Arhgef39

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 PL gene expression Arhgef39 0.03 0.02 3.0e-03 0.03 0.02 0.02 0.03 5.9e-04 1.5e-03 1.3e-03 9.2e-04
2 NAcc gene expression Arhgef39 0.06 0.06 2.8e-06 0.04 0.01 0.04 0.01 4.2e-07 1.2e-02 1.5e-06 2.2e-02
3 BLA gene expression Arhgef39 0.1 0.07 2.7e-05 0.06 0.08 0.07 0.07 4.8e-04 5.3e-05 8.9e-05 1.1e-04
4 Adipose gene expression Arhgef39 0.06 0.04 2.4e-04 0.03 0.03 0.03 0.02 3.1e-04 3.1e-04 3.2e-04 1.1e-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 density1.42.43.01.61.71.70.8
Area under the delay curve0.60.61.2-0.4-1.1-0.9-0.7
BMI with tail1.55.07.02.42.62.60.4
BMI without tail2.06.28.62.92.92.80.2
Body weight2.812.019.34.43.53.9-1.3
Weight adjusted by age0.20.30.50.70.00.3-0.6
Bone surface0.71.31.91.41.21.4-0.0
Bone volume0.71.21.61.21.21.30.4
Breakpoint value in progressive ratio session2.93.48.40.1-1.9-1.4-2.9
Number of licking bursts3.04.97.52.22.72.60.5
Context. condit. distance diff. score0.10.10.2-0.5-0.2-0.30.4
Locomotion velocity, session 13.13.311.81.1-0.30.1-3.4
Locomotion distance, session 10.91.13.51.00.10.3-1.9
Locomotion velocity, session 22.32.73.71.81.91.90.6
Locomotion distance, session 21.82.54.12.01.51.5-1.3
Locomotion velocity, session 30.60.72.60.4-0.3-0.1-1.6
Locomotion distance, session 32.02.23.31.81.21.6-1.3
Stereotopy head waving bouts, day 30.70.82.50.1-0.7-0.6-1.6
Stereotopy head waving duration, day 30.40.50.6-0.4-0.8-0.8-0.8
Locomotion velocity, session 70.00.10.1-0.2-0.2-0.30.0
Locomotion distance, session 70.30.30.50.70.30.4-0.7
Stereotopy head waving bouts, day 71.01.21.71.30.91.1-0.9
Stereotopy head waving duration, day 70.40.50.70.90.70.7-0.6
Locomotion velocity, session 80.40.41.60.2-0.2-0.3-1.3
Locomotion distance, session 80.30.51.40.60.30.2-1.2
Degree of sensitization distance0.91.01.4-1.1-1.0-1.20.4
Degree of sensitization stereotypy1.11.21.81.31.11.4-0.2
Conditioned locomotion0.30.41.10.2-0.4-0.2-1.1
Cocaine response after cond. corrected2.42.93.6-1.4-1.9-1.7-1.8
Cocaine response after cond. not corrected2.32.83.9-1.2-1.8-1.6-2.0
Cocaine response before conditioning0.60.71.20.81.10.90.2
Saline control response0.91.22.81.10.60.7-1.7
Bone: connectivity density0.91.41.61.31.21.31.0
Bone: cortical apparent density0.60.82.7-0.20.60.21.6
Bone: cortical area2.74.16.51.72.52.31.4
Bone: cortical porosity0.10.20.3-0.3-0.5-0.40.2
Bone: cortical porosity0.00.00.00.1-0.20.0-0.2
Bone: cortical thickness1.52.44.00.61.81.42.0
Bone: cortical thickness0.50.61.4-0.80.1-0.41.2
Bone: cortical tissue density0.50.62.3-0.30.50.11.5
Condit. Reinf. active minus inactive responses0.40.50.80.60.90.80.4
Condit. Reinf. active-inactive response ratio0.60.61.2-1.1-0.6-0.80.5
Condit. Reinf. active responses2.53.14.51.82.12.10.6
Condit. Reinf. inactive responses3.34.16.02.12.52.30.9
Incentive salience index mean3.64.46.22.42.42.5-0.2
Condit. Reinf. lever presses8.712.218.94.33.63.9-1.2
Condit. Reinf. active minus inactive responses0.60.71.10.81.01.10.4
Condit. Reinf. active-inactive response ratio0.20.20.30.20.40.50.6
Condit. Reinf. active responses1.92.63.61.81.91.90.2
Condit. Reinf. inactive responses2.63.45.12.02.32.00.7
Condit. Reinf. lever presses2.94.05.61.82.42.21.4
Condit. Reinf. lever reinforcers received2.23.14.22.02.02.00.2
Conditioned reinforcement - actives0.10.20.40.4-0.60.1-0.6
Conditioned reinforcement - inactives0.40.51.1-0.4-1.0-0.7-0.6
Conditioned locomotion0.30.41.20.5-0.50.1-1.1
Patch foraging indifference point 0 sec1.32.36.81.4-0.50.3-2.6
Patch foraging indifference point AUC6.28.913.23.63.03.6-0.8
Delay disc. indifference point, 0s delay1.11.21.9-0.9-1.4-1.3-0.8
Delay disc. indifference point, 16s delay1.51.72.5-0.7-1.6-1.3-1.4
Delay disc. indifference point, 2s delay0.10.10.3-0.10.30.30.5
Delay disc. indifference point, 24s delay0.10.10.1-0.3-0.3-0.40.1
Delay disc. indifference point, 4s delay0.10.10.2-0.3-0.4-0.3-0.2
Delay disc. indifference point, 8s delay0.10.10.20.50.00.2-0.1
Indifference point function ln k1.93.34.8-2.1-1.9-2.20.2
Indifference point function log k1.93.34.8-2.1-1.9-2.20.2
Patch foraging total patch changes 0 sec1.32.46.11.8-0.10.8-2.5
Patch foraging total patch changes 12 sec1.92.54.42.11.41.9-0.2
Patch foraging total patch changes 18 sec0.61.01.91.40.71.0-0.7
Patch foraging total patch changes 24 sec1.62.74.52.11.31.9-1.0
Patch foraging total patch changes 6 sec2.64.06.92.61.22.0-1.9
Patch foraging time to switch 0 sec1.73.55.7-2.4-1.6-2.11.2
Patch foraging water rate 0 sec1.12.43.51.91.11.7-1.3
Patch foraging water rate 12 sec0.10.10.50.1-0.2-0.0-0.7
Patch foraging water rate 18 sec0.40.60.80.50.90.80.7
Patch foraging water rate 24 sec0.40.62.1-0.30.40.21.4
Patch foraging water rate 6 sec0.40.51.20.51.10.8-0.2
Seeking ratio, delayed vs. immediate footshock3.74.57.62.82.32.30.2
Distance traveled before self-admin2.63.44.82.22.01.8-1.2
Distance traveled after self-admin1.21.53.20.81.81.20.8
Extensor digitorum longus weight4.216.726.55.14.24.7-0.6
Bone: elastic displacement4.75.48.8-3.0-2.2-2.41.4
Bone: elastic work2.83.78.5-2.1-0.7-1.22.9
Bone: endosteal estimation0.92.13.01.71.31.5-1.1
Bone: endosteal perimeter1.02.23.11.81.21.5-1.4
Epididymis fat weight0.31.11.81.01.31.30.5
Delta time in closed arm before/after self-admin1.00.91.50.41.20.81.2
Delta time in open arm before/after self-admin0.50.50.90.3-1.0-0.6-0.9
Diff in mean of infusions in LGA sessions0.20.30.7-0.60.1-0.20.9
Delay discount exponential model param0.50.51.00.31.00.80.7
Extinction: sum of active levers before priming2.73.04.9-1.3-2.2-2.2-0.6
Active lever presses in extinction session 60.30.30.6-0.2-0.8-0.6-0.2
Bone: final force1.42.33.91.62.01.70.3
Bone: final moment1.32.03.51.41.91.50.6
Food consumed during 24 hour testing period0.60.81.21.11.00.9-0.6
Glucose2.23.44.92.22.02.2-0.4
Heart weight0.71.11.91.41.01.1-0.0
Delay discount hyperbolic model param0.30.40.70.20.80.60.7
Intermittent access intake day 1-15 change0.51.12.10.81.41.10.6
Intermittent access intake escalation0.51.02.10.61.41.00.8
Intermittent access intake escalation 21.61.93.30.61.81.31.5
Intermitt. access day 1 inactive lever presses0.41.52.31.51.41.2-0.5
Intermitt. access day 15 inactive lever presses0.10.20.30.50.60.1-0.4
Intermitt. access escalation Index0.30.40.60.50.80.6-0.6
Intermittent access day 1 total infusions1.72.75.6-0.7-2.4-1.5-1.6
Intermittent access day 15 total infusions0.00.00.10.3-0.10.2-0.1
Intermittent access terminal intake (last 3 days)0.10.10.20.4-0.10.2-0.4
Intermittent access total infusions0.30.40.80.5-0.60.1-0.9
Intermittent access day 1 locomotion1.62.14.6-0.5-2.1-1.3-1.3
Intermittent access day 15 total locomotion0.81.43.2-0.5-1.8-1.1-0.9
Intermittent access total locomotion1.11.32.9-0.9-1.7-1.2-0.2
Intermittent access standard deviation0.20.40.80.90.60.6-0.3
Left kidney weight0.52.54.22.11.21.4-1.6
Right kidney weight0.41.72.91.71.31.4-0.4
Cocaine induced anxiety0.20.20.6-0.8-0.3-0.50.1
Post-drug Anxiety0.30.40.60.80.50.5-0.6
Baseline Anxiety0.80.91.61.31.01.00.1
Tail length1.56.09.23.02.72.7-0.4
Length with tail1.45.910.63.31.82.4-2.0
Length without tail0.31.13.60.8-0.50.0-1.9
Times rat made contact with spout0.50.60.80.60.90.80.7
Lifetime Intake0.70.82.30.5-0.9-0.1-1.5
Liver weight, left0.00.10.20.0-0.2-0.2-0.4
Liver weight, right0.61.01.5-1.2-1.0-1.10.5
Locomotor activity0.00.00.00.10.10.0-0.1
Locomotor testing distance0.30.61.2-0.3-0.7-0.7-1.1
Locomotor testing rearing0.40.71.21.10.80.7-0.7
Locomotion in novel chamber0.30.40.8-0.7-0.3-0.30.9
Locomotion in novel chamber post-restriction1.32.12.70.81.61.51.6
Fecal boli incidents, locomotor time 10.30.50.6-0.7-0.6-0.80.7
Change in fecal boli incidents, locomotor task0.50.51.00.70.20.6-1.0
Time >=10cm from walls, locomotor time 10.30.41.30.3-0.3-0.1-1.2
Bouts of movement, locomotor time 11.51.72.6-1.6-1.4-1.50.3
Total resting periods, locomotor time 12.02.23.7-1.9-1.4-1.60.8
Rest time, locomotor task time 12.12.65.8-2.0-0.3-0.92.4
Distance moved, locomotor task time 11.72.54.32.00.61.2-2.1
Vertical activity count, locomotor time 11.02.36.61.5-0.00.5-2.6
Time >=10cm from walls, locomotor time 20.10.20.30.60.30.2-0.4
Bouts of movement, locomotor time 20.40.61.21.10.70.8-0.2
Total resting periods, locomotor time 20.10.20.50.70.30.5-0.0
Rest time, locomotor task time 21.01.22.5-1.6-1.0-1.00.7
Distance moved, locomotor task time 20.60.71.30.71.20.80.6
Vertical activity count, locomotor time 20.50.71.21.10.80.7-0.6
Light reinforcement 11.53.811.31.80.40.5-3.4
Light reinforcement 22.33.612.21.2-0.8-0.2-3.5
Bone: marrow area1.02.23.11.81.51.7-0.8
Bone: maximum diameter2.34.26.02.22.52.40.6
Bone: maximum force2.95.17.82.42.82.50.5
Bone: maximum moment2.54.36.72.22.62.30.7
Mean time between licks in bursts0.20.50.9-0.8-0.6-0.90.3
Mean num. licks in bursts1.42.13.1-1.6-1.8-1.70.2
Cd content in liver0.50.60.90.80.90.9-0.5
Co content in liver0.70.81.0-0.7-1.0-1.0-1.0
Cu content in liver1.51.83.1-1.8-1.1-1.60.5
Fe content in liver1.21.41.9-0.9-1.3-1.4-1.1
K content in liver0.50.50.8-0.4-0.7-0.6-0.9
Mg content in liver0.60.61.3-0.7-1.1-0.8-0.3
Mn content in liver1.21.32.00.91.41.30.8
Na content in liver1.41.52.7-1.7-1.0-1.50.3
Rb content in liver5.05.98.8-3.0-2.6-2.8-0.2
Se content in liver2.42.83.71.91.91.80.6
Sr content in liver0.70.61.61.30.40.7-0.3
Zn content in liver0.10.10.10.10.40.20.3
Bone: minimum diameter0.10.10.4-0.20.10.10.7
Time in familiar zone, hab. session 11.91.86.4-0.90.3-0.02.5
Time in novel zone, hab. session 13.13.15.1-0.8-1.9-1.7-2.3
Total zone transitions, hab. session 10.00.00.00.20.10.10.1
Total locomotion distance, hab. session 10.81.12.10.51.10.91.4
Locomotion velocity, hab. session 11.72.43.41.41.91.71.1
Time in familiar zone, hab. session 21.11.13.1-1.0-0.2-0.61.8
Time in novel zone, hab. session 22.12.13.1-0.9-1.6-1.4-1.8
Total zone transitions, hab. session 20.60.81.21.10.60.7-1.1
Total locomotion distance, hab. session 20.70.91.21.11.11.1-0.0
Locomotion velocity, hab. session 20.91.21.71.31.31.30.1
Novel to familiar place preference ratio3.53.85.7-1.7-2.4-2.2-1.3
Novelty place preference4.44.76.9-2.1-2.6-2.5-1.1
Time in novel zone, NPP test5.45.88.4-2.4-2.9-2.8-1.2
Total zone transitions, NPP test0.81.21.91.30.70.8-1.4
Total locomotion distance, NPP test1.72.43.61.91.31.6-1.3
Locomotion velocity, NPP test2.23.04.72.21.71.9-1.0
Intraocular pressure2.02.84.12.01.52.0-1.0
Delta distance traveled before/after self-admin0.30.30.6-0.70.0-0.30.8
Delta ambulatory time before/after self-admin0.70.91.7-1.3-0.5-0.90.9
Parametrial fat weight0.20.41.1-0.2-0.4-0.6-1.1
Pavlov. Cond. lever latency5.77.110.9-3.3-2.8-3.10.7
Pavlov. Cond. magazine entry latency0.50.71.01.00.90.90.1
Pavlov. Cond. change in total contacts2.32.43.71.91.61.8-0.5
Pavlov. Cond. index score2.83.65.22.32.12.2-0.0
Pavlov. Cond. latency score2.63.24.92.21.92.1-0.1
Pavlov. Cond. lever contacts5.46.59.93.12.72.9-0.4
Pavlov. Cond. magazine entry number0.80.91.4-1.0-1.2-1.1-0.4
Pavlov. Cond. intertrial magazine entries0.20.20.30.50.50.60.2
Pavlov. Cond. lever-magazine prob. diff.2.93.64.92.22.12.20.2
Pavlov. Cond. response bias3.54.46.42.52.32.4-0.2
Pavlov. Cond. lever latency2.73.65.2-1.8-2.3-2.1-1.2
Pavlov. Cond. magazine entry latency0.30.30.4-0.6-0.3-0.50.7
Pavlov. Cond. change in total contacts1.42.34.50.71.71.22.1
Pavlov. Cond. index score0.70.92.20.31.00.71.5
Pavlov. Cond. latency score0.91.22.60.41.10.81.6
Pavlov. Cond. lever contacts2.02.84.01.52.01.81.2
Pavlov. Cond. magazine entry number0.70.92.80.1-0.8-0.4-1.7
Pavlov. Cond. intertrial magazine entries0.20.30.50.60.50.7-0.4
Pavlov. Cond. lever-magazine prob. diff.0.81.02.50.21.00.71.6
Pavlov. Cond. response bias1.21.72.40.91.51.21.5
Time in closed arm before self-admin0.30.30.6-0.8-0.7-0.50.1
Time in closed arm after self-admin0.70.81.8-1.10.2-0.21.4
Time in open arm before self-admin0.91.01.61.30.60.9-1.1
Time in open arm after self-admin1.41.53.41.80.20.8-1.4
Bone: periosteal estimation1.53.24.71.92.22.10.1
Bone: periosteal perimeter0.50.91.31.10.91.0-0.6
Bone: post-yield work2.02.94.72.21.61.7-1.2
Progressive ratio test 1 active lever presses1.41.73.5-0.2-1.6-0.9-1.9
Progressive ratio test 1 breakpoint1.21.53.1-0.1-1.5-0.8-1.7
Progressive ratio test 1 inactive lever presses1.11.64.51.30.10.5-2.1
Progressive ratio test 2 active lever presses2.02.34.1-0.3-2.0-1.1-2.0
Progressive ratio test 2 breakpoint2.12.44.3-0.4-2.1-1.2-2.0
Progressive ratio test 2 inactive lever presses0.20.30.60.7-0.30.2-0.8
Incentive Sensitization - Responses0.60.81.2-0.4-1.1-0.8-1.0
Incentive Sensitization - Breakpoint0.60.81.4-0.4-1.2-0.8-1.0
Sum of active levers in priming session hrs 5-63.43.25.3-1.2-2.3-2.0-1.4
Progressive ratio0.00.10.10.3-0.2-0.0-0.4
Food seeking constrained by brief footshock6.47.814.13.82.12.9-2.1
Seeking ratio, punishment vs. effort1.31.82.71.61.31.6-0.6
Retroperitoneal fat weight0.31.32.0-1.4-0.7-1.21.1
Reaction time number correct0.10.30.70.6-0.00.3-0.8
Reaction time mean minus median1.02.56.80.31.41.02.6
Reaction time mean minus median AUC0.92.23.90.81.61.42.0
Reaction time num false alarms0.20.20.60.30.30.30.8
Reaction time num false alarms AUC0.40.61.11.00.70.80.1
Reaction time trials correct on left0.10.30.70.6-0.00.3-0.8
Reaction time trials on left0.10.20.60.5-0.10.2-0.8
Reaction time mean1.72.85.9-2.0-0.4-1.12.4
Reaction time mean AUC1.93.06.4-2.1-0.5-1.12.5
Median of all reaction times2.73.87.2-2.7-1.2-1.91.7
Reaction time omissions1.42.03.2-1.8-1.3-1.70.4
Reaction time false alarm rate0.10.10.50.10.20.10.7
Reaction time premature initiation rate1.82.54.4-2.1-1.2-1.61.2
Reaction time premature initiations0.81.52.6-1.6-1.0-1.30.7
Std. dev. reaction times1.12.07.0-0.80.70.12.7
Reaction time trials completed0.10.20.60.5-0.10.2-0.8
Reaction time trials AUC0.10.20.60.5-0.10.2-0.8
Run reversals in cocaine runway, females0.30.30.9-0.40.30.20.9
Run reversals in cocaine runway, males0.00.00.1-0.1-0.2-0.20.1
Latency to leave start box in cocaine runway0.60.61.10.71.10.90.3
Latency to leave start box in cocaine runway, F0.10.10.2-0.1-0.3-0.3-0.5
Latency to leave start box in cocaine runway, M1.71.62.51.31.61.5-0.1
Std. dev. time between licks in bursts0.20.30.5-0.5-0.7-0.70.3
Total sessions with >9 infusions1.01.23.70.4-0.9-0.3-1.9
Short access day 1 total inactive lever presses0.81.03.10.80.30.5-1.8
Short access day 10 total inactive lever presses0.41.02.00.91.41.00.3
Short access day 1 total infusions1.11.44.80.4-0.8-0.3-2.2
Short access day 10 total infusions1.11.43.9-0.0-1.2-0.5-2.0
Short access total infusions1.62.05.2-0.0-1.5-0.8-2.3
Short access day 1 locomotion1.62.03.1-0.7-1.8-1.4-1.6
Short access day 10 total locomotion0.40.71.0-0.8-1.0-0.90.5
Short access total locomotion0.80.91.6-0.2-1.2-0.8-1.2
One hour access (0.3 mA shock)0.70.81.80.9-0.80.3-1.3
Compulsive drug intake0.50.60.90.60.70.71.0
One hour access (shock baseline)1.01.54.40.6-1.1-0.2-2.1
Social response proportion2.12.34.2-2.1-1.0-1.61.2
Social responses0.70.81.31.11.21.00.0
Social time0.10.10.3-0.5-0.0-0.5-0.0
Soleus weight0.82.27.50.6-0.8-0.5-2.7
Bone: stiffness3.65.89.12.63.02.70.3
Tibialis anterior weight6.421.632.85.74.95.2-1.5
Time to tail flick, vehicle, before self-admin0.40.40.5-0.7-0.7-0.50.6
Time to tail flick, vehicle, after self-admin0.10.10.10.20.30.30.3
Time to tail flick, test, before self-admin0.30.30.60.70.40.8-0.0
Time to tail flick, test, after self-admin2.62.73.81.31.81.91.4
Delta time to tail flick, vehicle, before/after SA0.20.10.30.40.60.30.0
Delta time to tail flick, test, before/after SA0.40.41.1-0.20.60.21.0
Tibia length0.30.83.00.2-0.2-0.4-1.7
Ambulatory time before self-admin1.92.84.52.11.61.6-1.3
Ambulatory time after self-admin0.30.40.70.70.80.6-0.1
Bone: tissue strength0.10.10.30.40.50.20.3
Total heroin consumption1.82.23.1-0.5-1.7-1.5-1.8
Bone: trabecular number1.21.92.41.51.51.50.9
Bone: trabecular spacing0.10.20.4-0.40.30.00.6
Bone: trabecular thickness0.10.10.3-0.2-0.3-0.20.6
Bone: trabecular tissue density2.33.44.92.12.22.0-0.4
Water consumed over 24 hours0.70.91.31.01.11.10.3
Number of responses in last shaping day2.52.88.90.1-1.1-0.9-3.0