Reaction time num false alarms1.41.93.61.8-1.9-0.60.6
Reaction time num false alarms AUC1.11.73.51.9-1.8-0.40.3
Reaction time trials correct on left0.30.62.30.4-0.4-0.11.5
Reaction time trials on left0.40.72.30.4-0.5-0.21.5
Reaction time mean0.40.61.0-1.00.2-0.9-0.8
Reaction time mean AUC0.40.71.1-1.10.4-0.9-0.8
Median of all reaction times0.70.91.8-1.40.3-1.3-0.5
Reaction time omissions2.02.97.90.8-1.8-2.80.1
Reaction time false alarm rate0.50.71.11.1-1.0-0.1-0.7
Reaction time premature initiation rate0.70.91.50.0-1.2-1.11.1
Reaction time premature initiations0.91.53.10.2-1.3-1.21.8
Std. dev. reaction times0.10.20.8-0.0-0.1-0.4-0.9
Reaction time trials completed0.40.72.30.4-0.5-0.21.5
Reaction time trials AUC0.30.51.80.3-0.3-0.11.4
Run reversals in cocaine runway, females0.50.51.8-0.3-0.2-1.3-0.1
Run reversals in cocaine runway, males1.21.22.60.90.61.0-1.6
Latency to leave start box in cocaine runway0.20.20.4-0.60.40.4-0.2
Latency to leave start box in cocaine runway, F0.20.20.70.10.10.8-0.3
Latency to leave start box in cocaine runway, M0.70.61.9-1.40.7-0.4-0.1
Std. dev. time between licks in bursts1.01.42.81.7-1.10.21.3
Total sessions with >9 infusions0.50.51.8-0.30.21.3-0.5
Short access day 1 total inactive lever presses0.10.10.4-0.0-0.10.60.1
Short access day 10 total inactive lever presses0.30.61.7-1.30.2-0.9-0.3
Short access day 1 total infusions0.10.10.4-0.6-0.2-0.20.2
Short access day 10 total infusions0.50.72.60.2-0.11.6-0.2
Short access total infusions0.30.41.4-0.1-0.11.20.3
Short access day 1 locomotion0.10.10.2-0.50.20.3-0.4
Short access day 10 total locomotion0.10.20.3-0.60.20.3-0.5
Short access total locomotion0.30.41.2-0.10.21.1-0.5
One hour access (0.3 mA shock)2.32.73.3-1.81.81.8-1.0
Compulsive drug intake1.41.73.7-1.91.40.7-0.9
One hour access (shock baseline)0.50.81.8-0.70.91.3-0.4
Social response proportion1.71.92.80.9-1.7-1.61.3
Social responses0.91.22.31.5-1.2-0.90.4
Social time1.72.34.41.1-1.6-2.11.1
Soleus weight0.10.30.6-0.80.6-0.30.2
Bone: stiffness3.15.18.1-2.82.80.6-2.0
Tibialis anterior weight8.227.739.0-4.16.14.2-6.2
Time to tail flick, vehicle, before self-admin0.40.40.9-0.40.70.2-0.9
Time to tail flick, vehicle, after self-admin0.30.40.9-0.60.4-0.9-0.5
Time to tail flick, test, before self-admin0.50.51.21.1-0.6-0.3-0.8
Time to tail flick, test, after self-admin1.21.21.8-1.20.8-1.3-1.0
Delta time to tail flick, vehicle, before/after SA0.30.20.4-0.3-0.1-0.70.6
Delta time to tail flick, test, before/after SA1.21.22.5-1.60.7-1.4-0.2
Tibia length0.41.23.4-1.80.6-1.00.0
Ambulatory time before self-admin0.00.10.10.1-0.10.30.3
Ambulatory time after self-admin1.61.82.9-1.0-0.9-1.61.7
Bone: tissue strength2.02.03.0-1.11.71.6-1.2
Total heroin consumption1.21.44.1-2.01.30.2-0.0
Bone: trabecular number0.30.61.5-0.80.0-1.20.4
Bone: trabecular spacing0.60.82.1-0.50.61.5-0.6
Bone: trabecular thickness0.10.10.20.10.1-0.3-0.5
Bone: trabecular tissue density1.01.53.0-0.10.91.5-1.7
Water consumed over 24 hours0.20.31.20.1-0.30.11.1
Number of responses in last shaping day2.22.43.51.9-1.7-1.80.2