Pde6c

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 Pde6c 0.07 0.05 8.5e-05 0.03 0.02 0.02 0.03 1.8e-04 1.6e-03 4.6e-03 7.6e-04
2 Adipose gene expression Pde6c 0.11 0.04 0.0e+00 0.1 0.14 0.13 0.13 1.1e-11 7.0e-15 5.7e-14 2.6e-14
3 Adipose mRNA stability Pde6c 0.05 0.02 2.9e-06 0.05 0.04 0.03 0.04 5.5e-06 2.7e-05 1.3e-04 1.9e-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
Bone: apparent density3.35.57.92.82.6-1.4
Area under the delay curve0.40.50.8-0.2-0.70.9
BMI with tail0.51.72.01.41.1-1.4
BMI without tail1.53.13.71.71.6-1.9
Body weight0.41.83.00.91.2-1.7
Weight adjusted by age0.10.10.20.4-0.30.0
Bone surface2.95.17.02.42.6-1.5
Bone volume3.25.46.72.52.6-1.9
Breakpoint value in progressive ratio session0.40.50.8-0.6-0.40.9
Number of licking bursts1.51.72.2-1.0-1.41.5
Context. condit. distance diff. score1.21.41.91.31.4-0.8
Locomotion velocity, session 12.12.33.0-1.3-1.51.7
Locomotion distance, session 10.81.11.2-1.0-1.11.0
Locomotion velocity, session 20.70.81.20.80.71.1
Locomotion distance, session 20.10.20.50.0-0.20.7
Locomotion velocity, session 30.30.40.50.70.6-0.5
Locomotion distance, session 30.70.81.30.50.8-1.1
Stereotopy head waving bouts, day 30.10.10.30.60.30.2
Stereotopy head waving duration, day 30.10.20.30.60.40.2
Locomotion velocity, session 73.74.14.31.92.1-2.0
Locomotion distance, session 72.53.13.71.61.9-1.8
Stereotopy head waving bouts, day 70.40.51.30.3-0.11.1
Stereotopy head waving duration, day 70.10.10.20.40.10.3
Locomotion velocity, session 80.30.30.50.70.6-0.1
Locomotion distance, session 80.50.71.31.10.80.2
Degree of sensitization distance0.20.20.30.50.50.3
Degree of sensitization stereotypy0.70.71.9-0.2-0.41.4
Conditioned locomotion0.80.92.70.20.1-1.7
Cocaine response after cond. corrected0.20.20.3-0.5-0.30.4
Cocaine response after cond. not corrected0.20.20.5-0.3-0.10.7
Cocaine response before conditioning0.20.20.70.20.10.8
Saline control response2.93.74.4-1.6-2.12.1
Bone: connectivity density4.87.510.53.23.0-1.7
Bone: cortical apparent density1.11.52.4-0.9-1.11.6
Bone: cortical area1.01.52.10.71.4-1.5
Bone: cortical porosity0.50.61.11.10.80.2
Bone: cortical porosity1.01.11.71.31.2-0.1
Bone: cortical thickness0.91.52.3-1.5-1.20.7
Bone: cortical thickness2.22.62.6-1.6-1.61.6
Bone: cortical tissue density1.11.42.5-0.8-1.11.6
Condit. Reinf. active minus inactive responses0.00.00.1-0.2-0.1-0.0
Condit. Reinf. active-inactive response ratio0.10.10.1-0.4-0.2-0.2
Condit. Reinf. active responses0.00.00.1-0.2-0.1-0.2
Condit. Reinf. inactive responses0.00.00.0-0.2-0.20.2
Incentive salience index mean0.50.61.0-1.0-0.80.5
Condit. Reinf. lever presses2.12.73.8-2.0-1.81.0
Condit. Reinf. active minus inactive responses2.53.13.41.71.7-1.8
Condit. Reinf. active-inactive response ratio1.31.31.61.21.0-1.2
Condit. Reinf. active responses0.81.12.20.60.9-1.5
Condit. Reinf. inactive responses0.40.51.2-1.1-0.6-0.0
Condit. Reinf. lever presses0.20.30.4-0.6-0.50.6
Condit. Reinf. lever reinforcers received0.40.51.10.30.5-1.1
Conditioned reinforcement - actives0.60.60.90.90.90.2
Conditioned reinforcement - inactives2.73.04.32.02.10.9
Conditioned locomotion0.30.41.00.10.51.0
Patch foraging indifference point 0 sec0.40.60.9-0.9-0.90.5
Patch foraging indifference point AUC5.15.97.4-2.5-2.02.7
Delay disc. indifference point, 0s delay1.41.52.81.71.0-0.8
Delay disc. indifference point, 16s delay0.80.82.1-0.3-0.51.5
Delay disc. indifference point, 2s delay0.00.00.00.0-0.20.2
Delay disc. indifference point, 24s delay1.31.31.6-1.2-0.91.3
Delay disc. indifference point, 4s delay0.70.71.6-0.0-0.71.3
Delay disc. indifference point, 8s delay2.02.13.1-1.4-1.71.1
Indifference point function ln k5.37.48.22.82.5-2.9
Indifference point function log k5.37.48.22.82.5-2.9
Patch foraging total patch changes 0 sec0.30.40.6-0.8-0.80.3
Patch foraging total patch changes 12 sec4.55.96.0-2.4-2.42.4
Patch foraging total patch changes 18 sec1.01.31.8-1.0-1.11.3
Patch foraging total patch changes 24 sec0.40.50.9-0.9-0.60.5
Patch foraging total patch changes 6 sec3.85.66.9-2.6-2.22.3
Patch foraging time to switch 0 sec1.11.72.3-1.1-1.51.2
Patch foraging water rate 0 sec1.52.42.81.61.7-1.4
Patch foraging water rate 12 sec0.71.11.40.81.2-1.1
Patch foraging water rate 18 sec1.62.23.01.51.7-1.2
Patch foraging water rate 24 sec0.91.31.31.11.1-1.2
Patch foraging water rate 6 sec0.10.20.20.40.5-0.4
Seeking ratio, delayed vs. immediate footshock0.00.10.1-0.2-0.3-0.2
Distance traveled before self-admin0.80.91.51.21.0-0.5
Distance traveled after self-admin2.62.94.72.21.9-0.6
Extensor digitorum longus weight0.21.01.40.71.0-1.2
Bone: elastic displacement0.20.20.30.5-0.2-0.6
Bone: elastic work0.60.81.61.30.6-0.6
Bone: endosteal estimation5.411.816.43.34.1-2.9
Bone: endosteal perimeter4.910.113.63.23.7-2.5
Epididymis fat weight1.22.86.61.00.9-2.6
Delta time in closed arm before/after self-admin0.40.40.8-0.9-0.3-0.4
Delta time in open arm before/after self-admin0.90.91.81.30.90.2
Diff in mean of infusions in LGA sessions2.02.33.01.41.7-1.3
Delay discount exponential model param0.50.61.00.40.8-1.0
Extinction: sum of active levers before priming0.10.10.2-0.30.4-0.0
Active lever presses in extinction session 62.22.13.61.91.7-0.2
Bone: final force0.10.10.3-0.10.6-0.1
Bone: final moment0.10.20.3-0.10.6-0.5
Food consumed during 24 hour testing period0.50.61.4-0.5-0.1-1.2
Glucose0.10.20.40.20.5-0.6
Heart weight0.30.41.0-1.0-0.3-0.5
Delay discount hyperbolic model param0.40.40.70.20.7-0.8
Intermittent access intake day 1-15 change3.73.64.62.22.1-1.3
Intermittent access intake escalation3.23.13.61.91.9-1.5
Intermittent access intake escalation 24.34.35.72.42.2-1.5
Intermitt. access day 1 inactive lever presses0.20.20.30.50.5-0.4
Intermitt. access day 15 inactive lever presses0.50.61.00.81.0-0.3
Intermitt. access escalation Index3.22.85.41.41.0-2.3
Intermittent access day 1 total infusions0.60.71.10.91.10.4
Intermittent access day 15 total infusions2.83.14.81.92.2-0.9
Intermittent access terminal intake (last 3 days)2.62.94.22.02.0-0.7
Intermittent access total infusions1.51.72.61.51.6-0.4
Intermittent access day 1 locomotion0.20.20.40.10.60.6
Intermittent access day 15 total locomotion0.60.61.7-0.4-0.21.3
Intermittent access total locomotion0.80.92.7-0.10.01.6
Intermittent access standard deviation3.33.55.62.12.4-0.8
Left kidney weight0.10.30.7-0.9-0.3-0.4
Right kidney weight0.71.93.9-2.0-1.30.4
Cocaine induced anxiety0.50.61.11.00.40.7
Post-drug Anxiety0.60.71.4-0.6-1.20.4
Baseline Anxiety1.41.52.3-1.5-1.0-1.0
Tail length0.30.91.40.31.1-1.2
Length with tail0.00.10.3-0.60.2-0.2
Length without tail0.20.50.7-0.8-0.40.9
Times rat made contact with spout0.40.50.80.90.5-0.6
Lifetime Intake0.70.81.31.11.1-0.0
Liver weight, left0.40.61.4-0.10.5-1.2
Liver weight, right0.20.30.7-0.30.2-0.9
Locomotor activity0.20.30.80.90.3-0.2
Locomotor testing distance0.30.51.21.10.4-0.1
Locomotor testing rearing0.91.32.71.61.1-0.3
Locomotion in novel chamber3.74.55.22.31.8-2.3
Locomotion in novel chamber post-restriction0.20.30.7-0.4-0.20.8
Fecal boli incidents, locomotor time 11.11.22.11.41.1-0.5
Change in fecal boli incidents, locomotor task1.31.21.7-1.3-1.10.9
Time >=10cm from walls, locomotor time 10.20.20.7-0.20.80.0
Bouts of movement, locomotor time 10.10.20.40.6-0.30.2
Total resting periods, locomotor time 10.20.30.40.5-0.30.6
Rest time, locomotor task time 10.80.92.51.60.40.1
Distance moved, locomotor task time 10.70.82.2-1.5-0.4-0.4
Vertical activity count, locomotor time 10.90.92.5-1.6-0.5-0.1
Time >=10cm from walls, locomotor time 20.30.30.50.70.70.2
Bouts of movement, locomotor time 22.83.05.6-0.9-1.62.4
Total resting periods, locomotor time 22.83.06.0-0.7-1.52.4
Rest time, locomotor task time 20.50.61.1-0.2-0.91.0
Distance moved, locomotor task time 21.01.12.10.21.1-1.5
Vertical activity count, locomotor time 20.60.71.20.20.9-1.1
Light reinforcement 10.10.30.3-0.4-0.60.6
Light reinforcement 21.11.51.8-1.0-1.31.3
Bone: marrow area5.511.916.63.34.1-2.9
Bone: maximum diameter5.810.713.73.43.7-2.7
Bone: maximum force0.61.12.20.91.5-0.5
Bone: maximum moment0.71.22.20.81.5-0.9
Mean time between licks in bursts0.10.10.2-0.4-0.4-0.1
Mean num. licks in bursts3.03.63.91.72.0-2.0
Cd content in liver1.11.22.0-1.4-1.20.5
Co content in liver0.40.50.5-0.6-0.7-0.7
Cu content in liver4.04.86.5-2.2-2.61.7
Fe content in liver1.72.03.6-1.4-1.90.8
K content in liver0.30.30.40.1-0.60.6
Mg content in liver0.90.91.4-0.6-1.21.0
Mn content in liver3.64.15.5-1.6-2.02.3
Na content in liver1.41.42.7-1.1-1.60.7
Rb content in liver0.60.71.70.40.5-1.3
Se content in liver17.521.428.4-4.7-5.33.7
Sr content in liver0.30.30.80.00.2-0.9
Zn content in liver1.21.32.4-1.2-1.60.1
Bone: minimum diameter7.714.318.73.44.3-3.5
Time in familiar zone, hab. session 10.20.20.30.30.3-0.5
Time in novel zone, hab. session 10.30.30.5-0.5-0.40.7
Total zone transitions, hab. session 10.10.10.2-0.2-0.20.4
Total locomotion distance, hab. session 11.11.62.0-1.2-1.41.2
Locomotion velocity, hab. session 12.13.03.8-1.7-1.91.5
Time in familiar zone, hab. session 20.20.20.3-0.3-0.3-0.6
Time in novel zone, hab. session 20.10.10.2-0.10.00.5
Total zone transitions, hab. session 20.91.21.6-1.3-1.10.9
Total locomotion distance, hab. session 21.01.31.9-1.4-1.30.7
Locomotion velocity, hab. session 21.31.82.1-1.4-1.51.0
Novel to familiar place preference ratio2.82.94.92.21.90.2
Novelty place preference3.13.15.32.32.00.2
Time in novel zone, NPP test3.23.35.52.32.10.1
Total zone transitions, NPP test1.01.42.3-1.5-1.20.6
Total locomotion distance, NPP test2.12.93.5-1.9-1.81.4
Locomotion velocity, NPP test2.12.93.5-1.9-1.81.4
Intraocular pressure0.20.30.4-0.7-0.50.5
Delta distance traveled before/after self-admin1.31.41.81.31.3-0.7
Delta ambulatory time before/after self-admin2.42.63.31.81.8-1.2
Parametrial fat weight0.20.40.8-0.5-0.2-0.9
Pavlov. Cond. lever latency0.00.00.0-0.1-0.1-0.1
Pavlov. Cond. magazine entry latency0.50.61.2-1.1-0.70.5
Pavlov. Cond. change in total contacts0.10.10.2-0.30.1-0.4
Pavlov. Cond. index score0.30.40.6-0.8-0.50.6
Pavlov. Cond. latency score0.20.30.4-0.7-0.50.5
Pavlov. Cond. lever contacts0.50.60.9-0.9-0.70.6
Pavlov. Cond. magazine entry number0.10.10.20.5-0.00.4
Pavlov. Cond. intertrial magazine entries0.00.00.0-0.1-0.1-0.2
Pavlov. Cond. lever-magazine prob. diff.0.30.40.6-0.8-0.60.5
Pavlov. Cond. response bias0.20.20.6-0.8-0.30.0
Pavlov. Cond. lever latency1.21.72.81.71.2-0.9
Pavlov. Cond. magazine entry latency0.10.10.3-0.10.2-0.5
Pavlov. Cond. change in total contacts0.30.50.9-1.0-0.60.3
Pavlov. Cond. index score0.40.51.1-1.1-0.60.5
Pavlov. Cond. latency score0.30.30.7-0.8-0.40.4
Pavlov. Cond. lever contacts1.01.42.2-1.5-1.10.9
Pavlov. Cond. magazine entry number1.11.32.31.51.1-0.5
Pavlov. Cond. intertrial magazine entries0.81.11.81.31.0-0.7
Pavlov. Cond. lever-magazine prob. diff.0.30.40.8-0.9-0.40.5
Pavlov. Cond. response bias0.91.22.1-1.4-1.00.7
Time in closed arm before self-admin1.31.42.81.71.2-0.3
Time in closed arm after self-admin0.10.10.1-0.3-0.3-0.0
Time in open arm before self-admin0.20.20.3-0.3-0.6-0.5
Time in open arm after self-admin0.20.20.30.50.10.5
Bone: periosteal estimation3.47.110.32.43.2-2.3
Bone: periosteal perimeter3.76.17.92.42.8-2.2
Bone: post-yield work0.91.32.40.91.6-0.8
Progressive ratio test 1 active lever presses0.60.60.91.00.90.0
Progressive ratio test 1 breakpoint0.70.71.11.01.00.0
Progressive ratio test 1 inactive lever presses2.93.14.62.12.1-0.6
Progressive ratio test 2 active lever presses2.32.43.71.91.8-0.5
Progressive ratio test 2 breakpoint2.93.35.02.22.1-0.5
Progressive ratio test 2 inactive lever presses1.72.03.61.91.50.2
Incentive Sensitization - Responses4.14.26.12.52.3-1.0
Incentive Sensitization - Breakpoint3.73.85.32.32.2-1.0
Sum of active levers in priming session hrs 5-60.10.10.2-0.00.1-0.5
Progressive ratio0.30.41.0-0.2-0.4-1.0
Food seeking constrained by brief footshock0.00.10.1-0.10.4-0.0
Seeking ratio, punishment vs. effort0.20.20.5-0.10.40.7
Retroperitoneal fat weight0.31.03.0-0.20.1-1.7
Reaction time number correct2.02.84.22.01.6-1.4
Reaction time mean minus median0.60.81.70.30.8-1.3
Reaction time mean minus median AUC0.50.61.80.20.3-1.3
Reaction time num false alarms0.20.20.5-0.7-0.20.2
Reaction time num false alarms AUC0.10.20.5-0.7-0.20.0
Reaction time trials correct on left2.02.84.22.01.6-1.4
Reaction time trials on left2.02.84.02.01.6-1.4
Reaction time mean0.40.51.3-1.1-0.6-0.1
Reaction time mean AUC0.70.92.0-1.4-0.90.2
Median of all reaction times0.60.81.6-1.3-0.80.2
Reaction time omissions1.92.66.00.81.1-2.5
Reaction time false alarm rate1.01.42.7-1.6-0.90.8
Reaction time premature initiation rate0.40.51.3-1.1-0.50.1
Reaction time premature initiations0.20.30.6-0.00.4-0.8
Std. dev. reaction times0.50.61.7-0.50.2-1.3
Reaction time trials completed2.02.84.02.01.6-1.4
Reaction time trials AUC1.72.53.61.91.4-1.3
Run reversals in cocaine runway, females0.10.10.1-0.3-0.30.1
Run reversals in cocaine runway, males3.53.44.8-2.2-1.71.6
Latency to leave start box in cocaine runway2.62.83.11.81.5-1.7
Latency to leave start box in cocaine runway, F3.33.65.12.32.0-1.4
Latency to leave start box in cocaine runway, M0.90.92.50.20.2-1.6
Std. dev. time between licks in bursts2.12.63.3-1.7-1.8-1.2
Total sessions with >9 infusions0.10.10.3-0.2-0.10.6
Short access day 1 total inactive lever presses1.51.73.21.81.30.1
Short access day 10 total inactive lever presses0.10.10.20.4-0.1-0.1
Short access day 1 total infusions0.30.30.5-0.4-0.60.7
Short access day 10 total infusions0.10.10.2-0.4-0.20.5
Short access total infusions0.10.10.10.30.30.4
Short access day 1 locomotion0.00.00.00.2-0.10.1
Short access day 10 total locomotion0.80.92.6-0.3-0.01.6
Short access total locomotion0.50.51.4-0.3-0.41.2
One hour access (0.3 mA shock)5.46.39.53.13.0-0.5
Compulsive drug intake3.83.94.02.02.0-1.9
One hour access (shock baseline)0.80.91.31.11.20.5
Social response proportion2.42.64.22.01.6-0.9
Social responses0.40.50.90.70.9-0.3
Social time0.71.01.2-1.0-0.91.1
Soleus weight1.33.74.61.82.2-1.8
Bone: stiffness0.81.32.51.01.6-0.6
Tibialis anterior weight0.62.02.41.51.6-1.0
Time to tail flick, vehicle, before self-admin0.80.81.6-0.3-0.81.3
Time to tail flick, vehicle, after self-admin0.40.40.70.70.8-0.4
Time to tail flick, test, before self-admin2.12.13.61.61.90.1
Time to tail flick, test, after self-admin1.31.41.91.41.1-1.0
Delta time to tail flick, vehicle, before/after SA1.71.72.41.11.5-1.2
Delta time to tail flick, test, before/after SA0.40.30.90.2-0.1-1.0
Tibia length0.00.10.3-0.5-0.3-0.0
Ambulatory time before self-admin0.60.60.91.00.6-0.8
Ambulatory time after self-admin4.75.28.52.92.5-0.7
Bone: tissue strength0.20.20.40.10.4-0.6
Total heroin consumption0.30.30.8-0.5-0.10.9
Bone: trabecular number3.14.96.42.52.5-1.4
Bone: trabecular spacing1.31.72.9-1.7-1.50.3
Bone: trabecular thickness2.83.43.81.92.0-1.6
Bone: trabecular tissue density0.50.71.01.00.9-0.4
Water consumed over 24 hours1.01.22.01.41.1-0.6
Number of responses in last shaping day0.50.51.10.50.2-1.0