Gramd4

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 BLA mRNA stability Gramd4 0.11 0.07 6.8e-05 0.05 0.06 0.05 0.05 1.9e-03 6.4e-04 9.6e-04 1.3e-03
2 Brain mRNA stability Gramd4 0.06 0.04 2.6e-06 0.07 0.06 0.06 0.04 1.5e-07 2.1e-06 4.3e-06 4.5e-05
3 PL mRNA stability Gramd4 0.05 0.04 2.6e-04 0.02 0.02 0.01 0.02 3.9e-03 4.3e-03 9.2e-03 2.0e-03
4 PL gene expression Gramd4 0.08 0.05 4.6e-06 0.03 0.06 0.05 0.05 4.2e-04 1.3e-06 3.4e-06 1.9e-06

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 density0.50.91.3-1.2-0.9-1.00.7
Area under the delay curve2.73.24.7-2.2-2.1-1.80.8
BMI with tail1.65.59.11.93.03.00.6
BMI without tail0.51.42.70.81.61.50.0
Body weight1.88.011.52.93.33.4-1.3
Weight adjusted by age1.21.93.91.22.01.5-0.1
Bone surface0.10.20.6-0.8-0.3-0.40.4
Bone volume0.20.40.8-0.9-0.6-0.70.4
Breakpoint value in progressive ratio session0.40.51.7-0.20.3-0.11.3
Number of licking bursts0.30.41.40.0-0.5-0.3-1.2
Context. condit. distance diff. score0.70.91.61.30.91.1-0.3
Locomotion velocity, session 11.61.72.31.50.81.3-1.4
Locomotion distance, session 10.20.20.6-0.0-0.5-0.2-0.8
Locomotion velocity, session 23.54.15.22.31.62.3-1.9
Locomotion distance, session 20.30.40.6-0.8-0.3-0.40.8
Locomotion velocity, session 34.14.69.02.50.91.6-3.0
Locomotion distance, session 31.01.03.40.8-0.20.2-1.8
Stereotopy head waving bouts, day 30.60.71.30.80.81.1-0.3
Stereotopy head waving duration, day 31.61.93.81.31.51.9-0.1
Locomotion velocity, session 71.92.12.51.51.21.4-1.6
Locomotion distance, session 70.40.61.20.80.50.4-1.1
Stereotopy head waving bouts, day 71.41.52.21.50.91.3-1.1
Stereotopy head waving duration, day 70.50.60.80.90.60.8-0.7
Locomotion velocity, session 83.94.67.32.42.32.7-0.4
Locomotion distance, session 80.50.71.31.10.70.8-0.7
Degree of sensitization distance0.70.71.30.51.10.70.9
Degree of sensitization stereotypy0.70.71.11.00.80.9-0.6
Conditioned locomotion0.10.10.20.30.40.3-0.0
Cocaine response after cond. corrected0.30.41.00.70.10.4-1.0
Cocaine response after cond. not corrected0.60.62.00.7-0.20.3-1.4
Cocaine response before conditioning0.20.30.7-0.3-0.8-0.5-0.5
Saline control response0.00.10.10.30.2-0.20.1
Bone: connectivity density0.10.20.4-0.6-0.5-0.50.0
Bone: cortical apparent density1.11.52.2-1.3-1.3-1.50.5
Bone: cortical area1.42.24.01.52.01.60.1
Bone: cortical porosity0.50.61.00.81.00.60.4
Bone: cortical porosity0.80.91.80.81.40.80.5
Bone: cortical thickness0.20.30.7-0.10.60.10.8
Bone: cortical thickness1.51.73.50.81.91.11.2
Bone: cortical tissue density0.81.11.7-1.1-1.1-1.30.4
Condit. Reinf. active minus inactive responses0.20.30.7-0.5-0.5-0.80.1
Condit. Reinf. active-inactive response ratio1.01.11.8-1.1-1.1-1.30.5
Condit. Reinf. active responses0.60.71.2-0.6-1.1-1.0-0.6
Condit. Reinf. inactive responses0.50.61.50.1-0.8-0.3-1.2
Incentive salience index mean0.30.41.00.60.30.1-1.0
Condit. Reinf. lever presses2.02.84.01.81.31.5-2.0
Condit. Reinf. active minus inactive responses0.30.30.50.30.70.60.6
Condit. Reinf. active-inactive response ratio0.00.10.10.00.30.20.3
Condit. Reinf. active responses1.11.52.51.01.61.50.6
Condit. Reinf. inactive responses2.12.74.51.42.02.10.2
Condit. Reinf. lever presses0.70.92.10.71.01.50.2
Condit. Reinf. lever reinforcers received0.71.01.60.71.31.20.6
Conditioned reinforcement - actives0.00.10.20.40.1-0.2-0.3
Conditioned reinforcement - inactives0.10.20.30.60.5-0.00.1
Conditioned locomotion1.51.93.11.80.91.3-1.4
Patch foraging indifference point 0 sec0.00.00.1-0.20.0-0.10.1
Patch foraging indifference point AUC0.10.20.4-0.6-0.6-0.3-0.1
Delay disc. indifference point, 0s delay0.00.00.00.00.20.00.0
Delay disc. indifference point, 16s delay3.23.65.4-2.3-2.0-2.00.9
Delay disc. indifference point, 2s delay0.60.71.2-1.1-0.6-0.90.7
Delay disc. indifference point, 24s delay0.20.20.6-0.5-0.1-0.10.8
Delay disc. indifference point, 4s delay4.74.98.2-2.9-2.3-2.11.4
Delay disc. indifference point, 8s delay2.93.45.2-2.2-2.3-1.70.9
Indifference point function ln k1.93.35.12.31.81.9-1.1
Indifference point function log k1.93.35.12.31.81.9-1.1
Patch foraging total patch changes 0 sec0.10.10.2-0.4-0.3-0.30.1
Patch foraging total patch changes 12 sec0.00.00.0-0.20.20.10.1
Patch foraging total patch changes 18 sec0.20.30.4-0.5-0.5-0.6-0.4
Patch foraging total patch changes 24 sec0.10.10.30.0-0.30.0-0.6
Patch foraging total patch changes 6 sec0.50.71.5-1.2-0.8-0.60.5
Patch foraging time to switch 0 sec0.30.60.9-0.9-0.1-0.70.9
Patch foraging water rate 0 sec0.30.61.20.70.81.10.0
Patch foraging water rate 12 sec0.51.11.81.20.70.8-1.3
Patch foraging water rate 18 sec0.20.20.30.50.40.5-0.5
Patch foraging water rate 24 sec0.30.40.60.80.80.60.0
Patch foraging water rate 6 sec0.40.51.70.60.00.0-1.3
Seeking ratio, delayed vs. immediate footshock1.31.62.2-1.4-1.2-1.50.7
Distance traveled before self-admin0.50.61.70.8-0.30.2-1.3
Distance traveled after self-admin0.40.51.10.71.10.6-0.0
Extensor digitorum longus weight0.41.41.91.31.31.4-0.6
Bone: elastic displacement0.50.60.70.90.80.4-0.8
Bone: elastic work2.73.56.61.82.62.00.0
Bone: endosteal estimation1.84.05.92.22.22.4-0.6
Bone: endosteal perimeter2.96.27.92.82.82.8-1.1
Epididymis fat weight0.41.23.20.91.80.90.4
Delta time in closed arm before/after self-admin0.30.30.7-0.40.6-0.20.8
Delta time in open arm before/after self-admin1.31.33.91.0-0.00.3-2.0
Diff in mean of infusions in LGA sessions0.50.61.00.61.00.40.8
Delay discount exponential model param3.03.34.82.22.11.8-0.8
Extinction: sum of active levers before priming0.50.51.7-0.50.2-0.31.3
Active lever presses in extinction session 60.90.91.40.71.21.20.3
Bone: final force0.81.32.10.31.51.11.4
Bone: final moment1.11.82.90.31.71.21.7
Food consumed during 24 hour testing period3.44.77.32.32.72.5-0.4
Glucose0.00.10.20.2-0.0-0.4-0.0
Heart weight1.42.23.80.81.91.90.8
Delay discount hyperbolic model param3.13.55.02.22.21.9-0.8
Intermittent access intake day 1-15 change0.51.12.51.21.60.6-0.0
Intermittent access intake escalation0.30.61.20.91.10.2-0.3
Intermittent access intake escalation 20.50.61.60.21.2-0.40.7
Intermitt. access day 1 inactive lever presses0.10.30.9-0.00.70.10.9
Intermitt. access day 15 inactive lever presses0.71.42.71.21.71.10.5
Intermitt. access escalation Index0.20.20.4-0.4-0.4-0.70.3
Intermittent access day 1 total infusions2.13.45.72.40.91.5-2.2
Intermittent access day 15 total infusions2.23.26.12.51.31.0-2.0
Intermittent access terminal intake (last 3 days)3.44.58.12.92.01.5-1.9
Intermittent access total infusions3.03.56.62.61.51.3-1.8
Intermittent access day 1 locomotion1.52.04.91.6-0.20.6-2.2
Intermittent access day 15 total locomotion2.44.47.72.81.31.8-2.3
Intermittent access total locomotion2.93.46.32.51.21.4-2.0
Intermittent access standard deviation0.92.03.81.61.91.2-0.2
Left kidney weight9.544.464.07.07.98.0-1.6
Right kidney weight9.141.664.46.48.07.8-0.7
Cocaine induced anxiety0.40.61.7-0.10.70.41.3
Post-drug Anxiety1.31.43.3-1.2-0.3-0.81.8
Baseline Anxiety0.50.61.2-0.2-1.1-0.7-0.8
Tail length0.31.34.30.5-0.5-0.6-2.1
Length with tail0.83.65.52.11.61.5-2.3
Length without tail1.23.97.02.02.62.2-0.2
Times rat made contact with spout1.01.21.61.10.71.2-1.3
Lifetime Intake2.83.46.42.51.51.3-1.8
Liver weight, left2.03.34.82.21.51.8-1.7
Liver weight, right2.34.07.62.30.91.6-2.8
Locomotor activity3.86.07.72.82.32.6-2.1
Locomotor testing distance0.50.81.11.00.70.9-1.0
Locomotor testing rearing0.91.82.21.51.01.5-1.3
Locomotion in novel chamber1.21.65.20.7-0.70.4-2.3
Locomotion in novel chamber post-restriction0.10.20.3-0.6-0.5-0.10.3
Fecal boli incidents, locomotor time 10.10.20.30.50.10.5-0.5
Change in fecal boli incidents, locomotor task0.10.10.20.2-0.10.2-0.4
Time >=10cm from walls, locomotor time 10.30.31.0-0.10.31.00.5
Bouts of movement, locomotor time 10.20.20.30.50.50.40.2
Total resting periods, locomotor time 10.30.30.8-0.10.60.30.9
Rest time, locomotor task time 10.70.81.60.81.01.3-0.5
Distance moved, locomotor task time 10.00.00.10.1-0.3-0.10.0
Vertical activity count, locomotor time 10.20.40.8-0.7-0.3-0.40.9
Time >=10cm from walls, locomotor time 20.40.71.3-0.11.10.51.1
Bouts of movement, locomotor time 21.01.62.2-1.4-0.5-1.31.5
Total resting periods, locomotor time 20.91.62.2-1.5-0.7-1.31.4
Rest time, locomotor task time 21.62.14.0-0.6-2.0-1.0-1.7
Distance moved, locomotor task time 21.61.93.51.41.91.40.3
Vertical activity count, locomotor time 21.72.35.11.12.31.40.9
Light reinforcement 10.82.02.91.41.21.7-1.3
Light reinforcement 22.84.45.62.32.42.3-1.0
Bone: marrow area1.73.85.62.12.22.4-0.6
Bone: maximum diameter4.99.113.73.23.73.5-0.6
Bone: maximum force1.01.83.00.41.61.21.7
Bone: maximum moment1.32.33.70.41.91.41.9
Mean time between licks in bursts0.20.50.7-0.8-0.8-0.8-0.3
Mean num. licks in bursts0.60.91.70.91.31.10.5
Cd content in liver0.10.10.30.10.50.40.3
Co content in liver0.10.10.20.20.30.2-0.4
Cu content in liver7.58.812.1-3.5-3.2-3.21.7
Fe content in liver0.40.51.4-0.20.70.21.2
K content in liver0.10.10.3-0.1-0.6-0.30.1
Mg content in liver0.50.50.7-0.7-0.8-0.60.7
Mn content in liver1.51.72.81.60.70.9-1.7
Na content in liver2.52.74.1-1.7-2.0-1.70.9
Rb content in liver1.72.05.2-1.5-0.2-0.82.3
Se content in liver0.20.20.30.1-0.6-0.3-0.5
Sr content in liver0.40.30.6-0.3-0.7-0.3-0.8
Zn content in liver0.20.20.50.1-0.7-0.1-0.5
Bone: minimum diameter1.73.04.62.11.71.8-1.2
Time in familiar zone, hab. session 11.01.02.00.91.01.4-0.3
Time in novel zone, hab. session 10.20.20.4-0.4-0.2-0.60.6
Total zone transitions, hab. session 11.82.54.4-1.6-2.1-1.70.7
Total locomotion distance, hab. session 10.10.20.40.2-0.4-0.1-0.6
Locomotion velocity, hab. session 10.20.20.80.3-0.3-0.1-0.9
Time in familiar zone, hab. session 20.40.51.30.70.10.2-1.1
Time in novel zone, hab. session 20.70.71.2-1.0-0.4-0.81.1
Total zone transitions, hab. session 20.20.31.0-0.10.40.21.0
Total locomotion distance, hab. session 20.10.10.20.30.50.10.1
Locomotion velocity, hab. session 20.00.10.20.20.40.00.0
Novel to familiar place preference ratio0.10.10.3-0.6-0.1-0.30.2
Novelty place preference0.00.00.0-0.20.10.0-0.1
Time in novel zone, NPP test0.00.00.1-0.20.20.0-0.0
Total zone transitions, NPP test0.81.21.7-1.2-1.1-1.30.6
Total locomotion distance, NPP test0.10.10.3-0.3-0.4-0.6-0.0
Locomotion velocity, NPP test0.10.20.3-0.3-0.5-0.6-0.3
Intraocular pressure1.21.73.81.4-0.11.1-1.9
Delta distance traveled before/after self-admin0.70.81.80.61.40.90.0
Delta ambulatory time before/after self-admin0.40.61.40.41.20.80.2
Parametrial fat weight0.30.81.8-0.4-1.1-0.3-1.3
Pavlov. Cond. lever latency1.41.82.4-1.6-1.1-1.11.5
Pavlov. Cond. magazine entry latency0.10.10.2-0.20.2-0.40.2
Pavlov. Cond. change in total contacts0.10.10.30.10.50.20.3
Pavlov. Cond. index score0.10.20.30.40.50.2-0.3
Pavlov. Cond. latency score0.30.30.50.70.70.4-0.4
Pavlov. Cond. lever contacts1.41.72.51.51.01.0-1.6
Pavlov. Cond. magazine entry number0.00.00.20.1-0.00.4-0.1
Pavlov. Cond. intertrial magazine entries0.81.01.6-1.0-1.1-1.30.2
Pavlov. Cond. lever-magazine prob. diff.0.10.10.10.30.30.1-0.4
Pavlov. Cond. response bias0.40.50.70.80.70.4-0.8
Pavlov. Cond. lever latency0.30.50.7-0.3-0.9-0.9-0.6
Pavlov. Cond. magazine entry latency2.63.26.2-2.0-0.9-1.32.5
Pavlov. Cond. change in total contacts0.61.03.6-0.60.40.11.9
Pavlov. Cond. index score0.50.72.2-0.8-0.0-0.11.5
Pavlov. Cond. latency score0.60.82.6-0.80.1-0.01.6
Pavlov. Cond. lever contacts0.30.40.60.10.80.60.8
Pavlov. Cond. magazine entry number0.91.12.61.10.40.6-1.6
Pavlov. Cond. intertrial magazine entries0.30.40.60.40.80.60.7
Pavlov. Cond. lever-magazine prob. diff.0.50.61.8-0.8-0.2-0.21.3
Pavlov. Cond. response bias0.30.41.3-0.60.2-0.11.1
Time in closed arm before self-admin1.31.72.9-1.0-1.7-1.70.2
Time in closed arm after self-admin0.30.30.5-0.2-0.7-0.7-0.4
Time in open arm before self-admin0.10.10.2-0.0-0.20.4-0.3
Time in open arm after self-admin0.10.10.20.20.10.3-0.5
Bone: periosteal estimation2.24.77.02.32.72.5-0.4
Bone: periosteal perimeter4.57.79.93.13.13.0-1.5
Bone: post-yield work1.01.43.0-1.5-0.5-0.51.7
Progressive ratio test 1 active lever presses1.31.63.81.4-0.10.7-2.0
Progressive ratio test 1 breakpoint1.21.53.81.3-0.20.6-1.9
Progressive ratio test 1 inactive lever presses0.91.42.21.50.61.1-1.3
Progressive ratio test 2 active lever presses0.20.20.40.70.60.20.0
Progressive ratio test 2 breakpoint0.20.20.50.70.60.2-0.1
Progressive ratio test 2 inactive lever presses0.20.30.90.90.50.3-0.3
Incentive Sensitization - Responses0.30.41.00.20.9-0.01.0
Incentive Sensitization - Breakpoint0.40.51.00.31.00.10.9
Sum of active levers in priming session hrs 5-60.30.30.8-0.40.0-0.30.9
Progressive ratio0.20.30.6-0.4-0.5-0.8-0.0
Food seeking constrained by brief footshock0.40.50.80.50.90.90.4
Seeking ratio, punishment vs. effort0.81.22.10.21.31.01.4
Retroperitoneal fat weight1.87.911.82.83.43.4-0.4
Reaction time number correct0.20.30.8-0.4-0.9-0.4-0.4
Reaction time mean minus median0.20.50.9-0.4-1.0-0.7-0.5
Reaction time mean minus median AUC0.20.51.10.0-1.0-0.1-1.0
Reaction time num false alarms0.60.92.70.9-0.30.3-1.6
Reaction time num false alarms AUC0.81.33.81.2-0.20.2-1.9
Reaction time trials correct on left0.20.30.8-0.4-0.9-0.4-0.4
Reaction time trials on left0.20.30.8-0.4-0.9-0.4-0.4
Reaction time mean2.33.64.5-2.1-1.8-2.01.6
Reaction time mean AUC2.43.84.7-2.2-2.0-2.11.5
Median of all reaction times3.24.65.7-2.4-1.8-2.22.1
Reaction time omissions0.71.11.7-1.3-1.0-1.10.6
Reaction time false alarm rate0.71.02.11.30.30.4-1.4
Reaction time premature initiation rate1.11.65.2-0.50.90.02.3
Reaction time premature initiations0.61.13.6-0.80.2-0.31.9
Std. dev. reaction times0.61.11.8-1.0-1.3-1.30.1
Reaction time trials completed0.20.30.8-0.4-0.9-0.4-0.4
Reaction time trials AUC0.10.20.4-0.2-0.6-0.2-0.4
Run reversals in cocaine runway, females0.20.20.60.0-0.5-0.2-0.8
Run reversals in cocaine runway, males1.91.93.71.60.51.1-1.9
Latency to leave start box in cocaine runway1.41.62.21.31.51.5-0.3
Latency to leave start box in cocaine runway, F1.21.42.21.21.51.4-0.2
Latency to leave start box in cocaine runway, M0.30.30.50.70.60.6-0.2
Std. dev. time between licks in bursts0.40.61.4-0.80.4-0.21.2
Total sessions with >9 infusions2.63.14.62.11.61.9-1.4
Short access day 1 total inactive lever presses2.63.45.61.92.42.1-0.3
Short access day 10 total inactive lever presses0.30.81.30.91.21.0-0.1
Short access day 1 total infusions1.52.03.31.81.21.3-1.3
Short access day 10 total infusions2.53.25.32.31.51.6-1.7
Short access total infusions2.53.25.32.31.71.7-1.2
Short access day 1 locomotion0.10.10.30.50.20.2-0.3
Short access day 10 total locomotion1.32.46.71.5-0.10.9-2.6
Short access total locomotion1.01.22.11.40.50.8-1.4
One hour access (0.3 mA shock)1.21.42.61.61.20.9-0.9
Compulsive drug intake0.40.41.2-0.60.4-0.21.1
One hour access (shock baseline)1.42.24.42.11.01.0-1.6
Social response proportion1.61.83.31.31.81.5-0.2
Social responses2.32.93.51.91.61.9-1.5
Social time0.40.52.00.4-0.2-0.1-1.4
Soleus weight0.20.61.00.51.00.80.6
Bone: stiffness1.62.68.5-1.40.0-0.32.9
Tibialis anterior weight0.20.71.0-1.0-0.8-0.70.9
Time to tail flick, vehicle, before self-admin0.20.20.60.0-0.8-0.1-0.5
Time to tail flick, vehicle, after self-admin0.10.10.30.4-0.2-0.0-0.5
Time to tail flick, test, before self-admin2.02.12.61.61.41.5-1.3
Time to tail flick, test, after self-admin0.30.30.9-0.10.6-0.21.0
Delta time to tail flick, vehicle, before/after SA0.60.61.30.41.10.90.5
Delta time to tail flick, test, before/after SA2.52.63.3-1.7-1.1-1.81.7
Tibia length0.10.20.40.60.60.3-0.2
Ambulatory time before self-admin0.60.92.70.9-0.40.1-1.6
Ambulatory time after self-admin0.10.10.20.20.5-0.2-0.1
Bone: tissue strength1.01.02.1-1.1-0.3-0.61.4
Total heroin consumption0.60.82.3-0.00.60.61.5
Bone: trabecular number0.40.60.9-0.7-1.0-0.9-0.3
Bone: trabecular spacing2.12.85.21.61.82.3-0.1
Bone: trabecular thickness0.10.10.5-0.1-0.2-0.7-0.2
Bone: trabecular tissue density1.62.43.0-1.6-1.7-1.71.1
Water consumed over 24 hours1.11.42.21.21.51.4-0.3
Number of responses in last shaping day0.10.10.2-0.5-0.3-0.20.3