Gfra2

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 gene expression Gfra2 0.04 0.03 1.6e-03 0.02 0 0 0.01 1.3e-03 1.2e-01 1.4e-01 4.5e-02
2 Brain gene expression Gfra2 0.06 0.05 2.4e-04 0.04 0.04 0.04 0.03 1.4e-04 2.5e-04 2.2e-04 4.0e-04
3 PL gene expression Gfra2 0.09 0.06 4.2e-08 0.06 0.06 0.06 0.05 3.5e-07 1.2e-06 4.4e-07 2.2e-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
Bone: apparent density0.71.12.0-1.20.2-1.4
Area under the delay curve0.30.30.9-0.0-1.00.2
BMI with tail0.72.44.22.11.21.2
BMI without tail0.62.03.91.42.00.0
Body weight0.41.63.11.3-0.21.7
Weight adjusted by age0.71.12.20.7-0.91.5
Bone surface0.61.11.9-1.4-0.7-1.0
Bone volume0.61.01.7-1.3-0.5-1.1
Breakpoint value in progressive ratio session0.10.10.10.1-0.30.3
Number of licking bursts0.00.00.10.10.3-0.0
Context. condit. distance diff. score4.65.512.11.83.5-1.1
Locomotion velocity, session 10.10.10.2-0.0-0.30.5
Locomotion distance, session 11.21.62.5-1.6-1.5-0.2
Locomotion velocity, session 20.60.71.2-1.1-0.9-0.1
Locomotion distance, session 22.83.96.1-2.4-2.5-0.1
Locomotion velocity, session 31.71.92.81.71.50.7
Locomotion distance, session 30.80.91.90.81.4-0.2
Stereotopy head waving bouts, day 30.30.40.80.5-0.20.9
Stereotopy head waving duration, day 31.21.52.91.0-0.71.7
Locomotion velocity, session 76.67.215.71.24.0-2.1
Locomotion distance, session 73.94.910.50.63.2-2.0
Stereotopy head waving bouts, day 71.01.21.80.3-1.31.4
Stereotopy head waving duration, day 71.21.52.60.8-1.11.6
Locomotion velocity, session 80.50.61.30.71.20.0
Locomotion distance, session 80.40.60.9-0.60.7-0.9
Degree of sensitization distance2.72.84.3-0.32.0-2.1
Degree of sensitization stereotypy0.60.71.30.5-0.71.1
Conditioned locomotion0.40.50.90.81.0-0.2
Cocaine response after cond. corrected2.02.53.51.91.90.5
Cocaine response after cond. not corrected1.01.11.71.21.30.4
Cocaine response before conditioning1.61.92.9-1.7-1.6-0.4
Saline control response0.81.11.6-1.3-1.2-0.4
Bone: connectivity density1.21.93.7-1.20.6-1.9
Bone: cortical apparent density1.72.44.81.52.2-0.3
Bone: cortical area0.40.50.8-0.9-0.90.0
Bone: cortical porosity1.51.63.4-0.4-1.81.1
Bone: cortical porosity1.61.84.0-0.7-2.00.9
Bone: cortical thickness0.00.10.2-0.4-0.2-0.0
Bone: cortical thickness0.80.91.81.01.3-0.0
Bone: cortical tissue density1.92.65.41.62.3-0.3
Condit. Reinf. active minus inactive responses0.50.61.3-0.2-1.10.7
Condit. Reinf. active-inactive response ratio1.31.42.41.30.01.6
Condit. Reinf. active responses1.11.42.6-1.2-1.60.0
Condit. Reinf. inactive responses4.15.08.7-2.9-1.8-1.7
Incentive salience index mean1.51.84.0-0.7-2.01.0
Condit. Reinf. lever presses1.72.45.1-1.3-2.30.7
Condit. Reinf. active minus inactive responses0.20.30.4-0.50.1-0.7
Condit. Reinf. active-inactive response ratio0.20.20.20.50.50.2
Condit. Reinf. active responses0.50.71.2-0.90.1-1.1
Condit. Reinf. inactive responses1.21.62.5-1.5-0.3-1.6
Condit. Reinf. lever presses1.11.52.3-1.4-1.5-0.4
Condit. Reinf. lever reinforcers received0.40.60.9-0.9-0.1-1.0
Conditioned reinforcement - actives0.60.91.5-0.31.1-1.2
Conditioned reinforcement - inactives2.43.55.3-2.3-0.6-2.2
Conditioned locomotion0.10.10.3-0.10.5-0.4
Patch foraging indifference point 0 sec3.76.911.7-3.4-2.4-1.7
Patch foraging indifference point AUC0.60.81.41.20.90.5
Delay disc. indifference point, 0s delay1.61.72.6-1.5-1.6-0.6
Delay disc. indifference point, 16s delay0.10.10.3-0.2-0.3-0.5
Delay disc. indifference point, 2s delay1.31.52.90.2-1.71.3
Delay disc. indifference point, 24s delay0.30.30.60.80.40.4
Delay disc. indifference point, 4s delay1.21.21.81.2-0.61.3
Delay disc. indifference point, 8s delay0.20.20.4-0.3-0.6-0.2
Indifference point function ln k0.50.81.6-0.9-1.3-0.0
Indifference point function log k0.50.81.6-0.9-1.3-0.0
Patch foraging total patch changes 0 sec3.46.310.3-3.2-2.5-1.5
Patch foraging total patch changes 12 sec1.72.23.3-1.8-1.6-0.9
Patch foraging total patch changes 18 sec1.01.62.6-1.6-0.2-1.4
Patch foraging total patch changes 24 sec1.01.83.5-1.4-1.90.0
Patch foraging total patch changes 6 sec0.20.30.6-0.8-0.3-0.5
Patch foraging time to switch 0 sec0.30.61.2-0.60.6-1.1
Patch foraging water rate 0 sec0.30.61.1-0.0-1.10.7
Patch foraging water rate 12 sec0.30.61.0-0.1-0.91.0
Patch foraging water rate 18 sec1.72.64.51.80.02.1
Patch foraging water rate 24 sec0.60.81.21.11.00.5
Patch foraging water rate 6 sec1.62.34.20.1-2.11.7
Seeking ratio, delayed vs. immediate footshock0.80.91.7-1.3-0.3-1.0
Distance traveled before self-admin1.31.73.7-0.6-1.91.0
Distance traveled after self-admin1.51.93.41.5-0.11.8
Extensor digitorum longus weight6.425.050.64.6-1.77.1
Bone: elastic displacement1.21.42.4-1.6-1.1-0.7
Bone: elastic work2.53.35.1-2.3-2.1-0.5
Bone: endosteal estimation0.20.41.0-0.5-1.00.4
Bone: endosteal perimeter0.51.02.2-0.9-1.50.3
Epididymis fat weight0.41.32.6-1.00.7-1.6
Delta time in closed arm before/after self-admin2.82.63.8-1.9-0.6-1.9
Delta time in open arm before/after self-admin0.10.10.20.40.20.2
Diff in mean of infusions in LGA sessions0.40.51.00.5-0.51.0
Delay discount exponential model param0.40.51.0-0.31.0-0.6
Extinction: sum of active levers before priming1.11.32.2-1.30.2-1.5
Active lever presses in extinction session 60.40.40.60.10.7-0.8
Bone: final force0.10.20.4-0.2-0.60.4
Bone: final moment0.40.61.1-0.7-1.10.4
Food consumed during 24 hour testing period0.91.32.2-1.5-1.1-0.6
Glucose0.60.91.61.11.2-0.0
Heart weight0.50.71.3-1.1-0.5-0.8
Delay discount hyperbolic model param0.50.61.1-0.31.1-0.7
Intermittent access intake day 1-15 change0.81.63.4-1.00.5-1.9
Intermittent access intake escalation0.91.83.6-1.30.1-1.9
Intermittent access intake escalation 20.70.81.7-0.30.7-1.3
Intermitt. access day 1 inactive lever presses0.00.10.20.40.3-0.2
Intermitt. access day 15 inactive lever presses0.10.20.2-0.4-0.4-0.4
Intermitt. access escalation Index0.10.10.4-0.1-0.60.3
Intermittent access day 1 total infusions0.00.00.0-0.1-0.1-0.1
Intermittent access day 15 total infusions1.11.62.8-1.4-0.2-1.7
Intermittent access terminal intake (last 3 days)0.60.71.6-0.40.6-1.3
Intermittent access total infusions0.60.71.5-0.60.6-1.2
Intermittent access day 1 locomotion0.40.50.9-0.7-1.0-0.1
Intermittent access day 15 total locomotion0.10.20.4-0.20.5-0.7
Intermittent access total locomotion0.00.10.1-0.3-0.0-0.3
Intermittent access standard deviation0.10.20.3-0.5-0.4-0.6
Left kidney weight0.10.61.1-0.7-1.00.4
Right kidney weight0.52.44.8-1.6-2.20.3
Cocaine induced anxiety1.92.65.3-1.6-2.30.0
Post-drug Anxiety2.83.04.6-2.1-1.8-1.0
Baseline Anxiety0.60.71.40.31.2-0.7
Tail length0.62.44.7-2.2-0.9-1.3
Length with tail0.41.63.2-1.1-1.80.5
Length without tail1.23.87.11.1-1.82.7
Times rat made contact with spout0.30.40.6-0.40.6-0.8
Lifetime Intake0.40.50.9-0.40.6-0.9
Liver weight, left1.52.54.4-0.2-2.11.7
Liver weight, right0.40.60.91.00.21.0
Locomotor activity5.68.820.3-1.9-4.51.6
Locomotor testing distance5.29.417.5-3.3-4.2-0.2
Locomotor testing rearing6.112.221.9-3.8-4.7-0.5
Locomotion in novel chamber0.50.71.0-1.0-0.4-0.8
Locomotion in novel chamber post-restriction0.30.51.20.6-0.31.1
Fecal boli incidents, locomotor time 10.50.81.20.3-1.11.1
Change in fecal boli incidents, locomotor task0.50.50.90.90.60.5
Time >=10cm from walls, locomotor time 10.70.81.2-1.00.0-1.1
Bouts of movement, locomotor time 12.93.35.22.20.12.3
Total resting periods, locomotor time 13.43.86.12.50.72.2
Rest time, locomotor task time 11.62.03.31.80.61.6
Distance moved, locomotor task time 11.31.93.7-1.40.4-1.9
Vertical activity count, locomotor time 10.92.23.9-2.0-1.3-1.0
Time >=10cm from walls, locomotor time 20.20.30.70.30.10.8
Bouts of movement, locomotor time 22.23.55.42.3-0.12.2
Total resting periods, locomotor time 22.34.06.42.5-0.12.4
Rest time, locomotor task time 21.62.13.81.91.01.2
Distance moved, locomotor task time 22.93.45.9-2.4-0.7-2.0
Vertical activity count, locomotor time 21.42.03.8-1.9-1.3-0.7
Light reinforcement 11.12.65.1-0.81.4-2.3
Light reinforcement 22.13.27.60.92.7-1.1
Bone: marrow area0.20.40.9-0.5-1.00.2
Bone: maximum diameter0.10.30.70.3-0.30.8
Bone: maximum force0.50.81.6-0.6-1.30.7
Bone: maximum moment0.91.53.0-1.1-1.70.6
Mean time between licks in bursts0.92.23.9-2.0-0.3-1.6
Mean num. licks in bursts0.10.20.3-0.30.2-0.6
Cd content in liver1.01.12.0-0.1-1.41.1
Co content in liver3.54.16.52.60.42.4
Cu content in liver0.30.30.60.80.10.6
Fe content in liver0.91.12.0-1.20.2-1.4
K content in liver0.60.61.2-0.20.8-1.1
Mg content in liver1.41.42.8-0.90.9-1.7
Mn content in liver1.51.62.8-1.4-0.1-1.7
Na content in liver3.13.37.8-1.0-2.81.0
Rb content in liver0.50.51.10.71.1-0.2
Se content in liver4.55.38.1-2.9-2.6-1.1
Sr content in liver0.20.20.3-0.5-0.5-0.2
Zn content in liver0.80.91.4-1.2-1.0-0.4
Bone: minimum diameter0.81.42.9-1.0-1.70.5
Time in familiar zone, hab. session 10.20.20.40.60.60.2
Time in novel zone, hab. session 11.11.12.01.40.41.1
Total zone transitions, hab. session 10.60.81.7-0.6-1.30.5
Total locomotion distance, hab. session 11.11.62.5-1.5-1.6-0.1
Locomotion velocity, hab. session 12.43.45.2-2.2-2.3-0.4
Time in familiar zone, hab. session 23.03.25.12.21.51.5
Time in novel zone, hab. session 21.21.21.7-1.3-1.0-0.9
Total zone transitions, hab. session 21.72.14.3-0.6-2.11.3
Total locomotion distance, hab. session 20.81.02.1-0.8-1.40.5
Locomotion velocity, hab. session 21.31.73.6-0.9-1.90.8
Novel to familiar place preference ratio1.31.42.2-1.5-0.6-1.3
Novelty place preference1.11.11.8-1.3-0.5-1.2
Time in novel zone, NPP test0.70.71.1-1.1-0.5-0.9
Total zone transitions, NPP test1.11.62.9-1.7-1.3-0.5
Total locomotion distance, NPP test3.44.68.5-2.9-1.3-1.9
Locomotion velocity, NPP test3.14.48.2-2.9-1.2-1.9
Intraocular pressure0.40.50.9-0.9-0.1-0.8
Delta distance traveled before/after self-admin4.44.78.22.91.61.8
Delta ambulatory time before/after self-admin3.44.27.42.71.31.9
Parametrial fat weight0.92.24.2-1.50.5-2.0
Pavlov. Cond. lever latency0.50.71.11.01.0-0.0
Pavlov. Cond. magazine entry latency0.00.00.1-0.30.0-0.2
Pavlov. Cond. change in total contacts1.01.11.8-0.3-1.31.1
Pavlov. Cond. index score0.30.40.7-0.6-0.80.3
Pavlov. Cond. latency score0.40.50.8-0.7-0.90.2
Pavlov. Cond. lever contacts0.50.50.8-0.9-0.9-0.1
Pavlov. Cond. magazine entry number0.20.20.5-0.10.3-0.7
Pavlov. Cond. intertrial magazine entries1.11.32.1-1.3-1.5-0.4
Pavlov. Cond. lever-magazine prob. diff.0.30.40.7-0.4-0.80.5
Pavlov. Cond. response bias0.10.10.2-0.1-0.40.5
Pavlov. Cond. lever latency1.72.35.11.12.3-0.7
Pavlov. Cond. magazine entry latency0.91.11.7-1.2-1.3-0.3
Pavlov. Cond. change in total contacts1.11.73.2-0.2-1.81.4
Pavlov. Cond. index score1.52.04.7-1.0-2.20.7
Pavlov. Cond. latency score1.62.14.7-1.1-2.20.6
Pavlov. Cond. lever contacts1.72.34.9-1.3-2.20.5
Pavlov. Cond. magazine entry number0.50.61.10.81.00.2
Pavlov. Cond. intertrial magazine entries2.74.07.7-2.00.6-2.8
Pavlov. Cond. lever-magazine prob. diff.1.31.74.0-0.8-2.00.8
Pavlov. Cond. response bias1.82.55.3-1.3-2.30.5
Time in closed arm before self-admin1.11.42.21.50.51.4
Time in closed arm after self-admin0.00.00.00.20.00.2
Time in open arm before self-admin0.10.10.3-0.4-0.6-0.0
Time in open arm after self-admin0.10.20.2-0.5-0.4-0.2
Bone: periosteal estimation0.30.61.2-0.7-1.10.3
Bone: periosteal perimeter0.30.40.9-0.6-1.00.2
Bone: post-yield work0.40.51.30.31.1-0.4
Progressive ratio test 1 active lever presses0.81.01.71.11.30.3
Progressive ratio test 1 breakpoint1.01.21.71.31.30.4
Progressive ratio test 1 inactive lever presses0.60.91.5-0.21.0-1.2
Progressive ratio test 2 active lever presses0.40.40.90.61.0-0.1
Progressive ratio test 2 breakpoint0.20.20.50.40.7-0.1
Progressive ratio test 2 inactive lever presses0.10.20.5-0.30.4-0.7
Incentive Sensitization - Responses0.10.10.2-0.40.0-0.5
Incentive Sensitization - Breakpoint0.20.20.3-0.6-0.1-0.6
Sum of active levers in priming session hrs 5-60.50.50.90.61.0-0.3
Progressive ratio0.20.30.60.80.50.1
Food seeking constrained by brief footshock6.07.412.03.52.71.7
Seeking ratio, punishment vs. effort0.91.32.01.40.91.0
Retroperitoneal fat weight0.10.51.10.11.0-0.7
Reaction time number correct0.61.11.71.30.61.1
Reaction time mean minus median0.20.61.2-0.6-1.10.4
Reaction time mean minus median AUC0.10.20.4-0.4-0.60.3
Reaction time num false alarms0.10.20.3-0.3-0.60.4
Reaction time num false alarms AUC0.10.10.2-0.3-0.50.3
Reaction time trials correct on left0.61.11.71.30.61.1
Reaction time trials on left0.50.91.51.20.60.9
Reaction time mean0.10.20.3-0.3-0.60.4
Reaction time mean AUC0.20.30.6-0.2-0.70.6
Median of all reaction times0.00.00.10.0-0.20.3
Reaction time omissions1.01.52.6-1.20.6-1.6
Reaction time false alarm rate0.20.20.5-0.7-0.3-0.3
Reaction time premature initiation rate1.82.54.32.10.71.6
Reaction time premature initiations2.34.17.12.71.12.0
Std. dev. reaction times0.20.30.6-0.4-0.80.4
Reaction time trials completed0.50.91.51.20.60.9
Reaction time trials AUC0.40.81.41.20.60.9
Run reversals in cocaine runway, females1.71.73.4-1.20.3-1.8
Run reversals in cocaine runway, males1.01.02.00.7-0.61.4
Latency to leave start box in cocaine runway0.20.20.60.2-0.10.8
Latency to leave start box in cocaine runway, F0.60.71.60.6-0.51.3
Latency to leave start box in cocaine runway, M0.10.10.2-0.4-0.0-0.3
Std. dev. time between licks in bursts3.64.98.6-2.9-2.1-1.3
Total sessions with >9 infusions0.10.10.10.20.30.2
Short access day 1 total inactive lever presses0.40.60.8-0.8-0.9-0.4
Short access day 10 total inactive lever presses0.10.20.5-0.10.2-0.7
Short access day 1 total infusions0.30.40.60.60.80.2
Short access day 10 total infusions0.30.40.8-0.3-0.90.5
Short access total infusions0.00.00.0-0.1-0.20.2
Short access day 1 locomotion0.60.81.5-0.1-1.20.9
Short access day 10 total locomotion0.20.40.8-0.6-0.9-0.0
Short access total locomotion0.70.92.0-0.7-1.40.4
One hour access (0.3 mA shock)0.70.81.3-1.1-0.6-0.9
Compulsive drug intake1.11.42.5-1.6-1.0-0.7
One hour access (shock baseline)0.00.00.1-0.1-0.3-0.0
Social response proportion2.62.94.72.02.20.3
Social responses0.60.81.5-0.20.9-1.2
Social time1.21.62.5-1.6-1.3-0.7
Soleus weight0.82.33.71.80.31.9
Bone: stiffness0.40.61.20.4-0.61.1
Tibialis anterior weight3.913.227.52.9-2.05.2
Time to tail flick, vehicle, before self-admin0.60.61.1-0.40.6-1.1
Time to tail flick, vehicle, after self-admin2.63.45.82.41.71.4
Time to tail flick, test, before self-admin2.02.13.1-1.7-0.3-1.8
Time to tail flick, test, after self-admin2.32.44.70.22.2-1.5
Delta time to tail flick, vehicle, before/after SA1.41.42.11.51.30.6
Delta time to tail flick, test, before/after SA2.92.96.31.62.5-0.1
Tibia length3.610.017.9-4.2-3.0-1.8
Ambulatory time before self-admin0.71.02.2-0.7-1.50.6
Ambulatory time after self-admin2.83.36.41.7-0.62.5
Bone: tissue strength0.20.20.5-0.7-0.4-0.2
Total heroin consumption0.40.40.70.1-0.80.8
Bone: trabecular number1.21.93.5-1.50.1-1.9
Bone: trabecular spacing1.21.63.01.3-0.31.7
Bone: trabecular thickness0.91.11.8-1.3-0.4-1.2
Bone: trabecular tissue density0.71.11.90.5-1.01.4
Water consumed over 24 hours0.60.91.70.3-0.91.3
Number of responses in last shaping day0.30.30.60.4-0.30.8