Lgi1

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 Lgi1 0.04 0.03 2.1e-03 0.01 0.01 0.01 0.02 1.0e-02 2.0e-02 1.1e-02 3.8e-03
2 Brain gene expression Lgi1 0.04 0.02 1.2e-04 0.03 0.03 0.02 0.03 2.2e-03 3.4e-04 4.3e-03 1.6e-03
3 Adipose gene expression Lgi1 0.03 0.02 3.6e-04 0.02 0.02 0.02 0.02 5.6e-03 1.8e-03 1.8e-03 4.1e-03
4 Brain mRNA stability Lgi1 0.03 0.02 5.8e-03 0.01 0.02 0.02 0.01 1.7e-02 7.4e-03 3.4e-03 1.5e-02

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 density2.75.06.6-2.52.62.11.7
Area under the delay curve0.50.71.40.8-0.3-0.9-1.2
BMI with tail0.31.03.0-1.70.70.70.4
BMI without tail0.00.10.3-0.6-0.2-0.2-0.1
Body weight0.20.81.1-1.00.60.81.1
Weight adjusted by age0.00.00.1-0.00.0-0.1-0.2
Bone surface2.85.67.6-2.82.52.31.9
Bone volume2.85.65.9-2.42.42.42.2
Breakpoint value in progressive ratio session0.20.41.00.30.2-0.7-1.0
Number of licking bursts0.72.23.11.6-1.0-1.4-1.8
Context. condit. distance diff. score1.72.02.4-1.21.61.41.5
Locomotion velocity, session 12.62.93.91.8-1.2-1.7-2.0
Locomotion distance, session 11.21.62.21.4-0.8-1.3-1.5
Locomotion velocity, session 20.60.81.6-1.01.30.2-0.7
Locomotion distance, session 20.20.31.0-0.30.3-0.4-1.0
Locomotion velocity, session 30.30.30.4-0.50.60.50.5
Locomotion distance, session 30.50.61.2-0.30.50.91.1
Stereotopy head waving bouts, day 30.00.00.10.00.30.20.2
Stereotopy head waving duration, day 30.10.10.2-0.10.40.20.1
Locomotion velocity, session 73.43.75.3-1.51.92.32.0
Locomotion distance, session 72.63.34.2-1.61.72.11.8
Stereotopy head waving bouts, day 70.40.40.60.7-0.1-0.7-0.8
Stereotopy head waving duration, day 70.10.10.40.6-0.1-0.2-0.1
Locomotion velocity, session 80.20.30.6-0.60.80.30.3
Locomotion distance, session 80.81.22.5-1.41.60.70.1
Degree of sensitization distance0.30.30.7-0.70.90.30.0
Degree of sensitization stereotypy0.91.01.31.0-0.5-1.1-1.1
Conditioned locomotion0.50.61.4-0.4-0.30.91.2
Cocaine response after cond. corrected0.00.00.1-0.0-0.2-0.2-0.3
Cocaine response after cond. not corrected0.00.00.1-0.00.0-0.3-0.2
Cocaine response before conditioning0.10.20.30.50.2-0.5-0.2
Saline control response2.33.24.51.9-1.2-2.1-1.8
Bone: connectivity density4.26.79.3-3.02.82.51.9
Bone: cortical apparent density0.81.31.91.2-0.7-1.3-1.4
Bone: cortical area0.91.53.1-0.80.91.21.8
Bone: cortical porosity1.31.42.7-1.31.60.90.3
Bone: cortical porosity1.41.62.7-1.41.71.10.7
Bone: cortical thickness1.11.83.21.8-1.3-1.3-0.6
Bone: cortical thickness2.63.24.02.0-1.4-2.0-1.7
Bone: cortical tissue density0.81.32.01.1-0.6-1.3-1.4
Condit. Reinf. active minus inactive responses0.00.10.20.4-0.1-0.1-0.2
Condit. Reinf. active-inactive response ratio0.10.10.20.4-0.4-0.1-0.2
Condit. Reinf. active responses0.00.00.20.4-0.10.00.1
Condit. Reinf. inactive responses0.00.00.00.20.0-0.10.1
Incentive salience index mean0.40.60.80.9-0.8-0.7-0.6
Condit. Reinf. lever presses1.52.32.71.6-1.6-1.6-1.2
Condit. Reinf. active minus inactive responses2.23.43.9-1.91.62.01.9
Condit. Reinf. active-inactive response ratio1.11.72.2-1.51.11.51.0
Condit. Reinf. active responses0.71.02.2-0.60.41.01.5
Condit. Reinf. inactive responses0.71.01.71.3-1.2-0.90.1
Condit. Reinf. lever presses0.30.40.60.6-0.6-0.7-0.5
Condit. Reinf. lever reinforcers received0.30.41.0-0.40.20.61.0
Conditioned reinforcement - actives0.00.20.7-0.20.8-0.1-0.1
Conditioned reinforcement - inactives0.41.03.1-0.61.80.60.6
Conditioned locomotion0.10.10.30.50.2-0.40.1
Patch foraging indifference point 0 sec0.41.11.61.1-1.3-1.0-0.8
Patch foraging indifference point AUC2.45.77.92.5-1.8-2.8-2.3
Delay disc. indifference point, 0s delay1.01.12.1-1.31.40.80.3
Delay disc. indifference point, 16s delay0.40.61.10.5-0.3-1.0-1.0
Delay disc. indifference point, 2s delay0.20.20.6-0.00.1-0.3-0.8
Delay disc. indifference point, 24s delay0.91.42.01.4-0.7-1.2-1.2
Delay disc. indifference point, 4s delay0.80.92.20.4-0.1-1.1-1.5
Delay disc. indifference point, 8s delay1.52.53.61.9-1.4-1.4-1.6
Indifference point function ln k2.16.48.0-2.62.12.82.6
Indifference point function log k2.16.48.0-2.62.12.82.6
Patch foraging total patch changes 0 sec0.41.11.71.1-1.3-1.0-0.7
Patch foraging total patch changes 12 sec5.87.89.03.0-2.5-2.9-2.7
Patch foraging total patch changes 18 sec1.02.33.21.3-1.2-1.8-1.7
Patch foraging total patch changes 24 sec0.31.01.41.2-0.9-1.0-0.8
Patch foraging total patch changes 6 sec4.47.58.62.9-2.5-2.8-2.6
Patch foraging time to switch 0 sec0.41.52.61.1-1.1-1.1-1.6
Patch foraging water rate 0 sec0.62.22.9-1.31.41.51.7
Patch foraging water rate 12 sec0.20.81.6-0.50.81.01.3
Patch foraging water rate 18 sec1.02.22.5-1.41.61.61.4
Patch foraging water rate 24 sec0.91.21.4-1.11.11.11.2
Patch foraging water rate 6 sec0.10.20.3-0.50.40.20.5
Seeking ratio, delayed vs. immediate footshock0.10.10.20.1-0.4-0.4-0.2
Distance traveled before self-admin0.40.91.6-1.31.20.70.1
Distance traveled after self-admin1.11.93.6-1.71.91.10.3
Extensor digitorum longus weight0.41.51.6-1.11.21.31.2
Bone: elastic displacement0.10.10.30.5-0.30.1-0.3
Bone: elastic work0.20.20.5-0.40.70.50.1
Bone: endosteal estimation5.513.314.8-3.93.73.63.4
Bone: endosteal perimeter4.611.313.7-3.73.43.33.0
Epididymis fat weight0.62.94.1-1.61.11.92.0
Delta time in closed arm before/after self-admin0.40.40.91.0-0.7-0.30.2
Delta time in open arm before/after self-admin1.31.53.4-1.81.50.3-0.5
Diff in mean of infusions in LGA sessions0.91.62.3-1.21.51.31.0
Delay discount exponential model param0.60.81.6-0.80.30.91.3
Extinction: sum of active levers before priming0.10.10.3-0.20.20.20.5
Active lever presses in extinction session 63.73.77.1-2.32.71.50.5
Bone: final force0.20.30.3-0.60.50.30.6
Bone: final moment0.20.30.6-0.50.40.50.8
Food consumed during 24 hour testing period0.10.20.50.7-0.4-0.30.2
Glucose0.20.30.8-0.20.20.50.9
Heart weight0.40.61.10.8-1.10.20.8
Delay discount hyperbolic model param0.50.71.4-0.70.30.81.2
Intermittent access intake day 1-15 change0.52.84.7-2.21.61.41.4
Intermittent access intake escalation0.73.85.8-2.41.91.71.6
Intermittent access intake escalation 22.74.66.3-2.52.42.01.5
Intermitt. access day 1 inactive lever presses0.00.10.2-0.40.50.2-0.1
Intermitt. access day 15 inactive lever presses0.20.81.2-0.20.91.11.1
Intermitt. access escalation Index0.10.40.80.1-0.10.80.9
Intermittent access day 1 total infusions0.10.31.2-0.21.10.10.3
Intermittent access day 15 total infusions1.12.73.1-1.61.81.41.8
Intermittent access terminal intake (last 3 days)1.32.23.3-1.31.81.31.5
Intermittent access total infusions0.80.91.5-0.61.20.81.1
Intermittent access day 1 locomotion0.20.40.6-0.60.80.30.6
Intermittent access day 15 total locomotion0.00.20.30.10.4-0.5-0.4
Intermittent access total locomotion0.40.51.4-0.61.20.10.1
Intermittent access standard deviation0.63.24.3-2.02.11.61.5
Left kidney weight0.00.30.90.9-0.6-0.30.0
Right kidney weight0.31.93.51.9-1.6-1.1-0.6
Cocaine induced anxiety0.61.82.4-1.61.21.31.2
Post-drug Anxiety0.30.40.8-0.3-0.40.60.9
Baseline Anxiety0.71.12.51.3-1.6-0.5-0.1
Tail length0.00.20.70.30.10.20.9
Length with tail0.00.20.40.60.10.00.7
Length without tail0.21.11.6-0.61.31.01.1
Times rat made contact with spout0.20.20.6-0.40.80.30.2
Lifetime Intake0.40.51.2-0.51.10.50.7
Liver weight, left0.10.10.20.3-0.4-0.20.2
Liver weight, right0.51.01.2-1.10.90.81.1
Locomotor activity0.00.10.1-0.20.40.3-0.1
Locomotor testing distance0.00.10.30.20.2-0.1-0.6
Locomotor testing rearing0.30.91.9-1.01.40.90.3
Locomotion in novel chamber3.34.45.8-2.42.32.11.4
Locomotion in novel chamber post-restriction0.10.30.7-0.20.1-0.8-0.7
Fecal boli incidents, locomotor time 10.41.12.0-1.01.40.80.8
Change in fecal boli incidents, locomotor task1.21.31.60.9-1.2-1.3-1.1
Time >=10cm from walls, locomotor time 10.30.41.3-0.00.40.41.1
Bouts of movement, locomotor time 10.20.30.60.8-0.3-0.4-0.5
Total resting periods, locomotor time 10.40.50.90.9-0.2-0.6-0.7
Rest time, locomotor task time 10.00.10.20.20.4-0.1-0.4
Distance moved, locomotor task time 10.10.20.50.4-0.7-0.30.1
Vertical activity count, locomotor time 10.00.20.7-0.1-0.8-0.20.3
Time >=10cm from walls, locomotor time 20.10.20.40.00.40.40.6
Bouts of movement, locomotor time 21.03.35.01.9-0.9-2.0-2.2
Total resting periods, locomotor time 20.83.35.01.8-0.8-2.0-2.2
Rest time, locomotor task time 20.40.71.60.6-0.2-0.8-1.3
Distance moved, locomotor task time 20.71.02.3-0.50.41.11.5
Vertical activity count, locomotor time 20.20.51.0-0.70.20.71.0
Light reinforcement 10.20.81.10.9-0.6-0.8-1.1
Light reinforcement 20.92.13.41.5-1.1-1.2-1.8
Bone: marrow area5.613.615.2-3.93.73.73.5
Bone: maximum diameter5.611.312.1-3.53.43.33.3
Bone: maximum force0.81.62.2-1.41.51.01.1
Bone: maximum moment0.91.71.8-1.31.41.21.3
Mean time between licks in bursts0.10.51.30.6-1.1-0.30.3
Mean num. licks in bursts1.43.74.4-2.11.71.82.1
Cd content in liver1.41.52.41.5-1.4-0.9-1.0
Co content in liver2.22.64.72.1-2.2-1.0-0.3
Cu content in liver5.86.99.72.4-2.0-2.8-3.1
Fe content in liver2.53.03.91.5-1.7-1.7-2.0
K content in liver0.70.71.8-0.30.4-0.9-1.4
Mg content in liver0.50.61.90.0-0.0-0.7-1.4
Mn content in liver2.62.96.01.0-0.7-2.0-2.4
Na content in liver1.21.32.80.5-0.6-1.4-1.7
Rb content in liver0.10.20.4-0.00.30.60.4
Se content in liver20.924.731.84.5-4.5-5.2-5.6
Sr content in liver0.50.40.70.5-0.4-0.8-0.7
Zn content in liver2.52.95.11.4-1.3-1.7-2.3
Bone: minimum diameter7.614.518.8-3.53.43.94.3
Time in familiar zone, hab. session 10.10.10.2-0.40.20.30.0
Time in novel zone, hab. session 10.30.30.50.4-0.3-0.7-0.7
Total zone transitions, hab. session 10.10.20.6-0.00.3-0.3-0.8
Total locomotion distance, hab. session 11.31.93.31.1-0.9-1.5-1.8
Locomotion velocity, hab. session 12.43.44.61.7-1.4-2.0-2.2
Time in familiar zone, hab. session 20.40.50.91.0-0.9-0.30.1
Time in novel zone, hab. session 20.00.00.1-0.10.3-0.1-0.3
Total zone transitions, hab. session 20.70.91.11.0-0.9-1.0-0.9
Total locomotion distance, hab. session 21.11.52.01.4-1.3-1.2-1.0
Locomotion velocity, hab. session 21.31.71.91.3-1.2-1.4-1.3
Novel to familiar place preference ratio2.93.87.0-2.22.61.60.9
Novelty place preference3.14.07.3-2.32.71.60.9
Time in novel zone, NPP test3.34.07.2-2.22.71.61.0
Total zone transitions, NPP test0.71.01.21.1-1.0-1.0-0.9
Total locomotion distance, NPP test2.23.13.51.9-1.6-1.9-1.7
Locomotion velocity, NPP test2.02.83.41.7-1.5-1.8-1.6
Intraocular pressure0.40.61.11.0-0.7-0.8-0.6
Delta distance traveled before/after self-admin1.21.31.6-1.11.31.11.1
Delta ambulatory time before/after self-admin1.32.22.5-1.31.51.61.6
Parametrial fat weight0.41.01.71.3-1.2-1.0-0.3
Pavlov. Cond. lever latency0.00.00.10.1-0.4-0.10.1
Pavlov. Cond. magazine entry latency0.50.61.11.0-0.9-0.7-0.4
Pavlov. Cond. change in total contacts0.00.00.10.2-0.20.20.2
Pavlov. Cond. index score0.20.30.50.7-0.4-0.6-0.6
Pavlov. Cond. latency score0.20.20.40.6-0.3-0.4-0.5
Pavlov. Cond. lever contacts0.20.20.20.5-0.3-0.4-0.5
Pavlov. Cond. magazine entry number0.10.10.2-0.40.4-0.0-0.1
Pavlov. Cond. intertrial magazine entries0.10.10.10.3-0.10.10.4
Pavlov. Cond. lever-magazine prob. diff.0.20.30.40.7-0.4-0.5-0.5
Pavlov. Cond. response bias0.10.10.20.4-0.4-0.1-0.1
Pavlov. Cond. lever latency0.91.31.7-1.21.31.20.7
Pavlov. Cond. magazine entry latency0.10.20.40.6-0.50.10.4
Pavlov. Cond. change in total contacts0.20.40.60.7-0.8-0.7-0.2
Pavlov. Cond. index score0.40.61.11.0-0.9-0.7-0.1
Pavlov. Cond. latency score0.30.40.80.9-0.7-0.50.1
Pavlov. Cond. lever contacts1.11.62.11.4-1.5-1.3-0.7
Pavlov. Cond. magazine entry number1.11.52.7-1.71.41.00.5
Pavlov. Cond. intertrial magazine entries0.61.42.3-1.51.31.00.7
Pavlov. Cond. lever-magazine prob. diff.0.30.50.80.9-0.8-0.7-0.1
Pavlov. Cond. response bias1.01.41.91.4-1.4-1.1-0.6
Time in closed arm before self-admin0.40.61.1-0.41.01.00.4
Time in closed arm after self-admin0.20.20.60.8-0.3-0.1-0.1
Time in open arm before self-admin0.10.20.50.4-0.70.00.2
Time in open arm after self-admin0.40.40.8-0.80.4-0.4-0.9
Bone: periosteal estimation3.68.58.8-3.02.92.82.9
Bone: periosteal perimeter3.26.46.7-2.62.42.52.6
Bone: post-yield work1.22.12.6-1.61.51.31.4
Progressive ratio test 1 active lever presses0.10.20.5-0.40.7-0.3-0.3
Progressive ratio test 1 breakpoint0.10.20.3-0.20.6-0.5-0.4
Progressive ratio test 1 inactive lever presses0.30.72.0-0.51.40.70.5
Progressive ratio test 2 active lever presses1.11.64.0-0.82.00.81.0
Progressive ratio test 2 breakpoint1.21.64.0-0.72.00.91.0
Progressive ratio test 2 inactive lever presses0.20.72.4-0.41.60.40.3
Incentive Sensitization - Responses0.92.45.1-0.92.31.31.4
Incentive Sensitization - Breakpoint1.02.24.6-0.82.11.31.4
Sum of active levers in priming session hrs 5-60.20.20.30.4-0.6-0.2-0.5
Progressive ratio0.10.30.70.6-0.90.20.3
Food seeking constrained by brief footshock0.10.10.40.60.2-0.3-0.2
Seeking ratio, punishment vs. effort0.20.30.60.30.4-0.7-0.8
Retroperitoneal fat weight0.10.40.70.8-0.60.20.7
Reaction time number correct1.14.06.3-2.51.91.91.4
Reaction time mean minus median0.10.82.10.1-0.11.01.4
Reaction time mean minus median AUC0.10.71.60.1-0.40.91.3
Reaction time num false alarms0.00.10.10.3-0.2-0.20.2
Reaction time num false alarms AUC0.00.10.10.3-0.2-0.20.3
Reaction time trials correct on left1.14.06.3-2.51.91.91.4
Reaction time trials on left1.13.96.0-2.51.91.91.5
Reaction time mean0.51.12.41.6-1.3-0.40.2
Reaction time mean AUC0.51.32.51.6-1.5-0.7-0.1
Median of all reaction times0.71.12.51.6-1.3-0.6-0.1
Reaction time omissions0.81.43.2-0.10.01.51.8
Reaction time false alarm rate0.91.22.21.5-1.1-1.1-0.4
Reaction time premature initiation rate0.40.71.51.2-0.9-0.60.0
Reaction time premature initiations0.10.30.9-0.00.10.50.9
Std. dev. reaction times0.30.91.80.9-0.90.61.3
Reaction time trials completed1.13.96.0-2.51.91.91.5
Reaction time trials AUC1.03.55.4-2.31.81.91.4
Run reversals in cocaine runway, females0.40.51.20.5-0.2-0.7-1.1
Run reversals in cocaine runway, males3.13.54.61.9-1.8-2.1-1.5
Latency to leave start box in cocaine runway1.92.64.3-1.21.11.92.1
Latency to leave start box in cocaine runway, F2.83.54.0-1.91.72.01.9
Latency to leave start box in cocaine runway, M0.30.30.90.1-0.10.60.9
Std. dev. time between licks in bursts1.32.44.31.5-2.1-1.4-1.0
Total sessions with >9 infusions0.30.30.70.3-0.2-0.8-0.7
Short access day 1 total inactive lever presses0.81.52.8-1.51.71.00.2
Short access day 10 total inactive lever presses0.00.10.20.20.10.40.3
Short access day 1 total infusions0.30.61.20.6-0.3-1.1-0.9
Short access day 10 total infusions0.81.31.91.4-0.8-1.2-1.0
Short access total infusions0.10.10.30.00.5-0.3-0.3
Short access day 1 locomotion0.10.20.2-0.40.5-0.1-0.5
Short access day 10 total locomotion0.00.20.40.1-0.1-0.5-0.6
Short access total locomotion0.10.20.60.20.1-0.4-0.8
One hour access (0.3 mA shock)3.54.16.9-1.62.61.81.9
Compulsive drug intake1.32.03.4-0.70.91.81.8
One hour access (shock baseline)0.10.30.8-0.50.90.00.3
Social response proportion2.43.04.8-2.21.91.61.0
Social responses0.50.71.1-1.01.00.60.5
Social time0.20.40.70.0-0.4-0.8-0.8
Soleus weight1.64.85.5-2.12.02.32.3
Bone: stiffness1.12.02.7-1.51.61.11.4
Tibialis anterior weight0.82.93.9-1.82.01.61.4
Time to tail flick, vehicle, before self-admin0.60.81.90.4-0.2-0.9-1.4
Time to tail flick, vehicle, after self-admin0.20.41.0-0.71.00.40.2
Time to tail flick, test, before self-admin0.80.91.8-0.81.30.80.9
Time to tail flick, test, after self-admin0.00.00.1-0.10.30.3-0.2
Delta time to tail flick, vehicle, before/after SA1.31.41.9-1.21.41.11.1
Delta time to tail flick, test, before/after SA0.20.20.30.5-0.5-0.3-0.6
Tibia length0.10.20.50.7-0.6-0.20.0
Ambulatory time before self-admin0.20.71.4-1.21.00.5-0.2
Ambulatory time after self-admin2.64.17.0-2.42.61.80.8
Bone: tissue strength0.40.40.9-0.20.20.71.0
Total heroin consumption0.10.10.10.20.3-0.3-0.3
Bone: trabecular number1.83.44.2-2.02.11.81.5
Bone: trabecular spacing1.21.73.11.8-1.6-1.0-0.4
Bone: trabecular thickness2.02.73.0-1.61.71.71.6
Bone: trabecular tissue density0.50.91.4-1.21.00.80.8
Water consumed over 24 hours0.40.72.0-0.61.40.50.3
Number of responses in last shaping day0.20.20.50.6-0.7-0.2-0.2