Plxdc1

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 Brain gene expression Plxdc1 0.05 0.04 3.5e-05 0.04 0.04 0.03 0.04 7.6e-05 7.3e-05 3.5e-04 1.8e-04
2 pVTA intron excision ratio chr10_82956547_82956821 0.39 0.22 9.6e-03 0.03 0.02 0 0.02 1.6e-02 5.3e-02 2.4e-01 5.5e-02
3 Brain mRNA stability Plxdc1 0.15 0.15 1.0e-05 0.06 0.04 0.06 0.06 2.4e-06 4.4e-05 4.0e-06 3.6e-06
4 Adipose gene expression Plxdc1 0.37 0.27 8.2e-13 0.11 0.11 0.11 0.11 4.7e-12 9.2e-12 4.5e-12 8.6e-12

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 density2.33.94.81.91.8-1.9-2.2
Area under the delay curve0.80.91.21.00.7-1.0-1.1
BMI with tail1.44.75.6-2.3-2.42.31.5
BMI without tail0.00.10.2-0.4-0.20.1-0.0
Body weight5.021.126.0-5.1-4.44.84.0
Weight adjusted by age0.40.40.9-0.4-1.00.30.6
Bone surface0.00.00.1-0.10.1-0.3-0.0
Bone volume0.10.20.30.40.4-0.6-0.4
Breakpoint value in progressive ratio session0.90.91.4-1.1-0.11.21.1
Number of licking bursts0.40.50.70.80.4-0.6-0.9
Context. condit. distance diff. score0.91.02.1-0.7-1.41.00.7
Locomotion velocity, session 10.50.60.9-1.0-0.40.70.9
Locomotion distance, session 12.43.15.1-2.3-1.21.61.7
Locomotion velocity, session 20.40.40.8-0.9-0.30.70.6
Locomotion distance, session 20.50.61.4-1.20.20.50.9
Locomotion velocity, session 30.10.10.2-0.4-0.10.40.0
Locomotion distance, session 30.40.40.6-0.8-0.60.60.6
Stereotopy head waving bouts, day 33.54.15.22.11.8-1.9-2.3
Stereotopy head waving duration, day 30.50.61.20.80.4-0.5-1.1
Locomotion velocity, session 70.80.81.0-0.9-1.01.00.8
Locomotion distance, session 70.10.20.4-0.3-0.30.40.6
Stereotopy head waving bouts, day 71.01.11.91.10.7-0.9-1.4
Stereotopy head waving duration, day 70.30.30.60.50.3-0.5-0.8
Locomotion velocity, session 87.28.69.8-3.0-3.03.12.6
Locomotion distance, session 81.31.92.5-1.6-1.21.21.5
Degree of sensitization distance0.50.50.7-0.5-0.80.90.7
Degree of sensitization stereotypy1.51.62.31.40.8-1.2-1.5
Conditioned locomotion0.10.10.20.30.4-0.3-0.4
Cocaine response after cond. corrected1.82.02.71.61.4-1.6-1.0
Cocaine response after cond. not corrected2.62.94.32.11.5-1.8-1.3
Cocaine response before conditioning0.50.61.21.10.2-0.5-1.0
Saline control response0.10.20.40.6-0.2-0.2-0.5
Bone: connectivity density3.25.06.52.22.0-2.2-2.5
Bone: cortical apparent density5.16.77.82.82.8-2.7-2.0
Bone: cortical area0.10.20.30.50.3-0.4-0.2
Bone: cortical porosity0.30.40.80.90.3-0.4-0.6
Bone: cortical porosity0.40.41.01.00.2-0.4-0.7
Bone: cortical thickness1.01.72.71.71.1-1.2-1.2
Bone: cortical thickness4.24.86.32.51.9-2.0-2.3
Bone: cortical tissue density5.16.77.82.82.8-2.7-2.0
Condit. Reinf. active minus inactive responses0.60.71.00.71.0-0.7-0.9
Condit. Reinf. active-inactive response ratio0.90.91.50.90.9-0.8-1.2
Condit. Reinf. active responses0.60.80.90.90.9-0.7-0.9
Condit. Reinf. inactive responses0.20.20.60.80.1-0.2-0.5
Incentive salience index mean1.62.02.71.31.6-1.3-1.4
Condit. Reinf. lever presses1.11.52.11.21.4-1.2-1.1
Condit. Reinf. active minus inactive responses0.50.70.80.80.9-0.8-0.8
Condit. Reinf. active-inactive response ratio0.40.40.70.50.8-0.6-0.5
Condit. Reinf. active responses1.11.61.81.21.3-1.2-1.3
Condit. Reinf. inactive responses2.32.82.91.71.7-1.6-1.7
Condit. Reinf. lever presses0.00.00.00.20.2-0.2-0.2
Condit. Reinf. lever reinforcers received1.11.62.01.21.4-1.2-1.2
Conditioned reinforcement - actives1.11.11.51.20.6-1.2-1.0
Conditioned reinforcement - inactives1.31.42.11.21.5-1.0-1.1
Conditioned locomotion1.11.31.51.20.9-1.1-1.2
Patch foraging indifference point 0 sec2.23.65.01.52.2-2.1-1.6
Patch foraging indifference point AUC0.20.20.7-0.20.1-0.40.9
Delay disc. indifference point, 0s delay1.21.31.61.21.3-1.2-1.0
Delay disc. indifference point, 16s delay0.60.70.80.90.7-0.9-0.7
Delay disc. indifference point, 2s delay2.22.53.01.71.4-1.7-1.5
Delay disc. indifference point, 24s delay0.10.10.10.30.1-0.3-0.3
Delay disc. indifference point, 4s delay0.60.61.10.80.8-1.1-0.4
Delay disc. indifference point, 8s delay0.80.81.70.80.5-0.8-1.3
Indifference point function ln k0.10.10.40.10.1-0.0-0.7
Indifference point function log k0.10.10.40.10.1-0.0-0.7
Patch foraging total patch changes 0 sec1.72.73.91.22.0-1.9-1.3
Patch foraging total patch changes 12 sec5.36.98.52.52.9-2.9-2.1
Patch foraging total patch changes 18 sec0.70.91.80.81.1-1.3-0.3
Patch foraging total patch changes 24 sec1.92.32.71.61.6-1.6-1.1
Patch foraging total patch changes 6 sec2.33.45.31.52.3-2.2-1.1
Patch foraging time to switch 0 sec0.00.10.10.20.2-0.1-0.4
Patch foraging water rate 0 sec0.00.00.1-0.10.3-0.0-0.0
Patch foraging water rate 12 sec0.40.60.8-0.7-0.60.80.9
Patch foraging water rate 18 sec0.60.71.70.80.6-0.5-1.3
Patch foraging water rate 24 sec0.40.51.20.60.6-0.4-1.1
Patch foraging water rate 6 sec1.11.62.71.11.6-1.1-1.2
Seeking ratio, delayed vs. immediate footshock0.10.10.30.00.10.00.5
Distance traveled before self-admin0.20.20.5-0.5-0.20.40.7
Distance traveled after self-admin1.51.72.0-1.4-1.31.31.1
Extensor digitorum longus weight9.136.040.4-5.8-6.46.15.7
Bone: elastic displacement0.00.00.10.1-0.10.0-0.3
Bone: elastic work0.00.00.00.0-0.1-0.00.0
Bone: endosteal estimation1.63.54.7-2.2-1.71.71.9
Bone: endosteal perimeter1.53.24.3-2.0-1.61.52.1
Epididymis fat weight0.20.50.7-0.8-0.70.80.6
Delta time in closed arm before/after self-admin3.83.74.8-1.9-2.12.21.4
Delta time in open arm before/after self-admin0.00.00.00.20.00.00.1
Diff in mean of infusions in LGA sessions0.40.40.8-0.5-0.70.9-0.0
Delay discount exponential model param0.50.50.7-0.7-0.40.70.9
Extinction: sum of active levers before priming0.70.71.0-0.9-1.00.90.4
Active lever presses in extinction session 61.11.02.80.51.7-0.9-0.4
Bone: final force1.01.62.11.41.1-1.3-1.2
Bone: final moment0.81.31.71.30.9-1.1-1.1
Food consumed during 24 hour testing period0.91.11.5-1.1-0.90.91.2
Glucose0.50.71.11.00.9-1.0-0.2
Heart weight2.73.84.7-2.2-1.92.21.6
Delay discount hyperbolic model param0.70.71.0-0.9-0.60.91.0
Intermittent access intake day 1-15 change0.20.20.60.40.0-0.2-0.8
Intermittent access intake escalation0.10.10.30.20.1-0.2-0.6
Intermittent access intake escalation 20.10.10.1-0.3-0.40.30.1
Intermitt. access day 1 inactive lever presses1.11.12.40.91.2-0.2-1.5
Intermitt. access day 15 inactive lever presses3.03.34.91.82.2-1.4-1.8
Intermitt. access escalation Index1.41.23.5-0.8-1.90.50.6
Intermittent access day 1 total infusions0.10.20.40.40.6-0.4-0.0
Intermittent access day 15 total infusions0.30.30.30.50.6-0.5-0.6
Intermittent access terminal intake (last 3 days)0.30.40.50.60.7-0.6-0.5
Intermittent access total infusions0.00.10.20.10.4-0.20.0
Intermittent access day 1 locomotion0.50.51.00.61.0-0.7-0.4
Intermittent access day 15 total locomotion0.60.71.00.80.7-0.7-1.0
Intermittent access total locomotion0.91.01.60.91.3-0.8-0.9
Intermittent access standard deviation0.40.51.10.41.1-0.3-0.7
Left kidney weight1.95.46.8-2.6-2.12.42.2
Right kidney weight0.41.11.4-1.2-1.01.10.8
Cocaine induced anxiety1.61.82.5-1.6-1.41.41.0
Post-drug Anxiety0.00.00.0-0.2-0.2-0.00.1
Baseline Anxiety2.42.53.41.81.3-1.9-1.3
Tail length0.72.13.2-1.8-0.81.21.8
Length with tail3.914.418.1-4.3-3.13.83.9
Length without tail4.59.911.4-3.3-2.93.43.0
Times rat made contact with spout0.91.01.31.10.9-0.9-1.1
Lifetime Intake0.00.00.20.10.4-0.1-0.0
Liver weight, left0.10.20.3-0.3-0.30.40.5
Liver weight, right0.10.20.50.20.7-0.4-0.1
Locomotor activity0.60.91.21.00.8-0.9-1.1
Locomotor testing distance2.84.76.42.31.7-2.1-2.5
Locomotor testing rearing6.710.311.53.03.4-3.4-3.1
Locomotion in novel chamber5.36.69.82.53.0-3.1-1.1
Locomotion in novel chamber post-restriction0.91.01.40.91.1-1.2-0.8
Fecal boli incidents, locomotor time 10.20.30.6-0.5-0.10.50.8
Change in fecal boli incidents, locomotor task0.10.10.20.4-0.0-0.5-0.2
Time >=10cm from walls, locomotor time 10.70.70.90.90.8-0.9-0.7
Bouts of movement, locomotor time 10.60.61.1-0.7-1.00.90.1
Total resting periods, locomotor time 10.91.01.8-0.9-1.31.10.3
Rest time, locomotor task time 10.00.00.20.00.0-0.1-0.4
Distance moved, locomotor task time 10.20.20.30.50.5-0.5-0.1
Vertical activity count, locomotor time 10.00.00.2-0.1-0.0-0.00.4
Time >=10cm from walls, locomotor time 21.81.93.11.51.4-1.8-0.5
Bouts of movement, locomotor time 20.20.20.60.20.1-0.0-0.8
Total resting periods, locomotor time 20.10.10.40.0-0.10.2-0.7
Rest time, locomotor task time 20.81.01.3-1.2-0.91.10.8
Distance moved, locomotor task time 20.10.10.20.10.4-0.40.4
Vertical activity count, locomotor time 20.00.00.0-0.1-0.10.00.0
Light reinforcement 12.64.76.01.92.1-2.2-2.5
Light reinforcement 20.81.11.41.01.0-0.9-1.2
Bone: marrow area1.53.34.5-2.1-1.61.61.9
Bone: maximum diameter0.00.00.10.10.2-0.30.2
Bone: maximum force0.00.00.10.30.1-0.3-0.2
Bone: maximum moment0.00.00.00.2-0.1-0.1-0.1
Mean time between licks in bursts1.21.72.0-1.4-1.11.31.4
Mean num. licks in bursts0.00.00.10.10.2-0.1-0.1
Cd content in liver0.30.30.60.30.5-0.5-0.8
Co content in liver1.21.41.6-1.3-1.11.21.2
Cu content in liver0.50.51.2-1.0-0.00.21.1
Fe content in liver1.21.51.8-1.3-1.11.11.3
K content in liver0.90.91.70.61.3-1.3-0.1
Mg content in liver0.60.61.10.61.0-1.0-0.0
Mn content in liver1.51.83.00.91.6-1.7-0.8
Na content in liver0.20.20.40.50.5-0.7-0.1
Rb content in liver1.82.33.41.21.8-1.7-1.1
Se content in liver3.13.85.81.82.4-2.2-1.2
Sr content in liver0.10.10.3-0.40.20.00.6
Zn content in liver2.02.22.71.41.6-1.5-1.3
Bone: minimum diameter0.30.60.8-0.9-0.60.40.9
Time in familiar zone, hab. session 10.40.40.50.70.6-0.4-0.6
Time in novel zone, hab. session 10.90.81.30.80.8-0.9-1.1
Total zone transitions, hab. session 12.12.93.4-1.8-1.61.71.7
Total locomotion distance, hab. session 10.00.10.1-0.2-0.30.40.0
Locomotion velocity, hab. session 10.60.91.0-1.0-1.01.00.8
Time in familiar zone, hab. session 20.50.60.70.70.8-0.7-0.7
Time in novel zone, hab. session 20.10.10.20.20.3-0.2-0.4
Total zone transitions, hab. session 20.40.50.9-0.9-0.60.70.7
Total locomotion distance, hab. session 20.10.20.3-0.4-0.40.5-0.1
Locomotion velocity, hab. session 20.30.40.6-0.6-0.70.80.3
Novel to familiar place preference ratio1.61.72.0-1.2-1.41.11.4
Novelty place preference1.21.21.8-0.9-1.41.01.1
Time in novel zone, NPP test0.40.40.9-0.4-0.90.60.6
Total zone transitions, NPP test0.20.30.5-0.7-0.30.40.7
Total locomotion distance, NPP test0.00.10.10.10.2-0.2-0.3
Locomotion velocity, NPP test0.10.20.4-0.6-0.40.40.4
Intraocular pressure1.72.43.6-1.4-1.91.61.2
Delta distance traveled before/after self-admin1.11.22.0-1.1-1.41.10.6
Delta ambulatory time before/after self-admin0.50.51.3-0.6-1.10.7-0.2
Parametrial fat weight0.81.62.81.01.2-0.9-1.7
Pavlov. Cond. lever latency2.83.64.0-2.0-2.01.71.9
Pavlov. Cond. magazine entry latency9.812.714.13.83.5-3.4-3.6
Pavlov. Cond. change in total contacts8.08.59.23.03.0-2.7-2.9
Pavlov. Cond. index score8.410.611.63.43.3-3.0-3.3
Pavlov. Cond. latency score6.48.19.13.02.9-2.6-2.8
Pavlov. Cond. lever contacts2.32.63.21.81.6-1.4-1.7
Pavlov. Cond. magazine entry number12.515.617.1-4.1-4.03.83.9
Pavlov. Cond. intertrial magazine entries1.41.71.9-1.4-1.31.31.3
Pavlov. Cond. lever-magazine prob. diff.9.411.713.03.63.4-3.2-3.4
Pavlov. Cond. response bias9.311.312.53.53.4-3.2-3.4
Pavlov. Cond. lever latency0.10.20.3-0.5-0.40.40.5
Pavlov. Cond. magazine entry latency0.10.20.3-0.2-0.50.30.5
Pavlov. Cond. change in total contacts0.60.81.20.81.0-1.1-0.6
Pavlov. Cond. index score0.10.10.20.50.3-0.3-0.2
Pavlov. Cond. latency score0.00.00.10.30.1-0.2-0.1
Pavlov. Cond. lever contacts0.60.81.11.00.8-0.8-0.9
Pavlov. Cond. magazine entry number0.00.00.1-0.3-0.00.10.2
Pavlov. Cond. intertrial magazine entries1.72.22.6-1.4-1.61.61.3
Pavlov. Cond. lever-magazine prob. diff.0.00.00.10.30.1-0.2-0.1
Pavlov. Cond. response bias0.81.01.31.11.0-1.0-0.9
Time in closed arm before self-admin1.31.51.81.21.1-1.3-1.3
Time in closed arm after self-admin0.60.60.9-0.8-1.00.70.6
Time in open arm before self-admin2.62.83.8-1.9-1.31.41.9
Time in open arm after self-admin0.60.61.0-0.8-0.50.81.0
Bone: periosteal estimation0.10.30.4-0.6-0.40.30.7
Bone: periosteal perimeter0.71.21.4-1.1-1.10.91.2
Bone: post-yield work1.01.41.9-1.2-1.41.30.7
Progressive ratio test 1 active lever presses1.31.32.01.21.1-1.4-0.8
Progressive ratio test 1 breakpoint1.21.21.71.21.0-1.3-0.9
Progressive ratio test 1 inactive lever presses1.21.32.01.01.3-0.7-1.4
Progressive ratio test 2 active lever presses1.21.31.91.11.3-1.4-0.7
Progressive ratio test 2 breakpoint0.91.01.41.11.1-1.2-0.7
Progressive ratio test 2 inactive lever presses0.10.20.60.20.8-0.20.1
Incentive Sensitization - Responses1.01.01.51.11.2-1.1-0.5
Incentive Sensitization - Breakpoint1.01.01.51.01.2-1.1-0.4
Sum of active levers in priming session hrs 5-60.70.71.40.71.2-0.6-0.7
Progressive ratio0.20.30.50.00.6-0.70.4
Food seeking constrained by brief footshock0.30.40.50.50.7-0.7-0.5
Seeking ratio, punishment vs. effort0.20.20.60.5-0.20.1-0.8
Retroperitoneal fat weight0.00.10.3-0.5-0.00.2-0.0
Reaction time number correct1.11.62.8-1.1-1.11.11.7
Reaction time mean minus median0.30.30.9-0.3-0.90.7-0.1
Reaction time mean minus median AUC0.20.30.60.6-0.3-0.0-0.8
Reaction time num false alarms0.81.01.11.11.0-1.0-1.0
Reaction time num false alarms AUC0.50.70.80.90.7-0.7-0.9
Reaction time trials correct on left1.11.62.8-1.1-1.11.11.7
Reaction time trials on left1.11.52.7-1.0-1.11.11.7
Reaction time mean0.00.00.10.1-0.30.2-0.3
Reaction time mean AUC0.00.10.10.0-0.30.1-0.3
Median of all reaction times0.20.30.40.60.4-0.4-0.6
Reaction time omissions0.71.01.41.00.8-1.1-1.2
Reaction time false alarm rate1.31.72.71.31.1-1.1-1.7
Reaction time premature initiation rate0.30.40.90.60.3-0.5-0.9
Reaction time premature initiations0.10.10.2-0.2-0.50.40.2
Std. dev. reaction times0.10.10.40.1-0.60.3-0.3
Reaction time trials completed1.11.52.7-1.0-1.11.11.7
Reaction time trials AUC0.91.42.5-0.9-1.01.01.6
Run reversals in cocaine runway, females2.52.42.9-1.6-1.61.71.3
Run reversals in cocaine runway, males0.50.50.90.70.9-0.7-0.4
Latency to leave start box in cocaine runway3.03.35.4-1.8-1.31.62.3
Latency to leave start box in cocaine runway, F3.13.45.8-1.7-1.51.62.4
Latency to leave start box in cocaine runway, M0.20.20.4-0.50.6-0.00.4
Std. dev. time between licks in bursts0.20.20.3-0.5-0.50.50.4
Total sessions with >9 infusions1.01.11.41.01.2-0.9-1.2
Short access day 1 total inactive lever presses1.51.62.41.31.4-0.7-1.5
Short access day 10 total inactive lever presses0.60.71.8-0.8-0.61.30.0
Short access day 1 total infusions0.40.41.20.41.1-0.2-0.3
Short access day 10 total infusions0.20.30.40.50.6-0.6-0.2
Short access total infusions0.10.10.20.00.50.00.1
Short access day 1 locomotion3.23.46.11.62.5-1.5-1.6
Short access day 10 total locomotion2.32.53.41.51.8-1.6-1.4
Short access total locomotion0.70.71.30.71.1-0.6-0.8
One hour access (0.3 mA shock)0.00.00.10.2-0.3-0.2-0.2
Compulsive drug intake0.10.10.1-0.2-0.40.2-0.0
One hour access (shock baseline)0.10.10.20.40.3-0.4-0.4
Social response proportion0.00.00.10.1-0.3-0.1-0.2
Social responses0.20.30.60.30.5-0.8-0.4
Social time0.00.00.1-0.1-0.4-0.1-0.1
Soleus weight0.30.91.91.20.4-0.6-1.4
Bone: stiffness0.00.10.10.30.2-0.4-0.1
Tibialis anterior weight1.55.16.1-2.1-2.52.32.1
Time to tail flick, vehicle, before self-admin0.20.20.40.40.1-0.4-0.6
Time to tail flick, vehicle, after self-admin0.10.10.20.30.4-0.5-0.2
Time to tail flick, test, before self-admin1.01.02.2-0.8-1.51.00.3
Time to tail flick, test, after self-admin0.20.20.60.30.8-0.3-0.0
Delta time to tail flick, vehicle, before/after SA0.40.40.40.60.7-0.5-0.6
Delta time to tail flick, test, before/after SA2.62.44.91.42.2-1.5-0.7
Tibia length1.02.83.5-1.5-1.91.81.5
Ambulatory time before self-admin0.40.40.9-0.7-0.30.41.0
Ambulatory time after self-admin2.62.83.5-1.9-1.71.81.3
Bone: tissue strength0.60.60.9-0.6-1.00.90.5
Total heroin consumption0.70.91.90.61.4-1.0-0.4
Bone: trabecular number5.28.18.52.92.7-2.9-2.9
Bone: trabecular spacing1.01.31.5-1.1-1.11.11.2
Bone: trabecular thickness0.00.00.10.2-0.10.1-0.4
Bone: trabecular tissue density0.00.00.00.10.10.0-0.1
Water consumed over 24 hours0.10.10.2-0.0-0.40.4-0.1
Number of responses in last shaping day0.20.20.7-0.10.90.20.3