Spindoc

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 pVTA isoform ratio NM_001399680.1 0.05 0.03 5.0e-03 0 0.01 -0 0 1.6e-01 9.2e-02 6.5e-01 1.7e-01
2 Adipose mRNA stability Spindoc 0.03 0.02 3.6e-03 0.02 0.01 0 0.01 1.7e-03 1.7e-02 8.8e-02 1.4e-02
3 BLA gene expression Spindoc 0.07 0.05 8.4e-03 0.01 0 0.01 0.01 8.7e-02 2.9e-01 1.1e-01 1.1e-01
4 NAcc mRNA stability Spindoc 0.03 0.02 3.7e-04 0.02 0.03 0.01 0.03 9.4e-04 5.8e-05 7.0e-03 6.1e-05

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 density1.22.32.71.6-1.5-1.5-1.3
Area under the delay curve0.20.30.60.4-0.6-0.5-0.8
BMI with tail6.121.222.94.6-4.5-4.5-4.8
BMI without tail0.73.85.52.1-1.6-1.7-2.3
Body weight3.917.223.64.7-3.3-3.5-4.9
Weight adjusted by age0.41.12.21.5-0.7-0.9-1.0
Bone surface4.38.514.63.8-2.6-2.5-2.4
Bone volume2.75.37.62.8-2.4-2.3-1.7
Breakpoint value in progressive ratio session0.61.13.31.8-0.1-0.1-0.9
Number of licking bursts0.00.10.30.5-0.1-0.3-0.2
Context. condit. distance diff. score0.20.20.6-0.8-0.3-0.40.1
Locomotion velocity, session 10.00.00.1-0.0-0.10.1-0.3
Locomotion distance, session 11.01.31.80.9-1.2-1.0-1.3
Locomotion velocity, session 21.61.93.01.7-1.0-0.8-1.7
Locomotion distance, session 20.20.30.70.5-0.3-0.0-0.8
Locomotion velocity, session 32.93.35.10.7-2.3-2.1-1.8
Locomotion distance, session 30.20.20.50.1-0.6-0.3-0.7
Stereotopy head waving bouts, day 31.31.52.70.2-1.5-1.7-1.0
Stereotopy head waving duration, day 30.30.40.9-0.2-0.8-0.9-0.2
Locomotion velocity, session 70.80.92.30.1-1.5-1.0-0.7
Locomotion distance, session 70.30.40.90.0-0.9-0.5-0.8
Stereotopy head waving bouts, day 70.50.60.80.8-0.9-0.9-0.2
Stereotopy head waving duration, day 70.91.22.21.5-0.9-0.9-0.8
Locomotion velocity, session 80.30.41.00.30.51.0-0.0
Locomotion distance, session 80.40.61.20.2-1.1-0.9-0.4
Degree of sensitization distance0.91.01.50.5-1.2-1.2-0.9
Degree of sensitization stereotypy0.70.81.61.3-0.9-0.8-0.5
Conditioned locomotion0.40.51.11.0-0.2-0.4-0.9
Cocaine response after cond. corrected0.20.31.1-1.10.10.30.2
Cocaine response after cond. not corrected0.10.10.5-0.7-0.20.10.0
Cocaine response before conditioning0.20.30.91.0-0.5-0.2-0.2
Saline control response1.52.14.12.0-0.8-0.3-1.9
Bone: connectivity density3.14.97.12.7-2.0-2.0-2.1
Bone: cortical apparent density0.50.81.7-0.51.31.00.6
Bone: cortical area1.11.82.21.5-1.3-1.2-1.3
Bone: cortical porosity0.50.61.1-0.20.81.10.7
Bone: cortical porosity0.30.30.90.20.60.90.3
Bone: cortical thickness0.50.91.51.00.60.7-1.2
Bone: cortical thickness0.30.30.6-0.10.50.8-0.6
Bone: cortical tissue density0.50.81.9-0.41.41.00.5
Condit. Reinf. active minus inactive responses0.30.30.50.6-0.4-0.6-0.7
Condit. Reinf. active-inactive response ratio0.10.10.3-0.10.50.40.2
Condit. Reinf. active responses0.81.01.70.7-1.0-1.3-0.9
Condit. Reinf. inactive responses0.81.12.20.5-1.2-1.5-0.6
Incentive salience index mean1.11.41.81.0-1.0-1.2-1.3
Condit. Reinf. lever presses1.62.32.61.4-1.6-1.6-1.5
Condit. Reinf. active minus inactive responses0.10.10.30.1-0.6-0.10.5
Condit. Reinf. active-inactive response ratio0.40.71.20.2-1.1-1.10.5
Condit. Reinf. active responses0.10.10.30.3-0.5-0.0-0.1
Condit. Reinf. inactive responses0.20.30.90.10.31.0-0.5
Condit. Reinf. lever presses1.52.23.81.9-1.5-1.1-1.2
Condit. Reinf. lever reinforcers received0.10.20.40.6-0.5-0.1-0.2
Conditioned reinforcement - actives0.10.20.50.5-0.3-0.20.7
Conditioned reinforcement - inactives0.30.71.5-0.3-1.2-1.10.5
Conditioned locomotion1.42.05.3-2.3-0.3-0.41.6
Patch foraging indifference point 0 sec0.10.30.50.3-0.7-0.5-0.6
Patch foraging indifference point AUC0.40.92.81.7-0.4-0.3-0.6
Delay disc. indifference point, 0s delay0.20.20.30.1-0.4-0.5-0.5
Delay disc. indifference point, 16s delay0.40.51.2-0.1-1.1-0.9-0.4
Delay disc. indifference point, 2s delay0.30.30.50.4-0.7-0.7-0.3
Delay disc. indifference point, 24s delay0.00.10.2-0.1-0.2-0.1-0.5
Delay disc. indifference point, 4s delay0.40.41.20.2-0.4-0.4-1.1
Delay disc. indifference point, 8s delay0.10.10.4-0.20.40.60.0
Indifference point function ln k1.13.29.6-3.10.90.81.3
Indifference point function log k1.13.29.6-3.10.90.81.3
Patch foraging total patch changes 0 sec0.00.10.3-0.0-0.3-0.1-0.5
Patch foraging total patch changes 12 sec2.22.95.72.4-1.1-0.6-2.1
Patch foraging total patch changes 18 sec0.10.31.01.0-0.3-0.1-0.4
Patch foraging total patch changes 24 sec1.24.16.42.1-1.9-1.4-2.5
Patch foraging total patch changes 6 sec0.91.52.41.3-1.1-0.8-1.5
Patch foraging time to switch 0 sec0.93.64.82.2-2.0-1.8-1.4
Patch foraging water rate 0 sec0.82.96.7-2.61.31.11.4
Patch foraging water rate 12 sec1.45.713.9-3.71.71.61.8
Patch foraging water rate 18 sec0.41.03.5-1.90.60.20.2
Patch foraging water rate 24 sec1.52.24.8-2.21.01.11.3
Patch foraging water rate 6 sec2.13.18.0-2.81.31.31.1
Seeking ratio, delayed vs. immediate footshock0.10.10.2-0.3-0.4-0.4-0.4
Distance traveled before self-admin1.12.52.91.7-1.5-1.6-1.4
Distance traveled after self-admin0.00.10.10.30.30.1-0.1
Extensor digitorum longus weight4.216.829.75.4-2.5-2.6-4.9
Bone: elastic displacement1.62.02.9-1.71.51.40.9
Bone: elastic work0.30.41.40.40.50.2-1.2
Bone: endosteal estimation1.53.67.30.8-2.4-2.7-0.8
Bone: endosteal perimeter1.43.57.10.8-2.5-2.7-0.3
Epididymis fat weight0.42.03.8-1.0-1.7-1.90.4
Delta time in closed arm before/after self-admin0.50.51.9-0.1-0.3-0.3-1.4
Delta time in open arm before/after self-admin0.80.91.51.2-1.0-0.9-0.6
Diff in mean of infusions in LGA sessions0.20.41.10.6-0.10.1-1.0
Delay discount exponential model param0.20.30.6-0.40.60.50.8
Extinction: sum of active levers before priming1.62.43.71.9-1.1-1.2-1.8
Active lever presses in extinction session 61.81.84.62.1-0.7-1.0-1.1
Bone: final force2.64.26.32.5-1.7-1.8-2.1
Bone: final moment2.64.26.12.5-1.7-1.8-2.1
Food consumed during 24 hour testing period0.00.00.10.2-0.2-0.00.3
Glucose0.40.71.3-0.8-1.1-0.90.2
Heart weight0.61.01.40.1-1.1-1.2-1.1
Delay discount hyperbolic model param0.30.30.5-0.50.60.50.7
Intermittent access intake day 1-15 change0.20.92.7-0.80.40.51.6
Intermittent access intake escalation0.21.13.3-0.70.60.61.8
Intermittent access intake escalation 20.20.41.3-0.4-0.1-0.01.1
Intermitt. access day 1 inactive lever presses0.11.02.3-0.60.90.91.5
Intermitt. access day 15 inactive lever presses0.42.04.00.1-2.0-1.9-0.5
Intermitt. access escalation Index0.41.33.2-1.80.70.70.9
Intermittent access day 1 total infusions1.13.36.50.2-2.5-2.5-0.7
Intermittent access day 15 total infusions0.51.31.8-0.9-1.1-1.11.3
Intermittent access terminal intake (last 3 days)1.42.55.10.0-2.3-2.20.2
Intermittent access total infusions1.92.34.8-0.1-2.2-2.10.0
Intermittent access day 1 locomotion1.22.24.20.0-2.0-2.0-0.7
Intermittent access day 15 total locomotion0.51.93.8-0.2-1.9-1.90.2
Intermittent access total locomotion3.94.79.50.0-3.1-3.0-0.3
Intermittent access standard deviation0.10.40.9-0.7-0.3-0.11.0
Left kidney weight0.11.12.60.1-1.4-1.6-0.3
Right kidney weight0.10.71.4-0.0-1.1-1.2-0.2
Cocaine induced anxiety0.00.00.10.30.20.10.3
Post-drug Anxiety0.10.10.50.7-0.1-0.2-0.3
Baseline Anxiety0.10.20.60.1-0.10.0-0.8
Tail length0.10.71.40.21.21.0-0.4
Length with tail0.52.14.32.10.1-0.1-2.1
Length without tail0.73.78.42.3-0.7-0.9-2.9
Times rat made contact with spout0.30.30.60.00.80.8-0.1
Lifetime Intake1.21.53.1-0.2-1.8-1.7-0.1
Liver weight, left0.30.51.2-1.10.60.50.6
Liver weight, right0.30.51.9-1.40.0-0.10.1
Locomotor activity1.72.64.5-2.11.51.51.2
Locomotor testing distance0.92.24.7-2.21.31.30.9
Locomotor testing rearing0.41.63.9-2.00.81.10.8
Locomotion in novel chamber0.60.91.8-1.3-0.3-0.61.1
Locomotion in novel chamber post-restriction0.51.53.1-1.60.40.41.8
Fecal boli incidents, locomotor time 10.10.30.40.6-0.6-0.30.5
Change in fecal boli incidents, locomotor task0.40.40.8-0.70.90.60.3
Time >=10cm from walls, locomotor time 10.50.71.00.4-1.0-1.00.7
Bouts of movement, locomotor time 11.41.83.8-0.21.62.01.1
Total resting periods, locomotor time 11.01.12.4-0.11.21.50.9
Rest time, locomotor task time 11.01.72.8-1.50.91.01.7
Distance moved, locomotor task time 10.30.81.01.0-0.7-0.8-1.0
Vertical activity count, locomotor time 10.00.10.4-0.60.10.10.4
Time >=10cm from walls, locomotor time 20.10.20.60.30.20.10.8
Bouts of movement, locomotor time 20.10.20.40.5-0.3-0.1-0.6
Total resting periods, locomotor time 20.00.10.10.3-0.3-0.0-0.4
Rest time, locomotor task time 20.71.32.3-1.50.40.71.4
Distance moved, locomotor task time 20.20.30.50.70.70.4-0.2
Vertical activity count, locomotor time 20.41.02.1-0.81.41.10.5
Light reinforcement 10.10.40.7-0.60.40.80.7
Light reinforcement 20.40.91.8-0.1-1.2-1.40.5
Bone: marrow area1.33.36.80.7-2.3-2.6-0.7
Bone: maximum diameter1.22.43.21.6-1.8-1.8-0.9
Bone: maximum force5.110.012.53.5-3.0-3.0-3.0
Bone: maximum moment5.09.511.73.4-3.0-3.0-3.0
Mean time between licks in bursts0.10.40.7-0.20.70.6-0.8
Mean num. licks in bursts0.20.60.8-0.80.70.90.5
Cd content in liver0.40.51.6-0.5-0.2-0.11.3
Co content in liver3.64.25.2-2.22.12.31.5
Cu content in liver0.20.30.4-0.40.50.60.5
Fe content in liver0.10.10.20.5-0.2-0.1-0.1
K content in liver1.21.22.01.0-1.0-0.8-1.4
Mg content in liver0.40.50.7-0.1-0.7-0.7-0.9
Mn content in liver2.22.44.22.1-1.3-1.3-1.5
Na content in liver0.50.60.70.7-0.8-0.6-0.9
Rb content in liver1.21.42.9-1.70.80.91.0
Se content in liver0.40.51.10.4-0.8-1.00.0
Sr content in liver1.10.91.91.4-0.6-0.4-1.1
Zn content in liver0.91.01.90.8-0.9-0.9-1.4
Bone: minimum diameter1.93.76.70.8-2.6-2.6-0.9
Time in familiar zone, hab. session 10.30.30.5-0.1-0.7-0.5-0.6
Time in novel zone, hab. session 10.70.80.8-0.90.90.90.8
Total zone transitions, hab. session 10.10.10.30.6-0.3-0.0-0.3
Total locomotion distance, hab. session 10.50.71.40.1-1.2-1.0-0.4
Locomotion velocity, hab. session 10.40.50.90.3-0.9-0.9-0.6
Time in familiar zone, hab. session 20.80.91.9-0.71.11.40.2
Time in novel zone, hab. session 21.01.11.80.8-1.3-1.3-0.7
Total zone transitions, hab. session 21.72.13.41.4-1.4-1.1-1.8
Total locomotion distance, hab. session 21.01.32.00.5-1.4-1.1-1.3
Locomotion velocity, hab. session 21.01.32.20.4-1.5-1.3-1.1
Novel to familiar place preference ratio1.31.72.81.7-1.3-1.1-1.0
Novelty place preference0.91.11.71.3-1.2-1.0-0.7
Time in novel zone, NPP test1.01.21.61.3-1.2-1.0-0.8
Total zone transitions, NPP test0.81.22.61.6-0.9-0.4-1.2
Total locomotion distance, NPP test0.30.40.60.3-0.7-0.5-0.7
Locomotion velocity, NPP test0.10.10.20.1-0.4-0.2-0.4
Intraocular pressure0.81.32.9-1.10.80.81.7
Delta distance traveled before/after self-admin1.71.92.8-1.41.71.50.9
Delta ambulatory time before/after self-admin1.11.92.8-1.21.71.50.9
Parametrial fat weight0.61.52.7-0.9-1.6-1.50.6
Pavlov. Cond. lever latency1.11.41.8-1.11.01.21.4
Pavlov. Cond. magazine entry latency1.82.42.91.5-1.5-1.7-1.4
Pavlov. Cond. change in total contacts0.91.01.51.0-1.2-1.2-0.5
Pavlov. Cond. index score0.60.70.90.9-0.7-0.9-0.8
Pavlov. Cond. latency score0.60.81.00.9-0.7-1.0-1.0
Pavlov. Cond. lever contacts0.91.11.50.9-0.9-1.2-1.2
Pavlov. Cond. magazine entry number0.30.40.7-0.80.40.60.4
Pavlov. Cond. intertrial magazine entries0.50.61.1-0.90.70.41.0
Pavlov. Cond. lever-magazine prob. diff.0.81.01.41.2-0.9-1.0-0.9
Pavlov. Cond. response bias0.60.80.90.9-0.8-1.0-0.8
Pavlov. Cond. lever latency1.01.52.0-1.41.41.00.9
Pavlov. Cond. magazine entry latency2.33.36.22.5-1.4-1.1-2.0
Pavlov. Cond. change in total contacts1.12.64.12.0-1.8-1.3-1.1
Pavlov. Cond. index score2.23.55.82.4-1.8-1.5-1.6
Pavlov. Cond. latency score2.23.65.62.4-1.9-1.6-1.6
Pavlov. Cond. lever contacts0.71.11.71.3-1.2-0.7-0.7
Pavlov. Cond. magazine entry number3.95.19.8-3.11.71.42.3
Pavlov. Cond. intertrial magazine entries0.61.42.4-1.20.90.91.6
Pavlov. Cond. lever-magazine prob. diff.2.43.76.42.5-1.8-1.4-1.7
Pavlov. Cond. response bias2.02.74.42.1-1.6-1.1-1.6
Time in closed arm before self-admin0.20.30.50.3-0.6-0.70.2
Time in closed arm after self-admin0.20.20.6-0.80.20.10.4
Time in open arm before self-admin1.31.52.3-1.51.41.30.2
Time in open arm after self-admin0.10.10.20.10.40.4-0.4
Bone: periosteal estimation1.84.36.91.6-2.4-2.6-1.4
Bone: periosteal perimeter1.22.33.21.4-1.8-1.8-1.0
Bone: post-yield work4.98.413.42.5-3.7-3.3-1.7
Progressive ratio test 1 active lever presses0.10.20.40.0-0.6-0.50.2
Progressive ratio test 1 breakpoint0.10.20.40.1-0.6-0.50.3
Progressive ratio test 1 inactive lever presses0.30.71.00.5-1.0-1.0-0.7
Progressive ratio test 2 active lever presses0.60.91.7-0.3-1.3-1.20.7
Progressive ratio test 2 breakpoint0.70.91.8-0.3-1.4-1.20.6
Progressive ratio test 2 inactive lever presses0.51.41.7-1.3-1.3-1.20.9
Incentive Sensitization - Responses0.82.23.91.1-2.0-1.7-0.9
Incentive Sensitization - Breakpoint0.92.03.80.9-2.0-1.7-0.8
Sum of active levers in priming session hrs 5-60.30.30.60.80.30.20.6
Progressive ratio0.72.23.51.9-1.4-1.5-1.1
Food seeking constrained by brief footshock0.00.00.00.0-0.00.2-0.2
Seeking ratio, punishment vs. effort0.71.53.6-1.91.01.10.5
Retroperitoneal fat weight1.35.918.1-4.3-0.3-0.42.3
Reaction time number correct0.00.10.20.20.50.3-0.4
Reaction time mean minus median0.21.14.12.0-0.4-0.1-0.2
Reaction time mean minus median AUC0.10.51.31.10.30.80.2
Reaction time num false alarms1.11.82.5-1.61.61.50.5
Reaction time num false alarms AUC0.61.32.2-1.01.41.50.2
Reaction time trials correct on left0.00.10.20.20.50.3-0.4
Reaction time trials on left0.00.20.30.30.50.4-0.4
Reaction time mean0.10.10.30.4-0.00.20.6
Reaction time mean AUC0.10.10.30.4-0.10.20.6
Median of all reaction times0.00.10.10.0-0.2-0.10.4
Reaction time omissions0.20.30.60.80.40.70.0
Reaction time false alarm rate0.60.81.2-1.10.91.00.4
Reaction time premature initiation rate1.82.87.41.4-0.7-1.1-2.7
Reaction time premature initiations0.82.36.61.5-0.1-0.5-2.6
Std. dev. reaction times0.20.50.70.60.50.90.9
Reaction time trials completed0.00.20.30.30.50.4-0.4
Reaction time trials AUC0.00.10.20.20.50.3-0.5
Run reversals in cocaine runway, females1.61.83.20.8-1.3-1.2-1.8
Run reversals in cocaine runway, males0.40.50.6-0.60.80.80.7
Latency to leave start box in cocaine runway0.30.40.90.1-0.9-1.0-0.0
Latency to leave start box in cocaine runway, F0.20.20.40.1-0.6-0.6-0.3
Latency to leave start box in cocaine runway, M0.10.10.20.1-0.2-0.40.4
Std. dev. time between licks in bursts0.30.50.8-0.80.70.9-0.2
Total sessions with >9 infusions0.10.10.20.2-0.4-0.40.1
Short access day 1 total inactive lever presses0.30.51.1-1.0-0.6-0.80.0
Short access day 10 total inactive lever presses0.11.01.4-1.20.90.81.0
Short access day 1 total infusions0.20.30.7-0.8-0.4-0.50.4
Short access day 10 total infusions1.01.73.10.6-1.8-1.7-0.7
Short access total infusions0.50.71.40.1-1.2-1.1-0.4
Short access day 1 locomotion0.30.51.0-0.3-0.8-1.00.1
Short access day 10 total locomotion0.51.83.40.4-1.8-1.8-0.7
Short access total locomotion0.91.42.80.1-1.7-1.6-0.4
One hour access (0.3 mA shock)1.11.32.1-1.0-1.5-1.30.6
Compulsive drug intake0.50.71.30.01.01.1-0.5
One hour access (shock baseline)0.61.51.9-1.1-1.2-1.21.4
Social response proportion0.10.10.40.7-0.10.0-0.3
Social responses0.30.40.90.10.90.90.0
Social time0.40.61.40.00.91.20.2
Soleus weight1.64.810.8-3.31.31.02.4
Bone: stiffness1.83.26.12.5-1.6-1.6-1.4
Tibialis anterior weight4.114.030.15.5-1.9-1.9-4.3
Time to tail flick, vehicle, before self-admin1.41.72.21.3-1.5-1.4-1.0
Time to tail flick, vehicle, after self-admin1.02.12.81.7-1.2-1.2-1.6
Time to tail flick, test, before self-admin1.82.03.20.0-1.7-1.8-1.4
Time to tail flick, test, after self-admin0.10.10.40.6-0.1-0.20.1
Delta time to tail flick, vehicle, before/after SA0.20.20.50.6-0.1-0.1-0.7
Delta time to tail flick, test, before/after SA1.31.62.40.21.51.51.3
Tibia length1.13.15.42.3-1.7-1.7-1.1
Ambulatory time before self-admin0.72.02.71.6-1.4-1.5-1.1
Ambulatory time after self-admin0.10.10.20.0-0.3-0.5-0.0
Bone: tissue strength0.10.10.2-0.30.30.40.4
Total heroin consumption1.31.54.02.00.1-0.2-1.4
Bone: trabecular number2.13.94.52.1-2.1-2.0-1.6
Bone: trabecular spacing1.82.63.3-1.71.81.81.1
Bone: trabecular thickness0.10.10.4-0.1-0.4-0.60.1
Bone: trabecular tissue density4.47.710.9-2.92.32.43.3
Water consumed over 24 hours0.10.30.40.50.70.4-0.4
Number of responses in last shaping day0.10.10.1-0.30.30.1-0.4