Plce1

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 Adipose gene expression ENSRNOG00000014276 0.11 0.07 8.9e-06 0.02 0.03 0.03 0.03 3.5e-03 2.4e-04 4.4e-04 1.1e-04
2 BLA gene expression ENSRNOG00000014276 0.12 0.07 4.6e-04 0.04 0.06 0.07 0.06 2.6e-03 2.2e-04 9.2e-05 4.2e-04
3 Brain gene expression ENSRNOG00000014276 0.06 0.04 1.0e-03 0.03 0.03 0.02 0.03 5.2e-04 1.8e-03 1.1e-02 1.2e-03
4 Liver mRNA stability ENSRNOG00000014276 0.32 0.12 2.6e-10 0.08 0.07 0.09 0.08 5.6e-09 1.2e-08 9.5e-10 4.5e-09

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 strong Z-scores (below -2 or above 2): lower negative Z-scores are darker blue, higher positive Z-scores are darker red.

Trait Avg chi2 ratio Avg chi2 Max chi2 1 2 3 4
BMI with tail1.03.35.52.31.11.3-2.1
BMI without tail1.63.34.11.71.71.8-2.0
Body weight0.41.73.20.51.81.6-0.9
Epididymis fat weight2.04.76.61.02.22.6-2.5
Glucose0.20.20.5-0.10.70.60.0
Heart weight0.50.82.2-1.50.40.6-0.6
Left kidney weight0.20.62.3-1.50.40.30.0
Right kidney weight0.82.27.6-2.7-0.4-0.40.9
Tail length0.61.72.7-1.51.61.20.7
Length with tail0.62.14.9-2.20.70.11.7
Length without tail1.02.25.0-1.7-0.4-0.82.2
Liver weight, left0.91.41.8-1.31.41.10.8
Liver weight, right0.40.60.9-0.90.90.80.4
Parametrial fat weight0.30.51.2-1.10.70.5-0.4
Retroperitoneal fat weight0.82.64.2-0.51.51.9-2.1
Intraocular pressure0.20.30.8-0.1-0.5-0.1-0.9
Extensor digitorum longus weight0.20.81.70.31.31.1-0.2
Soleus weight0.82.44.01.21.92.0-0.8
Tibialis anterior weight0.30.92.00.81.40.80.6
Tibia length0.20.61.3-1.10.2-0.20.9
Number of licking bursts1.41.62.9-0.4-1.6-1.70.8
Food consumed during 24 hour testing period0.10.10.5-0.7-0.10.10.2
Times rat made contact with spout0.10.20.60.80.10.0-0.2
Mean time between licks in bursts0.20.20.9-0.90.00.1-0.2
Mean num. licks in bursts2.02.53.81.11.91.9-1.1
Std. dev. time between licks in bursts0.70.81.7-1.3-0.8-0.5-0.8
Water consumed over 24 hours0.30.31.01.00.50.3-0.1
Indifference point 0 sec0.61.03.1-1.7-0.5-0.40.7
Indifference point AUC5.86.87.6-2.5-2.4-2.82.7
Indifference point function ln k4.86.88.62.32.82.9-2.3
Indifference point function log k4.86.88.62.32.82.9-2.3
Delay discounting total patch changes 0 sec0.50.82.8-1.7-0.4-0.30.4
Delay discounting total patch changes 12 sec3.54.66.2-2.0-2.5-2.51.5
Delay discounting total patch changes 18 sec1.31.73.0-0.8-1.4-1.71.1
Delay discounting total patch changes 24 sec1.41.84.1-2.0-0.3-0.61.6
Delay discounting total patch changes 6 sec3.96.08.2-2.9-2.2-2.42.3
Delay discounting time to switch 0 sec0.60.92.2-0.1-1.5-1.2-0.1
Delay discounting water rate 0 sec0.81.22.70.61.61.30.0
Delay discounting water rate 12 sec0.50.81.9-0.31.41.10.3
Delay discounting water rate 18 sec0.91.22.80.31.71.40.4
Delay discounting water rate 24 sec0.60.81.70.21.31.2-0.1
Delay discounting water rate 6 sec0.10.20.30.20.50.6-0.4
Locomotor activity0.10.10.20.40.40.2-0.1
Locomotor testing distance0.10.10.20.50.3-0.00.2
Locomotor testing rearing0.30.50.80.70.7-0.10.9
Light reinforcement 10.10.20.40.3-0.7-0.4-0.3
Light reinforcement 20.91.22.60.7-1.6-1.0-0.9
Reaction time number correct1.52.23.51.91.31.5-1.1
Reaction time mean minus median1.01.32.4-0.11.21.5-1.2
Reaction time mean minus median AUC1.21.62.8-0.01.01.6-1.7
Reaction time num false alarms0.60.82.2-1.50.0-0.01.0
Reaction time num false alarms AUC0.60.92.7-1.60.20.20.8
Reaction time trials correct on left1.52.23.51.91.31.5-1.1
Reaction time trials on left1.62.23.31.81.31.6-1.2
Reaction time mean0.50.72.6-1.60.00.3-0.1
Reaction time mean AUC0.60.72.8-1.7-0.3-0.0-0.0
Median of all reaction times0.50.72.6-1.6-0.2-0.00.1
Reaction time omissions3.34.46.80.22.32.6-2.4
Reaction time false alarm rate1.31.95.3-2.3-0.5-0.61.3
Reaction time premature initiation rate0.60.92.4-1.5-0.0-0.11.0
Reaction time premature initiations0.30.40.6-0.50.70.80.2
Std. dev. reaction times1.31.72.6-1.21.11.6-1.3
Reaction time trials completed1.62.23.31.81.31.6-1.2
Reaction time trials AUC1.52.13.21.81.31.5-1.2
Social response proportion2.62.87.32.71.01.0-1.4
Social responses0.30.41.21.10.40.3-0.6
Social time0.81.01.1-0.9-1.0-1.11.1
Conditioned locomotion1.21.52.20.31.31.4-1.5
Cocaine response after cond. corrected0.10.10.1-0.0-0.4-0.30.3
Cocaine response after cond. not corrected0.20.30.4-0.2-0.5-0.60.7
Cocaine response before conditioning0.30.40.5-0.5-0.6-0.70.6
Saline control response3.95.26.4-2.0-2.2-2.42.5
Condit. Reinf. active minus inactive responses2.43.03.71.71.91.8-1.4
Condit. Reinf. active-inactive response ratio2.12.23.92.01.21.1-1.5
Condit. Reinf. active responses1.01.42.40.11.51.6-1.1
Condit. Reinf. inactive responses0.91.24.5-2.10.00.20.3
Condit. Reinf. lever presses0.20.30.4-0.7-0.5-0.60.5
Condit. Reinf. lever reinforcers received0.50.71.1-0.11.01.1-0.7
Pavlov. Cond. lever latency1.11.53.31.80.90.9-1.1
Pavlov. Cond. magazine entry latency0.30.40.7-0.90.60.50.3
Pavlov. Cond. change in total contacts0.50.61.8-1.3-0.2-0.30.8
Pavlov. Cond. index score0.70.92.5-1.6-0.4-0.41.0
Pavlov. Cond. latency score0.60.82.0-1.4-0.2-0.31.0
Pavlov. Cond. lever contacts1.21.73.7-1.9-0.8-0.91.2
Pavlov. Cond. magazine entry number1.41.74.92.20.50.5-1.2
Pavlov. Cond. intertrial magazine entries0.91.22.01.40.70.8-1.3
Pavlov. Cond. lever-magazine prob. diff.0.81.02.3-1.5-0.3-0.51.2
Pavlov. Cond. response bias1.31.84.2-2.1-0.6-0.81.4
Conditioned reinforcement - actives0.70.72.10.4-0.1-0.71.5
Conditioned reinforcement - inactives0.80.92.61.60.3-0.30.8
Conditioned locomotion0.20.20.6-0.1-0.1-0.50.8
Intermittent access intake day 1-15 change1.11.12.31.31.50.70.3
Intermittent access intake escalation1.01.02.11.11.50.80.0
Intermittent access intake escalation 21.51.53.31.81.50.7-0.0
Intermitt. access day 1 inactive lever presses0.40.40.60.60.80.6-0.6
Intermitt. access day 15 inactive lever presses0.30.40.60.80.70.6-0.2
Intermitt. access escalation Index2.52.23.31.41.31.4-1.8
Intermittent access day 1 total infusions0.20.30.50.70.50.5-0.3
Intermittent access day 15 total infusions1.31.52.41.21.51.3-0.5
Intermittent access terminal intake (last 3 days)1.01.02.21.51.00.8-0.5
Intermittent access total infusions0.91.01.61.30.91.0-0.9
Intermittent access day 1 locomotion0.20.20.30.00.30.6-0.4
Intermittent access day 15 total locomotion1.01.11.5-0.8-0.8-1.21.2
Intermittent access total locomotion0.40.40.7-0.2-0.7-0.80.7
Intermittent access standard deviation1.71.83.71.41.91.2-0.1
Cocaine induced anxiety0.40.41.01.00.00.3-0.8
Post-drug Anxiety0.40.50.8-0.1-0.9-0.5-0.9
Baseline Anxiety0.40.41.4-1.2-0.4-0.30.1
Lifetime Intake0.40.51.01.00.50.6-0.6
Incentive Sensitization - Responses1.11.12.51.60.90.9-0.3
Incentive Sensitization - Breakpoint0.90.92.01.40.90.8-0.3
Progressive ratio test 1 active lever presses0.40.41.01.00.40.4-0.5
Progressive ratio test 1 breakpoint0.40.41.11.00.40.4-0.5
Progressive ratio test 1 inactive lever presses2.02.23.21.81.81.3-0.9
Progressive ratio test 2 active lever presses0.50.51.41.20.60.50.1
Progressive ratio test 2 breakpoint0.60.71.81.30.70.60.1
Progressive ratio test 2 inactive lever presses0.80.93.21.80.40.3-0.4
Total sessions with >9 infusions0.50.61.0-0.2-0.7-1.01.0
Short access day 1 total inactive lever presses3.84.310.03.20.60.8-2.5
Short access day 10 total inactive lever presses0.30.31.00.50.30.2-1.0
Short access day 1 total infusions0.30.30.80.3-0.9-0.5-0.5
Short access day 10 total infusions0.20.20.3-0.50.10.4-0.6
Short access total infusions0.10.10.10.4-0.2-0.20.1
Short access day 1 locomotion0.20.20.30.6-0.3-0.5-0.0
Short access day 10 total locomotion0.20.20.60.2-0.30.2-0.8
Short access total locomotion0.30.30.80.1-0.6-0.90.3
Compulsive drug intake2.92.96.01.52.41.6-0.9
One hour access (0.3 mA shock)1.72.04.32.11.51.2-0.2
One hour access (shock baseline)0.10.10.30.50.10.4-0.2
Number of responses in last shaping day1.31.32.91.50.30.3-1.7
Context. condit. distance diff. score0.70.91.31.10.90.9-0.7
Locomotion velocity, session 11.81.93.6-0.7-1.7-1.91.0
Locomotion distance, session 10.50.71.0-0.6-0.9-1.00.7
Locomotion velocity, session 21.31.53.70.5-0.7-1.21.9
Locomotion distance, session 20.50.72.2-0.2-0.4-0.61.5
Locomotion velocity, session 30.20.20.40.10.60.60.1
Locomotion distance, session 30.80.91.9-0.11.21.4-0.5
Stereotopy head waving bouts, day 30.20.30.60.7-0.10.0-0.8
Stereotopy head waving duration, day 30.40.51.21.1-0.20.0-0.9
Locomotion velocity, session 72.83.14.81.32.22.2-1.1
Locomotion distance, session 71.82.34.00.91.92.0-0.9
Stereotopy head waving bouts, day 70.70.81.50.6-1.0-1.20.4
Stereotopy head waving duration, day 70.20.30.50.7-0.4-0.5-0.5
Locomotion velocity, session 80.10.10.40.70.10.2-0.2
Locomotion distance, session 80.20.41.21.10.0-0.00.5
Degree of sensitization distance0.20.20.40.3-0.2-0.30.7
Degree of sensitization stereotypy1.11.32.50.0-1.3-1.60.9
Condit. Reinf. active minus inactive responses0.10.20.4-0.50.1-0.20.6
Condit. Reinf. active-inactive response ratio0.00.00.0-0.20.1-0.1-0.1
Condit. Reinf. active responses0.20.30.7-0.60.30.20.8
Condit. Reinf. inactive responses0.20.20.6-0.3-0.10.00.8
Incentive salience index mean0.81.01.8-1.4-0.4-0.51.3
Condit. Reinf. lever presses1.41.93.7-1.9-1.0-1.01.4
Time in familiar zone, hab. session 11.21.22.91.00.50.7-1.7
Time in novel zone, hab. session 10.80.81.7-0.7-0.7-0.81.3
Total zone transitions, hab. session 10.20.31.10.1-0.2-0.41.1
Total locomotion distance, hab. session 10.91.31.9-0.8-1.1-1.11.4
Locomotion velocity, hab. session 11.42.02.3-1.3-1.5-1.41.5
Time in familiar zone, hab. session 20.70.82.5-0.20.20.7-1.6
Time in novel zone, hab. session 20.40.41.2-0.0-0.3-0.61.1
Total zone transitions, hab. session 20.81.01.5-1.0-0.9-0.91.2
Total locomotion distance, hab. session 20.50.61.5-1.2-0.7-0.40.5
Locomotion velocity, hab. session 20.70.91.4-1.2-1.0-0.80.8
Novel to familiar place preference ratio1.31.45.02.20.2-0.20.7
Novelty place preference1.41.45.22.30.2-0.20.7
Time in novel zone, NPP test1.41.55.42.30.3-0.10.6
Total zone transitions, NPP test0.91.32.5-1.6-0.5-0.61.5
Total locomotion distance, NPP test1.62.22.8-1.7-1.4-1.31.5
Locomotion velocity, NPP test1.72.53.2-1.8-1.3-1.31.8
Pavlov. Cond. lever latency0.40.51.80.3-0.10.1-1.3
Pavlov. Cond. magazine entry latency0.91.12.6-1.6-0.4-0.41.3
Pavlov. Cond. change in total contacts0.20.20.3-0.50.50.40.3
Pavlov. Cond. index score0.91.12.6-1.2-0.4-0.51.6
Pavlov. Cond. latency score0.91.23.0-1.3-0.3-0.51.7
Pavlov. Cond. lever contacts1.01.22.7-1.3-0.4-0.51.7
Pavlov. Cond. magazine entry number0.20.30.50.7-0.5-0.6-0.1
Pavlov. Cond. intertrial magazine entries0.00.00.1-0.30.20.2-0.0
Pavlov. Cond. lever-magazine prob. diff.0.70.81.8-1.2-0.4-0.41.3
Pavlov. Cond. response bias0.50.61.4-1.20.10.11.0
Bone: apparent density1.52.65.92.41.71.1-0.5
Bone surface1.42.43.71.91.91.5-0.4
Bone volume1.72.95.01.72.21.8-0.6
Bone: connectivity density2.64.09.23.01.91.4-1.1
Bone: cortical apparent density1.11.43.10.3-1.8-1.6-0.2
Bone: cortical area1.11.63.4-0.81.81.6-0.0
Bone: cortical porosity0.50.52.11.4-0.0-0.10.3
Bone: cortical porosity0.50.51.61.30.40.30.3
Bone: cortical thickness1.01.65.1-2.3-0.6-0.60.7
Bone: cortical thickness1.72.02.5-1.5-1.6-1.60.9
Bone: cortical tissue density1.11.53.10.5-1.8-1.6-0.3
Bone: elastic displacement1.21.43.31.50.20.4-1.8
Bone: elastic work1.01.43.11.80.40.5-1.4
Bone: endosteal estimation2.96.212.71.83.63.0-0.2
Bone: endosteal perimeter2.34.89.51.83.12.5-0.2
Bone: final force0.50.71.6-1.00.60.11.2
Bone: final moment0.40.60.9-0.90.90.50.8
Bone: marrow area2.96.312.51.93.53.0-0.3
Bone: maximum diameter3.15.69.82.23.12.6-1.1
Bone: maximum force0.30.51.10.11.10.80.5
Bone: maximum moment0.50.81.80.11.41.2-0.0
Bone: minimum diameter4.58.216.51.64.13.6-1.0
Bone: periosteal estimation1.93.88.70.82.92.40.0
Bone: periosteal perimeter2.13.47.01.12.62.3-0.5
Bone: post-yield work0.40.51.10.21.01.0-0.1
Bone: stiffness0.40.61.3-0.11.10.80.7
Bone: tissue strength0.30.30.7-0.10.60.8-0.4
Bone: trabecular number1.62.55.02.21.71.2-0.9
Bone: trabecular spacing0.71.03.4-1.8-0.5-0.30.2
Bone: trabecular thickness1.62.03.11.31.81.5-0.8
Bone: trabecular tissue density0.20.30.60.80.60.4-0.2
Breakpoint value in progressive ratio session1.41.53.2-1.3-0.6-0.91.8
Distance traveled before self-admin0.60.61.40.60.7-0.51.2
Distance traveled after self-admin1.21.34.82.20.70.00.0
Delta time in closed arm before/after self-admin0.80.82.0-1.40.40.9-0.1
Delta time in open arm before/after self-admin0.80.82.01.4-0.3-0.60.8
Diff in mean of infusions in LGA sessions1.01.22.40.91.51.1-0.5
Extinction: sum of active levers before priming0.60.60.9-1.00.50.31.0
Active lever presses in extinction session 60.90.92.81.70.60.40.5
Delta distance traveled before/after self-admin1.51.63.11.80.70.9-1.4
Delta ambulatory time before/after self-admin2.22.44.22.01.21.4-1.5
Time in closed arm before self-admin0.70.82.91.70.60.3-0.1
Time in closed arm after self-admin0.40.40.9-0.90.10.00.9
Time in open arm before self-admin0.60.61.9-0.20.30.8-1.4
Time in open arm after self-admin0.30.30.40.6-0.5-0.60.4
Sum of active levers in priming session hrs 5-60.30.30.80.30.30.5-0.9
Time to tail flick, vehicle, before self-admin1.01.11.80.8-1.4-1.1-0.7
Time to tail flick, vehicle, after self-admin0.60.61.0-0.61.00.51.0
Time to tail flick, test, before self-admin0.70.71.71.30.90.40.5
Time to tail flick, test, after self-admin0.90.92.01.40.90.5-0.7
Delta time to tail flick, vehicle, before/after SA1.71.73.4-0.51.81.31.2
Delta time to tail flick, test, before/after SA0.10.10.30.20.20.1-0.5
Ambulatory time before self-admin0.40.51.00.60.4-0.61.0
Ambulatory time after self-admin2.42.79.63.11.00.3-0.2
Total heroin consumption0.40.51.1-1.1-0.3-0.20.9
Area under the delay curve0.70.81.4-0.4-1.1-1.20.7
Delay disc. indifference point, 0s delay0.50.61.91.40.50.2-0.3
Delay disc. indifference point, 16s delay1.71.72.2-0.8-1.4-1.41.5
Delay disc. indifference point, 2s delay0.30.30.60.7-0.3-0.3-0.7
Delay disc. indifference point, 24s delay2.62.53.4-1.4-1.5-1.61.9
Delay disc. indifference point, 4s delay1.11.22.0-0.2-1.3-1.41.0
Delay disc. indifference point, 8s delay1.41.52.4-1.1-1.5-1.40.5
Delay discount exponential model param0.91.01.60.51.11.3-0.9
Delay discount hyperbolic model param0.60.61.20.31.01.1-0.5
Fecal boli incidents, locomotor time 10.50.51.41.2-0.10.7-0.5
Change in fecal boli incidents, locomotor task1.21.11.4-1.2-0.8-1.11.1
Time >=10cm from walls, locomotor time 11.91.95.3-1.50.4-0.12.3
Bouts of movement, locomotor time 10.20.20.4-0.2-0.6-0.40.2
Total resting periods, locomotor time 10.70.71.1-0.3-1.0-1.00.9
Rest time, locomotor task time 10.60.71.21.1-0.6-0.90.6
Distance moved, locomotor task time 10.70.82.4-1.60.70.40.4
Vertical activity count, locomotor time 10.50.51.8-1.30.10.4-0.1
Time >=10cm from walls, locomotor time 20.80.92.7-0.40.6-0.51.7
Bouts of movement, locomotor time 23.33.55.6-1.0-2.2-2.41.5
Total resting periods, locomotor time 23.94.26.5-1.1-2.3-2.51.9
Rest time, locomotor task time 21.82.13.0-0.6-1.5-1.71.7
Distance moved, locomotor task time 21.61.84.10.02.01.6-0.7
Vertical activity count, locomotor time 20.60.71.20.10.91.1-0.9
Weight adjusted by age0.60.71.51.0-0.50.2-1.2
Seeking ratio, delayed vs. immediate footshock0.20.30.5-0.7-0.2-0.40.7
Locomotion in novel chamber1.92.36.12.51.21.1-0.8
Locomotion in novel chamber post-restriction1.92.25.4-0.4-0.9-1.62.3
Progressive ratio1.11.22.0-0.61.11.4-1.2
Food seeking constrained by brief footshock1.61.94.5-1.70.5-0.42.1
Seeking ratio, punishment vs. effort2.12.66.8-0.9-0.6-1.52.6
Run reversals in cocaine runway, females0.10.10.3-0.2-0.5-0.3-0.3
Run reversals in cocaine runway, males3.33.23.6-1.9-1.7-1.91.7
Latency to leave start box in cocaine runway3.94.25.51.62.42.2-2.0
Latency to leave start box in cocaine runway, F3.63.95.42.02.32.0-1.5
Latency to leave start box in cocaine runway, M1.51.52.50.11.21.3-1.6
Cd content in liver0.60.72.1-1.4-0.3-0.1-0.8
Co content in liver0.80.93.5-0.1-0.00.5-1.9
Cu content in liver4.96.09.5-1.5-2.9-3.12.0
Fe content in liver1.01.22.2-0.6-1.3-1.50.5
K content in liver1.31.33.0-0.1-0.9-1.21.7
Mg content in liver1.81.93.6-0.6-1.2-1.51.9
Mn content in liver3.74.27.1-0.4-2.7-2.61.7
Na content in liver2.12.33.9-0.2-2.0-1.91.3
Rb content in liver0.20.30.7-0.10.80.30.7
Se content in liver13.816.729.8-2.7-5.5-4.92.4
Sr content in liver0.10.00.1-0.2-0.2-0.0-0.3
Zn content in liver0.80.81.5-0.8-1.2-1.00.5