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 0.02 0.02 4.7e-03 0.01 0 0 0 4.2e-02 2.7e-01 2.4e-01 2.3e-01
2 NAcc gene expression Arhgef39 0.04 0.03 1.8e-05 0.03 0.04 0.04 0.04 9.9e-05 1.2e-05 3.3e-05 2.5e-05
3 BLA gene expression Arhgef39 0.09 0.06 4.1e-05 0.07 0.09 0.08 0.08 2.1e-04 2.2e-05 5.4e-05 5.8e-05
4 Adipose gene expression Arhgef39 0.06 0.04 1.8e-04 0.03 0.03 0.03 0.03 2.9e-04 2.2e-04 8.1e-04 4.9e-04

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 density1.11.92.6-1.21.61.61.0
Area under the delay curve0.60.61.10.5-0.8-0.8-1.0
BMI with tail2.37.610.1-2.53.13.22.1
BMI without tail5.110.514.4-3.63.83.70.7
Body weight3.213.517.8-4.24.24.21.1
Weight adjusted by age0.50.51.1-0.90.30.3-1.0
Bone surface0.61.01.4-1.11.21.2-0.0
Bone volume0.50.91.4-0.91.21.20.4
Breakpoint value in progressive ratio session1.01.13.5-0.2-0.6-0.6-1.9
Number of licking bursts4.24.96.4-2.32.52.51.3
Context. condit. distance diff. score0.10.10.20.4-0.3-0.20.3
Locomotion velocity, session 12.22.48.0-1.20.40.3-2.8
Locomotion distance, session 10.70.92.4-0.90.40.4-1.5
Locomotion velocity, session 22.53.03.5-1.81.91.91.3
Locomotion distance, session 21.72.33.9-2.01.61.5-0.9
Locomotion velocity, session 30.50.62.1-0.30.0-0.0-1.4
Locomotion distance, session 32.12.33.3-1.81.71.7-0.3
Stereotopy head waving bouts, day 30.80.93.00.1-0.5-0.6-1.7
Stereotopy head waving duration, day 30.60.71.40.5-0.8-0.8-1.2
Locomotion velocity, session 70.10.10.10.3-0.3-0.2-0.0
Locomotion distance, session 70.20.20.3-0.40.50.5-0.2
Stereotopy head waving bouts, day 72.02.33.3-1.81.71.70.0
Stereotopy head waving duration, day 70.50.60.9-1.00.80.8-0.4
Locomotion velocity, session 80.40.51.9-0.3-0.1-0.2-1.4
Locomotion distance, session 80.30.41.1-0.70.40.3-1.0
Degree of sensitization distance1.11.11.71.3-1.2-1.2-0.1
Degree of sensitization stereotypy1.31.41.9-1.31.31.40.3
Conditioned locomotion0.30.41.4-0.1-0.2-0.2-1.2
Cocaine response after cond. corrected2.52.84.31.4-1.6-1.6-2.1
Cocaine response after cond. not corrected2.52.85.51.1-1.4-1.5-2.3
Cocaine response before conditioning0.60.81.1-1.11.00.90.3
Saline control response0.81.11.4-1.20.90.8-1.2
Bone: connectivity density0.71.11.4-0.81.11.21.0
Bone: cortical apparent density0.60.72.60.6-0.1-0.11.6
Bone: cortical area2.13.24.0-1.72.02.01.4
Bone: cortical porosity0.30.40.50.6-0.7-0.7-0.2
Bone: cortical porosity0.00.00.0-0.10.00.0-0.0
Bone: cortical thickness1.01.73.1-0.71.21.31.8
Bone: cortical thickness0.20.20.40.7-0.3-0.30.4
Bone: cortical tissue density0.50.72.10.7-0.2-0.21.5
Condit. Reinf. active minus inactive responses0.60.60.9-0.90.80.80.6
Condit. Reinf. active-inactive response ratio0.50.60.80.9-0.8-0.80.1
Condit. Reinf. active responses2.93.54.6-2.22.12.01.1
Condit. Reinf. inactive responses3.44.15.0-2.12.22.21.4
Incentive salience index mean4.25.17.5-2.72.52.50.7
Condit. Reinf. lever presses9.612.819.4-4.44.04.00.3
Condit. Reinf. active minus inactive responses0.70.81.1-0.91.01.00.6
Condit. Reinf. active-inactive response ratio0.20.30.6-0.20.40.50.8
Condit. Reinf. active responses2.12.93.8-1.91.91.90.7
Condit. Reinf. inactive responses2.83.54.3-2.02.12.01.1
Condit. Reinf. lever presses2.53.43.8-1.72.02.01.7
Condit. Reinf. lever reinforcers received2.43.44.4-2.12.12.10.8
Conditioned reinforcement - actives0.30.30.3-0.50.50.60.6
Conditioned reinforcement - inactives0.00.00.10.1-0.3-0.2-0.2
Conditioned locomotion0.40.50.7-0.90.60.80.4
Patch foraging indifference point 0 sec1.01.64.1-1.30.60.7-2.0
Patch foraging indifference point AUC7.78.811.7-3.43.43.40.6
Delay disc. indifference point, 0s delay1.41.51.81.1-1.3-1.3-1.2
Delay disc. indifference point, 16s delay1.71.73.30.8-1.2-1.2-1.8
Delay disc. indifference point, 2s delay0.10.10.40.20.20.20.6
Delay disc. indifference point, 24s delay0.20.20.20.5-0.4-0.4-0.2
Delay disc. indifference point, 4s delay0.10.10.20.4-0.3-0.3-0.2
Delay disc. indifference point, 8s delay0.00.00.1-0.30.10.1-0.2
Indifference point function ln k2.43.44.52.0-2.1-2.1-0.7
Indifference point function log k2.43.44.52.0-2.1-2.1-0.7
Patch foraging total patch changes 0 sec1.21.92.8-1.61.01.1-1.7
Patch foraging total patch changes 12 sec2.43.14.2-1.92.02.10.6
Patch foraging total patch changes 18 sec0.70.91.4-1.21.11.1-0.2
Patch foraging total patch changes 24 sec2.53.14.3-2.12.02.0-0.2
Patch foraging total patch changes 6 sec2.94.36.7-2.62.22.3-0.7
Patch foraging time to switch 0 sec2.84.36.32.5-2.3-2.30.3
Patch foraging water rate 0 sec1.82.83.9-2.01.81.9-0.5
Patch foraging water rate 12 sec0.10.10.5-0.10.10.1-0.7
Patch foraging water rate 18 sec0.50.60.8-0.60.80.90.8
Patch foraging water rate 24 sec0.40.51.80.30.20.31.3
Patch foraging water rate 6 sec0.40.50.9-0.70.90.9-0.0
Seeking ratio, delayed vs. immediate footshock4.14.76.9-2.62.32.31.3
Distance traveled before self-admin3.73.95.7-2.42.22.2-0.5
Distance traveled after self-admin0.40.50.6-0.60.80.70.7
Extensor digitorum longus weight4.417.324.8-5.04.74.61.0
Bone: elastic displacement3.64.16.02.5-2.3-2.20.5
Bone: elastic work2.12.73.91.9-1.3-1.32.0
Bone: endosteal estimation0.91.93.2-1.81.51.4-0.7
Bone: endosteal perimeter1.02.13.5-1.91.51.4-0.9
Epididymis fat weight0.41.01.7-1.31.11.0-0.3
Delta time in closed arm before/after self-admin3.02.93.2-1.51.81.81.7
Delta time in open arm before/after self-admin0.60.61.10.1-0.8-0.8-1.0
Diff in mean of infusions in LGA sessions0.00.00.10.3-0.2-0.20.2
Delay discount exponential model param0.40.50.9-0.40.60.71.0
Extinction: sum of active levers before priming1.61.62.41.1-1.5-1.5-0.7
Active lever presses in extinction session 60.20.20.30.1-0.6-0.5-0.4
Bone: final force0.91.42.1-1.21.41.40.4
Bone: final moment0.61.01.5-1.01.21.20.6
Food consumed during 24 hour testing period0.70.81.3-1.11.00.9-0.4
Glucose1.11.62.3-1.51.51.40.2
Heart weight0.71.01.9-1.41.01.0-0.3
Delay discount hyperbolic model param0.40.40.8-0.30.60.60.9
Intermittent access intake day 1-15 change1.01.02.4-0.40.90.91.5
Intermittent access intake escalation1.31.32.1-0.71.21.21.4
Intermittent access intake escalation 21.81.84.1-0.41.21.22.0
Intermitt. access day 1 inactive lever presses0.60.70.9-0.90.91.00.2
Intermitt. access day 15 inactive lever presses0.10.20.4-0.40.10.1-0.7
Intermitt. access escalation Index1.00.91.3-1.11.00.9-0.6
Intermittent access day 1 total infusions0.40.51.3-0.0-0.6-0.5-1.1
Intermittent access day 15 total infusions0.60.71.0-1.00.80.90.5
Intermittent access terminal intake (last 3 days)0.70.81.1-1.10.91.00.4
Intermittent access total infusions0.91.01.7-1.31.01.10.2
Intermittent access day 1 locomotion0.50.50.80.2-0.9-0.8-0.9
Intermittent access day 15 total locomotion0.30.30.70.4-0.8-0.7-0.2
Intermittent access total locomotion0.20.20.30.3-0.6-0.40.4
Intermittent access standard deviation0.50.50.6-0.70.60.70.8
Left kidney weight0.51.42.6-1.61.11.1-0.8
Right kidney weight0.10.30.8-0.60.1-0.0-0.9
Cocaine induced anxiety1.31.52.01.4-1.3-1.3-0.7
Post-drug Anxiety0.20.20.3-0.50.50.3-0.4
Baseline Anxiety1.71.82.1-1.41.41.41.1
Tail length2.36.911.0-3.32.92.8-0.2
Length with tail0.93.26.0-2.51.81.7-0.9
Length without tail0.30.71.00.6-1.0-0.9-0.6
Times rat made contact with spout0.40.50.9-0.40.70.71.0
Lifetime Intake0.91.02.1-1.50.80.9-0.6
Liver weight, left0.20.40.6-0.80.70.6-0.2
Liver weight, right0.20.30.70.1-0.4-0.5-0.8
Locomotor activity0.00.00.0-0.20.10.0-0.1
Locomotor testing distance0.30.51.7-0.1-0.3-0.3-1.3
Locomotor testing rearing0.50.81.4-1.20.90.8-0.5
Locomotion in novel chamber0.30.31.20.20.10.11.1
Locomotion in novel chamber post-restriction2.12.54.3-1.01.61.62.1
Fecal boli incidents, locomotor time 10.40.50.70.7-0.8-0.80.3
Change in fecal boli incidents, locomotor task0.80.80.9-1.00.90.9-0.7
Time >=10cm from walls, locomotor time 10.30.31.1-0.2-0.0-0.0-1.0
Bouts of movement, locomotor time 11.71.92.81.7-1.5-1.5-0.3
Total resting periods, locomotor time 12.22.44.02.0-1.7-1.70.1
Rest time, locomotor task time 12.32.64.42.1-1.1-1.21.8
Distance moved, locomotor task time 12.12.33.9-2.01.41.4-1.2
Vertical activity count, locomotor time 11.81.83.6-1.50.90.8-1.9
Time >=10cm from walls, locomotor time 20.10.10.2-0.50.30.3-0.3
Bouts of movement, locomotor time 20.60.61.2-1.10.80.80.2
Total resting periods, locomotor time 20.30.30.5-0.70.50.50.2
Rest time, locomotor task time 21.01.12.41.6-1.0-1.00.2
Distance moved, locomotor task time 20.40.50.6-0.50.70.70.8
Vertical activity count, locomotor time 20.40.51.0-1.00.70.6-0.3
Light reinforcement 11.73.17.7-1.80.80.7-2.8
Light reinforcement 22.23.010.2-1.30.20.0-3.2
Bone: marrow area0.92.03.3-1.81.61.5-0.4
Bone: maximum diameter2.03.74.9-2.22.22.10.7
Bone: maximum force2.33.95.5-2.12.32.30.9
Bone: maximum moment1.83.14.2-1.82.02.01.0
Mean time between licks in bursts0.50.71.10.9-0.9-1.0-0.4
Mean num. licks in bursts1.92.33.11.7-1.8-1.7-0.4
Cd content in liver0.70.71.0-0.50.90.91.0
Co content in liver1.61.82.01.4-1.4-1.4-1.2
Cu content in liver1.11.42.61.6-1.2-1.20.3
Fe content in liver1.01.24.2-0.6-0.0-0.1-2.1
K content in liver0.50.50.90.5-0.6-0.6-1.0
Mg content in liver0.40.40.50.7-0.7-0.7-0.4
Mn content in liver0.40.41.0-0.30.50.51.0
Na content in liver1.71.82.41.5-1.5-1.6-0.7
Rb content in liver4.35.37.12.7-2.5-2.5-1.2
Se content in liver1.82.22.7-1.71.61.51.2
Sr content in liver0.70.61.2-1.10.80.70.4
Zn content in liver0.30.41.20.10.40.41.1
Bone: minimum diameter0.00.00.20.1-0.1-0.10.4
Time in familiar zone, hab. session 11.81.75.71.0-0.2-0.12.4
Time in novel zone, hab. session 13.73.78.60.8-1.6-1.7-2.9
Total zone transitions, hab. session 10.00.00.0-0.10.10.10.1
Total locomotion distance, hab. session 10.71.02.4-0.60.80.81.6
Locomotion velocity, hab. session 11.82.62.8-1.51.71.61.6
Time in familiar zone, hab. session 20.90.91.71.0-0.7-0.71.3
Time in novel zone, hab. session 22.12.14.40.9-1.3-1.3-2.1
Total zone transitions, hab. session 20.50.71.0-1.00.80.7-0.7
Total locomotion distance, hab. session 20.71.01.3-1.21.11.10.4
Locomotion velocity, hab. session 21.01.41.8-1.31.31.30.6
Novel to familiar place preference ratio3.73.84.41.6-2.1-2.1-2.0
Novelty place preference4.74.85.82.0-2.4-2.4-1.9
Time in novel zone, NPP test5.96.07.32.2-2.7-2.7-2.1
Total zone transitions, NPP test0.71.01.5-1.20.90.8-1.0
Total locomotion distance, NPP test1.72.43.8-2.01.71.6-0.5
Locomotion velocity, NPP test2.33.24.8-2.22.02.0-0.1
Intraocular pressure2.02.83.8-1.91.91.9-0.3
Delta distance traveled before/after self-admin0.70.81.11.0-1.0-1.00.1
Delta ambulatory time before/after self-admin1.71.92.71.6-1.5-1.60.1
Parametrial fat weight0.20.30.4-0.70.50.4-0.6
Pavlov. Cond. lever latency6.68.411.93.4-3.3-3.3-0.5
Pavlov. Cond. magazine entry latency0.40.50.7-0.80.80.70.4
Pavlov. Cond. change in total contacts2.42.63.8-1.91.81.80.2
Pavlov. Cond. index score2.93.75.0-2.22.22.10.8
Pavlov. Cond. latency score2.73.54.7-2.22.12.10.7
Pavlov. Cond. lever contacts5.16.08.0-2.82.82.80.7
Pavlov. Cond. magazine entry number0.70.91.11.1-1.0-1.0-0.5
Pavlov. Cond. intertrial magazine entries0.20.30.4-0.60.60.60.3
Pavlov. Cond. lever-magazine prob. diff.2.83.54.4-2.12.12.11.1
Pavlov. Cond. response bias2.93.54.9-2.22.12.10.6
Pavlov. Cond. lever latency2.83.84.41.9-2.1-2.1-1.8
Pavlov. Cond. magazine entry latency0.40.50.70.8-0.8-0.80.1
Pavlov. Cond. change in total contacts1.21.63.9-0.61.11.02.0
Pavlov. Cond. index score0.40.51.6-0.30.50.51.3
Pavlov. Cond. latency score0.70.82.2-0.40.70.71.5
Pavlov. Cond. lever contacts1.52.02.3-1.41.51.51.2
Pavlov. Cond. magazine entry number0.40.52.0-0.2-0.1-0.1-1.4
Pavlov. Cond. intertrial magazine entries0.40.50.8-0.80.80.90.1
Pavlov. Cond. lever-magazine prob. diff.0.40.61.8-0.20.50.41.3
Pavlov. Cond. response bias0.60.91.2-0.80.90.91.1
Time in closed arm before self-admin2.22.53.71.9-1.8-1.7-0.4
Time in closed arm after self-admin0.30.30.50.7-0.3-0.20.7
Time in open arm before self-admin2.12.33.9-2.01.61.5-0.6
Time in open arm after self-admin1.51.73.6-1.91.21.2-0.7
Bone: periosteal estimation1.32.63.7-1.91.91.80.2
Bone: periosteal perimeter0.50.81.4-1.20.90.8-0.7
Bone: post-yield work1.21.62.6-1.61.41.3-0.6
Progressive ratio test 1 active lever presses0.40.40.8-0.90.30.5-0.7
Progressive ratio test 1 breakpoint0.50.51.0-1.00.50.6-0.7
Progressive ratio test 1 inactive lever presses1.01.02.7-1.10.40.5-1.6
Progressive ratio test 2 active lever presses0.40.41.2-0.6-0.2-0.0-1.1
Progressive ratio test 2 breakpoint0.30.41.2-0.4-0.4-0.2-1.1
Progressive ratio test 2 inactive lever presses0.20.20.5-0.70.40.5-0.1
Incentive Sensitization - Responses0.10.10.5-0.1-0.2-0.2-0.7
Incentive Sensitization - Breakpoint0.20.20.5-0.0-0.4-0.3-0.7
Sum of active levers in priming session hrs 5-62.92.83.71.4-1.9-1.9-1.4
Progressive ratio0.00.00.1-0.1-0.2-0.1-0.2
Food seeking constrained by brief footshock6.98.414.2-3.83.13.1-0.6
Seeking ratio, punishment vs. effort1.62.02.8-1.71.61.6-0.0
Retroperitoneal fat weight0.10.20.30.5-0.5-0.60.3
Reaction time number correct0.10.20.3-0.40.30.3-0.5
Reaction time mean minus median1.52.06.5-0.40.90.92.5
Reaction time mean minus median AUC1.72.24.4-1.01.31.32.1
Reaction time num false alarms0.10.20.6-0.30.20.20.8
Reaction time num false alarms AUC0.40.61.0-1.00.70.70.4
Reaction time trials correct on left0.10.20.3-0.40.30.3-0.5
Reaction time trials on left0.10.10.3-0.30.20.2-0.5
Reaction time mean1.42.03.01.7-1.2-1.21.5
Reaction time mean AUC1.62.23.21.8-1.3-1.31.5
Median of all reaction times2.63.65.82.4-2.0-2.00.6
Reaction time omissions1.21.72.41.4-1.5-1.5-0.1
Reaction time false alarm rate0.10.10.4-0.1-0.0-0.00.7
Reaction time premature initiation rate2.12.74.82.2-1.7-1.60.7
Reaction time premature initiations1.21.73.01.7-1.4-1.30.4
Std. dev. reaction times0.81.24.40.5-0.0-0.12.1
Reaction time trials completed0.10.10.3-0.30.20.2-0.5
Reaction time trials AUC0.10.10.2-0.30.20.2-0.5
Run reversals in cocaine runway, females0.30.31.00.20.30.31.0
Run reversals in cocaine runway, males0.00.00.10.0-0.1-0.00.3
Latency to leave start box in cocaine runway0.60.70.9-0.70.90.90.7
Latency to leave start box in cocaine runway, F0.00.00.00.0-0.1-0.0-0.1
Latency to leave start box in cocaine runway, M1.01.01.4-1.21.21.1-0.2
Std. dev. time between licks in bursts0.30.40.60.7-0.7-0.8-0.2
Total sessions with >9 infusions0.80.92.8-0.7-0.2-0.1-1.7
Short access day 1 total inactive lever presses1.61.82.6-1.61.41.5-0.2
Short access day 10 total inactive lever presses0.10.10.2-0.20.50.40.1
Short access day 1 total infusions1.41.42.3-1.50.80.9-1.4
Short access day 10 total infusions0.70.81.3-1.10.60.7-1.1
Short access total infusions0.70.82.3-0.90.20.3-1.5
Short access day 1 locomotion0.20.20.6-0.2-0.4-0.4-0.8
Short access day 10 total locomotion0.40.40.60.6-0.7-0.70.6
Short access total locomotion0.20.20.5-0.50.10.1-0.7
One hour access (0.3 mA shock)0.60.71.5-1.20.80.8-0.4
Compulsive drug intake0.40.40.8-0.90.70.60.1
One hour access (shock baseline)0.40.51.0-1.00.50.6-0.6
Social response proportion2.32.54.02.0-1.7-1.80.3
Social responses0.50.60.9-1.00.90.80.3
Social time0.30.30.50.4-0.5-0.7-0.6
Soleus weight0.92.59.3-0.4-0.5-0.7-3.1
Bone: stiffness3.04.76.6-2.42.62.40.8
Tibialis anterior weight6.020.630.5-5.55.15.00.1
Time to tail flick, vehicle, before self-admin1.01.01.61.3-1.2-1.10.0
Time to tail flick, vehicle, after self-admin0.00.00.00.0-0.1-0.0-0.2
Time to tail flick, test, before self-admin0.30.30.4-0.40.60.70.6
Time to tail flick, test, after self-admin1.11.12.1-0.51.01.11.4
Delta time to tail flick, vehicle, before/after SA0.10.10.2-0.40.40.4-0.0
Delta time to tail flick, test, before/after SA0.10.10.10.3-0.2-0.20.3
Tibia length0.41.24.30.0-0.3-0.5-2.1
Ambulatory time before self-admin3.03.25.1-2.31.91.8-0.8
Ambulatory time after self-admin0.10.10.3-0.50.30.3-0.2
Bone: tissue strength0.00.00.1-0.10.20.10.2
Total heroin consumption0.70.92.20.3-0.8-0.8-1.5
Bone: trabecular number1.21.92.4-1.21.51.61.2
Bone: trabecular spacing0.10.20.60.2-0.00.00.8
Bone: trabecular thickness0.00.10.10.3-0.3-0.20.2
Bone: trabecular tissue density2.02.84.6-2.11.91.70.2
Water consumed over 24 hours0.70.81.2-0.91.01.10.6
Number of responses in last shaping day1.11.24.3-0.7-0.0-0.0-2.1