Prph

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 pVTA gene expression Prph 0.08 0.07 2.2e-05 0.05 0.05 0.05 0.05 1.2e-04 7.2e-05 7.2e-05 1.3e-04
2 LHb gene expression Prph 0.37 0.19 2.9e-08 0.22 0.26 0.24 0.26 6.0e-06 5.2e-07 1.6e-06 8.5e-07
3 Adipose gene expression Prph 0.09 0.08 5.6e-08 0.06 0.06 0.06 0.06 4.3e-07 4.9e-07 2.3e-07 8.5e-07

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
Bone: apparent density8.715.117.3-3.44.2-4.0
Area under the delay curve1.01.21.6-1.30.9-1.1
BMI with tail7.525.827.2-5.14.9-5.2
BMI without tail2.16.57.8-2.52.3-2.8
Body weight7.332.134.6-5.65.5-5.9
Weight adjusted by age2.23.34.7-1.31.9-2.2
Bone surface10.919.921.9-4.24.7-4.5
Bone volume8.314.816.4-3.74.1-3.8
Breakpoint value in progressive ratio session1.31.61.8-1.31.4-1.2
Number of licking bursts0.71.12.71.6-0.70.1
Context. condit. distance diff. score0.30.40.8-0.20.5-0.9
Locomotion velocity, session 11.71.93.01.7-1.01.3
Locomotion distance, session 13.34.25.51.9-1.82.3
Locomotion velocity, session 20.40.40.80.4-0.50.9
Locomotion distance, session 22.63.75.11.7-1.82.3
Locomotion velocity, session 35.05.76.62.6-2.22.4
Locomotion distance, session 35.05.46.52.0-2.42.5
Stereotopy head waving bouts, day 30.70.81.4-0.51.2-0.9
Stereotopy head waving duration, day 30.30.40.8-0.30.9-0.4
Locomotion velocity, session 70.70.82.11.4-0.60.2
Locomotion distance, session 72.02.54.32.1-1.50.9
Stereotopy head waving bouts, day 71.11.31.6-0.91.2-1.3
Stereotopy head waving duration, day 71.11.31.4-1.11.2-1.1
Locomotion velocity, session 80.20.20.60.80.0-0.0
Locomotion distance, session 81.21.72.11.4-1.31.2
Degree of sensitization distance0.60.61.4-0.30.7-1.2
Degree of sensitization stereotypy0.20.30.3-0.60.3-0.6
Conditioned locomotion0.00.10.10.40.10.1
Cocaine response after cond. corrected0.00.00.0-0.0-0.10.2
Cocaine response after cond. not corrected0.60.70.90.7-0.80.9
Cocaine response before conditioning3.44.14.42.0-2.12.0
Saline control response0.00.10.10.30.2-0.1
Bone: connectivity density5.78.910.9-2.53.3-3.1
Bone: cortical apparent density0.20.20.30.4-0.50.5
Bone: cortical area10.215.617.7-3.54.2-4.2
Bone: cortical porosity0.80.91.90.3-0.81.4
Bone: cortical porosity1.01.02.10.4-1.01.4
Bone: cortical thickness3.55.77.1-1.82.6-2.7
Bone: cortical thickness0.20.20.5-0.10.3-0.7
Bone: cortical tissue density0.20.30.40.5-0.60.6
Condit. Reinf. active minus inactive responses0.20.30.60.4-0.20.8
Condit. Reinf. active-inactive response ratio0.10.10.3-0.30.60.1
Condit. Reinf. active responses0.91.11.71.0-0.81.3
Condit. Reinf. inactive responses2.73.33.71.8-1.91.8
Incentive salience index mean0.00.00.00.20.10.2
Condit. Reinf. lever presses0.10.10.3-0.50.3-0.2
Condit. Reinf. active minus inactive responses0.00.10.2-0.4-0.10.0
Condit. Reinf. active-inactive response ratio0.20.20.3-0.2-0.60.5
Condit. Reinf. active responses0.10.10.30.0-0.50.3
Condit. Reinf. inactive responses0.40.60.70.8-0.80.6
Condit. Reinf. lever presses0.00.00.10.10.1-0.3
Condit. Reinf. lever reinforcers received0.30.40.70.5-0.80.6
Conditioned reinforcement - actives0.61.11.90.6-1.41.0
Conditioned reinforcement - inactives3.85.66.32.3-2.52.3
Conditioned locomotion0.20.20.30.5-0.50.4
Patch foraging indifference point 0 sec3.46.311.13.3-2.01.9
Patch foraging indifference point AUC0.70.91.21.0-1.10.7
Delay disc. indifference point, 0s delay1.41.52.1-1.51.2-1.1
Delay disc. indifference point, 16s delay1.11.21.6-1.30.9-1.1
Delay disc. indifference point, 2s delay1.41.61.9-1.41.2-1.1
Delay disc. indifference point, 24s delay1.01.11.5-0.81.0-1.2
Delay disc. indifference point, 4s delay0.80.81.7-1.30.6-0.6
Delay disc. indifference point, 8s delay2.12.53.0-1.51.5-1.7
Indifference point function ln k3.15.46.4-2.52.3-2.1
Indifference point function log k3.15.46.4-2.52.3-2.1
Patch foraging total patch changes 0 sec3.26.110.73.3-2.01.9
Patch foraging total patch changes 12 sec3.54.67.62.8-1.91.6
Patch foraging total patch changes 18 sec4.67.010.53.2-2.42.2
Patch foraging total patch changes 24 sec2.44.16.92.6-1.81.5
Patch foraging total patch changes 6 sec4.26.411.23.3-2.11.9
Patch foraging time to switch 0 sec1.73.63.71.9-1.91.9
Patch foraging water rate 0 sec2.65.45.7-2.42.3-2.3
Patch foraging water rate 12 sec2.55.35.7-2.42.3-2.2
Patch foraging water rate 18 sec0.40.60.8-0.90.6-0.8
Patch foraging water rate 24 sec3.75.26.9-2.62.2-2.0
Patch foraging water rate 6 sec4.66.78.6-2.92.5-2.3
Seeking ratio, delayed vs. immediate footshock0.10.10.2-0.40.3-0.3
Distance traveled before self-admin1.21.62.51.6-1.01.1
Distance traveled after self-admin0.70.91.81.3-0.50.8
Extensor digitorum longus weight4.818.920.8-4.63.9-4.5
Bone: elastic displacement5.26.06.92.6-2.12.6
Bone: elastic work0.10.10.2-0.00.20.4
Bone: endosteal estimation8.418.519.1-4.44.3-4.2
Bone: endosteal perimeter7.816.617.4-4.13.9-4.2
Epididymis fat weight0.72.43.1-1.31.8-1.6
Delta time in closed arm before/after self-admin0.00.00.00.0-0.10.1
Delta time in open arm before/after self-admin1.31.31.61.3-1.11.1
Diff in mean of infusions in LGA sessions1.01.31.6-1.21.2-0.9
Delay discount exponential model param1.01.21.61.3-0.81.1
Extinction: sum of active levers before priming1.81.92.6-1.61.4-1.1
Active lever presses in extinction session 60.70.71.2-0.51.1-0.8
Bone: final force11.318.019.9-4.54.3-3.9
Bone: final moment12.219.722.1-4.74.5-4.0
Food consumed during 24 hour testing period1.21.72.2-1.01.5-1.4
Glucose0.20.40.80.40.4-0.9
Heart weight0.20.30.5-0.60.3-0.7
Delay discount hyperbolic model param1.01.11.61.3-0.81.0
Intermittent access intake day 1-15 change0.10.10.2-0.5-0.4-0.2
Intermittent access intake escalation0.10.30.7-0.8-0.1-0.4
Intermittent access intake escalation 20.10.10.3-0.2-0.50.1
Intermitt. access day 1 inactive lever presses0.20.91.40.5-0.91.2
Intermitt. access day 15 inactive lever presses0.40.81.50.2-1.20.9
Intermitt. access escalation Index0.40.51.0-0.10.8-1.0
Intermittent access day 1 total infusions1.11.72.21.5-1.21.2
Intermittent access day 15 total infusions0.60.91.50.7-1.20.7
Intermittent access terminal intake (last 3 days)1.01.42.00.9-1.41.1
Intermittent access total infusions1.72.02.71.3-1.61.3
Intermittent access day 1 locomotion0.30.30.80.9-0.30.3
Intermittent access day 15 total locomotion0.20.30.60.8-0.60.1
Intermittent access total locomotion1.51.82.51.6-1.31.0
Intermittent access standard deviation0.10.30.6-0.0-0.80.4
Left kidney weight1.04.77.3-2.71.9-1.7
Right kidney weight4.520.623.9-4.94.4-4.3
Cocaine induced anxiety2.94.25.4-1.82.0-2.3
Post-drug Anxiety4.04.34.8-2.11.9-2.2
Baseline Anxiety0.10.10.2-0.50.10.0
Tail length0.00.10.20.20.0-0.4
Length with tail1.66.87.7-2.42.6-2.8
Length without tail5.417.518.4-4.14.3-4.1
Times rat made contact with spout0.20.20.40.6-0.30.3
Lifetime Intake2.32.83.51.6-1.91.5
Liver weight, left10.317.118.3-4.14.1-4.3
Liver weight, right2.95.05.9-2.42.2-2.1
Locomotor activity1.42.12.41.6-1.51.3
Locomotor testing distance3.05.56.22.5-2.42.1
Locomotor testing rearing1.93.84.42.1-2.11.7
Locomotion in novel chamber2.02.64.3-2.11.3-1.3
Locomotion in novel chamber post-restriction0.00.10.1-0.3-0.20.2
Fecal boli incidents, locomotor time 11.62.33.51.0-1.61.9
Change in fecal boli incidents, locomotor task0.50.50.9-0.21.0-0.7
Time >=10cm from walls, locomotor time 10.10.10.10.20.2-0.3
Bouts of movement, locomotor time 10.10.10.2-0.00.00.4
Total resting periods, locomotor time 10.50.51.00.6-0.51.0
Rest time, locomotor task time 10.60.81.11.0-0.61.0
Distance moved, locomotor task time 10.10.20.40.20.2-0.6
Vertical activity count, locomotor time 10.81.92.9-1.11.2-1.7
Time >=10cm from walls, locomotor time 20.50.71.10.4-0.91.0
Bouts of movement, locomotor time 22.13.33.4-1.71.9-1.9
Total resting periods, locomotor time 22.03.63.9-1.71.9-2.0
Rest time, locomotor task time 20.10.10.40.6-0.00.0
Distance moved, locomotor task time 20.00.00.1-0.1-0.20.2
Vertical activity count, locomotor time 20.10.20.3-0.40.1-0.6
Light reinforcement 11.74.15.61.7-2.41.9
Light reinforcement 20.50.81.30.5-1.10.9
Bone: marrow area8.217.818.0-4.24.2-4.2
Bone: maximum diameter4.07.49.3-2.42.7-3.1
Bone: maximum force16.228.730.3-5.55.5-5.1
Bone: maximum moment17.330.432.3-5.75.7-5.2
Mean time between licks in bursts0.10.20.30.3-0.40.6
Mean num. licks in bursts0.20.40.7-0.80.20.6
Cd content in liver0.70.80.90.7-0.90.9
Co content in liver0.10.10.30.4-0.6-0.0
Cu content in liver0.60.81.4-0.41.2-0.9
Fe content in liver1.62.02.41.4-1.51.3
K content in liver0.00.00.10.10.1-0.2
Mg content in liver0.20.20.20.5-0.30.5
Mn content in liver0.00.00.1-0.00.10.4
Na content in liver0.00.00.0-0.1-0.2-0.1
Rb content in liver0.50.61.81.3-0.1-0.2
Se content in liver2.12.53.61.9-1.41.3
Sr content in liver1.10.91.3-0.51.1-1.1
Zn content in liver1.01.11.31.1-1.01.0
Bone: minimum diameter9.617.618.4-4.04.3-4.3
Time in familiar zone, hab. session 10.20.20.40.3-0.40.6
Time in novel zone, hab. session 10.30.30.5-0.20.5-0.7
Total zone transitions, hab. session 10.20.30.50.3-0.70.6
Total locomotion distance, hab. session 10.00.10.10.40.10.2
Locomotion velocity, hab. session 10.00.00.10.30.20.1
Time in familiar zone, hab. session 20.50.51.1-1.00.7-0.4
Time in novel zone, hab. session 20.50.61.31.1-0.50.3
Total zone transitions, hab. session 20.30.40.60.5-0.60.8
Total locomotion distance, hab. session 20.20.30.50.6-0.20.7
Locomotion velocity, hab. session 20.10.20.30.5-0.10.5
Novel to familiar place preference ratio1.82.03.3-0.81.4-1.8
Novelty place preference1.31.42.6-0.51.2-1.6
Time in novel zone, NPP test1.11.22.3-0.41.1-1.5
Total zone transitions, NPP test1.92.83.71.9-1.41.7
Total locomotion distance, NPP test2.63.64.72.2-1.51.9
Locomotion velocity, NPP test1.62.23.21.8-1.11.5
Intraocular pressure7.310.511.03.2-3.23.3
Delta distance traveled before/after self-admin0.00.00.00.10.00.1
Delta ambulatory time before/after self-admin0.00.00.10.2-0.20.0
Parametrial fat weight0.71.72.61.0-1.61.2
Pavlov. Cond. lever latency0.10.10.30.30.50.0
Pavlov. Cond. magazine entry latency0.30.41.3-1.1-0.10.2
Pavlov. Cond. change in total contacts0.50.61.5-1.20.0-0.4
Pavlov. Cond. index score0.30.41.1-1.0-0.0-0.5
Pavlov. Cond. latency score0.20.30.8-0.9-0.1-0.4
Pavlov. Cond. lever contacts0.20.30.7-0.2-0.90.3
Pavlov. Cond. magazine entry number0.20.30.80.90.10.1
Pavlov. Cond. intertrial magazine entries1.51.83.61.9-0.61.2
Pavlov. Cond. lever-magazine prob. diff.0.60.71.6-1.30.2-0.7
Pavlov. Cond. response bias0.20.20.3-0.6-0.50.2
Pavlov. Cond. lever latency0.30.51.2-1.10.4-0.2
Pavlov. Cond. magazine entry latency0.70.91.3-0.11.2-1.1
Pavlov. Cond. change in total contacts1.22.03.3-0.71.5-1.8
Pavlov. Cond. index score0.50.71.10.30.9-1.0
Pavlov. Cond. latency score0.40.60.90.40.8-0.9
Pavlov. Cond. lever contacts0.20.30.90.9-0.20.0
Pavlov. Cond. magazine entry number1.82.23.30.5-1.71.8
Pavlov. Cond. intertrial magazine entries5.38.010.12.2-3.03.2
Pavlov. Cond. lever-magazine prob. diff.0.70.91.50.21.1-1.2
Pavlov. Cond. response bias0.10.20.30.50.2-0.4
Time in closed arm before self-admin2.53.24.1-1.61.7-2.0
Time in closed arm after self-admin0.30.30.5-0.70.4-0.6
Time in open arm before self-admin0.20.20.30.6-0.20.4
Time in open arm after self-admin0.20.20.40.6-0.20.5
Bone: periosteal estimation12.927.128.6-5.05.3-5.3
Bone: periosteal perimeter11.119.219.7-4.34.4-4.4
Bone: post-yield work9.914.514.9-3.93.8-3.8
Progressive ratio test 1 active lever presses6.17.69.03.0-2.82.4
Progressive ratio test 1 breakpoint5.77.08.62.9-2.72.3
Progressive ratio test 1 inactive lever presses1.52.13.20.9-1.81.5
Progressive ratio test 2 active lever presses1.61.92.81.2-1.71.2
Progressive ratio test 2 breakpoint1.51.82.61.2-1.61.1
Progressive ratio test 2 inactive lever presses0.91.42.30.8-1.51.1
Incentive Sensitization - Responses0.30.50.8-0.90.3-0.7
Incentive Sensitization - Breakpoint0.20.30.6-0.80.2-0.5
Sum of active levers in priming session hrs 5-60.00.00.00.20.20.1
Progressive ratio0.50.71.61.3-0.60.5
Food seeking constrained by brief footshock1.21.42.61.6-1.10.8
Seeking ratio, punishment vs. effort0.00.00.1-0.2-0.10.0
Retroperitoneal fat weight0.41.72.21.3-1.21.5
Reaction time number correct0.91.72.3-1.41.5-0.8
Reaction time mean minus median4.310.611.73.1-3.43.2
Reaction time mean minus median AUC2.87.18.02.5-2.82.7
Reaction time num false alarms1.72.42.71.6-1.51.6
Reaction time num false alarms AUC2.03.23.41.7-1.81.9
Reaction time trials correct on left0.91.72.3-1.41.5-0.8
Reaction time trials on left0.71.31.8-1.31.3-0.6
Reaction time mean0.61.01.31.1-1.10.8
Reaction time mean AUC0.40.60.80.9-0.80.5
Median of all reaction times0.00.00.10.20.0-0.3
Reaction time omissions9.614.015.63.4-3.84.0
Reaction time false alarm rate2.43.33.71.8-1.91.7
Reaction time premature initiation rate4.25.98.42.0-2.92.2
Reaction time premature initiations1.52.73.91.1-2.01.7
Std. dev. reaction times4.78.79.33.0-3.02.9
Reaction time trials completed0.71.31.8-1.31.3-0.6
Reaction time trials AUC1.12.12.9-1.61.7-0.9
Run reversals in cocaine runway, females0.20.20.4-0.60.2-0.3
Run reversals in cocaine runway, males1.21.21.41.0-1.11.2
Latency to leave start box in cocaine runway0.00.00.0-0.2-0.2-0.1
Latency to leave start box in cocaine runway, F0.80.91.20.7-1.10.9
Latency to leave start box in cocaine runway, M2.01.82.0-1.31.3-1.4
Std. dev. time between licks in bursts1.01.42.11.5-1.20.7
Total sessions with >9 infusions2.32.83.41.8-1.91.3
Short access day 1 total inactive lever presses1.82.32.81.5-1.71.4
Short access day 10 total inactive lever presses0.10.10.20.3-0.30.5
Short access day 1 total infusions1.01.31.91.4-1.10.9
Short access day 10 total infusions1.72.22.91.7-1.61.1
Short access total infusions2.93.64.82.2-2.01.5
Short access day 1 locomotion0.30.40.70.8-0.60.2
Short access day 10 total locomotion0.20.30.40.7-0.60.5
Short access total locomotion1.01.21.71.3-1.10.7
One hour access (0.3 mA shock)0.20.20.3-0.5-0.5-0.1
Compulsive drug intake0.10.10.3-0.50.00.1
One hour access (shock baseline)0.10.10.2-0.5-0.2-0.4
Social response proportion0.20.20.40.6-0.50.2
Social responses6.88.810.33.0-3.22.7
Social time0.10.20.5-0.70.10.1
Soleus weight0.82.43.6-1.91.4-1.4
Bone: stiffness19.732.034.0-5.85.6-5.5
Tibialis anterior weight1.86.18.4-2.91.6-2.7
Time to tail flick, vehicle, before self-admin1.61.72.31.1-1.21.5
Time to tail flick, vehicle, after self-admin0.20.30.8-0.90.3-0.3
Time to tail flick, test, before self-admin0.40.40.80.4-0.40.9
Time to tail flick, test, after self-admin0.90.91.2-1.10.9-0.9
Delta time to tail flick, vehicle, before/after SA0.70.60.9-0.90.7-0.8
Delta time to tail flick, test, before/after SA0.40.40.5-0.60.5-0.7
Tibia length7.019.224.2-3.54.6-4.9
Ambulatory time before self-admin2.13.13.71.9-1.61.8
Ambulatory time after self-admin1.72.03.01.7-1.21.2
Bone: tissue strength1.21.21.5-1.21.2-0.9
Total heroin consumption0.81.01.1-0.81.0-1.0
Bone: trabecular number5.48.910.8-2.53.3-3.1
Bone: trabecular spacing2.12.83.51.4-1.91.7
Bone: trabecular thickness0.10.10.1-0.2-0.30.3
Bone: trabecular tissue density0.00.00.1-0.3-0.10.1
Water consumed over 24 hours0.10.10.10.40.3-0.1
Number of responses in last shaping day0.10.10.20.3-0.4-0.1