Limd2

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 Eye isoform ratio XM_006247622.5 0.28 0.14 4.3e-03 0.18 0.15 0.06 0.12 1.1e-03 2.5e-03 4.0e-02 7.1e-03
2 NAcc gene expression Limd2 0.02 0.01 9.2e-05 0.02 0.03 0.01 0.02 9.6e-04 5.3e-05 8.4e-03 2.9e-04
3 Eye alternative TSS XM_006247622.5 0.22 0.12 8.1e-03 0.06 0.08 0 0.03 5.0e-02 2.1e-02 2.7e-01 1.1e-01

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 density0.10.20.4-0.4-0.6-0.0
Area under the delay curve0.10.10.10.3-0.3-0.2
BMI with tail1.96.810.5-1.7-3.22.6
BMI without tail2.111.117.6-2.3-4.23.2
Body weight4.218.526.2-3.3-5.14.3
Weight adjusted by age0.20.60.91.00.7-0.7
Bone surface2.34.65.1-2.3-2.31.9
Bone volume1.63.34.3-1.8-2.11.5
Breakpoint value in progressive ratio session0.20.40.8-0.90.00.6
Number of licking bursts0.00.10.2-0.40.2-0.0
Context. condit. distance diff. score0.00.00.1-0.20.30.1
Locomotion velocity, session 10.30.30.6-0.2-0.80.5
Locomotion distance, session 10.10.20.40.6-0.1-0.4
Locomotion velocity, session 20.40.40.9-1.00.10.6
Locomotion distance, session 20.10.20.50.20.7-0.4
Locomotion velocity, session 30.30.40.40.60.6-0.6
Locomotion distance, session 30.00.00.1-0.10.3-0.1
Stereotopy head waving bouts, day 30.70.81.21.10.6-1.0
Stereotopy head waving duration, day 30.60.70.80.90.7-0.9
Locomotion velocity, session 70.40.50.60.60.7-0.8
Locomotion distance, session 70.10.10.20.50.3-0.2
Stereotopy head waving bouts, day 70.91.01.50.71.2-1.1
Stereotopy head waving duration, day 72.22.84.51.02.1-1.7
Locomotion velocity, session 80.91.01.4-1.2-0.61.1
Locomotion distance, session 80.10.10.2-0.50.40.1
Degree of sensitization distance0.10.10.20.1-0.40.3
Degree of sensitization stereotypy1.11.22.10.71.5-1.1
Conditioned locomotion0.40.50.8-0.9-0.50.7
Cocaine response after cond. corrected0.40.51.31.10.2-0.5
Cocaine response after cond. not corrected0.40.61.01.00.7-0.7
Cocaine response before conditioning0.20.30.6-0.40.7-0.4
Saline control response2.83.94.7-2.1-1.62.2
Bone: connectivity density0.40.60.8-0.9-0.80.5
Bone: cortical apparent density4.87.58.92.82.3-3.0
Bone: cortical area0.50.82.0-0.3-1.40.7
Bone: cortical porosity7.68.39.9-2.7-2.83.1
Bone: cortical porosity5.96.57.4-2.2-2.72.7
Bone: cortical thickness6.410.616.44.02.1-3.4
Bone: cortical thickness3.74.65.32.31.8-2.3
Bone: cortical tissue density4.57.18.52.82.3-2.9
Condit. Reinf. active minus inactive responses3.13.54.3-2.1-1.61.9
Condit. Reinf. active-inactive response ratio1.11.21.5-1.2-0.81.2
Condit. Reinf. active responses3.64.76.3-2.5-1.82.1
Condit. Reinf. inactive responses0.91.22.0-1.4-1.00.8
Incentive salience index mean2.22.94.0-2.0-1.41.7
Condit. Reinf. lever presses0.30.51.0-1.0-0.30.6
Condit. Reinf. active minus inactive responses3.45.27.6-2.8-1.92.1
Condit. Reinf. active-inactive response ratio1.93.14.8-2.2-1.41.6
Condit. Reinf. active responses5.47.710.2-3.2-2.42.7
Condit. Reinf. inactive responses1.72.53.1-1.8-1.41.5
Condit. Reinf. lever presses1.82.73.3-1.8-1.41.7
Condit. Reinf. lever reinforcers received4.86.78.6-2.9-2.32.5
Conditioned reinforcement - actives0.31.01.5-0.6-1.21.1
Conditioned reinforcement - inactives0.61.82.7-0.9-1.61.4
Conditioned locomotion3.14.55.7-1.8-2.42.2
Patch foraging indifference point 0 sec2.05.57.1-2.7-2.32.1
Patch foraging indifference point AUC0.40.90.9-0.9-1.00.9
Delay disc. indifference point, 0s delay0.70.71.00.70.9-1.0
Delay disc. indifference point, 16s delay0.50.71.4-0.3-1.20.7
Delay disc. indifference point, 2s delay0.10.10.20.2-0.0-0.5
Delay disc. indifference point, 24s delay1.21.83.4-0.8-1.81.2
Delay disc. indifference point, 4s delay0.80.81.21.10.7-0.9
Delay disc. indifference point, 8s delay0.20.40.60.70.1-0.8
Indifference point function ln k0.20.60.70.80.6-0.9
Indifference point function log k0.20.60.70.80.6-0.9
Patch foraging total patch changes 0 sec2.05.96.9-2.6-2.42.2
Patch foraging total patch changes 12 sec4.15.48.1-2.8-1.82.2
Patch foraging total patch changes 18 sec1.94.65.2-2.3-2.02.1
Patch foraging total patch changes 24 sec1.03.34.0-2.0-1.91.6
Patch foraging total patch changes 6 sec1.83.13.3-1.8-1.81.7
Patch foraging time to switch 0 sec0.10.20.40.30.6-0.3
Patch foraging water rate 0 sec0.72.84.2-1.4-2.11.5
Patch foraging water rate 12 sec0.31.32.21.50.6-1.2
Patch foraging water rate 18 sec0.20.40.60.50.5-0.8
Patch foraging water rate 24 sec0.10.10.10.20.3-0.3
Patch foraging water rate 6 sec0.10.10.20.4-0.2-0.5
Seeking ratio, delayed vs. immediate footshock0.10.20.3-0.1-0.50.5
Distance traveled before self-admin0.20.40.50.60.7-0.6
Distance traveled after self-admin0.10.10.3-0.20.6-0.0
Extensor digitorum longus weight0.10.61.41.20.2-0.5
Bone: elastic displacement1.82.33.21.81.2-1.6
Bone: elastic work0.20.20.40.6-0.4-0.2
Bone: endosteal estimation14.034.240.0-6.3-5.25.9
Bone: endosteal perimeter14.936.638.7-6.2-5.76.2
Epididymis fat weight0.31.52.4-0.7-1.51.2
Delta time in closed arm before/after self-admin0.40.40.40.70.5-0.6
Delta time in open arm before/after self-admin0.00.00.0-0.10.00.1
Diff in mean of infusions in LGA sessions0.91.61.91.21.4-1.2
Delay discount exponential model param0.10.10.2-0.20.50.0
Extinction: sum of active levers before priming0.10.10.2-0.40.10.2
Active lever presses in extinction session 62.32.32.5-1.6-1.41.6
Bone: final force0.10.10.40.1-0.60.1
Bone: final moment0.10.10.40.1-0.60.0
Food consumed during 24 hour testing period2.44.85.5-1.9-2.42.3
Glucose0.91.52.51.61.0-1.0
Heart weight0.40.61.41.2-0.2-0.5
Delay discount hyperbolic model param0.10.10.2-0.20.40.1
Intermittent access intake day 1-15 change0.00.20.4-0.4-0.30.7
Intermittent access intake escalation0.20.91.3-0.8-0.91.2
Intermittent access intake escalation 20.71.11.6-0.9-1.01.3
Intermitt. access day 1 inactive lever presses0.44.65.4-2.3-2.02.1
Intermitt. access day 15 inactive lever presses0.63.34.2-1.8-2.01.7
Intermitt. access escalation Index0.92.73.51.51.9-1.5
Intermittent access day 1 total infusions0.30.81.0-1.0-0.90.9
Intermittent access day 15 total infusions1.33.33.6-1.6-1.91.9
Intermittent access terminal intake (last 3 days)2.84.95.2-2.1-2.22.3
Intermittent access total infusions2.93.53.6-1.9-1.81.9
Intermittent access day 1 locomotion2.64.95.9-1.9-2.42.2
Intermittent access day 15 total locomotion2.07.67.9-2.7-2.72.8
Intermittent access total locomotion7.69.19.6-2.9-3.13.1
Intermittent access standard deviation0.21.21.3-1.1-1.11.1
Left kidney weight0.10.71.10.80.6-1.1
Right kidney weight0.00.30.50.50.1-0.7
Cocaine induced anxiety0.30.81.11.00.6-0.9
Post-drug Anxiety0.80.91.31.10.6-1.0
Baseline Anxiety0.00.00.00.2-0.1-0.1
Tail length1.58.210.2-2.6-3.22.8
Length with tail1.67.08.3-2.4-2.92.6
Length without tail0.10.40.6-0.4-0.80.6
Times rat made contact with spout0.70.91.1-0.7-1.01.0
Lifetime Intake3.34.14.3-2.1-2.02.0
Liver weight, left2.95.06.9-2.6-1.82.2
Liver weight, right1.22.12.71.70.9-1.6
Locomotor activity0.40.60.8-0.9-0.40.9
Locomotor testing distance0.82.02.7-1.3-1.21.7
Locomotor testing rearing0.83.04.2-1.9-1.22.1
Locomotion in novel chamber0.10.20.50.70.2-0.2
Locomotion in novel chamber post-restriction0.20.70.9-0.9-0.90.7
Fecal boli incidents, locomotor time 10.00.10.2-0.1-0.30.4
Change in fecal boli incidents, locomotor task0.20.20.40.6-0.3-0.3
Time >=10cm from walls, locomotor time 12.22.73.91.32.0-1.5
Bouts of movement, locomotor time 10.30.41.01.00.1-0.5
Total resting periods, locomotor time 10.40.51.11.10.1-0.6
Rest time, locomotor task time 10.10.10.30.20.4-0.5
Distance moved, locomotor task time 10.20.50.8-0.4-0.90.7
Vertical activity count, locomotor time 10.00.20.4-0.2-0.70.5
Time >=10cm from walls, locomotor time 20.00.10.2-0.20.5-0.2
Bouts of movement, locomotor time 20.00.10.40.60.0-0.3
Total resting periods, locomotor time 20.10.40.70.90.3-0.5
Rest time, locomotor task time 22.23.73.81.91.9-2.0
Distance moved, locomotor task time 20.50.70.7-0.8-0.80.9
Vertical activity count, locomotor time 21.32.93.1-1.7-1.61.7
Light reinforcement 10.10.30.7-0.8-0.4-0.1
Light reinforcement 20.10.20.3-0.6-0.5-0.2
Bone: marrow area13.533.038.5-6.2-5.25.8
Bone: maximum diameter3.36.77.6-2.5-2.82.5
Bone: maximum force0.51.02.4-0.3-1.50.7
Bone: maximum moment0.51.02.4-0.4-1.50.7
Mean time between licks in bursts0.10.40.90.2-0.90.6
Mean num. licks in bursts0.20.51.00.0-1.00.7
Cd content in liver2.22.43.11.41.8-1.5
Co content in liver0.60.81.50.41.2-0.8
Cu content in liver0.50.50.9-1.0-0.60.6
Fe content in liver0.20.30.7-0.00.9-0.2
K content in liver0.20.20.3-0.60.3-0.0
Mg content in liver1.11.22.10.21.4-1.2
Mn content in liver1.41.62.40.31.6-1.5
Na content in liver0.50.61.4-1.20.20.5
Rb content in liver5.15.98.11.82.8-2.5
Se content in liver1.31.62.10.91.4-1.3
Sr content in liver1.00.91.1-1.0-1.00.8
Zn content in liver0.50.60.70.70.8-0.8
Bone: minimum diameter12.423.826.2-4.5-5.14.9
Time in familiar zone, hab. session 11.01.11.4-1.1-0.91.2
Time in novel zone, hab. session 11.21.41.81.30.9-1.3
Total zone transitions, hab. session 10.10.10.2-0.2-0.50.3
Total locomotion distance, hab. session 10.20.30.8-0.4-0.90.4
Locomotion velocity, hab. session 10.40.61.0-0.6-1.00.6
Time in familiar zone, hab. session 21.51.72.5-1.4-0.81.6
Time in novel zone, hab. session 22.02.13.01.70.8-1.7
Total zone transitions, hab. session 20.00.00.1-0.20.10.2
Total locomotion distance, hab. session 20.10.10.2-0.3-0.40.2
Locomotion velocity, hab. session 20.00.10.1-0.2-0.30.0
Novel to familiar place preference ratio0.20.30.6-0.2-0.80.5
Novelty place preference0.10.10.2-0.0-0.50.3
Time in novel zone, NPP test0.00.00.10.1-0.30.1
Total zone transitions, NPP test0.10.10.30.30.3-0.5
Total locomotion distance, NPP test0.10.10.2-0.2-0.40.0
Locomotion velocity, NPP test0.10.10.4-0.1-0.60.0
Intraocular pressure1.42.34.5-0.6-2.11.4
Delta distance traveled before/after self-admin0.10.10.1-0.20.4-0.0
Delta ambulatory time before/after self-admin0.00.10.2-0.40.00.2
Parametrial fat weight0.00.10.2-0.1-0.5-0.1
Pavlov. Cond. lever latency1.31.61.81.31.2-1.3
Pavlov. Cond. magazine entry latency3.03.95.0-2.2-1.71.9
Pavlov. Cond. change in total contacts2.52.73.0-1.7-1.51.7
Pavlov. Cond. index score2.63.23.9-2.0-1.61.8
Pavlov. Cond. latency score2.12.73.3-1.8-1.41.7
Pavlov. Cond. lever contacts1.92.32.6-1.6-1.41.6
Pavlov. Cond. magazine entry number2.12.63.61.91.3-1.6
Pavlov. Cond. intertrial magazine entries1.11.41.5-1.2-1.21.1
Pavlov. Cond. lever-magazine prob. diff.2.53.13.5-1.9-1.61.8
Pavlov. Cond. response bias2.93.64.6-2.1-1.71.8
Pavlov. Cond. lever latency0.30.40.70.90.3-0.6
Pavlov. Cond. magazine entry latency2.02.83.71.51.9-1.5
Pavlov. Cond. change in total contacts0.30.71.5-1.2-0.10.8
Pavlov. Cond. index score0.00.10.2-0.20.40.1
Pavlov. Cond. latency score0.10.10.30.10.6-0.1
Pavlov. Cond. lever contacts0.20.30.6-0.8-0.30.5
Pavlov. Cond. magazine entry number3.54.55.8-2.0-2.42.0
Pavlov. Cond. intertrial magazine entries9.120.023.6-4.2-4.94.3
Pavlov. Cond. lever-magazine prob. diff.0.10.10.3-0.10.6-0.1
Pavlov. Cond. response bias0.00.10.1-0.30.3-0.0
Time in closed arm before self-admin0.00.00.1-0.30.10.0
Time in closed arm after self-admin0.50.60.90.60.9-0.7
Time in open arm before self-admin0.91.11.61.30.8-1.0
Time in open arm after self-admin0.20.20.3-0.2-0.60.5
Bone: periosteal estimation7.417.517.7-4.2-4.24.1
Bone: periosteal perimeter3.77.38.1-2.6-2.82.7
Bone: post-yield work1.42.42.8-1.3-1.71.7
Progressive ratio test 1 active lever presses1.93.44.1-1.7-2.01.8
Progressive ratio test 1 breakpoint2.33.94.6-1.9-2.11.9
Progressive ratio test 1 inactive lever presses1.64.34.5-2.0-2.12.1
Progressive ratio test 2 active lever presses4.96.98.1-2.5-2.82.5
Progressive ratio test 2 breakpoint5.97.68.8-2.6-3.02.7
Progressive ratio test 2 inactive lever presses1.34.35.6-1.9-2.41.9
Incentive Sensitization - Responses1.74.65.0-2.0-2.22.1
Incentive Sensitization - Breakpoint2.04.64.9-2.0-2.22.2
Sum of active levers in priming session hrs 5-60.20.20.5-0.00.7-0.2
Progressive ratio0.00.00.0-0.1-0.00.0
Food seeking constrained by brief footshock4.05.06.1-2.5-1.72.4
Seeking ratio, punishment vs. effort1.12.52.8-1.7-1.31.7
Retroperitoneal fat weight0.41.82.8-1.1-1.71.2
Reaction time number correct0.31.01.31.10.6-1.1
Reaction time mean minus median0.00.20.50.70.2-0.3
Reaction time mean minus median AUC0.32.12.41.61.3-1.5
Reaction time num false alarms2.74.55.9-2.4-1.92.0
Reaction time num false alarms AUC2.04.66.1-2.5-1.92.0
Reaction time trials correct on left0.31.01.31.10.6-1.1
Reaction time trials on left0.31.01.31.10.6-1.1
Reaction time mean0.81.82.21.21.5-1.3
Reaction time mean AUC0.92.22.91.31.7-1.4
Median of all reaction times1.32.12.71.21.6-1.4
Reaction time omissions0.10.20.30.5-0.5-0.1
Reaction time false alarm rate3.85.26.8-2.6-1.92.3
Reaction time premature initiation rate0.81.31.9-0.9-1.41.1
Reaction time premature initiations0.20.51.0-0.4-1.00.5
Std. dev. reaction times0.20.70.91.00.8-0.8
Reaction time trials completed0.31.01.31.10.6-1.1
Reaction time trials AUC0.31.01.31.10.6-1.2
Run reversals in cocaine runway, females0.30.40.60.7-0.7-0.0
Run reversals in cocaine runway, males0.10.10.20.4-0.2-0.1
Latency to leave start box in cocaine runway0.10.10.20.30.3-0.4
Latency to leave start box in cocaine runway, F0.30.40.80.90.3-0.5
Latency to leave start box in cocaine runway, M0.30.30.8-0.90.20.1
Std. dev. time between licks in bursts0.00.00.10.1-0.30.1
Total sessions with >9 infusions0.30.40.8-0.3-0.90.6
Short access day 1 total inactive lever presses1.42.84.1-1.4-2.01.6
Short access day 10 total inactive lever presses0.00.30.7-0.3-0.90.4
Short access day 1 total infusions0.30.50.7-0.7-0.80.6
Short access day 10 total infusions2.54.24.3-2.0-2.12.1
Short access total infusions1.42.02.0-1.4-1.41.4
Short access day 1 locomotion1.93.15.5-0.9-2.31.7
Short access day 10 total locomotion2.39.29.7-2.9-3.13.1
Short access total locomotion3.24.86.4-1.7-2.52.3
One hour access (0.3 mA shock)1.41.72.1-1.2-1.31.4
Compulsive drug intake0.81.11.21.11.0-1.1
One hour access (shock baseline)1.02.62.8-1.6-1.51.7
Social response proportion0.10.10.20.5-0.30.1
Social responses0.20.20.3-0.4-0.40.5
Social time0.30.50.70.0-0.90.8
Soleus weight0.20.70.8-0.7-0.90.8
Bone: stiffness0.10.10.1-0.3-0.30.3
Tibialis anterior weight0.62.12.6-1.2-1.61.5
Time to tail flick, vehicle, before self-admin0.30.40.50.60.5-0.7
Time to tail flick, vehicle, after self-admin0.00.00.1-0.10.1-0.4
Time to tail flick, test, before self-admin0.00.00.1-0.10.30.1
Time to tail flick, test, after self-admin0.10.10.1-0.40.2-0.1
Delta time to tail flick, vehicle, before/after SA1.11.11.4-1.2-1.01.0
Delta time to tail flick, test, before/after SA0.10.20.3-0.20.5-0.5
Tibia length0.10.40.70.70.3-0.8
Ambulatory time before self-admin0.00.20.30.30.5-0.3
Ambulatory time after self-admin0.00.10.1-0.40.20.1
Bone: tissue strength2.22.32.91.71.3-1.5
Total heroin consumption0.30.40.9-0.90.20.5
Bone: trabecular number0.30.60.9-0.8-0.90.5
Bone: trabecular spacing0.00.10.20.00.40.2
Bone: trabecular thickness1.11.53.4-0.7-1.80.8
Bone: trabecular tissue density2.03.55.22.31.1-2.0
Water consumed over 24 hours0.00.00.10.1-0.30.1
Number of responses in last shaping day0.20.30.6-0.1-0.80.5