Pgap3

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 mRNA stability Pgap3 0.05 0.05 9.6e-03 0.01 0.01 0.01 0.01 8.0e-03 7.0e-02 1.5e-02 6.1e-02
2 Liver gene expression Pgap3 0.62 0.14 8.2e-05 0.02 0.03 0.03 0.04 3.0e-03 1.9e-04 2.0e-04 2.8e-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
Bone: apparent density1.01.72.71.70.8
Area under the delay curve0.00.10.10.20.3
BMI with tail2.88.910.0-3.2-2.8
BMI without tail0.00.10.2-0.4-0.1
Body weight5.121.425.6-5.1-4.1
Weight adjusted by age0.80.91.1-0.8-1.1
Bone surface0.20.40.6-0.3-0.8
Bone volume0.30.51.0-0.2-1.0
Breakpoint value in progressive ratio session0.10.10.2-0.1-0.4
Number of licking bursts0.40.51.0-0.2-1.0
Context. condit. distance diff. score0.20.30.3-0.60.5
Locomotion velocity, session 10.60.60.7-0.8-0.8
Locomotion distance, session 13.84.84.8-2.2-2.2
Locomotion velocity, session 20.00.00.1-0.20.3
Locomotion distance, session 21.11.62.1-1.0-1.4
Locomotion velocity, session 30.50.50.80.50.9
Locomotion distance, session 30.10.10.1-0.4-0.1
Stereotopy head waving bouts, day 32.53.03.61.91.5
Stereotopy head waving duration, day 30.10.10.10.40.3
Locomotion velocity, session 71.92.02.2-1.5-1.4
Locomotion distance, session 70.40.50.6-0.8-0.7
Stereotopy head waving bouts, day 70.10.10.20.40.2
Stereotopy head waving duration, day 70.10.10.10.40.3
Locomotion velocity, session 84.25.17.8-2.8-1.5
Locomotion distance, session 81.21.82.3-1.5-1.2
Degree of sensitization distance0.60.60.9-0.9-0.6
Degree of sensitization stereotypy0.10.10.20.5-0.0
Conditioned locomotion0.60.70.90.61.0
Cocaine response after cond. corrected0.30.40.8-0.1-0.9
Cocaine response after cond. not corrected0.50.51.0-0.0-1.0
Cocaine response before conditioning0.10.10.20.40.2
Saline control response1.01.41.9-0.9-1.4
Bone: connectivity density2.03.14.52.11.3
Bone: cortical apparent density6.99.111.53.42.6
Bone: cortical area0.00.00.00.0-0.2
Bone: cortical porosity0.20.20.4-0.3-0.6
Bone: cortical porosity0.70.71.1-0.6-1.1
Bone: cortical thickness0.81.31.61.31.0
Bone: cortical thickness5.05.87.42.72.0
Bone: cortical tissue density7.09.311.63.42.6
Condit. Reinf. active minus inactive responses1.71.92.01.31.4
Condit. Reinf. active-inactive response ratio3.13.43.91.72.0
Condit. Reinf. active responses1.21.51.61.31.2
Condit. Reinf. inactive responses0.10.10.2-0.0-0.5
Incentive salience index mean1.92.22.71.61.3
Condit. Reinf. lever presses0.40.50.90.90.4
Condit. Reinf. active minus inactive responses0.40.51.01.00.2
Condit. Reinf. active-inactive response ratio0.20.20.40.6-0.1
Condit. Reinf. active responses0.50.71.41.2-0.0
Condit. Reinf. inactive responses0.60.71.51.20.1
Condit. Reinf. lever presses0.10.20.20.50.4
Condit. Reinf. lever reinforcers received0.71.01.91.40.2
Conditioned reinforcement - actives0.40.40.60.80.4
Conditioned reinforcement - inactives2.32.63.31.81.4
Conditioned locomotion0.20.20.30.6-0.3
Patch foraging indifference point 0 sec2.84.65.12.32.0
Patch foraging indifference point AUC0.00.00.1-0.30.0
Delay disc. indifference point, 0s delay0.40.40.70.80.3
Delay disc. indifference point, 16s delay1.91.92.71.11.6
Delay disc. indifference point, 2s delay0.30.30.60.3-0.8
Delay disc. indifference point, 24s delay0.20.20.40.00.6
Delay disc. indifference point, 4s delay0.10.10.10.3-0.2
Delay disc. indifference point, 8s delay0.10.10.10.10.4
Indifference point function ln k0.20.30.50.30.7
Indifference point function log k0.20.30.50.30.7
Patch foraging total patch changes 0 sec2.33.74.02.01.8
Patch foraging total patch changes 12 sec2.63.45.62.41.1
Patch foraging total patch changes 18 sec0.70.91.11.00.9
Patch foraging total patch changes 24 sec1.01.21.41.21.0
Patch foraging total patch changes 6 sec2.23.24.42.11.4
Patch foraging time to switch 0 sec0.10.10.30.50.1
Patch foraging water rate 0 sec0.00.00.10.10.3
Patch foraging water rate 12 sec0.00.00.0-0.10.1
Patch foraging water rate 18 sec0.10.10.30.2-0.5
Patch foraging water rate 24 sec0.20.30.50.70.2
Patch foraging water rate 6 sec0.60.91.41.20.6
Seeking ratio, delayed vs. immediate footshock1.31.41.91.01.4
Distance traveled before self-admin0.30.30.6-0.1-0.8
Distance traveled after self-admin0.80.91.0-1.0-0.9
Extensor digitorum longus weight4.718.629.8-5.5-2.7
Bone: elastic displacement0.00.00.00.00.1
Bone: elastic work0.20.20.4-0.1-0.6
Bone: endosteal estimation2.75.96.3-2.5-2.3
Bone: endosteal perimeter1.12.33.1-1.8-1.3
Epididymis fat weight0.30.60.8-0.6-0.9
Delta time in closed arm before/after self-admin2.92.93.9-2.0-1.3
Delta time in open arm before/after self-admin0.00.00.0-0.0-0.1
Diff in mean of infusions in LGA sessions0.20.20.2-0.4-0.4
Delay discount exponential model param0.00.00.0-0.0-0.1
Extinction: sum of active levers before priming1.81.82.2-1.5-1.1
Active lever presses in extinction session 61.11.01.90.4-1.4
Bone: final force0.40.71.30.0-1.2
Bone: final moment0.50.91.7-0.2-1.3
Food consumed during 24 hour testing period0.80.91.1-1.1-0.9
Glucose0.20.30.5-0.1-0.7
Heart weight2.63.63.7-1.9-1.9
Delay discount hyperbolic model param0.00.00.0-0.1-0.1
Intermittent access intake day 1-15 change0.20.20.30.40.5
Intermittent access intake escalation0.20.10.20.40.4
Intermittent access intake escalation 20.10.10.1-0.4-0.1
Intermitt. access day 1 inactive lever presses1.31.42.21.50.7
Intermitt. access day 15 inactive lever presses3.13.44.62.21.5
Intermitt. access escalation Index1.51.42.1-1.5-0.8
Intermittent access day 1 total infusions0.20.20.30.6-0.1
Intermittent access day 15 total infusions0.40.40.60.80.5
Intermittent access terminal intake (last 3 days)0.40.40.70.80.5
Intermittent access total infusions0.10.10.30.50.2
Intermittent access day 1 locomotion0.50.50.90.90.3
Intermittent access day 15 total locomotion0.20.20.40.6-0.0
Intermittent access total locomotion0.91.01.41.20.7
Intermittent access standard deviation2.22.42.41.61.5
Left kidney weight0.20.50.9-1.00.1
Right kidney weight0.10.40.5-0.5-0.7
Cocaine induced anxiety3.64.14.4-2.0-2.1
Post-drug Anxiety0.80.91.2-0.8-1.1
Baseline Anxiety1.92.12.11.51.4
Tail length0.00.10.1-0.40.4
Length with tail1.45.07.5-2.7-1.6
Length without tail3.78.08.9-3.0-2.7
Times rat made contact with spout0.20.30.50.7-0.0
Lifetime Intake0.20.20.40.60.2
Liver weight, left0.00.00.00.1-0.1
Liver weight, right0.50.81.11.00.7
Locomotor activity0.20.30.60.1-0.7
Locomotor testing distance0.71.22.01.40.6
Locomotor testing rearing7.111.013.73.72.9
Locomotion in novel chamber2.73.36.22.50.7
Locomotion in novel chamber post-restriction0.70.81.60.1-1.3
Fecal boli incidents, locomotor time 10.30.30.4-0.5-0.7
Change in fecal boli incidents, locomotor task0.10.10.1-0.3-0.3
Time >=10cm from walls, locomotor time 10.80.81.10.81.0
Bouts of movement, locomotor time 10.20.20.4-0.6-0.1
Total resting periods, locomotor time 10.70.81.1-1.0-0.7
Rest time, locomotor task time 10.10.10.10.3-0.1
Distance moved, locomotor task time 10.00.00.0-0.10.0
Vertical activity count, locomotor time 11.01.01.2-1.1-0.9
Time >=10cm from walls, locomotor time 20.50.50.91.00.3
Bouts of movement, locomotor time 21.82.02.91.11.7
Total resting periods, locomotor time 21.92.13.11.01.8
Rest time, locomotor task time 20.40.50.7-0.8-0.5
Distance moved, locomotor task time 20.30.40.4-0.5-0.7
Vertical activity count, locomotor time 20.80.81.0-1.0-0.8
Light reinforcement 12.03.65.72.41.2
Light reinforcement 20.30.40.60.4-0.8
Bone: marrow area2.55.55.8-2.4-2.3
Bone: maximum diameter0.00.10.1-0.1-0.3
Bone: maximum force0.61.11.7-0.7-1.3
Bone: maximum moment0.81.31.9-0.9-1.4
Mean time between licks in bursts1.01.31.9-1.4-0.9
Mean num. licks in bursts0.40.50.60.70.8
Cd content in liver0.00.00.00.20.0
Co content in liver0.10.10.1-0.30.3
Cu content in liver0.40.50.70.50.8
Fe content in liver1.41.72.0-1.4-1.2
K content in liver0.90.91.01.00.8
Mg content in liver3.53.54.51.62.1
Mn content in liver3.64.14.12.02.0
Na content in liver0.40.40.8-0.3-0.9
Rb content in liver1.41.72.11.51.1
Se content in liver5.66.88.42.92.3
Sr content in liver0.90.80.90.81.0
Zn content in liver2.42.73.81.91.3
Bone: minimum diameter0.91.71.8-1.3-1.3
Time in familiar zone, hab. session 11.21.12.1-0.3-1.5
Time in novel zone, hab. session 12.82.73.51.31.9
Total zone transitions, hab. session 10.70.91.5-1.2-0.7
Total locomotion distance, hab. session 10.00.00.00.10.0
Locomotion velocity, hab. session 10.10.10.1-0.4-0.2
Time in familiar zone, hab. session 20.10.10.10.2-0.4
Time in novel zone, hab. session 21.01.01.10.91.1
Total zone transitions, hab. session 21.11.51.7-1.3-1.1
Total locomotion distance, hab. session 21.11.41.9-1.0-1.4
Locomotion velocity, hab. session 21.31.82.1-1.2-1.4
Novel to familiar place preference ratio0.30.30.4-0.50.7
Novelty place preference0.50.51.0-0.21.0
Time in novel zone, NPP test0.60.61.20.11.1
Total zone transitions, NPP test1.72.43.0-1.3-1.7
Total locomotion distance, NPP test0.91.21.9-0.6-1.4
Locomotion velocity, NPP test1.21.72.2-1.1-1.5
Intraocular pressure1.72.43.4-1.8-1.2
Delta distance traveled before/after self-admin0.50.51.0-1.0-0.2
Delta ambulatory time before/after self-admin0.60.71.3-1.1-0.3
Parametrial fat weight0.40.81.61.30.0
Pavlov. Cond. lever latency0.50.61.2-1.10.3
Pavlov. Cond. magazine entry latency4.15.29.23.01.1
Pavlov. Cond. change in total contacts7.88.311.23.32.3
Pavlov. Cond. index score2.53.16.02.40.5
Pavlov. Cond. latency score1.51.93.92.00.1
Pavlov. Cond. lever contacts0.40.50.70.8-0.5
Pavlov. Cond. magazine entry number5.77.112.1-3.5-1.5
Pavlov. Cond. intertrial magazine entries0.30.40.7-0.90.2
Pavlov. Cond. lever-magazine prob. diff.3.24.07.42.70.8
Pavlov. Cond. response bias4.45.38.93.01.3
Pavlov. Cond. lever latency0.10.10.2-0.40.1
Pavlov. Cond. magazine entry latency0.70.81.1-0.8-1.0
Pavlov. Cond. change in total contacts0.50.71.11.10.6
Pavlov. Cond. index score0.10.20.4-0.0-0.6
Pavlov. Cond. latency score0.20.20.4-0.2-0.7
Pavlov. Cond. lever contacts0.10.20.20.4-0.4
Pavlov. Cond. magazine entry number0.30.40.60.30.8
Pavlov. Cond. intertrial magazine entries0.40.50.8-0.30.9
Pavlov. Cond. lever-magazine prob. diff.0.20.30.5-0.2-0.7
Pavlov. Cond. response bias0.20.30.40.6-0.4
Time in closed arm before self-admin3.03.43.51.81.9
Time in closed arm after self-admin0.60.71.20.31.1
Time in open arm before self-admin2.12.33.1-1.8-1.2
Time in open arm after self-admin0.70.81.1-1.0-0.7
Bone: periosteal estimation0.81.61.9-1.1-1.4
Bone: periosteal perimeter1.52.62.6-1.6-1.6
Bone: post-yield work1.21.62.1-1.5-1.1
Progressive ratio test 1 active lever presses0.91.01.31.10.8
Progressive ratio test 1 breakpoint0.80.81.11.00.7
Progressive ratio test 1 inactive lever presses2.22.42.61.61.5
Progressive ratio test 2 active lever presses1.21.31.71.31.0
Progressive ratio test 2 breakpoint0.91.01.21.10.9
Progressive ratio test 2 inactive lever presses0.40.50.80.90.5
Incentive Sensitization - Responses0.80.81.21.10.7
Incentive Sensitization - Breakpoint0.70.71.11.00.6
Sum of active levers in priming session hrs 5-60.10.10.10.3-0.2
Progressive ratio0.10.10.1-0.1-0.4
Food seeking constrained by brief footshock0.00.00.10.3-0.1
Seeking ratio, punishment vs. effort0.10.10.10.30.4
Retroperitoneal fat weight0.00.10.2-0.2-0.5
Reaction time number correct2.23.24.3-1.5-2.1
Reaction time mean minus median0.20.30.5-0.7-0.3
Reaction time mean minus median AUC0.10.10.1-0.4-0.2
Reaction time num false alarms0.20.30.40.3-0.6
Reaction time num false alarms AUC0.20.30.70.1-0.8
Reaction time trials correct on left2.23.24.3-1.5-2.1
Reaction time trials on left2.23.14.2-1.4-2.1
Reaction time mean0.81.11.50.81.2
Reaction time mean AUC0.81.01.50.81.2
Median of all reaction times1.82.42.61.51.6
Reaction time omissions0.40.51.01.00.2
Reaction time false alarm rate0.30.40.60.80.3
Reaction time premature initiation rate0.10.10.20.3-0.4
Reaction time premature initiations1.01.42.3-0.7-1.5
Std. dev. reaction times0.00.00.0-0.10.1
Reaction time trials completed2.23.14.2-1.4-2.1
Reaction time trials AUC1.82.73.6-1.3-1.9
Run reversals in cocaine runway, females0.90.81.7-1.30.0
Run reversals in cocaine runway, males0.10.10.20.50.1
Latency to leave start box in cocaine runway0.80.91.2-1.1-0.7
Latency to leave start box in cocaine runway, F1.41.51.7-1.3-1.2
Latency to leave start box in cocaine runway, M1.11.11.30.91.1
Std. dev. time between licks in bursts0.20.20.3-0.5-0.4
Total sessions with >9 infusions1.21.31.41.11.2
Short access day 1 total inactive lever presses1.41.52.41.50.8
Short access day 10 total inactive lever presses0.20.20.4-0.6-0.1
Short access day 1 total infusions1.31.41.71.31.1
Short access day 10 total infusions0.20.30.50.7-0.2
Short access total infusions0.50.60.70.80.7
Short access day 1 locomotion3.53.84.82.21.7
Short access day 10 total locomotion1.11.21.81.30.8
Short access total locomotion1.21.31.31.11.2
One hour access (0.3 mA shock)0.00.00.10.10.3
Compulsive drug intake0.90.91.6-0.41.3
One hour access (shock baseline)0.20.20.30.6-0.4
Social response proportion0.20.20.2-0.5-0.5
Social responses0.20.30.5-0.3-0.7
Social time1.72.23.0-1.2-1.7
Soleus weight0.82.33.4-1.1-1.8
Bone: stiffness0.20.40.6-0.4-0.8
Tibialis anterior weight1.55.16.3-2.5-2.0
Time to tail flick, vehicle, before self-admin0.20.20.4-0.2-0.6
Time to tail flick, vehicle, after self-admin0.10.10.2-0.2-0.5
Time to tail flick, test, before self-admin1.71.72.4-1.6-0.9
Time to tail flick, test, after self-admin0.70.81.50.3-1.2
Delta time to tail flick, vehicle, before/after SA0.30.20.4-0.2-0.7
Delta time to tail flick, test, before/after SA1.61.42.81.70.1
Tibia length3.29.09.2-3.0-3.0
Ambulatory time before self-admin0.10.10.1-0.1-0.3
Ambulatory time after self-admin1.92.12.4-1.5-1.4
Bone: tissue strength0.90.91.2-1.1-0.8
Total heroin consumption0.70.91.00.9-1.0
Bone: trabecular number1.93.05.32.30.8
Bone: trabecular spacing3.03.94.1-2.0-1.9
Bone: trabecular thickness0.10.10.10.30.1
Bone: trabecular tissue density1.72.33.61.01.9
Water consumed over 24 hours0.30.30.5-0.4-0.7
Number of responses in last shaping day1.51.61.91.21.4