Ptk7

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 Ptk7 0.22 0.1 0.0e+00 0.22 0.22 0.22 0.21 2.0e-23 6.3e-24 1.7e-23 2.1e-23
2 Brain gene expression Ptk7 0.22 0.09 0.0e+00 0.28 0.25 0.26 0.28 8.2e-26 3.1e-23 1.9e-24 1.2e-25
3 Brain mRNA stability Ptk7 0.1 0.06 1.1e-05 0.03 0.05 0.05 0.05 9.9e-04 2.4e-05 1.6e-05 4.1e-05
4 PL mRNA stability Ptk7 0.04 0.04 9.0e-03 0.02 0.02 0.01 0.02 4.4e-03 5.4e-03 9.7e-03 2.5e-03

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 density1.32.24.3-1.3-0.92.11.4
Area under the delay curve5.26.19.6-2.8-3.1-0.6-2.5
BMI with tail2.48.315.03.93.5-2.30.4
BMI without tail3.09.016.84.14.0-1.31.4
Body weight2.711.720.84.64.5-0.72.4
Weight adjusted by age0.20.30.70.70.90.10.3
Bone surface1.73.14.2-2.0-1.72.11.1
Bone volume1.01.93.0-1.4-1.21.71.1
Breakpoint value in progressive ratio session0.60.71.40.10.0-1.1-1.2
Number of licking bursts2.03.25.01.92.20.81.9
Context. condit. distance diff. score0.30.40.90.40.40.70.9
Locomotion velocity, session 11.21.32.61.00.7-1.6-1.1
Locomotion distance, session 11.31.63.11.81.7-0.50.6
Locomotion velocity, session 23.94.58.02.82.6-1.80.1
Locomotion distance, session 20.91.22.31.51.3-1.0-0.0
Locomotion velocity, session 31.01.12.41.00.8-1.5-0.8
Locomotion distance, session 30.80.91.3-0.8-1.0-0.8-1.1
Stereotopy head waving bouts, day 30.80.91.71.31.2-0.30.5
Stereotopy head waving duration, day 31.31.63.01.71.5-1.00.1
Locomotion velocity, session 71.01.12.40.70.4-1.5-1.2
Locomotion distance, session 70.70.91.80.40.1-1.3-1.3
Stereotopy head waving bouts, day 70.30.41.00.30.30.61.0
Stereotopy head waving duration, day 70.50.61.2-0.3-0.11.01.1
Locomotion velocity, session 80.30.40.70.80.8-0.40.2
Locomotion distance, session 80.60.81.51.21.1-0.20.7
Degree of sensitization distance1.11.12.21.51.3-0.8-0.2
Degree of sensitization stereotypy0.50.50.6-0.8-0.70.80.6
Conditioned locomotion2.63.05.9-1.3-1.7-1.2-2.4
Cocaine response after cond. corrected0.10.10.2-0.5-0.50.2-0.2
Cocaine response after cond. not corrected0.20.30.4-0.6-0.6-0.1-0.5
Cocaine response before conditioning0.40.51.30.20.2-1.2-0.7
Saline control response0.00.00.10.1-0.1-0.3-0.1
Bone: connectivity density2.13.36.0-1.7-1.22.51.7
Bone: cortical apparent density0.30.40.6-0.7-0.8-0.1-0.7
Bone: cortical area0.50.81.31.10.8-1.1-0.1
Bone: cortical porosity0.10.10.20.20.20.10.4
Bone: cortical porosity0.10.10.20.30.2-0.4-0.2
Bone: cortical thickness0.61.01.61.21.0-1.3-0.3
Bone: cortical thickness0.20.20.4-0.3-0.20.60.6
Bone: cortical tissue density0.30.40.6-0.8-0.8-0.1-0.7
Condit. Reinf. active minus inactive responses1.01.12.01.41.4-0.30.5
Condit. Reinf. active-inactive response ratio0.30.30.50.50.50.40.7
Condit. Reinf. active responses1.72.13.81.92.0-0.20.9
Condit. Reinf. inactive responses1.41.72.81.71.7-0.21.0
Incentive salience index mean1.41.83.31.81.7-0.90.2
Condit. Reinf. lever presses2.43.46.42.52.3-1.20.5
Condit. Reinf. active minus inactive responses0.50.71.30.00.41.21.1
Condit. Reinf. active-inactive response ratio1.41.62.60.71.31.31.6
Condit. Reinf. active responses0.10.20.40.00.20.60.5
Condit. Reinf. inactive responses0.20.30.6-0.0-0.3-0.7-0.8
Condit. Reinf. lever presses0.70.91.30.70.90.91.1
Condit. Reinf. lever reinforcers received0.10.20.5-0.10.20.70.5
Conditioned reinforcement - actives1.01.73.3-0.2-0.7-1.7-1.8
Conditioned reinforcement - inactives0.30.51.00.80.5-1.0-0.3
Conditioned locomotion0.10.10.20.50.5-0.10.2
Patch foraging indifference point 0 sec0.40.81.41.21.2-0.30.6
Patch foraging indifference point AUC1.52.24.41.30.9-2.1-1.4
Delay disc. indifference point, 0s delay1.82.03.3-1.3-1.4-1.0-1.8
Delay disc. indifference point, 16s delay6.77.312.5-3.4-3.50.0-2.3
Delay disc. indifference point, 2s delay2.42.73.6-1.7-1.8-0.9-1.9
Delay disc. indifference point, 24s delay0.70.71.5-1.2-0.90.80.1
Delay disc. indifference point, 4s delay4.64.89.5-1.4-2.1-1.9-3.1
Delay disc. indifference point, 8s delay3.23.75.8-2.1-2.4-0.7-2.0
Indifference point function ln k0.30.50.9-0.9-0.8-0.0-0.5
Indifference point function log k0.30.50.9-0.9-0.8-0.0-0.5
Patch foraging total patch changes 0 sec0.51.01.81.41.3-0.40.6
Patch foraging total patch changes 12 sec1.01.22.01.41.0-1.4-0.3
Patch foraging total patch changes 18 sec1.21.92.91.61.2-1.7-0.6
Patch foraging total patch changes 24 sec0.50.81.41.20.8-1.1-0.2
Patch foraging total patch changes 6 sec1.52.24.22.01.9-0.80.8
Patch foraging time to switch 0 sec3.06.19.0-3.0-2.62.81.0
Patch foraging water rate 0 sec3.47.214.32.61.7-3.8-2.2
Patch foraging water rate 12 sec2.65.59.73.12.7-2.3-0.1
Patch foraging water rate 18 sec0.91.42.21.51.2-1.3-0.4
Patch foraging water rate 24 sec1.52.23.31.81.6-1.6-0.5
Patch foraging water rate 6 sec1.52.15.40.80.4-2.3-1.5
Seeking ratio, delayed vs. immediate footshock1.21.52.7-1.7-1.60.80.1
Distance traveled before self-admin0.10.20.30.30.0-0.6-0.5
Distance traveled after self-admin1.31.63.01.71.5-1.1-0.3
Extensor digitorum longus weight0.10.30.60.70.5-0.7-0.1
Bone: elastic displacement0.20.30.6-0.8-0.60.30.1
Bone: elastic work0.50.61.9-0.00.20.81.4
Bone: endosteal estimation0.30.61.1-1.0-1.00.60.2
Bone: endosteal perimeter0.00.00.10.20.10.10.3
Epididymis fat weight2.06.79.93.03.10.82.7
Delta time in closed arm before/after self-admin1.91.83.9-0.4-0.22.01.8
Delta time in open arm before/after self-admin1.01.02.2-0.0-0.2-1.5-1.3
Diff in mean of infusions in LGA sessions0.91.11.71.10.8-1.3-0.8
Delay discount exponential model param5.25.89.22.83.00.62.4
Extinction: sum of active levers before priming0.80.91.80.30.0-1.3-1.2
Active lever presses in extinction session 61.21.12.10.70.4-1.4-1.5
Bone: final force0.40.71.50.80.70.11.2
Bone: final moment0.30.40.70.90.6-0.50.7
Food consumed during 24 hour testing period0.81.01.71.00.8-1.3-1.0
Glucose4.06.311.43.43.3-0.71.5
Heart weight0.10.20.30.60.4-0.4-0.0
Delay discount hyperbolic model param4.75.28.32.62.90.62.3
Intermittent access intake day 1-15 change0.00.00.00.20.1-0.1-0.1
Intermittent access intake escalation0.00.00.00.1-0.00.10.0
Intermittent access intake escalation 20.10.10.2-0.1-0.3-0.3-0.5
Intermitt. access day 1 inactive lever presses0.41.52.70.81.21.21.6
Intermitt. access day 15 inactive lever presses0.20.40.60.70.80.10.6
Intermitt. access escalation Index0.00.00.0-0.1-0.0-0.1-0.0
Intermittent access day 1 total infusions0.30.40.80.90.8-0.20.4
Intermittent access day 15 total infusions0.20.20.50.70.6-0.10.3
Intermittent access terminal intake (last 3 days)0.00.00.00.1-0.1-0.20.0
Intermittent access total infusions0.10.10.20.50.3-0.30.0
Intermittent access day 1 locomotion0.50.61.01.00.9-0.20.7
Intermittent access day 15 total locomotion0.40.71.41.21.0-0.30.5
Intermittent access total locomotion0.40.50.70.80.80.20.8
Intermittent access standard deviation1.12.23.4-1.9-1.71.60.5
Left kidney weight0.94.48.52.92.6-1.30.6
Right kidney weight1.15.29.13.02.5-2.3-0.4
Cocaine induced anxiety0.60.92.20.00.31.51.1
Post-drug Anxiety0.70.71.8-0.00.31.41.0
Baseline Anxiety0.50.60.8-0.6-0.7-0.8-0.9
Tail length1.04.05.62.22.41.02.2
Length with tail1.25.49.91.82.11.93.1
Length without tail0.72.14.11.31.40.92.0
Times rat made contact with spout3.13.66.62.32.60.41.5
Lifetime Intake0.00.00.1-0.1-0.3-0.2-0.2
Liver weight, left0.81.43.40.80.5-1.8-1.1
Liver weight, right1.62.74.92.22.1-0.81.1
Locomotor activity1.93.04.61.82.10.71.9
Locomotor testing distance1.93.55.11.82.21.02.3
Locomotor testing rearing1.63.25.72.42.4-1.20.3
Locomotion in novel chamber0.60.71.3-0.9-1.2-0.3-0.8
Locomotion in novel chamber post-restriction1.32.24.5-0.6-1.1-1.7-2.1
Fecal boli incidents, locomotor time 11.31.93.4-0.2-0.8-1.8-1.8
Change in fecal boli incidents, locomotor task0.30.31.0-0.2-0.3-0.5-1.0
Time >=10cm from walls, locomotor time 10.60.61.20.70.4-1.1-0.8
Bouts of movement, locomotor time 10.40.40.8-0.4-0.30.80.9
Total resting periods, locomotor time 10.30.41.00.20.20.61.0
Rest time, locomotor task time 10.40.61.0-0.9-1.0-0.0-0.7
Distance moved, locomotor task time 10.20.20.40.20.30.60.6
Vertical activity count, locomotor time 10.10.30.6-0.8-0.70.2-0.2
Time >=10cm from walls, locomotor time 20.60.91.70.90.5-1.3-0.8
Bouts of movement, locomotor time 20.20.30.40.50.50.60.6
Total resting periods, locomotor time 20.20.30.80.10.20.90.6
Rest time, locomotor task time 20.40.50.9-0.9-1.00.6-0.0
Distance moved, locomotor task time 20.70.81.51.11.2-0.30.5
Vertical activity count, locomotor time 20.20.20.5-0.2-0.2-0.5-0.7
Light reinforcement 11.02.54.42.11.9-1.40.0
Light reinforcement 21.42.23.21.71.80.41.6
Bone: marrow area0.30.71.2-1.1-1.10.60.2
Bone: maximum diameter0.40.71.40.90.5-1.2-0.6
Bone: maximum force0.40.62.00.00.00.71.4
Bone: maximum moment0.10.20.80.1-0.00.20.9
Mean time between licks in bursts0.92.33.8-2.0-1.81.40.1
Mean num. licks in bursts0.40.61.1-0.7-0.8-0.5-1.1
Cd content in liver1.01.11.9-1.4-1.40.0-0.7
Co content in liver0.10.10.1-0.4-0.30.40.2
Cu content in liver0.50.61.5-0.3-0.4-0.8-1.2
Fe content in liver0.00.00.10.20.0-0.1-0.3
K content in liver2.72.65.2-0.6-0.22.32.2
Mg content in liver0.40.40.6-0.5-0.50.70.7
Mn content in liver0.20.20.50.50.70.30.4
Na content in liver0.40.50.90.90.8-0.30.4
Rb content in liver2.42.75.5-2.2-2.40.1-0.9
Se content in liver0.80.91.41.21.0-1.0-0.7
Sr content in liver0.70.61.11.00.9-0.7-0.1
Zn content in liver1.21.32.0-1.2-1.4-0.5-1.3
Bone: minimum diameter0.10.20.60.70.4-0.40.3
Time in familiar zone, hab. session 11.11.12.11.00.5-1.5-0.9
Time in novel zone, hab. session 10.60.61.1-1.1-0.70.7-0.0
Total zone transitions, hab. session 12.43.36.42.52.4-0.70.8
Total locomotion distance, hab. session 12.83.97.62.72.5-1.40.2
Locomotion velocity, hab. session 12.53.56.82.62.3-1.40.2
Time in familiar zone, hab. session 21.82.02.7-1.7-1.61.50.4
Time in novel zone, hab. session 20.80.81.50.70.7-1.2-0.8
Total zone transitions, hab. session 22.43.14.61.61.91.12.2
Total locomotion distance, hab. session 21.92.54.22.02.10.31.4
Locomotion velocity, hab. session 21.62.13.41.71.90.41.4
Novel to familiar place preference ratio0.10.10.10.30.3-0.10.0
Novelty place preference0.00.00.00.10.1-0.1-0.0
Time in novel zone, NPP test0.00.00.10.10.1-0.2-0.2
Total zone transitions, NPP test4.15.99.73.13.10.02.1
Total locomotion distance, NPP test3.75.18.72.82.90.11.9
Locomotion velocity, NPP test4.36.19.43.03.10.52.4
Intraocular pressure0.50.71.1-0.8-0.8-0.4-1.1
Delta distance traveled before/after self-admin1.51.63.21.71.8-0.20.7
Delta ambulatory time before/after self-admin1.72.14.21.92.0-0.30.6
Parametrial fat weight2.66.210.63.13.3-0.12.1
Pavlov. Cond. lever latency2.02.64.3-2.1-1.71.70.4
Pavlov. Cond. magazine entry latency1.72.24.71.10.7-2.2-1.6
Pavlov. Cond. change in total contacts2.22.43.81.71.4-1.9-0.9
Pavlov. Cond. index score2.73.45.02.11.7-2.2-0.9
Pavlov. Cond. latency score2.22.84.91.81.4-2.2-1.1
Pavlov. Cond. lever contacts2.32.84.62.11.9-1.7-0.3
Pavlov. Cond. magazine entry number2.53.24.9-2.0-1.62.21.1
Pavlov. Cond. intertrial magazine entries0.60.71.3-1.1-1.10.5-0.3
Pavlov. Cond. lever-magazine prob. diff.2.83.55.72.01.6-2.4-1.1
Pavlov. Cond. response bias3.03.85.92.42.1-2.1-0.6
Pavlov. Cond. lever latency2.12.83.8-1.8-1.9-1.0-1.8
Pavlov. Cond. magazine entry latency1.82.12.91.71.70.41.6
Pavlov. Cond. change in total contacts2.13.34.41.82.01.22.1
Pavlov. Cond. index score3.04.06.12.42.50.62.0
Pavlov. Cond. latency score3.24.26.52.52.60.62.0
Pavlov. Cond. lever contacts2.33.24.11.92.01.02.0
Pavlov. Cond. magazine entry number0.70.91.5-0.9-0.9-0.6-1.2
Pavlov. Cond. intertrial magazine entries0.10.10.3-0.0-0.0-0.4-0.5
Pavlov. Cond. lever-magazine prob. diff.3.24.26.42.42.50.72.0
Pavlov. Cond. response bias1.52.03.61.11.21.31.9
Time in closed arm before self-admin0.40.51.0-0.4-0.11.00.9
Time in closed arm after self-admin2.93.16.2-0.30.22.52.5
Time in open arm before self-admin1.61.73.11.81.4-1.2-0.5
Time in open arm after self-admin2.02.24.61.00.7-2.1-1.6
Bone: periosteal estimation0.10.10.40.40.1-0.6-0.1
Bone: periosteal perimeter0.50.91.71.31.1-0.20.8
Bone: post-yield work0.40.61.3-0.10.01.01.1
Progressive ratio test 1 active lever presses0.60.71.10.91.00.40.9
Progressive ratio test 1 breakpoint0.50.61.00.91.00.30.8
Progressive ratio test 1 inactive lever presses0.50.71.31.11.0-0.70.0
Progressive ratio test 2 active lever presses1.41.63.51.91.5-0.90.2
Progressive ratio test 2 breakpoint1.61.93.92.01.6-0.90.2
Progressive ratio test 2 inactive lever presses0.40.61.21.10.9-0.70.1
Incentive Sensitization - Responses0.71.02.21.51.2-0.8-0.1
Incentive Sensitization - Breakpoint0.81.12.31.51.2-0.8-0.1
Sum of active levers in priming session hrs 5-63.73.47.00.4-0.1-2.6-2.7
Progressive ratio0.30.40.7-0.8-0.80.5-0.1
Food seeking constrained by brief footshock0.30.30.70.20.30.60.9
Seeking ratio, punishment vs. effort0.20.30.40.60.7-0.40.2
Retroperitoneal fat weight1.97.914.63.83.4-2.40.1
Reaction time number correct1.22.45.1-0.1-0.5-2.0-2.3
Reaction time mean minus median0.10.20.5-0.4-0.10.70.4
Reaction time mean minus median AUC0.30.71.6-0.9-0.41.30.6
Reaction time num false alarms0.40.51.0-1.0-1.00.3-0.1
Reaction time num false alarms AUC0.20.30.6-0.8-0.80.1-0.2
Reaction time trials correct on left1.22.45.1-0.1-0.5-2.0-2.3
Reaction time trials on left1.22.24.7-0.0-0.5-1.9-2.2
Reaction time mean1.82.96.5-0.7-0.22.52.1
Reaction time mean AUC2.13.37.4-0.7-0.12.72.3
Median of all reaction times2.23.16.8-0.6-0.12.62.3
Reaction time omissions0.30.50.80.60.70.60.9
Reaction time false alarm rate0.71.01.6-1.0-0.81.30.9
Reaction time premature initiation rate0.60.91.71.31.3-0.50.2
Reaction time premature initiations0.91.62.61.41.1-1.6-1.0
Std. dev. reaction times1.12.04.7-0.7-0.22.21.7
Reaction time trials completed1.22.24.7-0.0-0.5-1.9-2.2
Reaction time trials AUC1.12.24.40.2-0.3-2.0-2.1
Run reversals in cocaine runway, females0.60.61.21.10.8-0.8-0.1
Run reversals in cocaine runway, males0.20.20.40.30.1-0.6-0.6
Latency to leave start box in cocaine runway0.91.02.01.41.3-0.60.2
Latency to leave start box in cocaine runway, F0.20.20.30.50.5-0.00.5
Latency to leave start box in cocaine runway, M2.72.55.02.22.0-1.0-0.2
Std. dev. time between licks in bursts1.01.42.8-1.3-1.7-0.1-1.0
Total sessions with >9 infusions0.30.30.7-0.1-0.3-0.8-0.8
Short access day 1 total inactive lever presses0.10.20.30.50.4-0.4-0.0
Short access day 10 total inactive lever presses0.00.10.20.30.40.10.3
Short access day 1 total infusions0.30.40.6-0.4-0.7-0.5-0.8
Short access day 10 total infusions0.00.10.1-0.2-0.30.20.2
Short access total infusions0.50.71.3-1.0-1.1-0.2-0.6
Short access day 1 locomotion0.10.10.2-0.3-0.5-0.2-0.2
Short access day 10 total locomotion0.51.01.6-1.2-0.91.30.6
Short access total locomotion0.40.50.9-0.8-0.9-0.3-0.6
One hour access (0.3 mA shock)0.70.81.60.0-0.3-1.2-1.2
Compulsive drug intake0.30.40.9-0.2-0.3-0.7-0.9
One hour access (shock baseline)0.20.30.50.70.6-0.30.3
Social response proportion1.01.11.6-1.2-1.31.20.2
Social responses1.41.83.1-1.7-1.81.1-0.1
Social time1.92.65.1-0.7-1.3-1.7-2.3
Soleus weight0.30.81.61.21.1-0.50.4
Bone: stiffness0.10.10.3-0.1-0.20.30.5
Tibialis anterior weight0.10.40.70.80.8-0.20.4
Time to tail flick, vehicle, before self-admin0.10.10.3-0.5-0.4-0.30.0
Time to tail flick, vehicle, after self-admin3.03.96.4-2.2-1.72.51.1
Time to tail flick, test, before self-admin3.43.65.3-1.5-2.1-1.5-2.3
Time to tail flick, test, after self-admin0.70.81.5-1.2-1.10.4-0.5
Delta time to tail flick, vehicle, before/after SA1.11.01.8-1.1-1.01.30.3
Delta time to tail flick, test, before/after SA3.43.56.70.21.02.62.5
Tibia length2.15.810.13.23.0-2.0-0.1
Ambulatory time before self-admin0.30.50.9-0.1-0.4-0.9-1.0
Ambulatory time after self-admin1.61.93.31.81.6-1.3-0.4
Bone: tissue strength0.00.00.1-0.2-0.2-0.2-0.1
Total heroin consumption0.10.10.30.60.0-0.2-0.2
Bone: trabecular number1.01.62.5-1.3-1.11.61.0
Bone: trabecular spacing0.91.22.01.00.7-1.4-1.1
Bone: trabecular thickness1.31.62.3-1.4-1.21.50.8
Bone: trabecular tissue density2.33.47.90.1-0.3-2.3-2.8
Water consumed over 24 hours1.82.54.62.22.0-1.2-0.0
Number of responses in last shaping day0.10.10.20.20.1-0.5-0.3