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 1.8e-03 0.02 0 0 0.01 1.9e-03 1.1e-01 1.1e-01 3.5e-02
2 Brain gene expression Gfra2 0.06 0.05 4.0e-04 0.03 0.03 0.03 0.03 5.5e-04 4.6e-04 1.0e-03 1.5e-03
3 PL gene expression Gfra2 0.09 0.06 1.9e-08 0.07 0.07 0.07 0.07 3.9e-08 4.1e-08 3.1e-08 6.2e-08

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 density0.91.52.61.3-0.31.6
Area under the delay curve0.00.00.00.0-0.20.1
BMI with tail0.93.04.4-2.11.4-1.7
BMI without tail0.30.71.40.11.20.8
Body weight0.20.81.6-0.6-0.6-1.3
Weight adjusted by age0.60.71.2-0.4-0.8-1.1
Bone surface0.71.31.81.3-0.81.2
Bone volume0.81.31.81.3-0.81.3
Breakpoint value in progressive ratio session0.00.00.1-0.20.0-0.2
Number of licking bursts0.10.10.2-0.30.4-0.2
Context. condit. distance diff. score4.04.811.1-1.83.30.1
Locomotion velocity, session 10.10.10.20.0-0.5-0.3
Locomotion distance, session 11.62.13.41.6-1.80.6
Locomotion velocity, session 20.70.81.21.0-1.10.5
Locomotion distance, session 23.24.57.62.3-2.80.9
Locomotion velocity, session 31.92.23.0-1.71.5-1.1
Locomotion distance, session 30.60.71.5-0.81.2-0.1
Stereotopy head waving bouts, day 30.30.30.6-0.5-0.3-0.8
Stereotopy head waving duration, day 31.01.32.4-0.9-0.8-1.5
Locomotion velocity, session 74.95.413.1-1.23.61.3
Locomotion distance, session 72.73.48.0-0.62.81.4
Stereotopy head waving bouts, day 70.70.81.2-0.4-1.0-1.1
Stereotopy head waving duration, day 71.01.32.5-0.9-0.7-1.6
Locomotion velocity, session 80.60.71.4-0.81.2-0.2
Locomotion distance, session 80.30.40.70.40.40.9
Degree of sensitization distance2.02.03.00.31.71.7
Degree of sensitization stereotypy0.50.51.1-0.6-0.4-1.0
Conditioned locomotion0.30.40.8-0.50.9-0.1
Cocaine response after cond. corrected2.62.94.1-1.92.0-1.1
Cocaine response after cond. not corrected1.21.31.8-1.21.3-0.8
Cocaine response before conditioning1.92.33.41.7-1.80.9
Saline control response0.71.01.31.1-1.00.7
Bone: connectivity density1.32.14.21.50.22.1
Bone: cortical apparent density2.53.26.2-1.82.5-0.5
Bone: cortical area0.10.20.30.5-0.50.2
Bone: cortical porosity1.41.53.70.5-1.9-0.7
Bone: cortical porosity1.41.63.80.9-1.9-0.3
Bone: cortical thickness0.00.00.10.20.00.2
Bone: cortical thickness0.70.91.8-0.91.4-0.1
Bone: cortical tissue density2.63.56.6-1.92.6-0.5
Condit. Reinf. active minus inactive responses0.30.30.80.2-0.9-0.4
Condit. Reinf. active-inactive response ratio1.41.52.4-1.40.3-1.6
Condit. Reinf. active responses1.21.42.51.3-1.60.4
Condit. Reinf. inactive responses5.66.69.63.1-2.12.4
Incentive salience index mean1.01.33.10.7-1.8-0.4
Condit. Reinf. lever presses1.82.45.01.4-2.20.1
Condit. Reinf. active minus inactive responses0.20.20.40.50.00.6
Condit. Reinf. active-inactive response ratio0.40.40.4-0.70.7-0.5
Condit. Reinf. active responses0.60.81.41.0-0.21.2
Condit. Reinf. inactive responses1.92.33.61.7-0.61.9
Condit. Reinf. lever presses1.41.92.81.5-1.70.8
Condit. Reinf. lever reinforcers received0.50.61.00.9-0.31.0
Conditioned reinforcement - actives1.31.31.90.21.41.3
Conditioned reinforcement - inactives2.12.44.01.7-0.52.0
Conditioned locomotion0.40.51.00.50.41.0
Patch foraging indifference point 0 sec5.99.512.63.6-3.02.6
Patch foraging indifference point AUC1.11.31.7-1.31.1-1.0
Delay disc. indifference point, 0s delay1.41.52.01.4-1.21.1
Delay disc. indifference point, 16s delay0.10.10.30.20.20.5
Delay disc. indifference point, 2s delay0.60.71.2-0.2-1.1-0.9
Delay disc. indifference point, 24s delay0.50.40.6-0.80.7-0.5
Delay disc. indifference point, 4s delay1.01.11.7-1.20.2-1.3
Delay disc. indifference point, 8s delay0.10.10.20.3-0.20.4
Indifference point function ln k0.91.22.21.1-1.50.4
Indifference point function log k0.91.22.21.1-1.50.4
Patch foraging total patch changes 0 sec5.58.811.83.4-3.02.4
Patch foraging total patch changes 12 sec2.02.73.61.9-1.51.4
Patch foraging total patch changes 18 sec1.62.13.21.7-0.41.8
Patch foraging total patch changes 24 sec1.72.13.71.5-1.90.6
Patch foraging total patch changes 6 sec0.30.50.80.9-0.40.7
Patch foraging time to switch 0 sec0.40.51.10.70.31.0
Patch foraging water rate 0 sec0.30.41.00.1-1.0-0.5
Patch foraging water rate 12 sec0.30.50.90.1-0.9-0.8
Patch foraging water rate 18 sec2.02.74.9-1.80.2-2.2
Patch foraging water rate 24 sec0.60.91.1-1.01.0-0.8
Patch foraging water rate 6 sec1.01.42.4-0.2-1.6-1.3
Seeking ratio, delayed vs. immediate footshock1.21.41.91.3-0.61.4
Distance traveled before self-admin1.11.23.00.5-1.7-0.6
Distance traveled after self-admin1.81.92.9-1.60.5-1.7
Extensor digitorum longus weight6.224.349.7-4.8-0.6-7.0
Bone: elastic displacement1.71.92.81.7-1.21.2
Bone: elastic work3.14.05.22.3-2.31.3
Bone: endosteal estimation0.10.30.60.2-0.8-0.3
Bone: endosteal perimeter0.30.71.60.6-1.3-0.1
Epididymis fat weight0.92.24.41.40.42.1
Delta time in closed arm before/after self-admin2.12.03.21.4-0.91.8
Delta time in open arm before/after self-admin0.10.10.4-0.20.6-0.0
Diff in mean of infusions in LGA sessions1.61.83.5-1.40.2-1.9
Delay discount exponential model param0.00.10.10.30.10.3
Extinction: sum of active levers before priming0.90.91.80.70.71.3
Active lever presses in extinction session 60.30.30.7-0.30.80.4
Bone: final force0.00.10.1-0.1-0.3-0.4
Bone: final moment0.20.30.60.3-0.8-0.2
Food consumed during 24 hour testing period1.11.31.71.3-1.20.9
Glucose0.71.12.1-1.11.5-0.2
Heart weight0.30.40.60.8-0.80.3
Delay discount hyperbolic model param0.10.20.20.30.30.5
Intermittent access intake day 1-15 change1.11.12.21.10.01.5
Intermittent access intake escalation0.60.61.30.70.21.2
Intermittent access intake escalation 20.20.20.40.30.20.6
Intermitt. access day 1 inactive lever presses0.00.00.10.10.10.3
Intermitt. access day 15 inactive lever presses0.40.50.80.7-0.90.3
Intermitt. access escalation Index0.50.40.6-0.80.4-0.7
Intermittent access day 1 total infusions0.00.00.00.00.20.1
Intermittent access day 15 total infusions0.40.40.90.50.41.0
Intermittent access terminal intake (last 3 days)0.20.20.5-0.20.70.3
Intermittent access total infusions0.30.30.7-0.00.80.5
Intermittent access day 1 locomotion0.40.50.60.8-0.50.7
Intermittent access day 15 total locomotion0.60.61.30.50.51.1
Intermittent access total locomotion0.30.30.50.6-0.10.7
Intermittent access standard deviation0.90.91.61.0-0.31.3
Left kidney weight0.20.61.30.2-1.1-0.7
Right kidney weight0.92.63.41.8-1.91.0
Cocaine induced anxiety2.42.86.01.5-2.40.3
Post-drug Anxiety1.41.62.11.4-1.21.1
Baseline Anxiety0.40.40.70.10.80.7
Tail length1.23.85.72.4-1.41.9
Length with tail0.51.83.91.2-2.00.0
Length without tail1.53.46.4-1.4-1.3-2.5
Times rat made contact with spout0.20.20.40.30.50.6
Lifetime Intake0.20.20.50.10.70.5
Liver weight, left1.01.53.4-1.1-0.3-1.8
Liver weight, right0.50.81.4-0.90.2-1.2
Locomotor activity4.36.816.71.9-4.1-0.4
Locomotor testing distance5.18.515.43.0-3.91.1
Locomotor testing rearing8.312.820.73.8-4.61.8
Locomotion in novel chamber0.60.80.91.0-0.80.9
Locomotion in novel chamber post-restriction0.30.40.7-0.70.1-0.9
Fecal boli incidents, locomotor time 10.30.30.5-0.1-0.7-0.7
Change in fecal boli incidents, locomotor task0.40.40.6-0.80.6-0.6
Time >=10cm from walls, locomotor time 10.90.91.61.0-0.41.3
Bouts of movement, locomotor time 13.43.76.3-2.10.4-2.5
Total resting periods, locomotor time 14.34.77.0-2.50.9-2.6
Rest time, locomotor task time 12.42.74.4-1.90.4-2.1
Distance moved, locomotor task time 11.81.93.81.40.12.0
Vertical activity count, locomotor time 12.62.73.71.9-1.51.4
Time >=10cm from walls, locomotor time 20.10.10.3-0.3-0.2-0.6
Bouts of movement, locomotor time 23.23.44.9-2.10.9-2.2
Total resting periods, locomotor time 24.14.36.0-2.41.1-2.4
Rest time, locomotor task time 22.73.14.3-2.11.5-1.7
Distance moved, locomotor task time 23.94.56.22.5-1.42.3
Vertical activity count, locomotor time 22.73.04.02.0-2.01.1
Light reinforcement 11.42.54.90.91.42.2
Light reinforcement 22.02.76.9-0.92.60.7
Bone: marrow area0.10.30.70.3-0.8-0.2
Bone: maximum diameter0.20.30.7-0.60.0-0.8
Bone: maximum force0.20.40.90.2-0.9-0.4
Bone: maximum moment0.50.92.10.8-1.4-0.1
Mean time between licks in bursts1.82.64.02.0-0.51.9
Mean num. licks in bursts0.20.20.40.40.00.7
Cd content in liver0.10.10.30.20.30.5
Co content in liver4.24.97.0-2.61.3-2.5
Cu content in liver0.40.50.8-0.90.3-0.9
Fe content in liver1.11.42.61.2-0.01.6
K content in liver0.30.30.40.20.60.6
Mg content in liver0.50.50.90.30.81.0
Mn content in liver1.21.32.51.2-0.11.6
Na content in liver3.94.29.51.7-3.10.0
Rb content in liver0.81.02.5-0.81.60.1
Se content in liver5.26.38.22.9-2.81.8
Sr content in liver0.50.40.60.8-0.30.8
Zn content in liver1.71.94.70.9-2.2-0.5
Bone: minimum diameter0.61.12.50.9-1.6-0.1
Time in familiar zone, hab. session 10.30.20.3-0.60.6-0.3
Time in novel zone, hab. session 11.41.31.9-1.40.7-1.3
Total zone transitions, hab. session 10.50.81.80.7-1.3-0.1
Total locomotion distance, hab. session 11.31.93.11.5-1.80.6
Locomotion velocity, hab. session 13.04.26.22.3-2.51.1
Time in familiar zone, hab. session 24.34.45.9-2.41.8-2.0
Time in novel zone, hab. session 21.71.72.31.5-1.21.2
Total zone transitions, hab. session 21.62.05.10.7-2.3-0.8
Total locomotion distance, hab. session 20.91.22.70.9-1.6-0.1
Locomotion velocity, hab. session 21.31.74.20.9-2.0-0.3
Novel to familiar place preference ratio1.81.92.51.6-0.81.5
Novelty place preference1.51.52.11.4-0.81.4
Time in novel zone, NPP test0.91.01.31.1-0.71.0
Total zone transitions, NPP test1.72.43.31.7-1.81.0
Total locomotion distance, NPP test4.56.28.93.0-1.92.5
Locomotion velocity, NPP test4.26.08.52.9-1.92.4
Intraocular pressure0.40.61.00.9-0.11.0
Delta distance traveled before/after self-admin5.35.77.7-2.82.1-2.2
Delta ambulatory time before/after self-admin4.14.56.4-2.51.8-2.0
Parametrial fat weight1.53.06.31.50.62.5
Pavlov. Cond. lever latency0.60.71.2-0.91.1-0.3
Pavlov. Cond. magazine entry latency0.00.00.10.2-0.10.3
Pavlov. Cond. change in total contacts0.60.71.50.2-1.2-0.7
Pavlov. Cond. index score0.30.30.70.5-0.9-0.0
Pavlov. Cond. latency score0.30.40.90.7-0.90.1
Pavlov. Cond. lever contacts0.60.71.21.0-1.10.4
Pavlov. Cond. magazine entry number0.20.20.40.30.30.6
Pavlov. Cond. intertrial magazine entries1.31.52.31.4-1.50.7
Pavlov. Cond. lever-magazine prob. diff.0.20.30.80.4-0.9-0.2
Pavlov. Cond. response bias0.10.10.30.1-0.6-0.3
Pavlov. Cond. lever latency1.11.53.5-1.01.90.1
Pavlov. Cond. magazine entry latency1.11.31.91.2-1.40.7
Pavlov. Cond. change in total contacts0.81.12.40.1-1.5-1.0
Pavlov. Cond. index score1.31.74.11.0-2.0-0.2
Pavlov. Cond. latency score1.51.94.31.1-2.10.0
Pavlov. Cond. lever contacts1.72.45.31.3-2.3-0.0
Pavlov. Cond. magazine entry number0.60.81.1-0.91.0-0.6
Pavlov. Cond. intertrial magazine entries3.03.97.82.00.12.8
Pavlov. Cond. lever-magazine prob. diff.1.11.33.30.8-1.8-0.3
Pavlov. Cond. response bias1.82.55.61.3-2.4-0.1
Time in closed arm before self-admin1.61.83.0-1.40.7-1.7
Time in closed arm after self-admin0.30.30.5-0.5-0.2-0.7
Time in open arm before self-admin0.10.10.3-0.1-0.5-0.2
Time in open arm after self-admin0.10.10.10.3-0.10.2
Bone: periosteal estimation0.10.20.60.4-0.8-0.1
Bone: periosteal perimeter0.10.20.50.5-0.70.0
Bone: post-yield work0.30.40.9-0.41.00.1
Progressive ratio test 1 active lever presses2.22.33.3-1.61.8-1.0
Progressive ratio test 1 breakpoint2.42.54.1-1.72.0-0.8
Progressive ratio test 1 inactive lever presses0.60.71.30.50.71.2
Progressive ratio test 2 active lever presses1.61.73.9-1.12.0-0.1
Progressive ratio test 2 breakpoint0.70.82.0-0.61.40.1
Progressive ratio test 2 inactive lever presses0.20.20.40.40.10.6
Incentive Sensitization - Responses0.40.40.80.40.50.9
Incentive Sensitization - Breakpoint0.60.61.20.60.31.1
Sum of active levers in priming session hrs 5-61.21.22.3-1.11.5-0.2
Progressive ratio0.20.20.3-0.40.50.3
Food seeking constrained by brief footshock6.47.910.6-3.33.0-2.1
Seeking ratio, punishment vs. effort1.41.82.2-1.41.1-1.5
Retroperitoneal fat weight0.20.61.6-0.41.20.4
Reaction time number correct0.81.21.6-1.30.8-1.2
Reaction time mean minus median0.40.61.40.5-1.2-0.2
Reaction time mean minus median AUC0.10.20.50.2-0.7-0.2
Reaction time num false alarms0.10.10.30.3-0.5-0.1
Reaction time num false alarms AUC0.10.10.20.4-0.50.0
Reaction time trials correct on left0.81.21.6-1.30.8-1.2
Reaction time trials on left0.71.01.4-1.20.8-1.0
Reaction time mean0.20.20.60.2-0.8-0.2
Reaction time mean AUC0.30.41.00.2-1.0-0.4
Median of all reaction times0.00.10.20.1-0.4-0.1
Reaction time omissions1.21.73.11.40.11.8
Reaction time false alarm rate0.20.30.50.7-0.40.5
Reaction time premature initiation rate2.02.63.7-1.91.2-1.7
Reaction time premature initiations3.24.56.2-2.51.6-2.1
Std. dev. reaction times0.30.40.90.4-1.0-0.2
Reaction time trials completed0.71.01.4-1.20.8-1.0
Reaction time trials AUC0.71.01.4-1.20.8-1.0
Run reversals in cocaine runway, females2.42.34.61.5-0.12.1
Run reversals in cocaine runway, males1.11.02.3-0.9-0.3-1.5
Latency to leave start box in cocaine runway0.30.30.7-0.3-0.3-0.8
Latency to leave start box in cocaine runway, F0.60.71.5-0.5-0.6-1.2
Latency to leave start box in cocaine runway, M1.00.91.41.2-0.31.2
Std. dev. time between licks in bursts4.75.68.22.9-2.21.9
Total sessions with >9 infusions0.40.40.9-0.51.0-0.2
Short access day 1 total inactive lever presses0.20.20.50.30.30.7
Short access day 10 total inactive lever presses0.20.20.30.10.40.5
Short access day 1 total infusions1.51.62.6-1.31.6-0.8
Short access day 10 total infusions0.40.40.60.8-0.80.3
Short access total infusions0.10.10.10.20.40.3
Short access day 1 locomotion0.20.20.50.1-0.7-0.3
Short access day 10 total locomotion0.70.81.01.0-0.71.0
Short access total locomotion1.11.11.41.2-0.81.1
One hour access (0.3 mA shock)0.20.20.40.5-0.10.6
Compulsive drug intake0.80.81.70.8-1.30.2
One hour access (shock baseline)0.10.10.2-0.30.5-0.1
Social response proportion3.53.76.4-2.02.5-0.9
Social responses0.50.61.00.40.81.0
Social time1.21.62.31.5-1.21.1
Soleus weight0.72.03.5-1.60.4-1.9
Bone: stiffness0.30.50.9-0.8-0.1-0.9
Tibialis anterior weight3.612.225.9-3.1-1.1-5.1
Time to tail flick, vehicle, before self-admin0.50.61.00.8-0.11.0
Time to tail flick, vehicle, after self-admin2.83.04.1-2.01.3-1.8
Time to tail flick, test, before self-admin1.41.41.91.4-1.01.2
Time to tail flick, test, after self-admin1.71.73.00.21.71.5
Delta time to tail flick, vehicle, before/after SA1.61.62.2-1.51.3-0.9
Delta time to tail flick, test, before/after SA2.72.55.9-1.22.4-0.1
Tibia length4.011.416.24.0-3.32.7
Ambulatory time before self-admin0.80.81.90.5-1.4-0.4
Ambulatory time after self-admin2.22.44.3-1.70.2-2.1
Bone: tissue strength0.40.40.70.8-0.70.4
Total heroin consumption0.20.20.50.1-0.7-0.4
Bone: trabecular number1.42.24.21.6-0.22.0
Bone: trabecular spacing1.21.63.0-1.3-0.1-1.7
Bone: trabecular thickness1.11.31.91.3-0.51.4
Bone: trabecular tissue density0.50.71.3-0.6-0.7-1.2
Water consumed over 24 hours0.50.61.1-0.3-0.8-1.1
Number of responses in last shaping day0.20.20.50.5-0.70.1