Hub : Genes

Gchfr

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 Adipose gene expression Gchfr 0.17 0.08 1.0e-07 0.07 0.06 0.07 0.07 1.7e-08 1.6e-07 7.9e-08 1.5e-08
2 pVTA gene expression Gchfr 0.05 0.03 3.8e-03 0.04 0.02 0.03 0.01 3.1e-04 8.9e-03 1.1e-03 5.8e-02
3 NAcc gene expression Gchfr 0.06 0.03 2.1e-06 0.05 0.04 0.04 0.04 9.7e-08 1.4e-06 7.1e-07 3.4e-07
4 Liver gene expression Gchfr 0.34 0.11 0.0e+00 0.29 0.28 0.28 0.29 1.4e-32 4.3e-31 3.5e-31 2.3e-32

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 density0.61.11.71.1-1.31.2-0.3
Area under the delay curve1.01.12.11.0-1.5-0.01.2
BMI with tail3.110.819.84.4-3.43.21.4
BMI without tail5.215.926.65.2-4.04.60.4
Body weight3.314.627.95.3-3.63.81.7
Weight adjusted by age0.60.91.71.3-0.30.31.3
Bone surface0.71.32.21.3-1.11.5-0.4
Bone volume0.91.62.21.3-1.51.5-0.3
Breakpoint value in progressive ratio session0.20.20.4-0.6-0.2-0.0-0.6
Number of licking bursts0.40.71.8-0.9-0.60.3-1.3
Context. condit. distance diff. score2.73.25.91.9-1.62.4-1.0
Locomotion velocity, session 13.03.25.4-2.31.6-2.30.1
Locomotion distance, session 11.41.72.7-1.61.4-1.5-0.0
Locomotion velocity, session 20.30.31.20.1-1.10.00.2
Locomotion distance, session 20.50.71.4-1.20.7-0.6-0.7
Locomotion velocity, session 30.40.51.2-0.7-1.1-0.6-0.1
Locomotion distance, session 31.21.32.3-0.2-1.50.9-1.5
Stereotopy head waving bouts, day 31.61.83.01.7-1.30.61.5
Stereotopy head waving duration, day 31.41.72.41.4-1.50.31.5
Locomotion velocity, session 70.80.81.20.7-1.11.1-0.7
Locomotion distance, session 70.60.81.60.5-0.31.3-1.2
Stereotopy head waving bouts, day 70.30.30.6-0.30.2-0.80.7
Stereotopy head waving duration, day 70.40.41.1-0.00.2-0.81.1
Locomotion velocity, session 81.21.43.01.2-1.71.10.1
Locomotion distance, session 81.01.52.80.8-0.91.7-1.3
Degree of sensitization distance0.60.62.20.21.5-0.10.5
Degree of sensitization stereotypy0.20.20.4-0.20.7-0.40.3
Conditioned locomotion1.92.23.71.7-1.41.9-0.2
Cocaine response after cond. corrected1.31.52.7-1.6-0.9-0.4-1.7
Cocaine response after cond. not corrected1.41.63.4-1.8-0.5-0.7-1.5
Cocaine response before conditioning0.50.61.0-0.31.0-0.90.7
Saline control response1.52.03.92.00.10.61.9
Bone: connectivity density0.30.40.90.90.30.10.9
Bone: cortical apparent density0.30.40.7-0.50.70.0-0.8
Bone: cortical area1.01.52.51.6-1.41.00.5
Bone: cortical porosity0.91.02.1-1.4-0.6-0.7-1.0
Bone: cortical porosity0.30.40.8-0.6-0.9-0.2-0.5
Bone: cortical thickness0.50.91.61.2-1.30.60.5
Bone: cortical thickness0.80.91.7-0.5-1.30.5-1.3
Bone: cortical tissue density0.30.40.6-0.60.7-0.0-0.8
Condit. Reinf. active minus inactive responses1.31.53.60.41.9-0.61.3
Condit. Reinf. active-inactive response ratio0.60.61.21.10.30.21.1
Condit. Reinf. active responses2.22.78.0-0.02.8-1.01.3
Condit. Reinf. inactive responses1.21.54.9-0.72.2-0.80.1
Incentive salience index mean2.53.18.3-0.42.9-1.41.4
Condit. Reinf. lever presses2.43.48.9-0.73.0-1.61.3
Condit. Reinf. active minus inactive responses0.81.12.41.50.71.00.7
Condit. Reinf. active-inactive response ratio0.60.71.61.30.41.00.3
Condit. Reinf. active responses1.21.63.71.90.81.01.1
Condit. Reinf. inactive responses0.91.12.51.20.7-0.11.6
Condit. Reinf. lever presses1.52.05.11.50.9-0.12.3
Condit. Reinf. lever reinforcers received1.31.83.31.81.20.61.4
Conditioned reinforcement - actives0.20.30.4-0.60.5-0.70.3
Conditioned reinforcement - inactives0.40.61.00.1-0.81.0-0.9
Conditioned locomotion1.11.42.9-0.30.8-1.41.7
Patch foraging indifference point 0 sec2.24.112.91.80.1-0.63.6
Patch foraging indifference point AUC1.01.42.4-1.61.3-1.2-0.1
Delay disc. indifference point, 0s delay1.21.33.50.10.4-1.21.9
Delay disc. indifference point, 16s delay0.40.41.1-0.2-1.0-0.60.5
Delay disc. indifference point, 2s delay0.91.02.31.5-0.40.90.7
Delay disc. indifference point, 24s delay1.21.32.6-1.20.9-1.60.6
Delay disc. indifference point, 4s delay0.30.30.60.5-0.8-0.00.7
Delay disc. indifference point, 8s delay2.12.44.61.6-2.10.31.5
Indifference point function ln k2.54.46.72.2-2.62.4-0.6
Indifference point function log k2.54.46.72.2-2.62.4-0.6
Patch foraging total patch changes 0 sec1.93.510.91.70.0-0.53.3
Patch foraging total patch changes 12 sec1.31.63.80.21.4-0.91.9
Patch foraging total patch changes 18 sec0.50.81.4-0.51.2-0.81.0
Patch foraging total patch changes 24 sec0.61.12.91.1-0.30.01.7
Patch foraging total patch changes 6 sec0.71.13.0-0.00.9-0.81.7
Patch foraging time to switch 0 sec1.02.14.0-0.22.0-1.31.6
Patch foraging water rate 0 sec1.02.03.21.2-1.71.8-0.8
Patch foraging water rate 12 sec1.32.85.6-0.0-1.71.6-2.4
Patch foraging water rate 18 sec1.01.53.60.1-1.91.0-1.2
Patch foraging water rate 24 sec1.82.64.00.9-1.82.0-1.5
Patch foraging water rate 6 sec1.31.95.4-0.9-0.70.9-2.3
Seeking ratio, delayed vs. immediate footshock0.70.92.10.8-0.31.4-0.9
Distance traveled before self-admin0.40.50.80.6-0.90.70.4
Distance traveled after self-admin0.10.10.30.2-0.20.50.2
Extensor digitorum longus weight0.20.92.90.5-1.70.6-0.2
Bone: elastic displacement0.20.30.6-0.20.2-0.70.8
Bone: elastic work0.40.61.50.9-0.30.01.2
Bone: endosteal estimation0.51.01.50.3-1.01.2-1.2
Bone: endosteal perimeter0.10.20.50.2-0.40.7-0.5
Epididymis fat weight0.20.61.70.7-1.30.60.2
Delta time in closed arm before/after self-admin0.50.41.00.2-0.10.9-1.0
Delta time in open arm before/after self-admin2.92.85.11.4-1.72.3-1.2
Diff in mean of infusions in LGA sessions0.70.81.70.01.3-0.61.1
Delay discount exponential model param0.70.81.7-0.81.3-0.0-1.0
Extinction: sum of active levers before priming0.91.01.7-1.30.7-1.30.2
Active lever presses in extinction session 60.40.40.8-0.90.3-0.80.2
Bone: final force0.91.52.61.6-0.91.5-0.2
Bone: final moment0.91.42.31.5-1.01.5-0.2
Food consumed during 24 hour testing period0.40.61.7-0.6-0.20.4-1.3
Glucose1.82.84.21.5-2.02.1-0.8
Heart weight2.43.76.42.5-1.82.30.1
Delay discount hyperbolic model param0.80.91.6-1.01.2-0.2-1.0
Intermittent access intake day 1-15 change1.53.24.20.6-2.02.0-2.0
Intermittent access intake escalation1.53.04.50.9-2.12.0-1.7
Intermittent access intake escalation 23.33.87.4-0.4-2.21.7-2.7
Intermitt. access day 1 inactive lever presses0.20.92.31.50.10.60.8
Intermitt. access day 15 inactive lever presses0.40.92.00.8-0.71.4-0.7
Intermitt. access escalation Index0.50.71.51.20.30.40.9
Intermittent access day 1 total infusions0.40.71.2-0.30.6-1.01.1
Intermittent access day 15 total infusions0.50.71.00.8-1.01.0-0.3
Intermittent access terminal intake (last 3 days)1.11.42.40.4-1.61.3-1.2
Intermittent access total infusions0.10.10.30.2-0.50.3-0.1
Intermittent access day 1 locomotion0.70.92.80.40.0-0.71.7
Intermittent access day 15 total locomotion0.81.52.30.9-1.51.5-1.0
Intermittent access total locomotion0.10.10.30.3-0.50.10.2
Intermittent access standard deviation1.02.13.60.1-1.61.5-1.9
Left kidney weight1.67.512.73.6-2.73.00.6
Right kidney weight2.310.619.24.4-3.23.31.3
Cocaine induced anxiety0.50.71.61.10.20.21.3
Post-drug Anxiety0.91.02.31.5-0.01.20.5
Baseline Anxiety0.30.30.70.3-0.10.8-0.7
Tail length1.97.412.83.2-2.43.6-0.7
Length with tail0.93.87.22.7-1.62.30.6
Length without tail0.31.11.91.2-1.40.90.4
Times rat made contact with spout0.20.20.70.10.2-0.50.8
Lifetime Intake0.10.10.2-0.2-0.4-0.20.1
Liver weight, left2.44.08.22.9-1.52.20.8
Liver weight, right1.42.44.52.1-1.61.11.2
Locomotor activity0.40.61.1-0.80.8-1.00.1
Locomotor testing distance0.40.71.1-0.90.8-1.10.1
Locomotor testing rearing0.71.52.7-1.41.6-1.0-0.5
Locomotion in novel chamber0.10.20.20.5-0.40.20.4
Locomotion in novel chamber post-restriction1.32.13.31.7-1.51.8-0.4
Fecal boli incidents, locomotor time 10.40.61.3-1.10.0-1.0-0.3
Change in fecal boli incidents, locomotor task1.91.93.31.6-1.21.8-0.3
Time >=10cm from walls, locomotor time 10.20.20.7-0.1-0.20.4-0.8
Bouts of movement, locomotor time 13.64.08.6-2.91.6-2.2-0.4
Total resting periods, locomotor time 13.64.07.9-2.81.9-2.2-0.4
Rest time, locomotor task time 10.10.20.5-0.40.7-0.20.2
Distance moved, locomotor task time 10.10.20.3-0.00.2-0.50.6
Vertical activity count, locomotor time 10.10.20.30.5-0.40.5-0.1
Time >=10cm from walls, locomotor time 23.75.412.13.5-1.52.21.6
Bouts of movement, locomotor time 20.00.00.10.2-0.2-0.00.3
Total resting periods, locomotor time 20.00.00.10.1-0.1-0.00.3
Rest time, locomotor task time 22.43.15.9-2.41.8-1.6-0.8
Distance moved, locomotor task time 21.31.53.21.8-0.50.81.4
Vertical activity count, locomotor time 22.02.86.02.4-1.11.71.0
Light reinforcement 12.45.813.81.52.3-1.43.7
Light reinforcement 21.21.93.6-1.31.9-1.50.5
Bone: marrow area0.40.91.50.4-1.01.2-1.1
Bone: maximum diameter0.61.12.01.4-1.01.10.3
Bone: maximum force1.22.14.52.1-1.11.60.6
Bone: maximum moment1.01.83.71.9-1.11.50.5
Mean time between licks in bursts0.40.92.1-1.5-0.0-0.6-1.0
Mean num. licks in bursts0.61.02.51.00.6-0.21.6
Cd content in liver0.30.30.50.7-0.70.50.2
Co content in liver0.40.51.5-0.5-1.2-0.4-0.2
Cu content in liver0.60.72.2-0.5-0.40.6-1.5
Fe content in liver1.01.24.1-0.62.0-0.4-0.2
K content in liver0.60.60.90.4-0.80.9-0.7
Mg content in liver2.62.64.50.8-2.11.8-1.4
Mn content in liver1.21.42.91.7-1.01.00.7
Na content in liver0.50.51.1-0.70.70.1-1.1
Rb content in liver3.23.77.32.0-2.71.9-0.0
Se content in liver0.20.30.50.6-0.50.7-0.2
Sr content in liver0.20.20.4-0.60.2-0.60.0
Zn content in liver0.70.82.5-0.40.20.8-1.6
Bone: minimum diameter0.61.22.41.2-1.60.40.8
Time in familiar zone, hab. session 11.31.22.9-1.70.6-1.0-0.9
Time in novel zone, hab. session 12.02.04.62.1-0.91.31.0
Total zone transitions, hab. session 10.81.11.6-1.21.2-1.30.1
Total locomotion distance, hab. session 10.71.01.4-1.01.2-1.20.3
Locomotion velocity, hab. session 11.31.82.6-1.31.6-1.60.5
Time in familiar zone, hab. session 20.00.00.1-0.0-0.3-0.00.0
Time in novel zone, hab. session 20.30.30.60.8-0.40.40.4
Total zone transitions, hab. session 20.30.40.8-0.90.4-0.5-0.5
Total locomotion distance, hab. session 20.10.20.5-0.10.7-0.30.2
Locomotion velocity, hab. session 20.30.41.0-0.31.0-0.50.4
Novel to familiar place preference ratio1.11.22.61.6-0.20.61.3
Novelty place preference1.01.12.31.5-0.20.61.3
Time in novel zone, NPP test1.01.12.41.5-0.30.71.2
Total zone transitions, NPP test1.11.63.4-1.80.2-0.6-1.6
Total locomotion distance, NPP test0.40.51.0-1.0-0.0-0.3-0.9
Locomotion velocity, NPP test0.40.61.3-1.10.0-0.4-0.9
Intraocular pressure1.42.04.3-1.60.8-2.10.7
Delta distance traveled before/after self-admin0.20.20.5-0.30.7-0.50.2
Delta ambulatory time before/after self-admin0.70.82.1-0.41.5-0.90.6
Parametrial fat weight0.41.02.00.31.3-0.61.4
Pavlov. Cond. lever latency0.81.02.20.6-1.51.0-0.6
Pavlov. Cond. magazine entry latency1.82.34.01.02.0-0.52.0
Pavlov. Cond. change in total contacts0.30.30.70.40.80.5-0.3
Pavlov. Cond. index score1.41.74.0-0.22.0-1.11.3
Pavlov. Cond. latency score1.62.04.1-0.12.0-1.31.5
Pavlov. Cond. lever contacts1.11.33.3-0.61.8-1.10.7
Pavlov. Cond. magazine entry number1.11.42.5-1.0-1.40.2-1.6
Pavlov. Cond. intertrial magazine entries0.80.92.2-0.5-1.00.6-1.5
Pavlov. Cond. lever-magazine prob. diff.1.11.43.4-0.41.9-1.00.9
Pavlov. Cond. response bias0.70.93.20.01.8-0.40.6
Pavlov. Cond. lever latency2.02.75.5-2.3-0.0-0.9-2.2
Pavlov. Cond. magazine entry latency1.31.52.61.50.90.51.6
Pavlov. Cond. change in total contacts0.91.53.01.70.90.91.1
Pavlov. Cond. index score1.52.14.32.10.61.01.6
Pavlov. Cond. latency score1.21.63.41.90.51.11.3
Pavlov. Cond. lever contacts2.33.16.12.50.20.82.4
Pavlov. Cond. magazine entry number1.11.32.8-1.7-0.7-0.9-1.1
Pavlov. Cond. intertrial magazine entries0.30.41.2-0.5-1.1-0.3-0.3
Pavlov. Cond. lever-magazine prob. diff.1.41.93.92.00.61.01.6
Pavlov. Cond. response bias2.63.57.42.70.41.02.4
Time in closed arm before self-admin1.72.23.5-1.61.7-1.90.0
Time in closed arm after self-admin1.01.02.6-0.91.6-0.9-0.2
Time in open arm before self-admin0.30.30.60.3-0.6-0.10.8
Time in open arm after self-admin3.63.96.81.5-2.62.4-1.0
Bone: periosteal estimation0.51.11.81.1-1.31.2-0.2
Bone: periosteal perimeter0.50.81.41.1-1.20.70.5
Bone: post-yield work0.40.61.5-0.3-0.30.8-1.2
Progressive ratio test 1 active lever presses0.10.20.2-0.20.4-0.50.5
Progressive ratio test 1 breakpoint0.10.20.2-0.20.5-0.50.5
Progressive ratio test 1 inactive lever presses0.10.10.30.10.6-0.0-0.0
Progressive ratio test 2 active lever presses0.00.00.10.30.10.10.3
Progressive ratio test 2 breakpoint0.10.10.20.5-0.00.30.3
Progressive ratio test 2 inactive lever presses0.10.20.40.5-0.30.6-0.1
Incentive Sensitization - Responses0.00.10.20.1-0.50.20.0
Incentive Sensitization - Breakpoint0.00.10.10.2-0.40.20.1
Sum of active levers in priming session hrs 5-60.70.72.1-0.6-0.30.5-1.4
Progressive ratio0.00.10.2-0.20.5-0.00.2
Food seeking constrained by brief footshock0.00.00.00.10.10.10.1
Seeking ratio, punishment vs. effort0.00.00.00.1-0.1-0.20.1
Retroperitoneal fat weight2.08.519.34.4-0.81.83.3
Reaction time number correct2.75.28.51.8-2.62.9-1.5
Reaction time mean minus median0.20.41.11.1-0.30.40.5
Reaction time mean minus median AUC0.71.84.12.0-1.01.20.7
Reaction time num false alarms0.00.00.10.30.10.20.1
Reaction time num false alarms AUC0.00.00.20.10.40.2-0.0
Reaction time trials correct on left2.75.28.51.8-2.62.9-1.5
Reaction time trials on left2.75.18.41.9-2.62.9-1.4
Reaction time mean0.20.41.0-0.51.0-0.5-0.1
Reaction time mean AUC0.10.10.4-0.20.6-0.3-0.1
Median of all reaction times0.81.22.4-1.21.5-0.9-0.3
Reaction time omissions0.60.92.21.20.30.21.5
Reaction time false alarm rate0.91.22.2-0.71.5-1.30.8
Reaction time premature initiation rate2.33.28.0-0.62.8-1.61.4
Reaction time premature initiations0.30.51.60.51.20.10.5
Std. dev. reaction times0.30.61.31.2-0.20.20.9
Reaction time trials completed2.75.18.41.9-2.62.9-1.4
Reaction time trials AUC2.75.28.91.9-2.43.0-1.5
Run reversals in cocaine runway, females1.41.43.0-0.2-1.01.3-1.7
Run reversals in cocaine runway, males0.10.10.3-0.50.2-0.2-0.5
Latency to leave start box in cocaine runway0.10.10.20.30.40.10.1
Latency to leave start box in cocaine runway, F0.20.20.4-0.60.3-0.6-0.1
Latency to leave start box in cocaine runway, M1.31.22.81.70.41.30.3
Std. dev. time between licks in bursts0.50.61.10.9-1.00.20.8
Total sessions with >9 infusions1.31.63.3-0.90.6-1.81.4
Short access day 1 total inactive lever presses0.40.51.50.6-1.20.5-0.0
Short access day 10 total inactive lever presses0.92.15.01.4-0.52.2-1.2
Short access day 1 total infusions0.50.71.5-1.10.1-1.20.4
Short access day 10 total infusions0.70.91.4-0.50.9-1.21.2
Short access total infusions0.50.71.5-0.90.2-1.20.7
Short access day 1 locomotion1.41.73.3-1.21.1-1.80.9
Short access day 10 total locomotion0.40.72.60.1-1.6-0.00.2
Short access total locomotion1.01.23.0-0.00.1-1.31.7
One hour access (0.3 mA shock)2.32.64.80.1-1.51.9-2.2
Compulsive drug intake1.51.83.4-0.2-1.31.4-1.8
One hour access (shock baseline)0.10.20.50.40.5-0.10.7
Social response proportion1.31.53.01.31.70.80.7
Social responses1.31.75.60.02.4-0.40.9
Social time0.10.10.20.50.10.50.1
Soleus weight0.00.00.1-0.20.30.1-0.2
Bone: stiffness0.81.32.91.7-0.61.30.3
Tibialis anterior weight0.10.40.80.9-0.00.9-0.2
Time to tail flick, vehicle, before self-admin0.20.20.4-0.0-0.4-0.60.5
Time to tail flick, vehicle, after self-admin0.50.72.10.2-1.50.4-0.6
Time to tail flick, test, before self-admin0.30.30.5-0.10.5-0.70.7
Time to tail flick, test, after self-admin0.40.40.80.8-0.50.30.9
Delta time to tail flick, vehicle, before/after SA2.52.44.11.3-1.72.0-1.0
Delta time to tail flick, test, before/after SA0.10.10.40.3-0.30.10.6
Tibia length0.61.75.01.30.4-0.32.2
Ambulatory time before self-admin0.40.60.90.6-0.90.40.9
Ambulatory time after self-admin0.00.00.1-0.10.30.10.1
Bone: tissue strength0.10.10.20.4-0.30.3-0.0
Total heroin consumption0.50.61.3-1.2-0.0-0.8-0.6
Bone: trabecular number1.83.05.21.7-1.82.3-1.0
Bone: trabecular spacing2.43.25.1-0.81.6-2.32.1
Bone: trabecular thickness0.50.61.7-0.5-0.30.6-1.3
Bone: trabecular tissue density2.43.610.0-2.00.10.3-3.2
Water consumed over 24 hours0.20.30.6-0.60.8-0.5-0.1
Number of responses in last shaping day1.21.31.9-0.81.2-1.41.1