RT1-Da

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 RT1-Da 0.15 0.06 2.7e-08 0.01 0.07 0.06 0.06 7.9e-03 4.4e-08 1.9e-07 9.0e-07
2 Liver gene expression RT1-Da 0.04 0.03 2.3e-03 0.01 0.03 0 0.01 7.1e-03 8.2e-04 2.7e-01 8.2e-03
3 Adipose isoform ratio NM_001008847.2 0.13 0.06 7.4e-13 0.12 0.11 0.1 0.06 5.5e-13 2.3e-12 1.2e-11 1.9e-07
4 Adipose isoform ratio XM_039098493.2 0.13 0.06 8.7e-13 0.12 0.11 0.1 0.07 5.5e-13 2.6e-12 1.3e-11 3.0e-08

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 density0.40.62.31.5-0.20.2-0.2
Area under the delay curve0.10.10.5-0.7-0.10.1-0.1
BMI with tail2.79.511.12.33.2-3.33.3
BMI without tail1.64.86.41.12.5-2.42.4
Body weight1.98.511.60.23.3-3.43.4
Weight adjusted by age0.50.71.6-1.30.6-0.70.7
Bone surface0.00.00.1-0.2-0.20.1-0.1
Bone volume0.10.10.50.70.1-0.20.2
Breakpoint value in progressive ratio session0.20.20.3-0.2-0.50.5-0.5
Number of licking bursts0.91.42.0-1.4-1.11.1-1.1
Context. condit. distance diff. score4.65.57.0-1.8-2.72.4-2.4
Locomotion velocity, session 13.13.34.0-1.5-2.01.9-1.9
Locomotion distance, session 10.20.30.70.8-0.50.4-0.4
Locomotion velocity, session 20.50.50.7-0.5-0.80.8-0.8
Locomotion distance, session 20.10.10.30.2-0.50.4-0.4
Locomotion velocity, session 30.20.20.70.80.4-0.10.1
Locomotion distance, session 30.80.81.20.5-0.91.1-1.1
Stereotopy head waving bouts, day 30.40.51.8-1.30.1-0.20.2
Stereotopy head waving duration, day 30.30.41.6-1.3-0.0-0.00.0
Locomotion velocity, session 70.70.71.50.3-1.20.8-0.8
Locomotion distance, session 72.02.53.90.1-2.01.7-1.7
Stereotopy head waving bouts, day 70.40.50.7-0.5-0.50.8-0.8
Stereotopy head waving duration, day 70.00.00.1-0.30.10.2-0.2
Locomotion velocity, session 84.85.77.9-2.8-2.22.2-2.2
Locomotion distance, session 82.53.65.1-1.2-2.32.0-2.0
Degree of sensitization distance0.60.71.4-1.2-0.80.5-0.5
Degree of sensitization stereotypy0.70.81.2-0.1-0.81.1-1.1
Conditioned locomotion0.60.71.0-0.10.8-1.01.0
Cocaine response after cond. corrected0.30.30.60.30.4-0.70.7
Cocaine response after cond. not corrected0.20.20.5-0.70.3-0.40.4
Cocaine response before conditioning0.50.62.1-1.40.20.3-0.3
Saline control response2.63.44.91.62.2-1.71.7
Bone: connectivity density0.20.20.91.0-0.1-0.10.1
Bone: cortical apparent density3.04.14.41.92.1-2.12.1
Bone: cortical area0.00.00.1-0.20.3-0.20.2
Bone: cortical porosity2.42.63.4-1.2-1.51.9-1.9
Bone: cortical porosity3.53.84.4-1.8-1.82.1-2.1
Bone: cortical thickness1.52.54.02.01.6-1.31.3
Bone: cortical thickness4.04.75.62.42.3-2.02.0
Bone: cortical tissue density2.73.74.01.72.0-2.02.0
Condit. Reinf. active minus inactive responses1.21.31.8-0.5-1.11.3-1.3
Condit. Reinf. active-inactive response ratio0.10.10.10.30.3-0.10.1
Condit. Reinf. active responses0.50.60.80.0-0.80.9-0.9
Condit. Reinf. inactive responses0.30.41.21.1-0.30.4-0.4
Incentive salience index mean2.12.63.1-1.1-1.71.7-1.7
Condit. Reinf. lever presses2.12.93.9-1.4-2.01.7-1.7
Condit. Reinf. active minus inactive responses0.20.20.6-0.8-0.00.3-0.3
Condit. Reinf. active-inactive response ratio0.70.82.4-1.6-0.40.6-0.6
Condit. Reinf. active responses0.10.10.1-0.2-0.10.4-0.4
Condit. Reinf. inactive responses0.50.61.31.10.7-0.60.6
Condit. Reinf. lever presses0.91.31.9-0.3-1.11.4-1.4
Condit. Reinf. lever reinforcers received0.20.30.5-0.4-0.40.7-0.7
Conditioned reinforcement - actives0.00.00.10.30.0-0.10.1
Conditioned reinforcement - inactives0.00.00.0-0.2-0.20.1-0.1
Conditioned locomotion0.20.20.4-0.6-0.60.4-0.4
Patch foraging indifference point 0 sec1.32.43.51.11.9-1.61.6
Patch foraging indifference point AUC0.20.20.3-0.5-0.20.5-0.5
Delay disc. indifference point, 0s delay0.30.41.1-1.0-0.50.3-0.3
Delay disc. indifference point, 16s delay0.10.10.20.50.3-0.20.2
Delay disc. indifference point, 2s delay1.31.53.6-1.9-0.90.9-0.9
Delay disc. indifference point, 24s delay0.20.20.5-0.7-0.20.4-0.4
Delay disc. indifference point, 4s delay0.20.20.4-0.70.4-0.20.2
Delay disc. indifference point, 8s delay0.10.10.3-0.5-0.30.2-0.2
Indifference point function ln k0.40.80.9-0.9-1.00.9-0.9
Indifference point function log k0.40.80.9-0.9-1.00.9-0.9
Patch foraging total patch changes 0 sec1.42.73.71.21.9-1.71.7
Patch foraging total patch changes 12 sec1.21.52.21.01.5-1.21.2
Patch foraging total patch changes 18 sec3.96.06.52.62.5-2.42.4
Patch foraging total patch changes 24 sec1.01.73.82.01.1-0.90.9
Patch foraging total patch changes 6 sec1.52.32.81.31.7-1.51.5
Patch foraging time to switch 0 sec1.93.94.81.81.8-2.22.2
Patch foraging water rate 0 sec0.10.10.2-0.50.3-0.30.3
Patch foraging water rate 12 sec0.20.51.41.20.5-0.40.4
Patch foraging water rate 18 sec0.30.40.60.50.8-0.70.7
Patch foraging water rate 24 sec0.30.50.80.90.7-0.50.5
Patch foraging water rate 6 sec0.50.70.70.90.8-0.80.8
Seeking ratio, delayed vs. immediate footshock0.60.71.50.71.2-0.70.7
Distance traveled before self-admin0.40.50.80.20.7-0.90.9
Distance traveled after self-admin0.60.71.30.01.2-0.80.8
Extensor digitorum longus weight0.10.41.2-1.1-0.60.3-0.3
Bone: elastic displacement0.00.00.10.3-0.20.1-0.1
Bone: elastic work0.10.10.10.00.2-0.30.3
Bone: endosteal estimation1.12.59.7-3.1-0.40.2-0.2
Bone: endosteal perimeter1.22.67.8-2.8-1.10.8-0.8
Epididymis fat weight10.335.139.36.35.7-5.95.9
Delta time in closed arm before/after self-admin0.30.30.4-0.30.4-0.60.6
Delta time in open arm before/after self-admin0.10.10.30.50.10.1-0.1
Diff in mean of infusions in LGA sessions0.20.20.50.2-0.70.4-0.4
Delay discount exponential model param0.20.20.60.80.2-0.30.3
Extinction: sum of active levers before priming0.70.71.2-1.1-0.80.7-0.7
Active lever presses in extinction session 60.00.00.00.2-0.2-0.00.0
Bone: final force2.54.05.41.12.3-2.22.2
Bone: final moment1.72.73.60.91.9-1.81.8
Food consumed during 24 hour testing period0.40.60.8-0.40.7-0.90.9
Glucose6.910.817.4-4.2-3.12.8-2.8
Heart weight0.30.52.1-1.50.00.1-0.1
Delay discount hyperbolic model param0.20.30.70.90.2-0.40.4
Intermittent access intake day 1-15 change0.00.00.00.10.2-0.00.0
Intermittent access intake escalation0.20.30.60.80.6-0.40.4
Intermittent access intake escalation 20.20.20.3-0.4-0.30.5-0.5
Intermitt. access day 1 inactive lever presses0.10.51.5-1.2-0.40.4-0.4
Intermitt. access day 15 inactive lever presses0.00.10.1-0.40.3-0.30.3
Intermitt. access escalation Index0.20.20.40.1-0.60.5-0.5
Intermittent access day 1 total infusions1.11.82.9-0.7-1.71.4-1.4
Intermittent access day 15 total infusions0.10.20.20.3-0.50.5-0.5
Intermittent access terminal intake (last 3 days)0.20.30.4-0.2-0.60.6-0.6
Intermittent access total infusions0.40.50.7-0.2-0.90.8-0.8
Intermittent access day 1 locomotion0.00.00.10.3-0.2-0.00.0
Intermittent access day 15 total locomotion0.30.50.70.10.8-0.80.8
Intermittent access total locomotion0.10.10.20.40.3-0.40.4
Intermittent access standard deviation1.02.02.70.81.6-1.61.6
Left kidney weight2.09.111.91.33.5-3.43.4
Right kidney weight2.29.812.71.23.5-3.63.6
Cocaine induced anxiety0.00.00.0-0.10.2-0.20.2
Post-drug Anxiety0.10.20.20.10.5-0.40.4
Baseline Anxiety0.00.00.0-0.20.2-0.20.2
Tail length0.62.28.7-3.0-0.10.3-0.3
Length with tail0.62.58.3-2.90.7-0.80.8
Length without tail1.54.97.0-1.02.1-2.62.6
Times rat made contact with spout0.40.51.91.40.20.1-0.1
Lifetime Intake0.30.40.6-0.3-0.80.7-0.7
Liver weight, left0.50.83.2-1.80.1-0.10.1
Liver weight, right1.22.07.1-2.7-0.70.5-0.5
Locomotor activity0.10.20.5-0.70.30.2-0.2
Locomotor testing distance0.00.10.3-0.50.3-0.10.1
Locomotor testing rearing0.20.40.5-0.50.7-0.60.6
Locomotion in novel chamber0.20.20.40.60.5-0.30.3
Locomotion in novel chamber post-restriction0.91.41.80.61.3-1.31.3
Fecal boli incidents, locomotor time 10.00.00.10.2-0.40.1-0.1
Change in fecal boli incidents, locomotor task0.50.51.8-1.40.1-0.10.1
Time >=10cm from walls, locomotor time 11.71.82.6-0.51.4-1.61.6
Bouts of movement, locomotor time 10.20.20.30.3-0.30.6-0.6
Total resting periods, locomotor time 10.30.30.50.0-0.40.7-0.7
Rest time, locomotor task time 10.60.70.9-0.7-0.80.9-0.9
Distance moved, locomotor task time 10.40.60.90.20.9-0.90.9
Vertical activity count, locomotor time 11.02.32.80.91.7-1.71.7
Time >=10cm from walls, locomotor time 20.50.82.1-1.40.5-0.70.7
Bouts of movement, locomotor time 20.20.30.5-0.2-0.20.7-0.7
Total resting periods, locomotor time 20.61.11.6-0.7-0.81.3-1.3
Rest time, locomotor task time 20.40.50.8-0.9-0.60.7-0.7
Distance moved, locomotor task time 21.11.31.90.51.1-1.41.4
Vertical activity count, locomotor time 20.70.91.40.20.9-1.21.2
Light reinforcement 11.33.13.91.11.9-2.02.0
Light reinforcement 20.60.91.30.01.0-1.11.1
Bone: marrow area1.12.39.2-3.0-0.20.0-0.0
Bone: maximum diameter1.42.65.1-2.3-1.41.3-1.3
Bone: maximum force1.11.92.50.51.5-1.61.6
Bone: maximum moment0.61.01.40.21.0-1.21.2
Mean time between licks in bursts1.94.65.1-2.2-2.12.1-2.1
Mean num. licks in bursts1.21.94.12.01.2-1.01.0
Cd content in liver0.70.81.10.70.5-1.11.1
Co content in liver2.12.43.01.01.7-1.71.7
Cu content in liver0.60.82.91.70.40.0-0.0
Fe content in liver1.31.61.61.21.2-1.31.3
K content in liver0.30.30.50.2-0.60.7-0.7
Mg content in liver2.02.02.3-1.2-1.41.5-1.5
Mn content in liver1.92.04.3-2.1-1.31.0-1.0
Na content in liver0.20.20.80.90.30.0-0.0
Rb content in liver0.00.00.1-0.1-0.3-0.00.0
Se content in liver4.95.86.2-2.5-2.22.5-2.5
Sr content in liver0.30.30.8-0.9-0.3-0.30.3
Zn content in liver0.30.30.7-0.8-0.50.5-0.5
Bone: minimum diameter0.81.44.8-2.2-0.70.4-0.4
Time in familiar zone, hab. session 10.80.83.01.7-0.10.2-0.2
Time in novel zone, hab. session 10.60.62.2-1.50.3-0.20.2
Total zone transitions, hab. session 10.10.20.20.2-0.50.5-0.5
Total locomotion distance, hab. session 10.10.20.20.4-0.40.4-0.4
Locomotion velocity, hab. session 10.10.20.20.2-0.40.5-0.5
Time in familiar zone, hab. session 21.51.63.01.71.2-1.01.0
Time in novel zone, hab. session 20.60.61.4-1.2-0.60.5-0.5
Total zone transitions, hab. session 20.50.70.91.00.7-0.80.8
Total locomotion distance, hab. session 20.30.41.31.10.2-0.30.3
Locomotion velocity, hab. session 20.10.20.70.8-0.20.1-0.1
Novel to familiar place preference ratio0.30.40.4-0.5-0.70.6-0.6
Novelty place preference0.50.50.5-0.7-0.70.7-0.7
Time in novel zone, NPP test0.50.50.6-0.7-0.70.7-0.7
Total zone transitions, NPP test0.30.50.90.2-1.00.7-0.7
Total locomotion distance, NPP test0.10.20.30.5-0.50.2-0.2
Locomotion velocity, NPP test0.20.30.50.7-0.60.3-0.3
Intraocular pressure0.40.61.31.10.4-0.70.7
Delta distance traveled before/after self-admin0.10.10.2-0.50.20.3-0.3
Delta ambulatory time before/after self-admin0.10.20.4-0.60.20.4-0.4
Parametrial fat weight4.19.711.72.43.1-3.43.4
Pavlov. Cond. lever latency9.011.312.72.73.6-3.63.6
Pavlov. Cond. magazine entry latency4.96.37.6-1.9-2.52.8-2.8
Pavlov. Cond. change in total contacts3.23.44.0-1.6-1.82.0-2.0
Pavlov. Cond. index score7.49.310.3-2.5-3.23.2-3.2
Pavlov. Cond. latency score7.99.911.2-2.6-3.33.3-3.3
Pavlov. Cond. lever contacts6.88.19.2-2.5-3.02.9-2.9
Pavlov. Cond. magazine entry number3.44.35.21.62.1-2.32.3
Pavlov. Cond. intertrial magazine entries1.51.82.81.71.2-1.21.2
Pavlov. Cond. lever-magazine prob. diff.7.28.910.0-2.4-3.13.2-3.2
Pavlov. Cond. response bias5.16.37.1-2.1-2.62.7-2.7
Pavlov. Cond. lever latency0.20.30.4-0.70.2-0.50.5
Pavlov. Cond. magazine entry latency0.80.91.2-1.0-1.10.9-0.9
Pavlov. Cond. change in total contacts0.20.30.40.0-0.40.7-0.7
Pavlov. Cond. index score0.40.60.8-0.3-0.80.9-0.9
Pavlov. Cond. latency score0.30.30.5-0.2-0.60.7-0.7
Pavlov. Cond. lever contacts0.10.20.40.6-0.10.4-0.4
Pavlov. Cond. magazine entry number0.10.10.20.30.4-0.30.3
Pavlov. Cond. intertrial magazine entries0.60.91.2-0.7-0.81.1-1.1
Pavlov. Cond. lever-magazine prob. diff.0.30.40.5-0.2-0.70.7-0.7
Pavlov. Cond. response bias0.40.50.8-0.0-0.80.9-0.9
Time in closed arm before self-admin0.20.20.5-0.7-0.40.4-0.4
Time in closed arm after self-admin0.00.00.1-0.3-0.1-0.10.1
Time in open arm before self-admin1.51.72.1-0.8-1.31.5-1.5
Time in open arm after self-admin0.50.60.9-0.3-0.70.9-0.9
Bone: periosteal estimation0.40.93.6-1.90.1-0.20.2
Bone: periosteal perimeter0.61.03.1-1.8-0.60.6-0.6
Bone: post-yield work0.60.92.7-1.6-0.70.5-0.5
Progressive ratio test 1 active lever presses0.40.40.6-0.7-0.80.6-0.6
Progressive ratio test 1 breakpoint0.40.50.6-0.8-0.80.6-0.6
Progressive ratio test 1 inactive lever presses0.60.81.01.00.7-0.90.9
Progressive ratio test 2 active lever presses0.10.20.20.2-0.50.4-0.4
Progressive ratio test 2 breakpoint0.20.20.30.3-0.50.4-0.4
Progressive ratio test 2 inactive lever presses1.01.61.9-1.3-1.41.2-1.2
Incentive Sensitization - Responses0.20.30.40.2-0.50.6-0.6
Incentive Sensitization - Breakpoint0.10.20.20.4-0.40.5-0.5
Sum of active levers in priming session hrs 5-61.41.31.5-1.0-1.11.2-1.2
Progressive ratio4.26.59.01.63.0-2.72.7
Food seeking constrained by brief footshock0.00.00.10.2-0.00.2-0.2
Seeking ratio, punishment vs. effort4.05.77.0-1.6-2.62.6-2.6
Retroperitoneal fat weight0.41.72.21.11.1-1.51.5
Reaction time number correct1.42.73.01.51.6-1.71.7
Reaction time mean minus median1.43.44.1-1.5-2.01.9-1.9
Reaction time mean minus median AUC1.84.76.2-1.8-2.52.1-2.1
Reaction time num false alarms0.30.40.5-0.7-0.40.6-0.6
Reaction time num false alarms AUC0.30.40.7-0.8-0.40.7-0.7
Reaction time trials correct on left1.42.73.01.51.6-1.71.7
Reaction time trials on left1.32.52.71.41.5-1.71.7
Reaction time mean1.93.13.8-1.9-2.01.5-1.5
Reaction time mean AUC1.93.03.8-1.9-1.91.5-1.5
Median of all reaction times1.21.72.6-1.6-1.51.0-1.0
Reaction time omissions0.91.41.7-1.2-1.31.1-1.1
Reaction time false alarm rate2.02.83.1-1.8-1.41.7-1.7
Reaction time premature initiation rate0.10.10.2-0.00.3-0.40.4
Reaction time premature initiations1.01.72.20.81.4-1.51.5
Std. dev. reaction times3.05.55.8-2.3-2.42.3-2.3
Reaction time trials completed1.32.52.71.41.5-1.71.7
Reaction time trials AUC1.42.73.01.51.6-1.71.7
Run reversals in cocaine runway, females0.40.40.60.80.5-0.70.7
Run reversals in cocaine runway, males1.11.11.2-0.8-1.11.1-1.1
Latency to leave start box in cocaine runway0.60.71.0-1.0-0.90.7-0.7
Latency to leave start box in cocaine runway, F0.60.60.9-0.8-1.00.7-0.7
Latency to leave start box in cocaine runway, M0.00.00.1-0.30.0-0.20.2
Std. dev. time between licks in bursts3.24.47.2-2.7-1.81.9-1.9
Total sessions with >9 infusions0.40.50.6-0.5-0.70.8-0.8
Short access day 1 total inactive lever presses1.72.33.1-1.8-1.51.3-1.3
Short access day 10 total inactive lever presses0.00.10.30.50.3-0.20.2
Short access day 1 total infusions1.21.71.9-1.2-1.41.3-1.3
Short access day 10 total infusions0.20.20.40.0-0.60.5-0.5
Short access total infusions0.70.81.2-0.7-1.10.9-0.9
Short access day 1 locomotion0.40.50.7-0.3-0.80.8-0.8
Short access day 10 total locomotion0.30.51.6-1.30.5-0.20.2
Short access total locomotion0.30.41.2-1.1-0.30.3-0.3
One hour access (0.3 mA shock)0.40.40.50.5-0.70.7-0.7
Compulsive drug intake0.10.10.1-0.4-0.20.2-0.2
One hour access (shock baseline)0.10.10.40.6-0.30.2-0.2
Social response proportion0.30.31.3-1.10.0-0.10.1
Social responses0.10.10.4-0.70.3-0.20.2
Social time0.60.91.3-1.1-0.80.9-0.9
Soleus weight1.54.514.1-3.8-1.50.9-0.9
Bone: stiffness1.42.32.61.21.6-1.61.6
Tibialis anterior weight0.51.62.51.61.3-1.11.1
Time to tail flick, vehicle, before self-admin1.41.42.11.51.1-1.11.1
Time to tail flick, vehicle, after self-admin0.70.91.0-0.9-0.91.0-1.0
Time to tail flick, test, before self-admin0.30.31.11.00.5-0.10.1
Time to tail flick, test, after self-admin1.21.31.80.3-1.21.4-1.4
Delta time to tail flick, vehicle, before/after SA1.91.92.5-0.8-1.61.4-1.4
Delta time to tail flick, test, before/after SA0.10.10.10.3-0.30.1-0.1
Tibia length0.30.93.1-1.80.5-0.40.4
Ambulatory time before self-admin0.00.10.10.20.2-0.30.3
Ambulatory time after self-admin0.20.20.5-0.20.7-0.30.3
Bone: tissue strength0.10.10.1-0.20.1-0.30.3
Total heroin consumption0.00.00.0-0.00.00.2-0.2
Bone: trabecular number0.50.93.31.8-0.20.3-0.3
Bone: trabecular spacing0.81.12.6-1.60.4-0.90.9
Bone: trabecular thickness0.50.72.71.60.2-0.10.1
Bone: trabecular tissue density0.50.80.8-0.9-0.80.9-0.9
Water consumed over 24 hours0.10.20.5-0.7-0.30.3-0.3
Number of responses in last shaping day2.83.16.3-2.5-1.31.4-1.4