Shld3

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 Shld3 0.06 0.06 1.9e-05 0.03 0.03 0.04 0.03 1.4e-04 1.3e-04 8.6e-05 1.3e-04
2 Brain gene expression Shld3 0.03 0.03 9.2e-03 0.03 0.02 0.02 0.02 1.1e-03 9.6e-03 7.9e-03 3.1e-03
3 PL gene expression Shld3 0.03 0.03 8.5e-03 0.02 -0 0 0.01 6.5e-03 6.8e-01 1.5e-01 2.1e-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
Bone: apparent density0.71.11.4-1.2-0.9-1.0
Area under the delay curve0.60.71.10.21.01.0
BMI with tail2.16.87.6-2.7-2.6-2.5
BMI without tail0.30.71.0-1.0-0.8-0.7
Body weight1.76.97.82.62.82.5
Weight adjusted by age0.30.30.40.60.50.5
Bone surface0.00.10.2-0.4-0.1-0.2
Bone volume0.10.20.4-0.6-0.3-0.4
Breakpoint value in progressive ratio session2.62.83.4-1.8-1.7-1.5
Number of licking bursts3.23.84.1-2.0-1.8-2.0
Context. condit. distance diff. score1.72.02.41.21.51.5
Locomotion velocity, session 10.40.40.50.70.50.7
Locomotion distance, session 10.81.01.11.01.11.0
Locomotion velocity, session 24.04.75.22.32.02.2
Locomotion distance, session 20.60.91.00.90.91.0
Locomotion velocity, session 34.75.55.62.42.32.3
Locomotion distance, session 37.27.98.12.72.82.8
Stereotopy head waving bouts, day 30.40.50.80.90.70.5
Stereotopy head waving duration, day 30.00.00.10.3-0.1-0.2
Locomotion velocity, session 70.10.10.10.30.20.2
Locomotion distance, session 70.30.40.50.60.70.6
Stereotopy head waving bouts, day 70.10.10.10.2-0.2-0.3
Stereotopy head waving duration, day 70.10.10.30.50.10.1
Locomotion velocity, session 82.63.13.31.81.71.7
Locomotion distance, session 84.05.96.62.22.52.6
Degree of sensitization distance3.33.33.6-1.7-1.9-1.9
Degree of sensitization stereotypy0.10.10.1-0.0-0.3-0.3
Conditioned locomotion0.10.10.1-0.3-0.2-0.4
Cocaine response after cond. corrected1.61.71.81.31.31.3
Cocaine response after cond. not corrected2.12.42.51.41.61.6
Cocaine response before conditioning0.30.40.40.50.70.7
Saline control response1.11.51.61.11.21.3
Bone: connectivity density0.10.10.1-0.3-0.2-0.3
Bone: cortical apparent density0.10.10.20.40.40.3
Bone: cortical area0.10.10.20.40.30.3
Bone: cortical porosity1.61.82.2-1.1-1.4-1.5
Bone: cortical porosity1.61.72.2-1.1-1.4-1.5
Bone: cortical thickness0.10.20.40.60.40.2
Bone: cortical thickness0.70.91.10.80.91.0
Bone: cortical tissue density0.10.20.20.50.40.4
Condit. Reinf. active minus inactive responses1.31.52.1-1.1-1.1-1.4
Condit. Reinf. active-inactive response ratio1.31.42.2-1.0-1.1-1.5
Condit. Reinf. active responses0.10.20.3-0.3-0.3-0.6
Condit. Reinf. inactive responses1.11.41.61.01.21.3
Incentive salience index mean1.01.21.6-1.0-1.0-1.3
Condit. Reinf. lever presses0.40.50.5-0.7-0.6-0.7
Condit. Reinf. active minus inactive responses3.64.54.72.22.12.1
Condit. Reinf. active-inactive response ratio2.22.33.11.81.51.3
Condit. Reinf. active responses1.31.81.91.41.41.3
Condit. Reinf. inactive responses0.10.10.20.20.40.4
Condit. Reinf. lever presses1.92.63.11.51.81.5
Condit. Reinf. lever reinforcers received1.82.52.71.61.61.5
Conditioned reinforcement - actives2.92.93.11.81.71.6
Conditioned reinforcement - inactives0.30.40.50.70.60.6
Conditioned locomotion0.60.71.11.00.70.8
Patch foraging indifference point 0 sec4.97.99.12.73.02.8
Patch foraging indifference point AUC1.31.52.2-1.2-1.5-1.0
Delay disc. indifference point, 0s delay0.10.20.2-0.4-0.4-0.4
Delay disc. indifference point, 16s delay1.01.01.60.51.31.1
Delay disc. indifference point, 2s delay0.10.10.1-0.2-0.2-0.4
Delay disc. indifference point, 24s delay1.01.01.60.21.31.2
Delay disc. indifference point, 4s delay0.00.00.10.10.20.2
Delay disc. indifference point, 8s delay0.30.30.5-0.20.70.7
Indifference point function ln k5.17.18.32.62.92.5
Indifference point function log k5.17.18.32.62.92.5
Patch foraging total patch changes 0 sec5.99.510.63.03.33.0
Patch foraging total patch changes 12 sec0.00.00.1-0.2-0.3-0.0
Patch foraging total patch changes 18 sec0.00.00.00.00.10.0
Patch foraging total patch changes 24 sec0.70.81.00.80.91.0
Patch foraging total patch changes 6 sec0.81.21.31.11.21.1
Patch foraging time to switch 0 sec6.19.410.6-3.2-2.9-3.0
Patch foraging water rate 0 sec5.48.69.43.12.92.8
Patch foraging water rate 12 sec5.38.18.32.82.92.8
Patch foraging water rate 18 sec6.18.28.32.92.82.9
Patch foraging water rate 24 sec2.43.33.92.01.81.7
Patch foraging water rate 6 sec13.820.220.94.54.44.6
Seeking ratio, delayed vs. immediate footshock1.51.82.2-1.5-1.2-1.3
Distance traveled before self-admin2.02.12.31.51.51.3
Distance traveled after self-admin1.51.71.81.31.31.2
Extensor digitorum longus weight4.116.117.4-3.8-4.2-4.1
Bone: elastic displacement1.41.61.7-1.3-1.1-1.3
Bone: elastic work0.60.81.1-1.1-0.7-0.9
Bone: endosteal estimation0.30.60.90.40.90.8
Bone: endosteal perimeter0.00.00.1-0.4-0.00.0
Epididymis fat weight0.00.00.10.00.0-0.3
Delta time in closed arm before/after self-admin3.83.75.1-2.3-1.7-1.7
Delta time in open arm before/after self-admin0.00.00.00.1-0.10.0
Diff in mean of infusions in LGA sessions0.20.20.3-0.4-0.6-0.3
Delay discount exponential model param0.60.71.1-0.3-1.0-0.9
Extinction: sum of active levers before priming1.21.21.7-1.3-1.1-0.9
Active lever presses in extinction session 62.12.12.3-1.5-1.4-1.4
Bone: final force0.71.11.21.01.11.1
Bone: final moment0.91.51.71.11.31.2
Food consumed during 24 hour testing period0.91.11.21.11.11.0
Glucose0.81.11.8-0.6-1.1-1.3
Heart weight0.40.60.8-0.6-0.9-0.8
Delay discount hyperbolic model param0.40.50.7-0.3-0.9-0.8
Intermittent access intake day 1-15 change0.10.10.10.30.20.3
Intermittent access intake escalation0.20.20.30.50.40.4
Intermittent access intake escalation 20.00.00.0-0.1-0.1-0.0
Intermitt. access day 1 inactive lever presses2.62.83.2-1.6-1.6-1.8
Intermitt. access day 15 inactive lever presses3.03.23.7-1.8-1.7-1.9
Intermitt. access escalation Index0.20.20.30.60.50.3
Intermittent access day 1 total infusions1.01.11.81.31.00.7
Intermittent access day 15 total infusions2.02.33.21.81.41.2
Intermittent access terminal intake (last 3 days)1.01.01.51.21.00.8
Intermittent access total infusions2.42.63.82.01.61.3
Intermittent access day 1 locomotion2.42.53.61.91.51.3
Intermittent access day 15 total locomotion1.92.13.01.71.31.3
Intermittent access total locomotion4.65.37.02.72.22.1
Intermittent access standard deviation0.60.60.8-0.7-0.9-0.8
Left kidney weight1.02.72.91.71.71.6
Right kidney weight0.20.70.70.80.80.8
Cocaine induced anxiety0.91.01.30.81.01.1
Post-drug Anxiety1.31.41.71.01.21.3
Baseline Anxiety0.00.00.0-0.00.20.1
Tail length8.525.726.45.15.15.0
Length with tail12.445.546.86.86.86.5
Length without tail7.115.616.14.04.03.8
Times rat made contact with spout0.40.40.5-0.7-0.6-0.7
Lifetime Intake2.12.33.41.81.51.2
Liver weight, left0.50.81.71.30.70.5
Liver weight, right0.00.10.1-0.3-0.3-0.2
Locomotor activity0.30.50.70.40.80.8
Locomotor testing distance0.30.40.9-1.0-0.4-0.4
Locomotor testing rearing0.20.20.5-0.7-0.3-0.4
Locomotion in novel chamber0.81.01.1-1.0-1.0-1.0
Locomotion in novel chamber post-restriction0.00.00.1-0.3-0.2-0.1
Fecal boli incidents, locomotor time 12.12.32.7-1.6-1.3-1.6
Change in fecal boli incidents, locomotor task0.10.10.20.0-0.4-0.4
Time >=10cm from walls, locomotor time 11.51.51.7-1.3-1.0-1.3
Bouts of movement, locomotor time 10.40.40.7-0.9-0.5-0.4
Total resting periods, locomotor time 10.10.10.4-0.6-0.2-0.1
Rest time, locomotor task time 11.71.92.4-1.5-1.3-1.3
Distance moved, locomotor task time 11.71.92.41.61.21.3
Vertical activity count, locomotor time 11.11.21.61.30.91.1
Time >=10cm from walls, locomotor time 20.70.71.1-1.0-0.7-0.7
Bouts of movement, locomotor time 20.10.20.30.10.40.5
Total resting periods, locomotor time 20.10.10.2-0.4-0.0-0.0
Rest time, locomotor task time 23.44.04.5-2.1-1.8-2.1
Distance moved, locomotor task time 22.02.32.81.61.21.7
Vertical activity count, locomotor time 20.40.40.90.90.30.6
Light reinforcement 12.64.85.02.12.22.2
Light reinforcement 20.10.10.2-0.3-0.3-0.4
Bone: marrow area0.30.60.80.40.90.8
Bone: maximum diameter0.50.91.1-1.0-0.9-0.8
Bone: maximum force0.10.20.30.30.50.6
Bone: maximum moment0.30.50.70.50.80.8
Mean time between licks in bursts0.10.10.1-0.2-0.3-0.3
Mean num. licks in bursts2.12.52.71.61.51.6
Cd content in liver0.40.40.60.70.40.7
Co content in liver0.20.20.30.20.60.4
Cu content in liver0.30.40.70.80.60.4
Fe content in liver1.62.02.51.61.31.3
K content in liver2.52.43.71.41.31.9
Mg content in liver0.30.40.90.30.30.9
Mn content in liver0.30.40.50.70.60.5
Na content in liver0.20.30.30.40.60.5
Rb content in liver0.91.21.51.01.21.0
Se content in liver0.10.10.2-0.2-0.5-0.4
Sr content in liver2.62.43.0-1.7-1.5-1.4
Zn content in liver0.00.00.1-0.20.00.3
Bone: minimum diameter2.03.84.21.81.92.0
Time in familiar zone, hab. session 14.34.04.32.12.01.9
Time in novel zone, hab. session 16.05.96.1-2.5-2.4-2.4
Total zone transitions, hab. session 10.00.00.10.10.00.2
Total locomotion distance, hab. session 10.00.10.2-0.00.20.4
Locomotion velocity, hab. session 10.00.00.10.00.20.3
Time in familiar zone, hab. session 21.41.51.61.21.21.2
Time in novel zone, hab. session 21.91.92.1-1.3-1.4-1.4
Total zone transitions, hab. session 20.10.20.20.40.30.4
Total locomotion distance, hab. session 20.00.00.1-0.3-0.20.0
Locomotion velocity, hab. session 20.00.10.20.10.10.4
Novel to familiar place preference ratio2.22.22.4-1.6-1.3-1.6
Novelty place preference1.61.61.9-1.3-1.1-1.4
Time in novel zone, NPP test1.81.82.1-1.4-1.2-1.4
Total zone transitions, NPP test1.52.22.41.51.41.5
Total locomotion distance, NPP test0.10.10.20.30.30.5
Locomotion velocity, NPP test0.60.91.00.90.91.0
Intraocular pressure3.24.56.4-1.8-1.9-2.5
Delta distance traveled before/after self-admin0.50.50.60.60.70.8
Delta ambulatory time before/after self-admin0.50.50.60.60.80.8
Parametrial fat weight0.00.00.1-0.0-0.1-0.2
Pavlov. Cond. lever latency0.00.10.1-0.1-0.3-0.3
Pavlov. Cond. magazine entry latency2.12.73.81.31.61.9
Pavlov. Cond. change in total contacts3.43.64.41.71.92.1
Pavlov. Cond. index score0.50.71.10.50.81.0
Pavlov. Cond. latency score0.20.20.40.20.50.7
Pavlov. Cond. lever contacts0.40.50.80.50.70.9
Pavlov. Cond. magazine entry number2.22.84.1-1.2-1.6-2.0
Pavlov. Cond. intertrial magazine entries4.96.07.2-2.3-2.3-2.7
Pavlov. Cond. lever-magazine prob. diff.0.80.91.40.71.01.2
Pavlov. Cond. response bias2.12.63.61.31.61.9
Pavlov. Cond. lever latency1.92.53.1-1.4-1.8-1.6
Pavlov. Cond. magazine entry latency0.91.01.30.81.11.1
Pavlov. Cond. change in total contacts5.27.27.82.52.82.8
Pavlov. Cond. index score2.53.33.91.52.01.9
Pavlov. Cond. latency score2.63.33.91.52.01.9
Pavlov. Cond. lever contacts2.02.73.31.51.81.6
Pavlov. Cond. magazine entry number1.72.12.6-1.1-1.5-1.6
Pavlov. Cond. intertrial magazine entries0.10.10.30.50.20.1
Pavlov. Cond. lever-magazine prob. diff.2.73.54.11.62.01.9
Pavlov. Cond. response bias1.62.22.61.31.61.5
Time in closed arm before self-admin0.00.00.10.10.20.3
Time in closed arm after self-admin0.70.70.9-0.9-0.8-0.8
Time in open arm before self-admin0.00.10.10.30.20.2
Time in open arm after self-admin0.20.20.3-0.3-0.6-0.5
Bone: periosteal estimation0.20.40.50.40.70.6
Bone: periosteal perimeter0.00.10.10.00.40.3
Bone: post-yield work0.00.00.00.1-0.0-0.0
Progressive ratio test 1 active lever presses1.11.21.71.31.20.7
Progressive ratio test 1 breakpoint1.31.31.71.31.30.8
Progressive ratio test 1 inactive lever presses0.60.70.90.81.00.6
Progressive ratio test 2 active lever presses0.40.40.50.70.70.4
Progressive ratio test 2 breakpoint0.30.30.40.60.60.3
Progressive ratio test 2 inactive lever presses0.30.30.50.70.60.2
Incentive Sensitization - Responses0.70.70.80.70.90.8
Incentive Sensitization - Breakpoint0.40.40.50.60.70.7
Sum of active levers in priming session hrs 5-61.11.11.4-0.9-1.2-1.1
Progressive ratio0.00.00.00.1-0.20.0
Food seeking constrained by brief footshock2.43.03.51.61.91.7
Seeking ratio, punishment vs. effort0.60.71.10.71.10.8
Retroperitoneal fat weight0.62.12.8-1.3-1.4-1.7
Reaction time number correct8.712.613.63.73.43.5
Reaction time mean minus median0.10.10.10.20.40.2
Reaction time mean minus median AUC0.30.40.60.60.80.5
Reaction time num false alarms0.70.91.1-1.0-0.8-1.0
Reaction time num false alarms AUC1.21.62.0-1.3-1.1-1.4
Reaction time trials correct on left8.712.613.63.73.43.5
Reaction time trials on left9.012.813.93.73.53.5
Reaction time mean1.41.92.0-1.4-1.3-1.4
Reaction time mean AUC1.21.61.7-1.3-1.2-1.3
Median of all reaction times2.43.33.4-1.8-1.8-1.8
Reaction time omissions0.20.20.40.60.50.2
Reaction time false alarm rate6.18.59.2-3.0-2.7-3.0
Reaction time premature initiation rate4.05.36.02.12.42.4
Reaction time premature initiations11.416.016.63.84.14.1
Std. dev. reaction times0.10.10.2-0.3-0.2-0.4
Reaction time trials completed9.012.813.93.73.53.5
Reaction time trials AUC8.111.712.73.63.33.4
Run reversals in cocaine runway, females0.70.70.9-0.9-0.9-0.6
Run reversals in cocaine runway, males0.10.10.2-0.40.10.0
Latency to leave start box in cocaine runway2.62.83.1-1.7-1.8-1.6
Latency to leave start box in cocaine runway, F0.40.40.4-0.6-0.6-0.6
Latency to leave start box in cocaine runway, M2.92.83.2-1.7-1.8-1.5
Std. dev. time between licks in bursts1.01.21.3-1.1-1.1-1.1
Total sessions with >9 infusions0.80.81.31.10.90.6
Short access day 1 total inactive lever presses0.10.10.20.4-0.10.1
Short access day 10 total inactive lever presses0.50.60.8-0.9-0.6-0.7
Short access day 1 total infusions1.21.21.81.31.10.9
Short access day 10 total infusions1.41.52.11.41.30.9
Short access total infusions1.71.92.81.71.41.1
Short access day 1 locomotion0.30.30.70.80.40.2
Short access day 10 total locomotion0.00.00.00.1-0.2-0.1
Short access total locomotion1.41.52.91.70.90.9
One hour access (0.3 mA shock)1.11.31.91.41.10.9
Compulsive drug intake0.10.10.2-0.4-0.3-0.4
One hour access (shock baseline)2.12.43.21.81.51.4
Social response proportion0.00.00.0-0.2-0.1-0.1
Social responses1.52.02.81.11.41.7
Social time0.00.00.00.10.10.0
Soleus weight0.20.50.8-0.5-0.7-0.9
Bone: stiffness0.30.50.80.50.80.9
Tibialis anterior weight2.58.69.2-2.8-3.0-2.9
Time to tail flick, vehicle, before self-admin4.95.05.42.22.22.3
Time to tail flick, vehicle, after self-admin1.71.92.51.11.31.6
Time to tail flick, test, before self-admin0.10.10.20.40.30.4
Time to tail flick, test, after self-admin0.90.91.3-0.6-1.1-1.1
Delta time to tail flick, vehicle, before/after SA1.31.31.7-1.3-1.1-1.0
Delta time to tail flick, test, before/after SA0.10.10.2-0.3-0.4-0.4
Tibia length6.718.820.34.54.54.0
Ambulatory time before self-admin0.70.70.90.90.80.8
Ambulatory time after self-admin0.91.01.30.91.11.0
Bone: tissue strength0.90.91.1-0.9-0.9-1.0
Total heroin consumption1.51.82.1-1.1-1.5-1.4
Bone: trabecular number0.00.00.1-0.3-0.0-0.1
Bone: trabecular spacing0.10.20.30.1-0.5-0.5
Bone: trabecular thickness0.91.12.0-1.4-0.8-0.8
Bone: trabecular tissue density2.53.53.6-1.9-1.8-1.8
Water consumed over 24 hours0.50.70.7-0.8-0.8-0.9
Number of responses in last shaping day0.50.50.8-0.3-0.7-0.9