RT1-M5

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 PL gene expression RT1-M5 0.09 0.05 4.7e-12 0.12 0.11 0.1 0.1 1.3e-12 1.3e-11 2.6e-11 2.1e-11
2 IC gene expression RT1-M5 0.09 0.06 6.2e-03 0.05 0.04 0.03 0.04 3.0e-03 9.5e-03 1.6e-02 1.1e-02
3 Adipose gene expression RT1-M5 0.05 0.03 1.9e-05 0.04 0.04 0.04 0.04 3.0e-05 1.1e-05 2.1e-05 2.0e-05
4 Brain gene expression RT1-M5 0.05 0.03 9.0e-04 0.04 0.02 0.03 0.03 1.3e-04 2.6e-03 8.7e-04 6.5e-04

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 density1.42.53.01.51.7-1.61.5
Area under the delay curve1.92.23.3-1.8-1.51.6-0.7
BMI with tail1.65.58.0-1.8-2.22.4-2.8
BMI without tail2.78.29.4-2.8-2.93.1-2.6
Body weight5.122.430.4-5.4-5.54.7-2.9
Weight adjusted by age1.82.76.9-1.6-2.61.10.5
Bone surface0.30.62.0-0.4-0.2-0.41.4
Bone volume0.20.41.5-0.2-0.0-0.41.2
Breakpoint value in progressive ratio session0.50.61.21.00.5-0.2-1.1
Number of licking bursts0.00.00.0-0.2-0.00.0-0.2
Context. condit. distance diff. score5.26.38.02.22.4-2.82.5
Locomotion velocity, session 10.20.20.30.20.3-0.50.6
Locomotion distance, session 10.60.71.21.11.1-0.70.3
Locomotion velocity, session 20.40.41.3-0.3-0.20.6-1.1
Locomotion distance, session 20.71.01.21.11.0-1.00.9
Locomotion velocity, session 30.50.61.8-0.00.10.7-1.3
Locomotion distance, session 31.31.42.01.41.4-1.20.5
Stereotopy head waving bouts, day 30.80.91.6-1.3-1.00.8-0.6
Stereotopy head waving duration, day 30.80.91.6-1.3-1.01.0-0.6
Locomotion velocity, session 73.94.34.52.12.1-2.12.0
Locomotion distance, session 73.13.94.12.02.0-2.01.8
Stereotopy head waving bouts, day 71.71.92.9-1.7-1.51.5-0.7
Stereotopy head waving duration, day 71.82.23.1-1.8-1.61.6-0.9
Locomotion velocity, session 80.30.41.2-0.4-0.4-0.41.1
Locomotion distance, session 83.75.36.62.21.9-2.62.5
Degree of sensitization distance0.30.30.9-0.10.1-0.40.9
Degree of sensitization stereotypy0.60.71.0-1.0-0.80.9-0.5
Conditioned locomotion2.93.33.7-1.7-1.71.9-1.9
Cocaine response after cond. corrected0.30.40.90.60.60.2-1.0
Cocaine response after cond. not corrected0.40.50.6-0.7-0.50.8-0.8
Cocaine response before conditioning3.74.58.0-2.8-2.71.60.2
Saline control response1.01.41.8-1.2-1.31.3-0.8
Bone: connectivity density2.94.55.11.82.2-2.32.2
Bone: cortical apparent density0.50.71.0-0.5-0.71.0-1.0
Bone: cortical area0.60.92.3-1.0-1.50.70.3
Bone: cortical porosity0.10.10.1-0.4-0.30.3-0.0
Bone: cortical porosity0.20.20.2-0.4-0.50.10.5
Bone: cortical thickness1.11.82.6-1.1-1.61.5-1.1
Bone: cortical thickness0.50.61.4-0.2-0.60.9-1.2
Bone: cortical tissue density0.40.60.9-0.5-0.60.9-1.0
Condit. Reinf. active minus inactive responses0.10.10.10.40.4-0.30.1
Condit. Reinf. active-inactive response ratio0.80.81.5-0.8-0.50.9-1.2
Condit. Reinf. active responses0.50.61.31.10.8-0.70.3
Condit. Reinf. inactive responses2.32.85.12.31.6-1.61.0
Incentive salience index mean0.40.50.70.80.8-0.80.2
Condit. Reinf. lever presses1.92.64.02.01.6-1.80.7
Condit. Reinf. active minus inactive responses0.40.51.0-0.8-1.00.70.0
Condit. Reinf. active-inactive response ratio1.51.72.3-1.5-1.51.3-0.7
Condit. Reinf. active responses0.30.40.80.60.3-0.60.9
Condit. Reinf. inactive responses1.31.62.11.41.2-1.31.1
Condit. Reinf. lever presses2.53.44.61.81.4-1.92.2
Condit. Reinf. lever reinforcers received0.50.71.20.70.6-0.81.1
Conditioned reinforcement - actives0.50.91.6-1.1-1.30.9-0.1
Conditioned reinforcement - inactives0.50.72.0-0.6-1.40.6-0.2
Conditioned locomotion0.20.30.5-0.7-0.60.4-0.4
Patch foraging indifference point 0 sec0.30.62.10.00.4-0.61.4
Patch foraging indifference point AUC0.91.32.4-1.2-1.61.1-0.2
Delay disc. indifference point, 0s delay0.80.91.3-0.9-0.61.1-1.0
Delay disc. indifference point, 16s delay1.11.21.6-1.2-1.11.3-0.7
Delay disc. indifference point, 2s delay2.12.32.8-1.7-1.61.6-1.1
Delay disc. indifference point, 24s delay0.50.61.1-1.0-0.80.8-0.0
Delay disc. indifference point, 4s delay3.43.64.6-2.1-2.12.0-1.2
Delay disc. indifference point, 8s delay0.30.40.8-0.9-0.70.30.4
Indifference point function ln k0.30.61.00.60.2-1.01.0
Indifference point function log k0.30.61.00.60.2-1.01.0
Patch foraging total patch changes 0 sec0.30.62.1-0.10.3-0.41.4
Patch foraging total patch changes 12 sec0.10.20.6-0.1-0.20.10.8
Patch foraging total patch changes 18 sec0.30.40.90.50.9-0.60.5
Patch foraging total patch changes 24 sec0.50.81.30.70.9-0.71.2
Patch foraging total patch changes 6 sec0.20.30.6-0.7-0.30.60.4
Patch foraging time to switch 0 sec0.50.93.1-0.00.60.5-1.8
Patch foraging water rate 0 sec0.51.13.9-0.2-0.6-0.42.0
Patch foraging water rate 12 sec0.00.10.20.40.1-0.20.3
Patch foraging water rate 18 sec0.10.10.30.2-0.0-0.00.5
Patch foraging water rate 24 sec0.20.30.5-0.7-0.30.6-0.1
Patch foraging water rate 6 sec0.00.10.20.40.3-0.20.1
Seeking ratio, delayed vs. immediate footshock0.70.91.8-0.6-0.70.9-1.3
Distance traveled before self-admin0.20.30.80.30.1-0.60.9
Distance traveled after self-admin0.20.20.5-0.7-0.40.4-0.3
Extensor digitorum longus weight0.51.96.10.00.2-1.12.5
Bone: elastic displacement0.40.50.7-0.7-0.20.8-0.9
Bone: elastic work1.01.31.6-1.3-0.91.2-1.2
Bone: endosteal estimation1.32.75.7-2.4-2.01.00.4
Bone: endosteal perimeter0.51.13.4-0.3-0.2-1.01.8
Epididymis fat weight1.13.88.4-0.9-0.72.3-2.9
Delta time in closed arm before/after self-admin0.40.40.7-0.6-0.80.6-0.2
Delta time in open arm before/after self-admin0.30.31.1-0.2-0.0-0.31.1
Diff in mean of infusions in LGA sessions2.12.54.72.21.8-1.50.1
Delay discount exponential model param2.02.33.41.81.6-1.60.8
Extinction: sum of active levers before priming0.80.81.91.40.8-0.7-0.7
Active lever presses in extinction session 60.90.93.00.50.10.6-1.7
Bone: final force2.03.14.3-1.9-2.11.9-1.1
Bone: final moment1.42.23.5-1.7-1.91.5-0.5
Food consumed during 24 hour testing period0.40.60.8-0.9-0.80.7-0.7
Glucose2.03.16.00.91.2-2.12.4
Heart weight2.23.55.7-2.3-2.41.7-0.3
Delay discount hyperbolic model param2.12.43.31.81.6-1.70.9
Intermittent access intake day 1-15 change0.00.10.3-0.0-0.00.1-0.5
Intermittent access intake escalation0.30.61.3-0.6-0.50.8-1.1
Intermittent access intake escalation 20.10.10.3-0.2-0.3-0.20.6
Intermitt. access day 1 inactive lever presses0.00.00.1-0.0-0.3-0.2-0.2
Intermitt. access day 15 inactive lever presses0.20.40.9-0.9-0.60.50.0
Intermitt. access escalation Index1.21.73.21.81.4-1.0-0.9
Intermittent access day 1 total infusions0.00.00.10.30.00.10.0
Intermittent access day 15 total infusions0.60.91.5-0.7-0.51.2-1.2
Intermittent access terminal intake (last 3 days)0.50.61.2-0.8-0.61.1-0.6
Intermittent access total infusions0.30.40.8-0.6-0.50.9-0.4
Intermittent access day 1 locomotion0.40.51.0-0.5-0.50.8-1.0
Intermittent access day 15 total locomotion2.13.84.4-2.0-2.02.1-1.6
Intermittent access total locomotion2.73.23.8-1.9-1.91.9-1.5
Intermittent access standard deviation0.61.32.7-1.2-1.60.90.5
Left kidney weight2.411.116.4-4.0-3.93.3-1.4
Right kidney weight3.415.622.4-4.7-4.73.9-1.7
Cocaine induced anxiety0.50.71.00.70.9-1.00.8
Post-drug Anxiety0.60.60.80.90.4-0.80.8
Baseline Anxiety0.30.30.91.00.2-0.2-0.5
Tail length2.39.015.6-3.9-3.72.6-0.3
Length with tail3.113.423.3-4.8-4.72.90.4
Length without tail3.310.716.7-4.0-4.13.0-1.0
Times rat made contact with spout1.11.32.31.51.5-0.9-0.1
Lifetime Intake0.50.61.0-0.8-0.91.0-0.3
Liver weight, left0.30.51.0-0.8-1.00.20.3
Liver weight, right2.13.76.6-2.6-2.31.6-0.7
Locomotor activity0.50.82.3-0.8-0.5-0.31.5
Locomotor testing distance0.51.02.7-0.20.6-0.91.6
Locomotor testing rearing0.10.30.6-0.60.0-0.20.8
Locomotion in novel chamber0.10.10.3-0.4-0.40.10.5
Locomotion in novel chamber post-restriction0.50.81.4-0.9-1.21.0-0.3
Fecal boli incidents, locomotor time 11.01.52.41.31.5-1.00.9
Change in fecal boli incidents, locomotor task2.62.63.0-1.4-1.71.6-1.6
Time >=10cm from walls, locomotor time 10.60.61.2-1.1-0.60.8-0.6
Bouts of movement, locomotor time 11.41.63.60.80.7-1.31.9
Total resting periods, locomotor time 10.50.61.50.50.4-0.71.2
Rest time, locomotor task time 10.30.40.5-0.7-0.70.7-0.5
Distance moved, locomotor task time 10.10.20.4-0.2-0.4-0.10.7
Vertical activity count, locomotor time 10.10.20.50.0-0.4-0.30.7
Time >=10cm from walls, locomotor time 20.30.40.8-0.8-0.90.40.3
Bouts of movement, locomotor time 20.20.40.7-0.8-0.70.40.4
Total resting periods, locomotor time 20.20.30.4-0.6-0.60.10.6
Rest time, locomotor task time 20.10.10.20.30.3-0.40.3
Distance moved, locomotor task time 20.20.30.4-0.6-0.60.60.1
Vertical activity count, locomotor time 20.00.00.1-0.0-0.3-0.10.3
Light reinforcement 10.00.00.1-0.0-0.00.3-0.2
Light reinforcement 21.42.23.1-1.7-1.81.5-0.5
Bone: marrow area1.22.75.6-2.4-2.01.00.3
Bone: maximum diameter0.40.72.1-0.3-0.4-0.61.5
Bone: maximum force1.62.84.2-2.0-2.01.6-0.7
Bone: maximum moment1.12.03.4-1.8-1.91.20.0
Mean time between licks in bursts0.10.31.0-0.1-0.1-0.61.0
Mean num. licks in bursts0.20.40.80.90.7-0.50.1
Cd content in liver0.10.10.40.1-0.0-0.20.6
Co content in liver0.30.30.5-0.4-0.60.7-0.4
Cu content in liver0.80.91.61.31.1-0.90.4
Fe content in liver1.41.73.5-0.9-0.81.5-1.9
K content in liver0.50.50.80.80.9-0.70.2
Mg content in liver0.70.71.10.80.8-1.00.7
Mn content in liver1.71.92.61.31.4-1.61.2
Na content in liver0.10.10.3-0.30.00.3-0.6
Rb content in liver0.60.70.90.80.7-1.00.8
Se content in liver0.10.10.2-0.3-0.2-0.20.5
Sr content in liver0.60.61.0-0.6-1.00.6-0.7
Zn content in liver0.70.71.60.50.4-0.91.3
Bone: minimum diameter0.20.40.8-0.5-0.6-0.30.9
Time in familiar zone, hab. session 11.41.32.81.31.7-0.9-0.1
Time in novel zone, hab. session 11.31.32.2-1.0-1.30.21.5
Total zone transitions, hab. session 10.91.31.51.21.1-1.21.1
Total locomotion distance, hab. session 10.50.70.90.91.0-0.90.6
Locomotion velocity, hab. session 10.20.30.60.80.7-0.5-0.0
Time in familiar zone, hab. session 20.50.61.00.91.0-0.6-0.1
Time in novel zone, hab. session 20.60.61.1-1.0-1.10.70.2
Total zone transitions, hab. session 20.00.00.10.20.10.0-0.3
Total locomotion distance, hab. session 20.71.01.61.21.3-0.90.4
Locomotion velocity, hab. session 20.91.21.81.31.3-1.00.4
Novel to familiar place preference ratio0.20.20.3-0.5-0.50.40.0
Novelty place preference0.40.40.7-0.8-0.80.6-0.0
Time in novel zone, NPP test0.60.71.1-1.0-1.00.7-0.0
Total zone transitions, NPP test1.31.92.51.01.4-1.51.6
Total locomotion distance, NPP test0.91.21.81.01.3-1.00.9
Locomotion velocity, NPP test1.52.23.31.61.8-1.41.0
Intraocular pressure0.81.21.41.10.9-1.11.2
Delta distance traveled before/after self-admin1.81.92.9-1.7-1.01.5-1.2
Delta ambulatory time before/after self-admin1.21.42.1-1.4-0.91.3-1.1
Parametrial fat weight0.81.92.7-1.4-1.71.4-0.9
Pavlov. Cond. lever latency0.30.30.6-0.2-0.50.7-0.8
Pavlov. Cond. magazine entry latency0.91.11.61.31.1-1.20.3
Pavlov. Cond. change in total contacts0.60.61.2-1.1-0.80.6-0.3
Pavlov. Cond. index score0.50.60.90.80.9-1.00.3
Pavlov. Cond. latency score0.30.40.70.60.7-0.80.3
Pavlov. Cond. lever contacts0.20.20.30.10.4-0.60.6
Pavlov. Cond. magazine entry number1.11.42.1-1.4-1.41.20.0
Pavlov. Cond. intertrial magazine entries0.20.20.50.70.4-0.30.5
Pavlov. Cond. lever-magazine prob. diff.0.70.91.21.01.1-1.10.3
Pavlov. Cond. response bias0.60.71.10.91.0-1.00.2
Pavlov. Cond. lever latency0.81.01.5-1.0-0.81.0-1.2
Pavlov. Cond. magazine entry latency0.20.20.3-0.6-0.50.4-0.2
Pavlov. Cond. change in total contacts0.10.10.2-0.3-0.50.20.2
Pavlov. Cond. index score0.10.10.50.10.0-0.30.7
Pavlov. Cond. latency score0.00.00.20.0-0.1-0.20.4
Pavlov. Cond. lever contacts0.50.71.20.70.5-0.81.1
Pavlov. Cond. magazine entry number0.20.20.40.60.5-0.4-0.0
Pavlov. Cond. intertrial magazine entries0.40.60.80.90.7-0.90.6
Pavlov. Cond. lever-magazine prob. diff.0.20.20.60.10.2-0.40.8
Pavlov. Cond. response bias0.40.51.20.40.4-0.71.1
Time in closed arm before self-admin0.10.10.4-0.1-0.00.2-0.6
Time in closed arm after self-admin2.32.42.9-1.4-1.51.6-1.7
Time in open arm before self-admin0.20.20.60.80.0-0.50.1
Time in open arm after self-admin1.11.31.81.10.7-1.21.3
Bone: periosteal estimation1.22.64.7-2.1-2.21.00.4
Bone: periosteal perimeter0.50.81.5-1.0-1.20.10.8
Bone: post-yield work1.42.16.00.30.1-1.52.5
Progressive ratio test 1 active lever presses0.60.81.5-0.4-0.61.0-1.2
Progressive ratio test 1 breakpoint0.70.81.4-0.5-0.71.0-1.2
Progressive ratio test 1 inactive lever presses0.10.10.20.3-0.50.1-0.5
Progressive ratio test 2 active lever presses0.20.20.60.20.20.6-0.7
Progressive ratio test 2 breakpoint0.30.30.80.10.10.7-0.9
Progressive ratio test 2 inactive lever presses0.20.30.6-0.4-0.80.6-0.1
Incentive Sensitization - Responses0.30.40.80.90.8-0.2-0.2
Incentive Sensitization - Breakpoint0.30.40.80.90.8-0.2-0.2
Sum of active levers in priming session hrs 5-60.20.20.50.50.7-0.40.1
Progressive ratio4.77.38.8-2.3-2.62.9-3.0
Food seeking constrained by brief footshock0.10.10.30.30.1-0.20.5
Seeking ratio, punishment vs. effort4.15.98.12.12.1-2.62.8
Retroperitoneal fat weight0.52.23.7-1.6-1.91.4-0.6
Reaction time number correct0.20.40.7-0.5-0.40.8-0.7
Reaction time mean minus median0.20.51.2-0.1-0.2-0.71.1
Reaction time mean minus median AUC0.30.61.8-0.0-0.4-0.81.3
Reaction time num false alarms0.00.10.2-0.4-0.20.10.0
Reaction time num false alarms AUC0.00.10.2-0.4-0.10.00.2
Reaction time trials correct on left0.20.40.7-0.5-0.40.8-0.7
Reaction time trials on left0.20.40.7-0.5-0.50.8-0.7
Reaction time mean1.11.73.70.50.7-1.51.9
Reaction time mean AUC0.91.53.70.40.6-1.41.9
Median of all reaction times1.21.63.20.60.9-1.51.8
Reaction time omissions0.00.10.1-0.10.3-0.30.2
Reaction time false alarm rate0.20.20.6-0.10.1-0.50.8
Reaction time premature initiation rate0.50.71.0-0.8-0.81.0-0.7
Reaction time premature initiations0.91.62.4-1.2-1.01.6-1.2
Std. dev. reaction times0.30.61.8-0.1-0.1-0.81.3
Reaction time trials completed0.20.40.7-0.5-0.50.8-0.7
Reaction time trials AUC0.20.40.6-0.5-0.40.8-0.7
Run reversals in cocaine runway, females0.50.50.90.60.3-0.71.0
Run reversals in cocaine runway, males0.70.71.7-1.3-1.00.60.1
Latency to leave start box in cocaine runway0.10.10.30.0-0.00.4-0.5
Latency to leave start box in cocaine runway, F0.60.71.01.00.7-0.70.9
Latency to leave start box in cocaine runway, M3.12.93.7-1.5-1.41.9-1.9
Std. dev. time between licks in bursts0.20.20.7-0.1-0.2-0.40.9
Total sessions with >9 infusions0.60.81.0-0.8-1.01.0-0.7
Short access day 1 total inactive lever presses0.71.02.5-0.9-1.60.7-0.1
Short access day 10 total inactive lever presses0.71.72.91.71.0-1.60.4
Short access day 1 total infusions0.10.20.70.0-0.2-0.10.8
Short access day 10 total infusions0.40.50.8-0.7-0.90.80.1
Short access total infusions0.40.60.9-0.8-1.00.80.1
Short access day 1 locomotion0.50.61.10.70.4-0.81.1
Short access day 10 total locomotion0.40.71.5-0.9-1.20.5-0.2
Short access total locomotion0.30.40.9-0.6-1.00.4-0.3
One hour access (0.3 mA shock)1.21.42.11.51.4-1.20.6
Compulsive drug intake2.83.35.42.12.3-1.90.3
One hour access (shock baseline)0.20.30.5-0.6-0.70.60.4
Social response proportion0.20.30.80.10.3-0.40.9
Social responses0.10.10.1-0.3-0.20.4-0.2
Social time0.00.00.10.1-0.0-0.4-0.1
Soleus weight0.41.23.5-0.50.3-0.91.9
Bone: stiffness0.30.40.6-0.6-0.80.7-0.6
Tibialis anterior weight0.00.10.20.10.50.1-0.0
Time to tail flick, vehicle, before self-admin0.50.50.70.90.9-0.6-0.5
Time to tail flick, vehicle, after self-admin0.30.40.50.70.7-0.6-0.1
Time to tail flick, test, before self-admin0.10.10.20.4-0.20.2-0.2
Time to tail flick, test, after self-admin0.10.20.50.2-0.7-0.3-0.2
Delta time to tail flick, vehicle, before/after SA0.00.00.0-0.00.0-0.00.2
Delta time to tail flick, test, before/after SA0.10.10.30.30.3-0.5-0.0
Tibia length1.54.16.5-2.6-2.51.7-0.8
Ambulatory time before self-admin0.10.10.30.30.1-0.40.6
Ambulatory time after self-admin0.30.30.5-0.7-0.30.6-0.6
Bone: tissue strength0.50.50.8-0.9-0.80.8-0.3
Total heroin consumption0.10.20.20.40.5-0.40.3
Bone: trabecular number0.81.32.01.11.4-1.10.9
Bone: trabecular spacing2.93.96.1-2.0-2.52.0-1.3
Bone: trabecular thickness1.51.92.71.41.7-1.41.1
Bone: trabecular tissue density0.91.32.1-1.3-1.41.1-0.2
Water consumed over 24 hours0.10.10.2-0.2-0.10.2-0.5
Number of responses in last shaping day0.40.41.0-1.0-0.70.20.3