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 9.6e-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 7.9e-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 1.1e-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 3.7e-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 density0.30.62.31.5-0.2-0.20.2
Area under the delay curve0.10.10.5-0.7-0.1-0.10.1
BMI with tail2.79.511.12.33.23.3-3.3
BMI without tail0.94.86.41.12.52.4-2.4
Body weight1.98.511.60.23.33.4-3.4
Weight adjusted by age0.30.71.6-1.30.60.7-0.7
Bone surface0.00.00.1-0.2-0.2-0.10.1
Bone volume0.10.10.50.70.10.2-0.2
Breakpoint value in progressive ratio session0.10.20.3-0.2-0.5-0.50.5
Number of licking bursts0.51.42.0-1.4-1.1-1.11.1
Context. condit. distance diff. score4.65.57.0-1.8-2.7-2.42.4
Locomotion velocity, session 12.93.34.0-1.5-2.0-1.91.9
Locomotion distance, session 10.20.30.70.8-0.5-0.40.4
Locomotion velocity, session 20.40.50.7-0.5-0.8-0.80.8
Locomotion distance, session 20.10.10.30.2-0.5-0.40.4
Locomotion velocity, session 30.20.20.70.80.40.1-0.1
Locomotion distance, session 30.70.81.20.5-0.9-1.11.1
Stereotopy head waving bouts, day 30.40.51.8-1.30.10.2-0.2
Stereotopy head waving duration, day 30.30.41.6-1.3-0.00.0-0.0
Locomotion velocity, session 70.70.71.50.3-1.2-0.80.8
Locomotion distance, session 72.02.53.90.1-2.0-1.71.7
Stereotopy head waving bouts, day 70.40.50.7-0.5-0.5-0.80.8
Stereotopy head waving duration, day 70.00.00.1-0.30.1-0.20.2
Locomotion velocity, session 84.85.77.9-2.8-2.2-2.22.2
Locomotion distance, session 82.53.65.1-1.2-2.3-2.02.0
Degree of sensitization distance0.60.71.4-1.2-0.8-0.50.5
Degree of sensitization stereotypy0.70.81.2-0.1-0.8-1.11.1
Conditioned locomotion0.60.71.0-0.10.81.0-1.0
Cocaine response after cond. corrected0.20.30.60.30.40.7-0.7
Cocaine response after cond. not corrected0.20.20.5-0.70.30.4-0.4
Cocaine response before conditioning0.50.62.1-1.40.2-0.30.3
Saline control response2.53.44.91.62.21.7-1.7
Bone: connectivity density0.10.20.91.0-0.10.1-0.1
Bone: cortical apparent density2.64.14.41.92.12.1-2.1
Bone: cortical area0.00.00.1-0.20.30.2-0.2
Bone: cortical porosity2.42.63.4-1.2-1.5-1.91.9
Bone: cortical porosity3.53.84.4-1.8-1.8-2.12.1
Bone: cortical thickness1.52.54.02.01.61.3-1.3
Bone: cortical thickness3.94.75.62.42.32.0-2.0
Bone: cortical tissue density2.33.74.01.72.02.0-2.0
Condit. Reinf. active minus inactive responses1.11.31.8-0.5-1.1-1.31.3
Condit. Reinf. active-inactive response ratio0.10.10.10.30.30.1-0.1
Condit. Reinf. active responses0.40.60.80.0-0.8-0.90.9
Condit. Reinf. inactive responses0.30.41.21.1-0.3-0.40.4
Incentive salience index mean2.02.63.1-1.1-1.7-1.71.7
Condit. Reinf. lever presses1.92.93.9-1.4-2.0-1.71.7
Condit. Reinf. active minus inactive responses0.10.20.6-0.8-0.0-0.30.3
Condit. Reinf. active-inactive response ratio0.50.82.4-1.6-0.4-0.60.6
Condit. Reinf. active responses0.10.10.1-0.2-0.1-0.40.4
Condit. Reinf. inactive responses0.40.61.31.10.70.6-0.6
Condit. Reinf. lever presses0.91.31.9-0.3-1.1-1.41.4
Condit. Reinf. lever reinforcers received0.20.30.5-0.4-0.4-0.70.7
Conditioned reinforcement - actives0.00.00.10.30.00.1-0.1
Conditioned reinforcement - inactives0.00.00.0-0.2-0.2-0.10.1
Conditioned locomotion0.20.20.4-0.6-0.6-0.40.4
Patch foraging indifference point 0 sec0.92.43.51.11.91.6-1.6
Patch foraging indifference point AUC0.10.20.3-0.5-0.2-0.50.5
Delay disc. indifference point, 0s delay0.30.41.1-1.0-0.5-0.30.3
Delay disc. indifference point, 16s delay0.10.10.20.50.30.2-0.2
Delay disc. indifference point, 2s delay1.31.53.6-1.9-0.9-0.90.9
Delay disc. indifference point, 24s delay0.10.20.5-0.7-0.2-0.40.4
Delay disc. indifference point, 4s delay0.20.20.4-0.70.40.2-0.2
Delay disc. indifference point, 8s delay0.10.10.3-0.5-0.3-0.20.2
Indifference point function ln k0.30.80.9-0.9-1.0-0.90.9
Indifference point function log k0.30.80.9-0.9-1.0-0.90.9
Patch foraging total patch changes 0 sec0.92.73.71.21.91.7-1.7
Patch foraging total patch changes 12 sec1.11.52.21.01.51.2-1.2
Patch foraging total patch changes 18 sec2.56.06.52.62.52.4-2.4
Patch foraging total patch changes 24 sec0.51.73.82.01.10.9-0.9
Patch foraging total patch changes 6 sec1.32.32.81.31.71.5-1.5
Patch foraging time to switch 0 sec1.03.94.81.81.82.2-2.2
Patch foraging water rate 0 sec0.00.10.2-0.50.30.3-0.3
Patch foraging water rate 12 sec0.10.51.41.20.50.4-0.4
Patch foraging water rate 18 sec0.20.40.60.50.80.7-0.7
Patch foraging water rate 24 sec0.30.50.80.90.70.5-0.5
Patch foraging water rate 6 sec0.50.70.70.90.80.8-0.8
Seeking ratio, delayed vs. immediate footshock0.50.71.50.71.20.7-0.7
Distance traveled before self-admin0.20.50.80.20.70.9-0.9
Distance traveled after self-admin0.40.71.30.01.20.8-0.8
Extensor digitorum longus weight0.10.41.2-1.1-0.6-0.30.3
Bone: elastic displacement0.00.00.10.3-0.2-0.10.1
Bone: elastic work0.10.10.10.00.20.3-0.3
Bone: endosteal estimation1.02.59.7-3.1-0.4-0.20.2
Bone: endosteal perimeter1.12.67.8-2.8-1.1-0.80.8
Epididymis fat weight6.935.139.36.35.75.9-5.9
Delta time in closed arm before/after self-admin0.30.30.4-0.30.40.6-0.6
Delta time in open arm before/after self-admin0.10.10.30.50.1-0.10.1
Diff in mean of infusions in LGA sessions0.10.20.50.2-0.7-0.40.4
Delay discount exponential model param0.10.20.60.80.20.3-0.3
Extinction: sum of active levers before priming0.50.71.2-1.1-0.8-0.70.7
Active lever presses in extinction session 60.00.00.00.2-0.20.0-0.0
Bone: final force2.54.05.41.12.32.2-2.2
Bone: final moment1.72.73.60.91.91.8-1.8
Food consumed during 24 hour testing period0.30.60.8-0.40.70.9-0.9
Glucose6.810.817.4-4.2-3.1-2.82.8
Heart weight0.30.52.1-1.50.0-0.10.1
Delay discount hyperbolic model param0.20.30.70.90.20.4-0.4
Intermittent access intake day 1-15 change0.00.00.00.10.20.0-0.0
Intermittent access intake escalation0.10.30.60.80.60.4-0.4
Intermittent access intake escalation 20.10.20.3-0.4-0.3-0.50.5
Intermitt. access day 1 inactive lever presses0.00.51.5-1.2-0.4-0.40.4
Intermitt. access day 15 inactive lever presses0.00.10.1-0.40.30.3-0.3
Intermitt. access escalation Index0.10.20.40.1-0.6-0.50.5
Intermittent access day 1 total infusions0.61.82.9-0.7-1.7-1.41.4
Intermittent access day 15 total infusions0.10.20.20.3-0.5-0.50.5
Intermittent access terminal intake (last 3 days)0.20.30.4-0.2-0.6-0.60.6
Intermittent access total infusions0.40.50.7-0.2-0.9-0.80.8
Intermittent access day 1 locomotion0.00.00.10.3-0.20.0-0.0
Intermittent access day 15 total locomotion0.10.50.70.10.80.8-0.8
Intermittent access total locomotion0.10.10.20.40.30.4-0.4
Intermittent access standard deviation0.42.02.70.81.61.6-1.6
Left kidney weight1.19.111.91.33.53.4-3.4
Right kidney weight1.49.812.71.23.53.6-3.6
Cocaine induced anxiety0.00.00.0-0.10.20.2-0.2
Post-drug Anxiety0.10.20.20.10.50.4-0.4
Baseline Anxiety0.00.00.0-0.20.20.2-0.2
Tail length0.42.28.7-3.0-0.1-0.30.3
Length with tail0.62.58.3-2.90.70.8-0.8
Length without tail0.94.97.0-1.02.12.6-2.6
Times rat made contact with spout0.40.51.91.40.2-0.10.1
Lifetime Intake0.30.40.6-0.3-0.8-0.70.7
Liver weight, left0.50.83.2-1.80.10.1-0.1
Liver weight, right1.22.07.1-2.7-0.7-0.50.5
Locomotor activity0.10.20.5-0.70.3-0.20.2
Locomotor testing distance0.00.10.3-0.50.30.1-0.1
Locomotor testing rearing0.10.40.5-0.50.70.6-0.6
Locomotion in novel chamber0.20.20.40.60.50.3-0.3
Locomotion in novel chamber post-restriction0.51.41.80.61.31.3-1.3
Fecal boli incidents, locomotor time 10.00.00.10.2-0.4-0.10.1
Change in fecal boli incidents, locomotor task0.40.51.8-1.40.10.1-0.1
Time >=10cm from walls, locomotor time 11.51.82.6-0.51.41.6-1.6
Bouts of movement, locomotor time 10.20.20.30.3-0.3-0.60.6
Total resting periods, locomotor time 10.20.30.50.0-0.4-0.70.7
Rest time, locomotor task time 10.40.70.9-0.7-0.8-0.90.9
Distance moved, locomotor task time 10.20.60.90.20.90.9-0.9
Vertical activity count, locomotor time 10.32.32.80.91.71.7-1.7
Time >=10cm from walls, locomotor time 20.30.82.1-1.40.50.7-0.7
Bouts of movement, locomotor time 20.10.30.5-0.2-0.2-0.70.7
Total resting periods, locomotor time 20.31.11.6-0.7-0.8-1.31.3
Rest time, locomotor task time 20.30.50.8-0.9-0.6-0.70.7
Distance moved, locomotor task time 21.01.31.90.51.11.4-1.4
Vertical activity count, locomotor time 20.40.91.40.20.91.2-1.2
Light reinforcement 10.73.13.91.11.92.0-2.0
Light reinforcement 20.40.91.30.01.01.1-1.1
Bone: marrow area0.92.39.2-3.0-0.2-0.00.0
Bone: maximum diameter1.32.65.1-2.3-1.4-1.31.3
Bone: maximum force0.91.92.50.51.51.6-1.6
Bone: maximum moment0.51.01.40.21.01.2-1.2
Mean time between licks in bursts0.84.65.1-2.2-2.1-2.12.1
Mean num. licks in bursts0.71.94.12.01.21.0-1.0
Cd content in liver0.70.81.10.70.51.1-1.1
Co content in liver2.12.43.01.01.71.7-1.7
Cu content in liver0.60.82.91.70.4-0.00.0
Fe content in liver1.31.61.61.21.21.3-1.3
K content in liver0.30.30.50.2-0.6-0.70.7
Mg content in liver1.82.02.3-1.2-1.4-1.51.5
Mn content in liver1.82.04.3-2.1-1.3-1.01.0
Na content in liver0.20.20.80.90.3-0.00.0
Rb content in liver0.00.00.1-0.1-0.30.0-0.0
Se content in liver4.95.86.2-2.5-2.2-2.52.5
Sr content in liver0.30.30.8-0.9-0.30.3-0.3
Zn content in liver0.30.30.7-0.8-0.5-0.50.5
Bone: minimum diameter0.71.44.8-2.2-0.7-0.40.4
Time in familiar zone, hab. session 10.70.83.01.7-0.1-0.20.2
Time in novel zone, hab. session 10.50.62.2-1.50.30.2-0.2
Total zone transitions, hab. session 10.10.20.20.2-0.5-0.50.5
Total locomotion distance, hab. session 10.10.20.20.4-0.4-0.40.4
Locomotion velocity, hab. session 10.10.20.20.2-0.4-0.50.5
Time in familiar zone, hab. session 21.41.63.01.71.21.0-1.0
Time in novel zone, hab. session 20.50.61.4-1.2-0.6-0.50.5
Total zone transitions, hab. session 20.50.70.91.00.70.8-0.8
Total locomotion distance, hab. session 20.30.41.31.10.20.3-0.3
Locomotion velocity, hab. session 20.10.20.70.8-0.2-0.10.1
Novel to familiar place preference ratio0.30.40.4-0.5-0.7-0.60.6
Novelty place preference0.40.50.5-0.7-0.7-0.70.7
Time in novel zone, NPP test0.40.50.6-0.7-0.7-0.70.7
Total zone transitions, NPP test0.30.50.90.2-1.0-0.70.7
Total locomotion distance, NPP test0.10.20.30.5-0.5-0.20.2
Locomotion velocity, NPP test0.20.30.50.7-0.6-0.30.3
Intraocular pressure0.40.61.31.10.40.7-0.7
Delta distance traveled before/after self-admin0.10.10.2-0.50.2-0.30.3
Delta ambulatory time before/after self-admin0.10.20.4-0.60.2-0.40.4
Parametrial fat weight4.19.711.72.43.13.4-3.4
Pavlov. Cond. lever latency8.911.312.72.73.63.6-3.6
Pavlov. Cond. magazine entry latency4.96.37.6-1.9-2.5-2.82.8
Pavlov. Cond. change in total contacts3.23.44.0-1.6-1.8-2.02.0
Pavlov. Cond. index score7.39.310.3-2.5-3.2-3.23.2
Pavlov. Cond. latency score7.89.911.2-2.6-3.3-3.33.3
Pavlov. Cond. lever contacts6.78.19.2-2.5-3.0-2.92.9
Pavlov. Cond. magazine entry number3.44.35.21.62.12.3-2.3
Pavlov. Cond. intertrial magazine entries1.51.82.81.71.21.2-1.2
Pavlov. Cond. lever-magazine prob. diff.7.28.910.0-2.4-3.1-3.23.2
Pavlov. Cond. response bias5.16.37.1-2.1-2.6-2.72.7
Pavlov. Cond. lever latency0.20.30.4-0.70.20.5-0.5
Pavlov. Cond. magazine entry latency0.70.91.2-1.0-1.1-0.90.9
Pavlov. Cond. change in total contacts0.10.30.40.0-0.4-0.70.7
Pavlov. Cond. index score0.40.60.8-0.3-0.8-0.90.9
Pavlov. Cond. latency score0.20.30.5-0.2-0.6-0.70.7
Pavlov. Cond. lever contacts0.10.20.40.6-0.1-0.40.4
Pavlov. Cond. magazine entry number0.10.10.20.30.40.3-0.3
Pavlov. Cond. intertrial magazine entries0.40.91.2-0.7-0.8-1.11.1
Pavlov. Cond. lever-magazine prob. diff.0.30.40.5-0.2-0.7-0.70.7
Pavlov. Cond. response bias0.40.50.8-0.0-0.8-0.90.9
Time in closed arm before self-admin0.10.20.5-0.7-0.4-0.40.4
Time in closed arm after self-admin0.00.00.1-0.3-0.10.1-0.1
Time in open arm before self-admin1.41.72.1-0.8-1.3-1.51.5
Time in open arm after self-admin0.50.60.9-0.3-0.7-0.90.9
Bone: periosteal estimation0.40.93.6-1.90.10.2-0.2
Bone: periosteal perimeter0.51.03.1-1.8-0.6-0.60.6
Bone: post-yield work0.50.92.7-1.6-0.7-0.50.5
Progressive ratio test 1 active lever presses0.20.40.6-0.7-0.8-0.60.6
Progressive ratio test 1 breakpoint0.30.50.6-0.8-0.8-0.60.6
Progressive ratio test 1 inactive lever presses0.30.81.01.00.70.9-0.9
Progressive ratio test 2 active lever presses0.10.20.20.2-0.5-0.40.4
Progressive ratio test 2 breakpoint0.10.20.30.3-0.5-0.40.4
Progressive ratio test 2 inactive lever presses0.51.61.9-1.3-1.4-1.21.2
Incentive Sensitization - Responses0.10.30.40.2-0.5-0.60.6
Incentive Sensitization - Breakpoint0.10.20.20.4-0.4-0.50.5
Sum of active levers in priming session hrs 5-61.31.31.5-1.0-1.1-1.21.2
Progressive ratio2.26.59.01.63.02.7-2.7
Food seeking constrained by brief footshock0.00.00.10.2-0.0-0.20.2
Seeking ratio, punishment vs. effort2.65.77.0-1.6-2.6-2.62.6
Retroperitoneal fat weight0.41.72.21.11.11.5-1.5
Reaction time number correct0.82.73.01.51.61.7-1.7
Reaction time mean minus median0.53.44.1-1.5-2.0-1.91.9
Reaction time mean minus median AUC0.74.76.2-1.8-2.5-2.12.1
Reaction time num false alarms0.20.40.5-0.7-0.4-0.60.6
Reaction time num false alarms AUC0.20.40.7-0.8-0.4-0.70.7
Reaction time trials correct on left0.82.73.01.51.61.7-1.7
Reaction time trials on left0.72.52.71.41.51.7-1.7
Reaction time mean1.43.13.8-1.9-2.0-1.51.5
Reaction time mean AUC1.23.03.8-1.9-1.9-1.51.5
Median of all reaction times1.11.72.6-1.6-1.5-1.01.0
Reaction time omissions0.81.41.7-1.2-1.3-1.11.1
Reaction time false alarm rate2.02.83.1-1.8-1.4-1.71.7
Reaction time premature initiation rate0.10.10.2-0.00.30.4-0.4
Reaction time premature initiations0.61.72.20.81.41.5-1.5
Std. dev. reaction times1.75.55.8-2.3-2.4-2.32.3
Reaction time trials completed0.72.52.71.41.51.7-1.7
Reaction time trials AUC0.82.73.01.51.61.7-1.7
Run reversals in cocaine runway, females0.40.40.60.80.50.7-0.7
Run reversals in cocaine runway, males1.01.11.2-0.8-1.1-1.11.1
Latency to leave start box in cocaine runway0.50.71.0-1.0-0.9-0.70.7
Latency to leave start box in cocaine runway, F0.50.60.9-0.8-1.0-0.70.7
Latency to leave start box in cocaine runway, M0.00.00.1-0.30.00.2-0.2
Std. dev. time between licks in bursts2.34.47.2-2.7-1.8-1.91.9
Total sessions with >9 infusions0.40.50.6-0.5-0.7-0.80.8
Short access day 1 total inactive lever presses1.12.33.1-1.8-1.5-1.31.3
Short access day 10 total inactive lever presses0.00.10.30.50.30.2-0.2
Short access day 1 total infusions0.81.71.9-1.2-1.4-1.31.3
Short access day 10 total infusions0.10.20.40.0-0.6-0.50.5
Short access total infusions0.60.81.2-0.7-1.1-0.90.9
Short access day 1 locomotion0.30.50.7-0.3-0.8-0.80.8
Short access day 10 total locomotion0.10.51.6-1.30.50.2-0.2
Short access total locomotion0.20.41.2-1.1-0.3-0.30.3
One hour access (0.3 mA shock)0.40.40.50.5-0.7-0.70.7
Compulsive drug intake0.10.10.1-0.4-0.2-0.20.2
One hour access (shock baseline)0.10.10.40.6-0.3-0.20.2
Social response proportion0.30.31.3-1.10.00.1-0.1
Social responses0.10.10.4-0.70.30.2-0.2
Social time0.50.91.3-1.1-0.8-0.90.9
Soleus weight1.54.514.1-3.8-1.5-0.90.9
Bone: stiffness1.32.32.61.21.61.6-1.6
Tibialis anterior weight0.51.62.51.61.31.1-1.1
Time to tail flick, vehicle, before self-admin1.11.42.11.51.11.1-1.1
Time to tail flick, vehicle, after self-admin0.40.91.0-0.9-0.9-1.01.0
Time to tail flick, test, before self-admin0.30.31.11.00.50.1-0.1
Time to tail flick, test, after self-admin1.21.31.80.3-1.2-1.41.4
Delta time to tail flick, vehicle, before/after SA1.71.92.5-0.8-1.6-1.41.4
Delta time to tail flick, test, before/after SA0.00.10.10.3-0.3-0.10.1
Tibia length0.30.93.1-1.80.50.4-0.4
Ambulatory time before self-admin0.00.10.10.20.20.3-0.3
Ambulatory time after self-admin0.10.20.5-0.20.70.3-0.3
Bone: tissue strength0.00.10.1-0.20.10.3-0.3
Total heroin consumption0.00.00.0-0.00.0-0.20.2
Bone: trabecular number0.50.93.31.8-0.2-0.30.3
Bone: trabecular spacing0.71.12.6-1.60.40.9-0.9
Bone: trabecular thickness0.50.72.71.60.20.1-0.1
Bone: trabecular tissue density0.40.80.8-0.9-0.8-0.90.9
Water consumed over 24 hours0.10.20.5-0.7-0.3-0.30.3
Number of responses in last shaping day2.43.16.3-2.5-1.3-1.41.4