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 8.6e-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 9.3e-05
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 density1.32.43.0-1.6-1.71.7-0.8
Area under the delay curve0.40.61.20.41.1-0.90.7
BMI with tail1.45.07.0-2.4-2.62.6-0.4
BMI without tail1.26.28.6-2.9-2.92.8-0.2
Body weight2.712.019.3-4.4-3.53.91.3
Weight adjusted by age0.10.30.5-0.7-0.00.30.6
Bone surface0.71.31.9-1.4-1.21.40.0
Bone volume0.61.21.6-1.2-1.21.3-0.4
Breakpoint value in progressive ratio session1.93.48.4-0.11.9-1.42.9
Number of licking bursts1.64.97.5-2.2-2.72.6-0.5
Context. condit. distance diff. score0.10.10.20.50.2-0.3-0.4
Locomotion velocity, session 12.93.311.8-1.10.30.13.4
Locomotion distance, session 10.91.13.5-1.0-0.10.31.9
Locomotion velocity, session 22.32.73.7-1.8-1.91.9-0.6
Locomotion distance, session 21.82.54.1-2.0-1.51.51.3
Locomotion velocity, session 30.60.72.6-0.40.3-0.11.6
Locomotion distance, session 31.92.23.3-1.8-1.21.61.3
Stereotopy head waving bouts, day 30.70.82.5-0.10.7-0.61.6
Stereotopy head waving duration, day 30.40.50.60.40.8-0.80.8
Locomotion velocity, session 70.00.10.10.20.2-0.3-0.0
Locomotion distance, session 70.20.30.5-0.7-0.30.40.7
Stereotopy head waving bouts, day 71.01.21.7-1.3-0.91.10.9
Stereotopy head waving duration, day 70.40.50.7-0.9-0.70.70.6
Locomotion velocity, session 80.40.41.6-0.20.2-0.31.3
Locomotion distance, session 80.30.51.4-0.6-0.30.21.2
Degree of sensitization distance0.91.01.41.11.0-1.2-0.4
Degree of sensitization stereotypy1.11.21.8-1.3-1.11.40.2
Conditioned locomotion0.30.41.1-0.20.4-0.21.1
Cocaine response after cond. corrected1.92.93.61.41.9-1.71.8
Cocaine response after cond. not corrected1.92.83.91.21.8-1.62.0
Cocaine response before conditioning0.60.71.2-0.8-1.10.9-0.2
Saline control response0.91.22.8-1.1-0.60.71.7
Bone: connectivity density0.91.41.6-1.3-1.21.3-1.0
Bone: cortical apparent density0.50.82.70.2-0.60.2-1.6
Bone: cortical area2.54.16.5-1.7-2.52.3-1.4
Bone: cortical porosity0.10.20.30.30.5-0.4-0.2
Bone: cortical porosity0.00.00.0-0.10.20.00.2
Bone: cortical thickness1.52.44.0-0.6-1.81.4-2.0
Bone: cortical thickness0.50.61.40.8-0.1-0.4-1.2
Bone: cortical tissue density0.40.62.30.3-0.50.1-1.5
Condit. Reinf. active minus inactive responses0.40.50.8-0.6-0.90.8-0.4
Condit. Reinf. active-inactive response ratio0.60.61.21.10.6-0.8-0.5
Condit. Reinf. active responses2.43.14.5-1.8-2.12.1-0.6
Condit. Reinf. inactive responses3.14.16.0-2.1-2.52.3-0.9
Incentive salience index mean3.44.46.2-2.4-2.42.50.2
Condit. Reinf. lever presses8.112.218.9-4.3-3.63.91.2
Condit. Reinf. active minus inactive responses0.50.71.1-0.8-1.01.1-0.4
Condit. Reinf. active-inactive response ratio0.10.20.3-0.2-0.40.5-0.6
Condit. Reinf. active responses1.82.63.6-1.8-1.91.9-0.2
Condit. Reinf. inactive responses2.33.45.1-2.0-2.32.0-0.7
Condit. Reinf. lever presses2.74.05.6-1.8-2.42.2-1.4
Condit. Reinf. lever reinforcers received2.23.14.2-2.0-2.02.0-0.2
Conditioned reinforcement - actives0.10.20.4-0.40.60.10.6
Conditioned reinforcement - inactives0.20.51.10.41.0-0.70.6
Conditioned locomotion0.30.41.2-0.50.50.11.1
Patch foraging indifference point 0 sec0.82.36.8-1.40.50.32.6
Patch foraging indifference point AUC3.78.913.2-3.6-3.03.60.8
Delay disc. indifference point, 0s delay1.11.21.90.91.4-1.30.8
Delay disc. indifference point, 16s delay1.21.72.50.71.6-1.31.4
Delay disc. indifference point, 2s delay0.10.10.30.1-0.30.3-0.5
Delay disc. indifference point, 24s delay0.00.10.10.30.3-0.4-0.1
Delay disc. indifference point, 4s delay0.10.10.20.30.4-0.30.2
Delay disc. indifference point, 8s delay0.00.10.2-0.5-0.00.20.1
Indifference point function ln k1.13.34.82.11.9-2.2-0.2
Indifference point function log k1.13.34.82.11.9-2.2-0.2
Patch foraging total patch changes 0 sec0.82.46.1-1.80.10.82.5
Patch foraging total patch changes 12 sec1.92.54.4-2.1-1.41.90.2
Patch foraging total patch changes 18 sec0.41.01.9-1.4-0.71.00.7
Patch foraging total patch changes 24 sec0.82.74.5-2.1-1.31.91.0
Patch foraging total patch changes 6 sec2.34.06.9-2.6-1.22.01.9
Patch foraging time to switch 0 sec0.93.55.72.41.6-2.1-1.2
Patch foraging water rate 0 sec0.62.43.5-1.9-1.11.71.3
Patch foraging water rate 12 sec0.00.10.5-0.10.2-0.00.7
Patch foraging water rate 18 sec0.30.60.8-0.5-0.90.8-0.7
Patch foraging water rate 24 sec0.40.62.10.3-0.40.2-1.4
Patch foraging water rate 6 sec0.40.51.2-0.5-1.10.80.2
Seeking ratio, delayed vs. immediate footshock3.14.57.6-2.8-2.32.3-0.2
Distance traveled before self-admin1.63.44.8-2.2-2.01.81.2
Distance traveled after self-admin0.81.53.2-0.8-1.81.2-0.8
Extensor digitorum longus weight4.216.726.5-5.1-4.24.70.6
Bone: elastic displacement4.35.48.83.02.2-2.4-1.4
Bone: elastic work2.83.78.52.10.7-1.2-2.9
Bone: endosteal estimation0.82.13.0-1.7-1.31.51.1
Bone: endosteal perimeter0.92.23.1-1.8-1.21.51.4
Epididymis fat weight0.21.11.8-1.0-1.31.3-0.5
Delta time in closed arm before/after self-admin1.00.91.5-0.4-1.20.8-1.2
Delta time in open arm before/after self-admin0.50.50.9-0.31.0-0.60.9
Diff in mean of infusions in LGA sessions0.20.30.70.6-0.1-0.2-0.9
Delay discount exponential model param0.40.51.0-0.3-1.00.8-0.7
Extinction: sum of active levers before priming1.93.04.91.32.2-2.20.6
Active lever presses in extinction session 60.30.30.60.20.8-0.60.2
Bone: final force1.42.33.9-1.6-2.01.7-0.3
Bone: final moment1.22.03.5-1.4-1.91.5-0.6
Food consumed during 24 hour testing period0.40.81.2-1.1-1.00.90.6
Glucose2.23.44.9-2.2-2.02.20.4
Heart weight0.71.11.9-1.4-1.01.10.0
Delay discount hyperbolic model param0.30.40.7-0.2-0.80.6-0.7
Intermittent access intake day 1-15 change0.21.12.1-0.8-1.41.1-0.6
Intermittent access intake escalation0.21.02.1-0.6-1.41.0-0.8
Intermittent access intake escalation 21.11.93.3-0.6-1.81.3-1.5
Intermitt. access day 1 inactive lever presses0.11.52.3-1.5-1.41.20.5
Intermitt. access day 15 inactive lever presses0.00.20.3-0.5-0.60.10.4
Intermitt. access escalation Index0.10.40.6-0.5-0.80.60.6
Intermittent access day 1 total infusions0.92.75.60.72.4-1.51.6
Intermittent access day 15 total infusions0.00.00.1-0.30.10.20.1
Intermittent access terminal intake (last 3 days)0.10.10.2-0.40.10.20.4
Intermittent access total infusions0.30.40.8-0.50.60.10.9
Intermittent access day 1 locomotion1.12.14.60.52.1-1.31.3
Intermittent access day 15 total locomotion0.41.43.20.51.8-1.10.9
Intermittent access total locomotion1.11.32.90.91.7-1.20.2
Intermittent access standard deviation0.10.40.8-0.9-0.60.60.3
Left kidney weight0.32.54.2-2.1-1.21.41.6
Right kidney weight0.21.72.9-1.7-1.31.40.4
Cocaine induced anxiety0.10.20.60.80.3-0.5-0.1
Post-drug Anxiety0.30.40.6-0.8-0.50.50.6
Baseline Anxiety0.50.91.6-1.3-1.01.0-0.1
Tail length1.16.09.2-3.0-2.72.70.4
Length with tail1.35.910.6-3.3-1.82.42.0
Length without tail0.21.13.6-0.80.50.01.9
Times rat made contact with spout0.50.60.8-0.6-0.90.8-0.7
Lifetime Intake0.70.82.3-0.50.9-0.11.5
Liver weight, left0.00.10.2-0.00.2-0.20.4
Liver weight, right0.61.01.51.21.0-1.1-0.5
Locomotor activity0.00.00.0-0.1-0.10.00.1
Locomotor testing distance0.20.61.20.30.7-0.71.1
Locomotor testing rearing0.20.71.2-1.1-0.80.70.7
Locomotion in novel chamber0.30.40.80.70.3-0.3-0.9
Locomotion in novel chamber post-restriction0.72.12.7-0.8-1.61.5-1.6
Fecal boli incidents, locomotor time 10.20.50.60.70.6-0.8-0.7
Change in fecal boli incidents, locomotor task0.40.51.0-0.7-0.20.61.0
Time >=10cm from walls, locomotor time 10.30.41.3-0.30.3-0.11.2
Bouts of movement, locomotor time 11.31.72.61.61.4-1.5-0.3
Total resting periods, locomotor time 11.92.23.71.91.4-1.6-0.8
Rest time, locomotor task time 11.62.65.82.00.3-0.9-2.4
Distance moved, locomotor task time 10.92.54.3-2.0-0.61.22.1
Vertical activity count, locomotor time 10.32.36.6-1.50.00.52.6
Time >=10cm from walls, locomotor time 20.10.20.3-0.6-0.30.20.4
Bouts of movement, locomotor time 20.20.61.2-1.1-0.70.80.2
Total resting periods, locomotor time 20.10.20.5-0.7-0.30.50.0
Rest time, locomotor task time 20.71.22.51.61.0-1.0-0.7
Distance moved, locomotor task time 20.50.71.3-0.7-1.20.8-0.6
Vertical activity count, locomotor time 20.30.71.2-1.1-0.80.70.6
Light reinforcement 10.83.811.3-1.8-0.40.53.4
Light reinforcement 21.63.612.2-1.20.8-0.23.5
Bone: marrow area0.92.23.1-1.8-1.51.70.8
Bone: maximum diameter2.14.26.0-2.2-2.52.4-0.6
Bone: maximum force2.65.17.8-2.4-2.82.5-0.5
Bone: maximum moment2.34.36.7-2.2-2.62.3-0.7
Mean time between licks in bursts0.10.50.90.80.6-0.9-0.3
Mean num. licks in bursts0.82.13.11.61.8-1.7-0.2
Cd content in liver0.50.60.9-0.8-0.90.90.5
Co content in liver0.70.81.00.71.0-1.01.0
Cu content in liver1.51.83.11.81.1-1.6-0.5
Fe content in liver1.21.41.90.91.3-1.41.1
K content in liver0.50.50.80.40.7-0.60.9
Mg content in liver0.60.61.30.71.1-0.80.3
Mn content in liver1.21.32.0-0.9-1.41.3-0.8
Na content in liver1.41.52.71.71.0-1.5-0.3
Rb content in liver5.05.98.83.02.6-2.80.2
Se content in liver2.42.83.7-1.9-1.91.8-0.6
Sr content in liver0.70.61.6-1.3-0.40.70.3
Zn content in liver0.10.10.1-0.1-0.40.2-0.3
Bone: minimum diameter0.10.10.40.2-0.10.1-0.7
Time in familiar zone, hab. session 11.61.86.40.9-0.3-0.0-2.5
Time in novel zone, hab. session 12.83.15.10.81.9-1.72.3
Total zone transitions, hab. session 10.00.00.0-0.2-0.10.1-0.1
Total locomotion distance, hab. session 10.81.12.1-0.5-1.10.9-1.4
Locomotion velocity, hab. session 11.72.43.4-1.4-1.91.7-1.1
Time in familiar zone, hab. session 21.01.13.11.00.2-0.6-1.8
Time in novel zone, hab. session 22.02.13.10.91.6-1.41.8
Total zone transitions, hab. session 20.60.81.2-1.1-0.60.71.1
Total locomotion distance, hab. session 20.70.91.2-1.1-1.11.10.0
Locomotion velocity, hab. session 20.91.21.7-1.3-1.31.3-0.1
Novel to familiar place preference ratio2.93.85.71.72.4-2.21.3
Novelty place preference3.74.76.92.12.6-2.51.1
Time in novel zone, NPP test4.75.88.42.42.9-2.81.2
Total zone transitions, NPP test0.81.21.9-1.3-0.70.81.4
Total locomotion distance, NPP test1.72.43.6-1.9-1.31.61.3
Locomotion velocity, NPP test2.13.04.7-2.2-1.71.91.0
Intraocular pressure1.72.84.1-2.0-1.52.01.0
Delta distance traveled before/after self-admin0.30.30.60.7-0.0-0.3-0.8
Delta ambulatory time before/after self-admin0.50.91.71.30.5-0.9-0.9
Parametrial fat weight0.20.41.10.20.4-0.61.1
Pavlov. Cond. lever latency5.67.110.93.32.8-3.1-0.7
Pavlov. Cond. magazine entry latency0.50.71.0-1.0-0.90.9-0.1
Pavlov. Cond. change in total contacts2.32.43.7-1.9-1.61.80.5
Pavlov. Cond. index score2.83.65.2-2.3-2.12.20.0
Pavlov. Cond. latency score2.53.24.9-2.2-1.92.10.1
Pavlov. Cond. lever contacts5.46.59.9-3.1-2.72.90.4
Pavlov. Cond. magazine entry number0.70.91.41.01.2-1.10.4
Pavlov. Cond. intertrial magazine entries0.20.20.3-0.5-0.50.6-0.2
Pavlov. Cond. lever-magazine prob. diff.2.93.64.9-2.2-2.12.2-0.2
Pavlov. Cond. response bias3.54.46.4-2.5-2.32.40.2
Pavlov. Cond. lever latency2.63.65.21.82.3-2.11.2
Pavlov. Cond. magazine entry latency0.20.30.40.60.3-0.5-0.7
Pavlov. Cond. change in total contacts1.02.34.5-0.7-1.71.2-2.1
Pavlov. Cond. index score0.60.92.2-0.3-1.00.7-1.5
Pavlov. Cond. latency score0.71.22.6-0.4-1.10.8-1.6
Pavlov. Cond. lever contacts1.92.84.0-1.5-2.01.8-1.2
Pavlov. Cond. magazine entry number0.70.92.8-0.10.8-0.41.7
Pavlov. Cond. intertrial magazine entries0.10.30.5-0.6-0.50.70.4
Pavlov. Cond. lever-magazine prob. diff.0.71.02.5-0.2-1.00.7-1.6
Pavlov. Cond. response bias1.21.72.4-0.9-1.51.2-1.5
Time in closed arm before self-admin0.20.30.60.80.7-0.5-0.1
Time in closed arm after self-admin0.70.81.81.1-0.2-0.2-1.4
Time in open arm before self-admin0.81.01.6-1.3-0.60.91.1
Time in open arm after self-admin1.41.53.4-1.8-0.20.81.4
Bone: periosteal estimation1.33.24.7-1.9-2.22.1-0.1
Bone: periosteal perimeter0.50.91.3-1.1-0.91.00.6
Bone: post-yield work1.72.94.7-2.2-1.61.71.2
Progressive ratio test 1 active lever presses1.01.73.50.21.6-0.91.9
Progressive ratio test 1 breakpoint0.91.53.10.11.5-0.81.7
Progressive ratio test 1 inactive lever presses0.61.64.5-1.3-0.10.52.1
Progressive ratio test 2 active lever presses1.72.34.10.32.0-1.12.0
Progressive ratio test 2 breakpoint1.92.44.30.42.1-1.22.0
Progressive ratio test 2 inactive lever presses0.10.30.6-0.70.30.20.8
Incentive Sensitization - Responses0.30.81.20.41.1-0.81.0
Incentive Sensitization - Breakpoint0.40.81.40.41.2-0.81.0
Sum of active levers in priming session hrs 5-63.43.25.31.22.3-2.01.4
Progressive ratio0.00.10.1-0.30.2-0.00.4
Food seeking constrained by brief footshock6.27.814.1-3.8-2.12.92.1
Seeking ratio, punishment vs. effort0.81.82.7-1.6-1.31.60.6
Retroperitoneal fat weight0.31.32.01.40.7-1.2-1.1
Reaction time number correct0.10.30.7-0.60.00.30.8
Reaction time mean minus median0.42.56.8-0.3-1.41.0-2.6
Reaction time mean minus median AUC0.32.23.9-0.8-1.61.4-2.0
Reaction time num false alarms0.10.20.6-0.3-0.30.3-0.8
Reaction time num false alarms AUC0.20.61.1-1.0-0.70.8-0.1
Reaction time trials correct on left0.10.30.7-0.60.00.30.8
Reaction time trials on left0.10.20.6-0.50.10.20.8
Reaction time mean1.32.85.92.00.4-1.1-2.4
Reaction time mean AUC1.33.06.42.10.5-1.1-2.5
Median of all reaction times2.43.87.22.71.2-1.9-1.7
Reaction time omissions1.22.03.21.81.3-1.7-0.4
Reaction time false alarm rate0.10.10.5-0.1-0.20.1-0.7
Reaction time premature initiation rate1.62.54.42.11.2-1.6-1.2
Reaction time premature initiations0.51.52.61.61.0-1.3-0.7
Std. dev. reaction times0.62.07.00.8-0.70.1-2.7
Reaction time trials completed0.10.20.6-0.50.10.20.8
Reaction time trials AUC0.10.20.6-0.50.10.20.8
Run reversals in cocaine runway, females0.30.30.90.4-0.30.2-0.9
Run reversals in cocaine runway, males0.00.00.10.10.2-0.2-0.1
Latency to leave start box in cocaine runway0.50.61.1-0.7-1.10.9-0.3
Latency to leave start box in cocaine runway, F0.10.10.20.10.3-0.30.5
Latency to leave start box in cocaine runway, M1.71.62.5-1.3-1.61.50.1
Std. dev. time between licks in bursts0.20.30.50.50.7-0.7-0.3
Total sessions with >9 infusions1.01.23.7-0.40.9-0.31.9
Short access day 1 total inactive lever presses0.51.03.1-0.8-0.30.51.8
Short access day 10 total inactive lever presses0.11.02.0-0.9-1.41.0-0.3
Short access day 1 total infusions0.71.44.8-0.40.8-0.32.2
Short access day 10 total infusions0.91.43.90.01.2-0.52.0
Short access total infusions1.42.05.20.01.5-0.82.3
Short access day 1 locomotion1.22.03.10.71.8-1.41.6
Short access day 10 total locomotion0.20.71.00.81.0-0.9-0.5
Short access total locomotion0.60.91.60.21.2-0.81.2
One hour access (0.3 mA shock)0.70.81.8-0.90.80.31.3
Compulsive drug intake0.40.60.9-0.6-0.70.7-1.0
One hour access (shock baseline)0.61.54.4-0.61.1-0.22.1
Social response proportion1.82.34.22.11.0-1.6-1.2
Social responses0.60.81.3-1.1-1.21.0-0.0
Social time0.10.10.30.50.0-0.50.0
Soleus weight0.82.27.5-0.60.8-0.52.7
Bone: stiffness3.25.89.1-2.6-3.02.7-0.3
Tibialis anterior weight6.321.632.8-5.7-4.95.21.5
Time to tail flick, vehicle, before self-admin0.30.40.50.70.7-0.5-0.6
Time to tail flick, vehicle, after self-admin0.00.10.1-0.2-0.30.3-0.3
Time to tail flick, test, before self-admin0.30.30.6-0.7-0.40.80.0
Time to tail flick, test, after self-admin2.62.73.8-1.3-1.81.9-1.4
Delta time to tail flick, vehicle, before/after SA0.10.10.3-0.4-0.60.3-0.0
Delta time to tail flick, test, before/after SA0.30.41.10.2-0.60.2-1.0
Tibia length0.30.83.0-0.20.2-0.41.7
Ambulatory time before self-admin0.92.84.5-2.1-1.61.61.3
Ambulatory time after self-admin0.20.40.7-0.7-0.80.60.1
Bone: tissue strength0.10.10.3-0.4-0.50.2-0.3
Total heroin consumption1.82.23.10.51.7-1.51.8
Bone: trabecular number1.01.92.4-1.5-1.51.5-0.9
Bone: trabecular spacing0.10.20.40.4-0.30.0-0.6
Bone: trabecular thickness0.10.10.30.20.3-0.2-0.6
Bone: trabecular tissue density1.93.44.9-2.1-2.22.00.4
Water consumed over 24 hours0.50.91.3-1.0-1.11.1-0.3
Number of responses in last shaping day2.12.88.9-0.11.1-0.93.0