Pcp2

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 ENSRNOG00000000993 0.12 0.06 3.1e-08 0.1 0.08 0.08 0.09 1.8e-09 4.1e-08 5.0e-08 1.6e-08
2 Brain intron excision ratio chr12:1683275:1683377 0.03 0.02 7.5e-03 0.01 0.01 0 0.01 2.7e-02 3.4e-02 1.6e-01 8.6e-02
3 Brain intron excision ratio chr12:1683275:1683586 0.05 0.03 4.1e-03 0.02 0.03 0.02 0.02 2.4e-03 1.2e-03 3.8e-03 6.8e-03
4 Brain mRNA stability ENSRNOG00000000993 0.1 0.05 1.1e-07 0.05 0.07 0.07 0.07 1.8e-05 3.2e-07 3.5e-07 7.3e-07

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 strong Z-scores (below -2 or above 2): lower negative Z-scores are darker blue, higher positive Z-scores are darker red.

Trait Avg chi2 ratio Avg chi2 Max chi2 1 2 3 4
BMI with tail2.47.811.53.4-3.02.0-2.5
BMI without tail4.39.111.53.4-3.42.8-2.4
Body weight9.941.765.88.1-7.05.7-4.5
Epididymis fat weight0.10.20.30.4-0.6-0.1-0.4
Glucose0.20.30.90.2-0.10.5-1.0
Heart weight0.40.61.7-0.31.30.80.4
Left kidney weight4.813.621.14.6-4.03.8-1.9
Right kidney weight4.212.018.84.3-3.83.4-1.9
Tail length6.619.826.05.1-5.14.4-2.9
Length with tail10.538.658.17.6-6.86.0-3.9
Length without tail5.812.621.94.7-3.63.0-2.5
Liver weight, left0.40.71.9-0.30.5-0.81.4
Liver weight, right0.71.22.41.6-1.20.9-0.1
Parametrial fat weight0.00.10.10.3-0.20.3-0.2
Retroperitoneal fat weight0.20.82.40.5-0.6-0.4-1.5
Intraocular pressure0.30.40.80.9-0.90.30.2
Extensor digitorum longus weight3.313.421.64.6-4.33.0-2.0
Soleus weight0.41.12.11.4-1.40.50.1
Tibialis anterior weight5.619.229.15.4-5.13.7-2.9
Tibia length3.18.811.93.4-3.23.0-2.1
Number of licking bursts0.20.20.7-0.30.10.80.3
Food consumed during 24 hour testing period0.20.20.5-0.30.5-0.20.7
Times rat made contact with spout1.21.42.01.2-1.11.4-0.9
Mean time between licks in bursts1.62.22.7-1.61.6-1.51.2
Mean num. licks in bursts0.20.20.40.7-0.4-0.1-0.5
Std. dev. time between licks in bursts0.00.00.10.2-0.30.10.2
Water consumed over 24 hours0.60.71.20.9-0.81.1-0.1
Indifference point 0 sec1.93.04.5-1.41.5-1.82.1
Indifference point AUC0.10.20.40.6-0.20.60.0
Indifference point function ln k0.20.30.6-0.50.6-0.40.8
Indifference point function log k0.20.30.6-0.50.6-0.40.8
Delay discounting total patch changes 0 sec2.74.36.4-1.71.9-2.12.5
Delay discounting total patch changes 12 sec0.50.71.1-0.50.6-1.01.0
Delay discounting total patch changes 18 sec1.92.64.0-1.11.6-1.52.0
Delay discounting total patch changes 24 sec2.43.05.0-1.51.4-1.62.2
Delay discounting total patch changes 6 sec1.42.13.3-1.11.5-1.41.8
Delay discounting time to switch 0 sec0.40.72.40.2-0.5-0.1-1.6
Delay discounting water rate 0 sec0.81.24.3-0.20.6-0.42.1
Delay discounting water rate 12 sec0.30.51.4-0.40.5-0.31.2
Delay discounting water rate 18 sec0.00.00.1-0.0-0.00.20.3
Delay discounting water rate 24 sec0.20.30.40.5-0.40.50.6
Delay discounting water rate 6 sec0.40.61.6-0.00.4-0.71.3
Locomotor activity1.62.64.22.0-1.22.1-1.0
Locomotor testing distance0.10.20.30.50.10.30.6
Locomotor testing rearing0.91.41.9-0.91.1-1.31.4
Light reinforcement 10.40.81.50.6-0.90.7-1.2
Light reinforcement 20.20.20.3-0.50.4-0.30.5
Reaction time number correct0.30.51.2-0.30.6-0.21.1
Reaction time mean minus median4.05.26.72.2-2.61.8-2.4
Reaction time mean minus median AUC0.40.61.00.5-1.00.5-0.9
Reaction time num false alarms0.30.40.70.50.10.7-0.8
Reaction time num false alarms AUC0.10.20.20.50.30.4-0.5
Reaction time trials correct on left0.30.51.2-0.30.6-0.21.1
Reaction time trials on left0.30.41.1-0.30.6-0.21.1
Reaction time mean0.50.62.40.1-0.10.4-1.5
Reaction time mean AUC0.30.41.7-0.10.10.2-1.3
Median of all reaction times0.40.51.0-0.70.8-0.2-1.0
Reaction time omissions0.10.20.60.2-0.00.2-0.8
Reaction time false alarm rate0.30.51.10.7-0.20.6-1.0
Reaction time premature initiation rate0.40.60.80.6-0.70.8-0.9
Reaction time premature initiations0.10.20.30.4-0.40.6-0.3
Std. dev. reaction times1.42.03.41.2-1.41.0-1.8
Reaction time trials completed0.30.41.1-0.30.6-0.21.1
Reaction time trials AUC0.40.61.4-0.50.8-0.41.2
Social response proportion8.89.511.93.1-3.03.5-2.7
Social responses1.21.52.41.5-1.11.5-0.7
Social time0.30.30.9-0.90.6-0.1-0.2
Conditioned locomotion0.60.71.3-0.70.5-1.21.0
Cocaine response after cond. corrected0.10.10.30.3-0.3-0.2-0.5
Cocaine response after cond. not corrected0.40.40.60.7-0.6-0.1-0.8
Cocaine response before conditioning0.30.30.70.8-0.70.2-0.4
Saline control response0.40.61.00.8-0.81.00.3
Condit. Reinf. active minus inactive responses3.54.45.62.1-1.92.4-2.0
Condit. Reinf. active-inactive response ratio2.93.04.51.5-1.42.1-1.8
Condit. Reinf. active responses3.24.45.32.3-2.12.1-1.9
Condit. Reinf. inactive responses0.20.20.50.7-0.60.2-0.1
Condit. Reinf. lever presses0.20.30.60.8-0.60.3-0.5
Condit. Reinf. lever reinforcers received2.63.64.12.0-1.82.0-1.8
Pavlov. Cond. lever latency0.71.01.5-1.00.8-1.01.2
Pavlov. Cond. magazine entry latency0.50.61.70.4-0.30.5-1.3
Pavlov. Cond. change in total contacts0.20.30.40.4-0.30.7-0.6
Pavlov. Cond. index score0.30.41.00.5-0.30.6-1.0
Pavlov. Cond. latency score0.30.41.00.5-0.30.5-1.0
Pavlov. Cond. lever contacts0.40.61.00.8-0.60.5-1.0
Pavlov. Cond. magazine entry number0.20.20.70.0-0.2-0.30.8
Pavlov. Cond. intertrial magazine entries0.10.10.20.4-0.40.50.2
Pavlov. Cond. lever-magazine prob. diff.0.30.41.00.5-0.20.6-1.0
Pavlov. Cond. response bias0.30.51.10.6-0.40.5-1.0
Conditioned reinforcement - actives3.03.04.51.9-1.72.1-0.9
Conditioned reinforcement - inactives0.20.20.6-0.30.5-0.10.8
Conditioned locomotion1.11.32.01.4-1.31.3-0.4
Intermittent access intake day 1-15 change0.10.10.40.20.10.20.7
Intermittent access intake escalation0.10.10.20.4-0.10.30.5
Intermittent access intake escalation 20.30.30.6-0.40.5-0.30.8
Intermitt. access day 1 inactive lever presses0.80.81.7-0.81.0-0.51.3
Intermitt. access day 15 inactive lever presses0.40.50.8-0.60.6-0.90.6
Intermitt. access escalation Index0.30.20.3-0.60.5-0.40.5
Intermittent access day 1 total infusions0.10.10.2-0.40.4-0.1-0.1
Intermittent access day 15 total infusions0.10.10.3-0.30.5-0.20.5
Intermittent access terminal intake (last 3 days)0.20.20.3-0.40.5-0.40.4
Intermittent access total infusions0.00.00.1-0.20.2-0.1-0.2
Intermittent access day 1 locomotion0.50.50.7-0.90.8-0.80.1
Intermittent access day 15 total locomotion0.10.10.1-0.30.4-0.10.4
Intermittent access total locomotion0.20.20.4-0.60.7-0.40.1
Intermittent access standard deviation0.40.40.8-0.30.5-0.70.9
Cocaine induced anxiety0.10.10.3-0.20.1-0.50.0
Post-drug Anxiety0.20.30.6-0.50.3-0.4-0.8
Baseline Anxiety0.30.30.8-0.50.3-0.1-0.9
Lifetime Intake0.00.00.1-0.10.2-0.2-0.3
Incentive Sensitization - Responses0.00.00.0-0.20.20.10.2
Incentive Sensitization - Breakpoint0.00.00.0-0.20.20.10.2
Progressive ratio test 1 active lever presses0.30.30.50.6-0.40.7-0.3
Progressive ratio test 1 breakpoint0.50.50.90.7-0.60.9-0.5
Progressive ratio test 1 inactive lever presses0.10.10.30.10.10.40.5
Progressive ratio test 2 active lever presses0.60.71.40.8-0.71.2-0.4
Progressive ratio test 2 breakpoint0.50.61.40.6-0.51.2-0.5
Progressive ratio test 2 inactive lever presses0.30.41.50.10.30.21.2
Total sessions with >9 infusions0.20.30.30.6-0.50.4-0.5
Short access day 1 total inactive lever presses0.20.20.3-0.30.5-0.30.6
Short access day 10 total inactive lever presses0.20.20.80.3-0.0-0.20.9
Short access day 1 total infusions1.01.11.7-1.11.0-1.30.6
Short access day 10 total infusions0.40.40.7-0.70.7-0.80.3
Short access total infusions0.10.10.3-0.0-0.0-0.2-0.6
Short access day 1 locomotion0.20.20.6-0.20.10.3-0.8
Short access day 10 total locomotion1.21.31.7-1.11.1-1.31.0
Short access total locomotion0.20.20.2-0.50.4-0.5-0.3
Compulsive drug intake2.72.74.2-2.01.9-1.41.1
One hour access (0.3 mA shock)0.70.81.4-0.91.1-0.31.2
One hour access (shock baseline)0.50.60.90.9-0.80.9-0.2
Number of responses in last shaping day0.10.10.1-0.20.3-0.20.4
Context. condit. distance diff. score3.34.06.22.5-2.41.6-1.4
Locomotion velocity, session 10.10.10.2-0.20.10.1-0.4
Locomotion distance, session 10.50.61.2-0.91.1-0.50.4
Locomotion velocity, session 20.10.20.40.1-0.00.6-0.5
Locomotion distance, session 20.81.11.8-1.21.4-0.50.8
Locomotion velocity, session 30.30.40.70.8-0.70.4-0.4
Locomotion distance, session 30.60.71.0-0.70.8-0.81.0
Stereotopy head waving bouts, day 30.60.71.41.0-1.20.60.0
Stereotopy head waving duration, day 30.00.00.0-0.0-0.1-0.10.0
Locomotion velocity, session 71.41.52.91.0-0.71.3-1.7
Locomotion distance, session 70.40.50.80.5-0.50.9-0.9
Stereotopy head waving bouts, day 70.40.40.6-0.70.8-0.60.4
Stereotopy head waving duration, day 70.30.30.6-0.70.7-0.40.2
Locomotion velocity, session 81.01.21.31.1-0.91.1-1.2
Locomotion distance, session 81.32.02.81.7-1.51.3-1.1
Degree of sensitization distance0.40.40.90.0-0.10.8-0.9
Degree of sensitization stereotypy0.10.10.2-0.30.4-0.2-0.0
Condit. Reinf. active minus inactive responses0.10.10.1-0.10.2-0.3-0.4
Condit. Reinf. active-inactive response ratio0.20.20.70.4-0.30.2-0.8
Condit. Reinf. active responses0.10.10.1-0.20.4-0.3-0.0
Condit. Reinf. inactive responses0.30.40.6-0.70.8-0.50.6
Incentive salience index mean0.10.20.4-0.30.5-0.60.1
Condit. Reinf. lever presses0.20.30.4-0.30.5-0.70.4
Time in familiar zone, hab. session 11.41.31.7-1.21.0-1.31.1
Time in novel zone, hab. session 11.31.21.51.2-1.01.2-1.0
Total zone transitions, hab. session 10.20.30.7-0.80.8-0.2-0.0
Total locomotion distance, hab. session 10.00.10.1-0.30.2-0.2-0.3
Locomotion velocity, hab. session 10.20.20.4-0.70.5-0.4-0.2
Time in familiar zone, hab. session 20.00.00.10.1-0.2-0.2-0.2
Time in novel zone, hab. session 20.10.10.1-0.40.40.00.1
Total zone transitions, hab. session 20.20.30.80.3-0.40.9-0.4
Total locomotion distance, hab. session 20.00.00.1-0.20.20.2-0.1
Locomotion velocity, hab. session 20.00.00.1-0.30.20.2-0.1
Novel to familiar place preference ratio0.10.10.4-0.0-0.00.6-0.4
Novelty place preference0.10.10.2-0.30.20.4-0.2
Time in novel zone, NPP test0.10.10.2-0.10.00.5-0.3
Total zone transitions, NPP test0.10.20.30.4-0.40.6-0.4
Total locomotion distance, NPP test0.30.40.70.7-0.60.5-0.9
Locomotion velocity, NPP test0.30.40.50.7-0.60.6-0.7
Pavlov. Cond. lever latency0.70.81.60.9-1.30.9-0.2
Pavlov. Cond. magazine entry latency0.40.60.80.9-0.70.8-0.6
Pavlov. Cond. change in total contacts0.70.71.60.9-0.50.6-1.3
Pavlov. Cond. index score0.10.20.30.5-0.20.2-0.5
Pavlov. Cond. latency score0.10.10.40.4-0.10.1-0.6
Pavlov. Cond. lever contacts0.30.40.7-0.50.9-0.70.0
Pavlov. Cond. magazine entry number0.60.71.1-1.10.9-0.80.6
Pavlov. Cond. intertrial magazine entries1.31.52.1-1.31.4-1.11.0
Pavlov. Cond. lever-magazine prob. diff.0.10.10.20.5-0.20.1-0.5
Pavlov. Cond. response bias0.20.30.50.7-0.50.3-0.5
Bone: apparent density0.61.02.01.4-1.3-0.10.7
Bone surface1.83.15.92.4-2.40.9-0.5
Bone volume0.61.02.01.4-1.4-0.20.4
Bone: connectivity density1.82.85.32.3-2.21.0-0.1
Bone: cortical apparent density0.20.30.80.2-0.20.5-0.9
Bone: cortical area3.04.56.02.4-2.41.8-1.8
Bone: cortical porosity0.00.00.1-0.10.1-0.10.2
Bone: cortical porosity0.10.10.2-0.50.4-0.30.3
Bone: cortical thickness2.64.35.72.4-2.31.8-1.7
Bone: cortical thickness1.31.51.91.4-1.31.3-0.7
Bone: cortical tissue density0.10.20.60.0-0.00.3-0.7
Bone: elastic displacement0.10.10.30.6-0.30.30.1
Bone: elastic work1.21.62.81.7-1.61.0-0.3
Bone: endosteal estimation0.10.20.70.1-0.2-0.00.9
Bone: endosteal perimeter0.10.30.70.6-0.80.30.2
Bone: final force2.74.45.62.2-2.42.2-1.5
Bone: final moment2.13.54.42.0-2.11.9-1.3
Bone: marrow area0.10.20.9-0.0-0.1-0.10.9
Bone: maximum diameter0.71.32.21.4-1.50.8-0.5
Bone: maximum force1.32.33.51.7-1.91.4-0.8
Bone: maximum moment0.91.62.51.5-1.61.2-0.6
Bone: minimum diameter0.00.00.0-0.10.2-0.10.2
Bone: periosteal estimation0.81.62.71.5-1.61.1-0.5
Bone: periosteal perimeter0.71.22.01.3-1.40.8-0.8
Bone: post-yield work0.10.10.20.2-0.2-0.40.4
Bone: stiffness0.91.41.81.1-1.31.3-0.9
Bone: tissue strength1.41.41.8-1.11.1-1.21.3
Bone: trabecular number1.21.83.41.8-1.80.7-0.1
Bone: trabecular spacing1.82.33.4-1.81.8-1.40.8
Bone: trabecular thickness1.82.24.22.1-2.00.7-0.3
Bone: trabecular tissue density3.95.58.32.0-2.12.3-2.9
Breakpoint value in progressive ratio session1.41.51.91.3-1.21.0-1.4
Distance traveled before self-admin0.10.10.3-0.10.00.3-0.6
Distance traveled after self-admin0.10.10.10.2-0.00.4-0.3
Delta time in closed arm before/after self-admin0.20.20.40.3-0.40.7-0.4
Delta time in open arm before/after self-admin1.71.62.2-1.31.5-1.50.6
Diff in mean of infusions in LGA sessions0.00.00.00.2-0.1-0.10.1
Extinction: sum of active levers before priming0.10.10.2-0.40.4-0.4-0.3
Active lever presses in extinction session 60.10.10.10.3-0.30.0-0.1
Delta distance traveled before/after self-admin0.10.10.20.10.20.10.4
Delta ambulatory time before/after self-admin0.20.30.4-0.40.7-0.40.6
Time in closed arm before self-admin0.20.30.40.5-0.60.50.4
Time in closed arm after self-admin0.20.20.40.2-0.50.60.4
Time in open arm before self-admin0.40.40.70.6-0.40.8-0.6
Time in open arm after self-admin0.00.10.10.10.2-0.3-0.3
Sum of active levers in priming session hrs 5-60.20.20.50.3-0.2-0.2-0.7
Time to tail flick, vehicle, before self-admin1.01.02.40.4-0.61.0-1.6
Time to tail flick, vehicle, after self-admin0.10.10.30.00.00.4-0.5
Time to tail flick, test, before self-admin0.50.50.90.9-0.60.7-0.3
Time to tail flick, test, after self-admin0.50.50.80.7-0.70.5-0.9
Delta time to tail flick, vehicle, before/after SA0.90.91.0-0.90.9-0.91.0
Delta time to tail flick, test, before/after SA0.20.20.5-0.50.3-0.70.2
Ambulatory time before self-admin0.30.30.60.3-0.50.4-0.8
Ambulatory time after self-admin0.10.10.10.3-0.10.2-0.4
Total heroin consumption0.50.50.9-0.90.9-0.7-0.2
Area under the delay curve1.41.53.20.9-0.81.1-1.8
Delay disc. indifference point, 0s delay4.85.28.02.1-2.12.0-2.8
Delay disc. indifference point, 16s delay0.40.40.80.4-0.30.6-0.9
Delay disc. indifference point, 2s delay1.01.23.30.7-0.70.5-1.8
Delay disc. indifference point, 24s delay0.20.10.4-0.10.20.4-0.6
Delay disc. indifference point, 4s delay0.50.61.60.5-0.40.4-1.3
Delay disc. indifference point, 8s delay0.20.20.50.4-0.20.5-0.7
Delay discount exponential model param1.11.12.6-0.80.6-0.91.6
Delay discount hyperbolic model param1.01.02.6-0.70.6-0.81.6
Fecal boli incidents, locomotor time 10.70.81.21.0-1.11.0-0.4
Change in fecal boli incidents, locomotor task0.20.20.3-0.50.5-0.50.1
Time >=10cm from walls, locomotor time 10.20.20.6-0.0-0.1-0.4-0.8
Bouts of movement, locomotor time 10.50.50.90.8-0.60.9-0.3
Total resting periods, locomotor time 10.50.60.90.9-0.70.9-0.4
Rest time, locomotor task time 10.50.50.80.8-0.90.6-0.5
Distance moved, locomotor task time 10.00.00.1-0.20.30.0-0.0
Vertical activity count, locomotor time 10.10.10.40.3-0.10.6-0.1
Time >=10cm from walls, locomotor time 21.81.92.51.4-1.60.8-1.6
Bouts of movement, locomotor time 20.40.40.70.9-0.70.5-0.1
Total resting periods, locomotor time 20.20.20.50.7-0.60.4-0.0
Rest time, locomotor task time 20.10.10.3-0.20.2-0.60.2
Distance moved, locomotor task time 20.10.10.3-0.00.00.50.0
Vertical activity count, locomotor time 20.60.61.50.8-0.71.20.0
Weight adjusted by age0.20.20.30.5-0.3-0.20.5
Seeking ratio, delayed vs. immediate footshock3.13.64.7-2.22.1-1.61.6
Locomotion in novel chamber0.10.20.4-0.20.40.30.6
Locomotion in novel chamber post-restriction1.01.22.01.2-1.11.4-0.3
Progressive ratio1.01.21.7-1.31.3-0.90.8
Food seeking constrained by brief footshock4.25.25.4-2.32.2-2.32.2
Seeking ratio, punishment vs. effort0.10.10.10.3-0.4-0.10.3
Run reversals in cocaine runway, females0.60.60.7-0.80.7-0.90.6
Run reversals in cocaine runway, males0.90.91.5-0.81.0-0.51.2
Latency to leave start box in cocaine runway0.60.61.00.7-0.70.8-1.0
Latency to leave start box in cocaine runway, F0.50.50.60.7-0.70.8-0.8
Latency to leave start box in cocaine runway, M0.10.10.1-0.30.3-0.20.2
Cd content in liver3.53.85.4-2.12.3-1.41.9
Co content in liver0.91.12.2-0.90.9-0.71.5
Cu content in liver1.21.52.2-0.91.5-1.21.3
Fe content in liver0.81.02.01.4-1.30.6-0.3
K content in liver0.00.00.10.40.1-0.1-0.2
Mg content in liver0.30.30.70.8-0.30.6-0.4
Mn content in liver0.50.50.9-0.80.9-0.60.6
Na content in liver0.60.70.80.9-0.90.7-0.9
Rb content in liver1.62.02.9-1.31.7-1.60.9
Se content in liver2.22.64.12.0-1.60.9-1.7
Sr content in liver0.50.51.2-0.60.2-0.61.1
Zn content in liver0.40.40.70.8-0.80.30.5