Tk1

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 Liver gene expression Tk1 0.17 0.1 6.1e-09 0.06 0.07 0.07 0.05 1.1e-07 2.3e-08 2.2e-08 1.8e-06
2 IL alternative polyA NM_052800.1 0.12 0.1 8.2e-03 0.03 0.03 0.06 0.03 6.8e-02 7.9e-02 1.3e-02 6.7e-02
3 Adipose intron excision ratio chr10_103045009_103045844 0.02 0.02 8.5e-03 0.01 0.01 0 0.01 1.8e-02 2.5e-02 2.5e-01 4.6e-02

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 density1.01.62.61.60.4-1.4
Area under the delay curve2.12.34.6-0.1-2.11.5
BMI with tail1.44.48.3-1.92.9-1.2
BMI without tail1.22.53.80.91.9-1.7
Body weight0.52.36.0-2.50.40.8
Weight adjusted by age0.00.10.1-0.2-0.30.1
Bone surface1.22.25.70.5-2.40.7
Bone volume0.61.02.00.9-1.4-0.3
Breakpoint value in progressive ratio session0.30.30.6-0.60.2-0.8
Number of licking bursts0.00.10.10.1-0.30.2
Context. condit. distance diff. score0.10.10.2-0.5-0.40.1
Locomotion velocity, session 10.91.01.9-0.3-0.91.4
Locomotion distance, session 11.82.42.71.31.7-1.6
Locomotion velocity, session 20.40.40.50.70.6-0.7
Locomotion distance, session 24.56.36.92.32.6-2.6
Locomotion velocity, session 30.40.40.70.3-0.70.8
Locomotion distance, session 30.60.71.8-0.11.3-0.5
Stereotopy head waving bouts, day 31.61.93.2-1.8-1.21.1
Stereotopy head waving duration, day 31.72.12.7-1.5-1.61.1
Locomotion velocity, session 70.20.30.60.8-0.40.0
Locomotion distance, session 72.73.44.41.91.5-2.1
Stereotopy head waving bouts, day 73.03.43.8-2.0-1.71.8
Stereotopy head waving duration, day 75.26.37.5-2.1-2.72.6
Locomotion velocity, session 80.91.12.10.0-1.51.1
Locomotion distance, session 82.33.44.71.51.8-2.2
Degree of sensitization distance2.92.95.92.40.2-1.7
Degree of sensitization stereotypy1.31.41.5-1.2-1.11.2
Conditioned locomotion0.20.20.40.30.2-0.6
Cocaine response after cond. corrected0.20.30.7-0.90.00.2
Cocaine response after cond. not corrected0.10.10.2-0.3-0.40.3
Cocaine response before conditioning0.70.91.61.3-0.90.3
Saline control response1.41.82.31.5-1.21.2
Bone: connectivity density1.32.15.32.30.3-1.0
Bone: cortical apparent density2.12.75.50.22.3-1.6
Bone: cortical area2.53.79.5-3.1-0.51.2
Bone: cortical porosity2.02.23.0-1.0-1.71.6
Bone: cortical porosity2.72.94.3-1.1-2.11.8
Bone: cortical thickness2.44.06.7-2.62.3-0.0
Bone: cortical thickness1.11.32.3-1.51.3-0.0
Bone: cortical tissue density2.12.85.40.32.3-1.7
Condit. Reinf. active minus inactive responses0.20.20.40.6-0.3-0.2
Condit. Reinf. active-inactive response ratio0.30.30.50.7-0.5-0.3
Condit. Reinf. active responses0.40.51.31.10.0-0.4
Condit. Reinf. inactive responses0.50.61.11.10.6-0.5
Incentive salience index mean0.20.20.30.5-0.60.2
Condit. Reinf. lever presses0.10.10.20.4-0.3-0.0
Condit. Reinf. active minus inactive responses0.80.92.00.1-1.40.9
Condit. Reinf. active-inactive response ratio0.40.40.60.2-0.80.7
Condit. Reinf. active responses0.10.20.30.6-0.5-0.2
Condit. Reinf. inactive responses0.50.60.91.00.2-0.8
Condit. Reinf. lever presses0.81.12.11.50.1-1.1
Condit. Reinf. lever reinforcers received0.20.20.40.5-0.1-0.6
Conditioned reinforcement - actives0.91.01.40.61.0-1.2
Conditioned reinforcement - inactives0.20.30.5-0.7-0.00.5
Conditioned locomotion1.21.52.50.61.3-1.6
Patch foraging indifference point 0 sec0.71.11.80.90.8-1.4
Patch foraging indifference point AUC1.61.84.52.10.6-0.7
Delay disc. indifference point, 0s delay1.82.02.9-0.6-1.61.7
Delay disc. indifference point, 16s delay0.30.30.70.9-0.0-0.4
Delay disc. indifference point, 2s delay1.11.22.80.2-1.70.9
Delay disc. indifference point, 24s delay0.10.10.20.4-0.40.1
Delay disc. indifference point, 4s delay2.22.34.2-0.2-2.01.6
Delay disc. indifference point, 8s delay5.05.18.3-0.9-2.92.5
Indifference point function ln k1.31.83.0-1.71.3-0.7
Indifference point function log k1.31.83.0-1.71.3-0.7
Patch foraging total patch changes 0 sec1.01.62.71.11.1-1.6
Patch foraging total patch changes 12 sec2.93.85.22.31.7-1.8
Patch foraging total patch changes 18 sec2.02.65.82.40.2-1.4
Patch foraging total patch changes 24 sec0.60.71.60.5-1.30.6
Patch foraging total patch changes 6 sec1.62.32.81.71.4-1.5
Patch foraging time to switch 0 sec0.20.30.5-0.5-0.50.7
Patch foraging water rate 0 sec0.40.71.11.10.3-0.9
Patch foraging water rate 12 sec1.52.24.0-1.02.0-1.3
Patch foraging water rate 18 sec0.40.51.00.20.7-1.0
Patch foraging water rate 24 sec1.52.23.21.31.2-1.8
Patch foraging water rate 6 sec0.50.71.3-0.71.2-0.6
Seeking ratio, delayed vs. immediate footshock0.20.20.50.70.10.2
Distance traveled before self-admin1.61.72.7-0.5-1.51.6
Distance traveled after self-admin1.31.42.11.20.7-1.5
Extensor digitorum longus weight1.35.07.11.32.7-2.5
Bone: elastic displacement1.61.84.00.12.0-1.2
Bone: elastic work0.91.22.6-1.61.0-0.0
Bone: endosteal estimation1.22.77.7-0.3-2.80.4
Bone: endosteal perimeter4.49.220.5-1.5-4.52.2
Epididymis fat weight0.40.91.4-1.21.0-0.6
Delta time in closed arm before/after self-admin0.70.71.30.1-1.10.8
Delta time in open arm before/after self-admin0.80.81.51.20.5-0.8
Diff in mean of infusions in LGA sessions0.40.50.8-0.9-0.8-0.2
Delay discount exponential model param2.52.75.30.22.3-1.6
Extinction: sum of active levers before priming0.20.20.3-0.50.5-0.3
Active lever presses in extinction session 60.60.61.0-0.11.0-0.8
Bone: final force1.01.63.5-1.9-0.31.1
Bone: final moment1.11.74.0-2.0-0.41.1
Food consumed during 24 hour testing period0.91.11.91.0-1.40.7
Glucose0.30.40.8-0.50.9-0.4
Heart weight1.11.52.9-1.71.2-0.3
Delay discount hyperbolic model param2.32.55.00.22.2-1.5
Intermittent access intake day 1-15 change0.50.51.00.3-0.61.0
Intermittent access intake escalation0.50.50.60.7-0.70.8
Intermittent access intake escalation 20.30.30.91.0-0.10.2
Intermitt. access day 1 inactive lever presses2.12.22.6-1.3-1.51.6
Intermitt. access day 15 inactive lever presses0.30.30.70.80.3-0.3
Intermitt. access escalation Index1.21.12.0-0.1-1.41.1
Intermittent access day 1 total infusions0.50.51.1-1.10.5-0.5
Intermittent access day 15 total infusions0.00.00.10.0-0.30.2
Intermittent access terminal intake (last 3 days)0.10.10.2-0.4-0.40.4
Intermittent access total infusions0.10.20.5-0.7-0.0-0.0
Intermittent access day 1 locomotion0.70.81.40.20.9-1.2
Intermittent access day 15 total locomotion0.20.20.4-0.70.3-0.1
Intermittent access total locomotion0.40.50.8-0.00.8-0.9
Intermittent access standard deviation3.43.65.1-2.3-1.32.0
Left kidney weight2.57.010.9-3.3-1.92.5
Right kidney weight1.02.75.2-2.3-0.81.5
Cocaine induced anxiety0.91.01.6-0.0-1.21.3
Post-drug Anxiety0.50.50.90.9-0.70.5
Baseline Anxiety0.10.10.3-0.20.5-0.4
Tail length0.41.43.01.7-1.00.1
Length with tail1.24.35.5-1.5-2.42.2
Length without tail3.37.213.3-3.6-1.52.4
Times rat made contact with spout0.40.41.11.1-0.1-0.3
Lifetime Intake0.30.30.9-1.00.10.0
Liver weight, left2.23.54.2-2.1-1.52.0
Liver weight, right0.81.32.1-1.4-0.51.2
Locomotor activity0.00.00.10.1-0.2-0.2
Locomotor testing distance0.10.10.30.1-0.6-0.3
Locomotor testing rearing0.81.22.61.60.1-1.0
Locomotion in novel chamber1.01.23.11.8-0.7-0.2
Locomotion in novel chamber post-restriction0.20.20.70.1-0.80.2
Fecal boli incidents, locomotor time 10.70.71.60.10.7-1.3
Change in fecal boli incidents, locomotor task0.10.10.3-0.00.5-0.4
Time >=10cm from walls, locomotor time 10.50.51.00.6-1.00.5
Bouts of movement, locomotor time 10.20.20.4-0.40.6-0.3
Total resting periods, locomotor time 10.20.20.4-0.20.7-0.4
Rest time, locomotor task time 10.70.81.4-1.20.9-0.1
Distance moved, locomotor task time 10.40.41.01.0-0.50.1
Vertical activity count, locomotor time 11.21.23.21.80.2-0.7
Time >=10cm from walls, locomotor time 20.30.30.60.50.7-0.3
Bouts of movement, locomotor time 20.10.10.3-0.5-0.20.2
Total resting periods, locomotor time 20.10.10.2-0.5-0.30.1
Rest time, locomotor task time 20.30.41.0-1.0-0.40.1
Distance moved, locomotor task time 20.10.20.40.30.60.0
Vertical activity count, locomotor time 20.20.20.40.20.6-0.5
Light reinforcement 11.62.93.21.71.8-1.6
Light reinforcement 20.10.20.20.50.50.1
Bone: marrow area1.32.77.9-0.4-2.80.4
Bone: maximum diameter5.410.012.8-3.2-3.62.6
Bone: maximum force1.01.74.7-2.2-0.10.7
Bone: maximum moment1.11.95.2-2.3-0.20.7
Mean time between licks in bursts0.00.00.0-0.00.00.0
Mean num. licks in bursts0.40.50.70.70.6-0.9
Cd content in liver1.61.83.90.12.0-1.2
Co content in liver0.80.91.50.11.2-1.1
Cu content in liver0.10.10.2-0.50.00.0
Fe content in liver0.60.82.00.4-1.40.4
K content in liver0.20.20.30.5-0.60.4
Mg content in liver1.31.41.91.40.9-1.1
Mn content in liver0.80.91.6-0.5-1.01.3
Na content in liver0.90.91.80.0-1.31.0
Rb content in liver2.42.93.41.81.7-1.6
Se content in liver0.81.02.41.5-0.70.1
Sr content in liver0.40.40.6-0.80.70.1
Zn content in liver1.21.32.4-1.5-0.81.0
Bone: minimum diameter2.24.16.8-1.8-2.61.5
Time in familiar zone, hab. session 10.10.10.10.10.4-0.1
Time in novel zone, hab. session 10.40.40.6-0.2-0.70.8
Total zone transitions, hab. session 11.52.22.51.61.2-1.6
Total locomotion distance, hab. session 11.31.82.31.31.2-1.5
Locomotion velocity, hab. session 11.72.53.31.31.5-1.8
Time in familiar zone, hab. session 20.30.30.6-0.10.8-0.4
Time in novel zone, hab. session 20.40.40.7-0.3-0.80.7
Total zone transitions, hab. session 25.26.88.42.42.5-2.9
Total locomotion distance, hab. session 25.26.88.32.02.9-2.9
Locomotion velocity, hab. session 25.06.78.02.12.8-2.8
Novel to familiar place preference ratio2.22.33.31.21.4-1.8
Novelty place preference1.61.72.51.11.1-1.6
Time in novel zone, NPP test2.02.12.91.21.3-1.7
Total zone transitions, NPP test3.24.65.32.02.1-2.3
Total locomotion distance, NPP test6.58.911.02.23.3-3.3
Locomotion velocity, NPP test5.47.79.72.13.0-3.1
Intraocular pressure0.70.91.80.70.7-1.4
Delta distance traveled before/after self-admin3.43.75.41.41.9-2.3
Delta ambulatory time before/after self-admin3.63.95.81.61.9-2.4
Parametrial fat weight0.10.20.4-0.60.3-0.1
Pavlov. Cond. lever latency0.60.81.01.00.7-0.9
Pavlov. Cond. magazine entry latency2.63.44.7-1.2-2.22.0
Pavlov. Cond. change in total contacts0.40.40.7-0.30.8-0.7
Pavlov. Cond. index score1.62.02.2-1.3-1.51.5
Pavlov. Cond. latency score2.02.62.9-1.5-1.61.7
Pavlov. Cond. lever contacts0.20.20.4-0.7-0.10.3
Pavlov. Cond. magazine entry number3.03.84.31.82.1-2.0
Pavlov. Cond. intertrial magazine entries1.92.33.31.81.2-1.5
Pavlov. Cond. lever-magazine prob. diff.1.11.41.7-1.0-1.31.2
Pavlov. Cond. response bias1.41.71.8-1.3-1.31.3
Pavlov. Cond. lever latency1.11.42.3-1.5-0.11.4
Pavlov. Cond. magazine entry latency0.60.71.40.00.9-1.2
Pavlov. Cond. change in total contacts0.91.32.31.00.7-1.5
Pavlov. Cond. index score0.70.91.71.00.2-1.3
Pavlov. Cond. latency score0.50.61.10.80.0-1.1
Pavlov. Cond. lever contacts1.21.63.31.8-0.3-1.2
Pavlov. Cond. magazine entry number0.91.12.1-0.5-0.91.5
Pavlov. Cond. intertrial magazine entries1.41.83.01.5-1.70.4
Pavlov. Cond. lever-magazine prob. diff.0.81.01.91.10.3-1.4
Pavlov. Cond. response bias0.81.01.71.20.3-1.3
Time in closed arm before self-admin0.30.30.7-0.50.9-0.2
Time in closed arm after self-admin1.61.72.8-1.7-0.91.2
Time in open arm before self-admin0.30.30.5-0.7-0.10.6
Time in open arm after self-admin0.50.60.91.00.6-0.7
Bone: periosteal estimation1.83.75.2-2.2-2.31.1
Bone: periosteal perimeter4.67.79.7-3.1-2.82.4
Bone: post-yield work0.60.81.40.50.8-1.2
Progressive ratio test 1 active lever presses0.10.10.20.30.1-0.4
Progressive ratio test 1 breakpoint0.10.10.20.00.2-0.4
Progressive ratio test 1 inactive lever presses0.30.30.5-0.3-0.70.6
Progressive ratio test 2 active lever presses0.30.30.6-0.10.6-0.8
Progressive ratio test 2 breakpoint0.30.40.6-0.00.7-0.8
Progressive ratio test 2 inactive lever presses0.00.00.1-0.30.3-0.0
Incentive Sensitization - Responses0.60.61.6-1.3-0.00.4
Incentive Sensitization - Breakpoint0.70.71.8-1.3-0.20.6
Sum of active levers in priming session hrs 5-60.20.20.4-0.6-0.3-0.2
Progressive ratio0.20.30.3-0.60.4-0.6
Food seeking constrained by brief footshock0.50.61.2-1.1-0.40.6
Seeking ratio, punishment vs. effort0.50.61.00.0-0.91.0
Retroperitoneal fat weight0.30.91.5-1.2-0.70.8
Reaction time number correct2.84.06.62.61.3-1.9
Reaction time mean minus median0.60.81.5-1.2-0.20.9
Reaction time mean minus median AUC1.01.32.0-1.0-0.91.4
Reaction time num false alarms0.10.10.30.20.1-0.5
Reaction time num false alarms AUC0.20.30.70.50.3-0.8
Reaction time trials correct on left2.84.06.62.61.3-1.9
Reaction time trials on left2.83.96.52.61.3-1.9
Reaction time mean0.00.00.1-0.4-0.00.2
Reaction time mean AUC0.10.10.1-0.30.3-0.1
Median of all reaction times0.00.00.0-0.1-0.1-0.0
Reaction time omissions0.60.80.9-0.9-0.91.0
Reaction time false alarm rate0.20.30.7-0.8-0.40.3
Reaction time premature initiation rate3.04.06.01.12.4-2.2
Reaction time premature initiations5.57.89.52.32.9-3.1
Std. dev. reaction times0.10.20.4-0.70.30.2
Reaction time trials completed2.83.96.52.61.3-1.9
Reaction time trials AUC3.34.87.62.81.5-2.1
Run reversals in cocaine runway, females0.10.10.1-0.3-0.30.1
Run reversals in cocaine runway, males1.01.01.7-1.11.3-0.4
Latency to leave start box in cocaine runway0.70.81.4-0.01.2-1.0
Latency to leave start box in cocaine runway, F0.70.81.40.61.2-0.8
Latency to leave start box in cocaine runway, M1.21.12.20.11.1-1.5
Std. dev. time between licks in bursts1.21.52.91.70.4-1.1
Total sessions with >9 infusions1.01.13.0-1.70.10.4
Short access day 1 total inactive lever presses0.30.30.8-0.9-0.10.3
Short access day 10 total inactive lever presses1.01.11.9-0.6-0.91.4
Short access day 1 total infusions1.01.12.8-1.7-0.20.7
Short access day 10 total infusions1.11.22.7-1.6-0.70.6
Short access total infusions0.50.61.5-1.20.5-0.0
Short access day 1 locomotion0.40.41.1-1.00.10.3
Short access day 10 total locomotion0.40.51.3-1.10.10.3
Short access total locomotion1.41.43.9-2.00.50.4
One hour access (0.3 mA shock)0.20.30.60.10.5-0.8
Compulsive drug intake1.11.12.40.11.6-0.9
One hour access (shock baseline)0.20.20.50.3-0.70.1
Social response proportion0.70.71.30.21.1-0.9
Social responses0.10.10.20.40.5-0.1
Social time0.70.91.80.11.3-1.0
Soleus weight0.82.24.60.62.1-1.3
Bone: stiffness1.11.73.7-1.9-0.51.1
Tibialis anterior weight0.20.71.40.01.2-0.8
Time to tail flick, vehicle, before self-admin0.50.50.60.70.8-0.6
Time to tail flick, vehicle, after self-admin1.61.74.3-2.10.70.7
Time to tail flick, test, before self-admin0.50.51.01.0-0.6-0.1
Time to tail flick, test, after self-admin0.40.51.0-1.0-0.40.5
Delta time to tail flick, vehicle, before/after SA0.30.30.7-0.80.40.1
Delta time to tail flick, test, before/after SA1.31.22.8-1.70.10.8
Tibia length10.830.337.7-5.2-5.16.1
Ambulatory time before self-admin2.32.43.7-0.8-1.71.9
Ambulatory time after self-admin0.40.40.60.60.5-0.8
Bone: tissue strength1.31.22.2-0.11.5-1.2
Total heroin consumption1.92.23.7-1.9-1.31.1
Bone: trabecular number0.50.82.01.4-0.3-0.4
Bone: trabecular spacing0.30.30.7-0.8-0.40.4
Bone: trabecular thickness0.50.61.01.00.2-0.9
Bone: trabecular tissue density0.20.30.5-0.7-0.40.5
Water consumed over 24 hours0.40.41.31.1-0.20.1
Number of responses in last shaping day1.81.93.2-1.8-0.91.3