Hub : Genes

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 Brain gene expression ENSRNOG00000066555 0.03 0.03 5.1e-03 0.01 0.01 0.01 0.01 4.4e-02 2.9e-02 7.2e-02 8.0e-02
2 Liver gene expression ENSRNOG00000066555 0.04 0.04 2.6e-04 0.02 0.02 0.02 0.01 4.5e-03 3.2e-03 5.3e-03 7.3e-03

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 strong Z-scores (below -2 or above 2): lower negative Z-scores are darker blue, higher positive Z-scores are darker red.

Trait Avg chi2 ratio Avg chi2 Max chi2 1 2
BMI with tail1.85.96.02.42.4
BMI without tail0.30.60.60.80.8
Body weight1.87.57.6-2.7-2.8
Epididymis fat weight0.00.00.00.00.0
Glucose0.71.01.11.01.0
Heart weight0.40.50.50.70.7
Left kidney weight1.02.92.9-1.7-1.7
Right kidney weight0.30.80.8-0.9-0.9
Tail length8.425.525.6-5.1-5.0
Length with tail12.445.445.5-6.7-6.7
Length without tail7.416.216.2-4.0-4.0
Liver weight, left0.40.70.7-0.8-0.8
Liver weight, right0.10.10.10.30.3
Parametrial fat weight0.00.00.00.10.1
Retroperitoneal fat weight0.62.02.11.41.4
Intraocular pressure3.65.15.22.22.3
Extensor digitorum longus weight3.915.615.63.94.0
Soleus weight0.20.40.50.70.7
Tibialis anterior weight2.48.18.12.92.8
Tibia length6.418.018.2-4.3-4.2
Number of licking bursts3.44.14.12.02.0
Food consumed during 24 hour testing period0.91.11.1-1.1-1.0
Times rat made contact with spout0.40.50.50.70.7
Mean time between licks in bursts0.10.10.10.30.3
Mean num. licks in bursts2.22.62.6-1.6-1.6
Std. dev. time between licks in bursts1.01.21.21.11.1
Water consumed over 24 hours0.60.70.80.90.9
Indifference point 0 sec4.47.17.2-2.7-2.7
Indifference point AUC1.01.21.21.11.1
Indifference point function ln k4.46.36.3-2.5-2.5
Indifference point function log k4.46.36.3-2.5-2.5
Delay discounting total patch changes 0 sec5.48.78.8-3.0-2.9
Delay discounting total patch changes 12 sec0.00.00.00.10.1
Delay discounting total patch changes 18 sec0.00.00.0-0.0-0.0
Delay discounting total patch changes 24 sec0.70.90.9-0.9-0.9
Delay discounting total patch changes 6 sec0.81.31.3-1.1-1.1
Delay discounting time to switch 0 sec6.29.49.53.13.1
Delay discounting water rate 0 sec5.48.78.7-2.9-2.9
Delay discounting water rate 12 sec5.27.87.8-2.8-2.8
Delay discounting water rate 18 sec6.48.58.5-2.9-2.9
Delay discounting water rate 24 sec2.94.04.0-2.0-2.0
Delay discounting water rate 6 sec13.920.220.2-4.5-4.5
Locomotor activity0.20.40.4-0.6-0.6
Locomotor testing distance0.40.60.60.80.8
Locomotor testing rearing0.30.40.40.70.7
Light reinforcement 12.24.14.2-2.0-2.0
Light reinforcement 20.10.10.10.40.4
Reaction time number correct9.113.013.0-3.6-3.6
Reaction time mean minus median0.10.10.1-0.3-0.3
Reaction time mean minus median AUC0.40.50.5-0.7-0.7
Reaction time num false alarms0.60.80.80.90.9
Reaction time num false alarms AUC1.11.61.61.21.3
Reaction time trials correct on left9.113.013.0-3.6-3.6
Reaction time trials on left9.313.213.2-3.6-3.6
Reaction time mean1.42.02.01.41.4
Reaction time mean AUC1.31.71.71.31.3
Median of all reaction times2.63.53.51.91.9
Reaction time omissions0.10.20.2-0.4-0.4
Reaction time false alarm rate6.18.68.72.92.9
Reaction time premature initiation rate3.85.05.1-2.2-2.3
Reaction time premature initiations11.215.916.0-4.0-4.0
Std. dev. reaction times0.00.10.10.30.3
Reaction time trials completed9.313.213.2-3.6-3.6
Reaction time trials AUC8.412.012.0-3.5-3.5
Social response proportion0.10.10.10.30.3
Social responses1.21.51.6-1.2-1.2
Social time0.00.00.00.10.1
Conditioned locomotion0.10.10.10.30.3
Cocaine response after cond. corrected1.51.71.7-1.3-1.3
Cocaine response after cond. not corrected2.02.32.3-1.5-1.5
Cocaine response before conditioning0.30.30.4-0.6-0.6
Saline control response1.01.41.4-1.2-1.2
Condit. Reinf. active minus inactive responses3.74.64.6-2.1-2.1
Condit. Reinf. active-inactive response ratio2.22.32.4-1.5-1.5
Condit. Reinf. active responses1.21.71.7-1.3-1.3
Condit. Reinf. inactive responses0.10.10.1-0.3-0.3
Condit. Reinf. lever presses1.72.32.3-1.5-1.5
Condit. Reinf. lever reinforcers received1.72.42.4-1.5-1.5
Pavlov. Cond. lever latency1.72.32.41.51.5
Pavlov. Cond. magazine entry latency0.91.01.0-1.0-1.0
Pavlov. Cond. change in total contacts4.96.96.9-2.6-2.6
Pavlov. Cond. index score2.43.13.2-1.8-1.8
Pavlov. Cond. latency score2.53.13.1-1.8-1.8
Pavlov. Cond. lever contacts1.82.52.5-1.6-1.6
Pavlov. Cond. magazine entry number1.72.12.21.41.5
Pavlov. Cond. intertrial magazine entries0.00.10.1-0.3-0.2
Pavlov. Cond. lever-magazine prob. diff.2.53.33.3-1.8-1.8
Pavlov. Cond. response bias1.52.12.2-1.5-1.5
Conditioned reinforcement - actives2.82.72.8-1.7-1.7
Conditioned reinforcement - inactives0.20.30.3-0.5-0.5
Conditioned locomotion0.70.80.8-0.9-0.9
Intermittent access intake day 1-15 change0.10.10.1-0.2-0.2
Intermittent access intake escalation0.10.10.1-0.4-0.4
Intermittent access intake escalation 20.00.00.00.00.1
Intermitt. access day 1 inactive lever presses2.72.92.91.71.7
Intermitt. access day 15 inactive lever presses3.13.43.41.81.9
Intermitt. access escalation Index0.20.20.2-0.4-0.4
Intermittent access day 1 total infusions0.91.11.1-1.0-1.0
Intermittent access day 15 total infusions1.82.02.1-1.4-1.4
Intermittent access terminal intake (last 3 days)0.80.90.9-1.0-0.9
Intermittent access total infusions2.22.42.5-1.6-1.5
Intermittent access day 1 locomotion2.72.72.8-1.7-1.6
Intermittent access day 15 total locomotion2.02.22.2-1.5-1.5
Intermittent access total locomotion5.15.75.8-2.4-2.4
Intermittent access standard deviation0.40.50.50.70.7
Cocaine induced anxiety0.70.90.9-0.9-0.9
Post-drug Anxiety1.21.31.3-1.1-1.2
Baseline Anxiety0.00.00.0-0.1-0.1
Lifetime Intake2.02.22.2-1.5-1.5
Incentive Sensitization - Responses0.50.50.6-0.7-0.7
Incentive Sensitization - Breakpoint0.30.30.3-0.6-0.6
Progressive ratio test 1 active lever presses1.01.11.1-1.0-1.0
Progressive ratio test 1 breakpoint1.21.21.2-1.1-1.1
Progressive ratio test 1 inactive lever presses0.50.50.5-0.7-0.7
Progressive ratio test 2 active lever presses0.30.30.3-0.5-0.5
Progressive ratio test 2 breakpoint0.20.20.2-0.5-0.4
Progressive ratio test 2 inactive lever presses0.10.20.2-0.4-0.4
Total sessions with >9 infusions0.90.90.9-1.0-1.0
Short access day 1 total inactive lever presses0.00.00.0-0.1-0.1
Short access day 10 total inactive lever presses0.60.60.60.80.8
Short access day 1 total infusions1.31.41.4-1.2-1.1
Short access day 10 total infusions1.41.51.6-1.3-1.2
Short access total infusions1.92.12.1-1.5-1.4
Short access day 1 locomotion0.40.40.4-0.7-0.6
Short access day 10 total locomotion0.00.00.0-0.0-0.0
Short access total locomotion2.02.02.1-1.4-1.4
Compulsive drug intake0.20.20.20.50.4
One hour access (0.3 mA shock)1.11.21.2-1.1-1.1
One hour access (shock baseline)2.22.62.6-1.6-1.6
Number of responses in last shaping day0.40.40.40.60.6
Context. condit. distance diff. score1.51.91.9-1.4-1.4
Locomotion velocity, session 10.40.40.4-0.6-0.6
Locomotion distance, session 10.70.90.9-0.9-0.9
Locomotion velocity, session 24.24.94.9-2.2-2.2
Locomotion distance, session 20.60.90.9-0.9-0.9
Locomotion velocity, session 34.75.55.5-2.3-2.4
Locomotion distance, session 37.48.08.0-2.8-2.8
Stereotopy head waving bouts, day 30.30.30.4-0.6-0.6
Stereotopy head waving duration, day 30.00.00.00.00.1
Locomotion velocity, session 70.10.10.1-0.4-0.3
Locomotion distance, session 70.40.50.5-0.7-0.7
Stereotopy head waving bouts, day 70.00.00.00.10.1
Stereotopy head waving duration, day 70.10.10.1-0.3-0.3
Locomotion velocity, session 82.63.13.1-1.8-1.8
Locomotion distance, session 83.95.75.8-2.4-2.4
Degree of sensitization distance3.23.23.21.81.8
Degree of sensitization stereotypy0.00.00.00.10.2
Condit. Reinf. active minus inactive responses1.51.71.71.31.3
Condit. Reinf. active-inactive response ratio1.61.71.71.31.3
Condit. Reinf. active responses0.20.20.20.50.5
Condit. Reinf. inactive responses1.21.41.4-1.2-1.2
Incentive salience index mean1.11.31.41.11.2
Condit. Reinf. lever presses0.40.50.50.70.7
Time in familiar zone, hab. session 14.64.44.4-2.1-2.1
Time in novel zone, hab. session 16.46.36.32.52.5
Total zone transitions, hab. session 10.00.00.0-0.1-0.2
Total locomotion distance, hab. session 10.00.00.1-0.2-0.2
Locomotion velocity, hab. session 10.00.00.0-0.2-0.2
Time in familiar zone, hab. session 21.61.71.7-1.3-1.3
Time in novel zone, hab. session 22.12.12.11.41.4
Total zone transitions, hab. session 20.10.20.2-0.4-0.4
Total locomotion distance, hab. session 20.00.00.00.10.1
Locomotion velocity, hab. session 20.00.10.1-0.2-0.2
Novel to familiar place preference ratio2.22.32.31.51.5
Novelty place preference1.71.71.71.31.3
Time in novel zone, NPP test1.81.91.91.41.4
Total zone transitions, NPP test1.62.32.3-1.5-1.5
Total locomotion distance, NPP test0.10.10.1-0.4-0.4
Locomotion velocity, NPP test0.60.90.9-0.9-0.9
Pavlov. Cond. lever latency0.00.00.00.20.2
Pavlov. Cond. magazine entry latency2.12.72.7-1.6-1.6
Pavlov. Cond. change in total contacts3.33.53.5-1.9-1.9
Pavlov. Cond. index score0.50.60.7-0.8-0.8
Pavlov. Cond. latency score0.10.20.2-0.4-0.4
Pavlov. Cond. lever contacts0.40.50.5-0.7-0.7
Pavlov. Cond. magazine entry number2.12.72.71.61.7
Pavlov. Cond. intertrial magazine entries5.36.46.52.52.5
Pavlov. Cond. lever-magazine prob. diff.0.70.90.9-0.9-1.0
Pavlov. Cond. response bias2.22.72.7-1.6-1.6
Bone: apparent density0.71.11.11.11.1
Bone surface0.00.10.10.20.2
Bone volume0.10.20.20.50.5
Bone: connectivity density0.10.10.10.30.3
Bone: cortical apparent density0.10.20.2-0.4-0.4
Bone: cortical area0.10.10.1-0.4-0.4
Bone: cortical porosity1.41.51.51.21.2
Bone: cortical porosity1.41.51.61.21.3
Bone: cortical thickness0.10.20.2-0.5-0.4
Bone: cortical thickness0.81.01.0-1.0-1.0
Bone: cortical tissue density0.10.20.2-0.4-0.4
Bone: elastic displacement1.41.61.61.31.3
Bone: elastic work0.70.90.90.90.9
Bone: endosteal estimation0.20.40.4-0.6-0.6
Bone: endosteal perimeter0.00.00.00.20.2
Bone: final force0.61.01.1-1.0-1.0
Bone: final moment0.81.41.4-1.2-1.2
Bone: marrow area0.20.40.4-0.6-0.6
Bone: maximum diameter0.50.80.80.90.9
Bone: maximum force0.10.20.2-0.4-0.4
Bone: maximum moment0.20.40.4-0.6-0.6
Bone: minimum diameter1.93.63.6-1.9-1.9
Bone: periosteal estimation0.10.30.3-0.5-0.5
Bone: periosteal perimeter0.00.00.0-0.2-0.2
Bone: post-yield work0.00.00.00.00.0
Bone: stiffness0.30.50.5-0.7-0.7
Bone: tissue strength1.01.01.01.01.0
Bone: trabecular number0.00.00.00.20.1
Bone: trabecular spacing0.00.00.00.20.2
Bone: trabecular thickness1.11.31.31.21.1
Bone: trabecular tissue density2.43.43.41.81.8
Breakpoint value in progressive ratio session2.93.23.21.81.8
Distance traveled before self-admin2.22.32.3-1.5-1.5
Distance traveled after self-admin1.51.71.7-1.3-1.3
Delta time in closed arm before/after self-admin4.34.24.22.12.0
Delta time in open arm before/after self-admin0.00.00.00.00.0
Diff in mean of infusions in LGA sessions0.30.30.30.50.5
Extinction: sum of active levers before priming1.71.71.71.31.3
Active lever presses in extinction session 62.42.32.31.51.5
Delta distance traveled before/after self-admin0.40.40.4-0.7-0.7
Delta ambulatory time before/after self-admin0.40.50.5-0.7-0.7
Time in closed arm before self-admin0.00.00.0-0.2-0.2
Time in closed arm after self-admin0.50.50.50.70.7
Time in open arm before self-admin0.10.10.1-0.3-0.3
Time in open arm after self-admin0.30.30.30.60.6
Sum of active levers in priming session hrs 5-61.01.01.01.01.0
Time to tail flick, vehicle, before self-admin4.54.54.5-2.1-2.1
Time to tail flick, vehicle, after self-admin1.71.81.9-1.4-1.4
Time to tail flick, test, before self-admin0.10.10.1-0.4-0.4
Time to tail flick, test, after self-admin0.50.60.60.70.8
Delta time to tail flick, vehicle, before/after SA1.11.11.11.01.0
Delta time to tail flick, test, before/after SA0.10.10.10.30.3
Ambulatory time before self-admin0.80.80.8-0.9-0.9
Ambulatory time after self-admin0.91.01.0-1.0-1.0
Total heroin consumption1.31.61.61.21.3
Area under the delay curve0.40.40.4-0.6-0.6
Delay disc. indifference point, 0s delay0.10.10.10.40.4
Delay disc. indifference point, 16s delay0.70.70.7-0.8-0.9
Delay disc. indifference point, 2s delay0.00.00.00.20.2
Delay disc. indifference point, 24s delay0.60.50.6-0.7-0.8
Delay disc. indifference point, 4s delay0.00.00.0-0.1-0.1
Delay disc. indifference point, 8s delay0.00.00.0-0.2-0.2
Delay discount exponential model param0.40.40.40.60.6
Delay discount hyperbolic model param0.30.30.30.50.5
Fecal boli incidents, locomotor time 12.52.72.71.61.6
Change in fecal boli incidents, locomotor task0.00.00.0-0.0-0.0
Time >=10cm from walls, locomotor time 11.81.81.81.31.3
Bouts of movement, locomotor time 10.40.50.50.70.7
Total resting periods, locomotor time 10.10.10.10.40.4
Rest time, locomotor task time 11.92.12.11.41.4
Distance moved, locomotor task time 12.12.32.4-1.5-1.5
Vertical activity count, locomotor time 11.61.71.7-1.3-1.3
Time >=10cm from walls, locomotor time 20.80.90.90.90.9
Bouts of movement, locomotor time 20.10.20.2-0.4-0.4
Total resting periods, locomotor time 20.00.00.00.10.1
Rest time, locomotor task time 23.94.54.52.12.1
Distance moved, locomotor task time 22.22.62.6-1.6-1.6
Vertical activity count, locomotor time 20.60.60.6-0.8-0.8
Weight adjusted by age0.20.20.2-0.5-0.5
Seeking ratio, delayed vs. immediate footshock1.41.71.71.31.3
Locomotion in novel chamber0.91.11.11.11.0
Locomotion in novel chamber post-restriction0.10.10.10.30.3
Progressive ratio0.00.00.00.10.1
Food seeking constrained by brief footshock2.22.72.8-1.7-1.7
Seeking ratio, punishment vs. effort0.70.80.8-0.9-0.9
Run reversals in cocaine runway, females0.60.60.60.80.8
Run reversals in cocaine runway, males0.00.00.00.0-0.0
Latency to leave start box in cocaine runway2.42.72.71.61.6
Latency to leave start box in cocaine runway, F0.40.40.40.60.6
Latency to leave start box in cocaine runway, M2.62.52.61.61.6
Cd content in liver0.50.50.6-0.7-0.7
Co content in liver0.10.20.2-0.4-0.4
Cu content in liver0.20.30.3-0.5-0.5
Fe content in liver1.51.81.9-1.4-1.4
K content in liver2.72.72.7-1.6-1.7
Mg content in liver0.40.40.5-0.6-0.7
Mn content in liver0.40.40.4-0.7-0.7
Na content in liver0.20.30.3-0.5-0.5
Rb content in liver0.91.11.1-1.0-1.0
Se content in liver0.10.10.10.40.4
Sr content in liver2.52.32.31.51.5
Zn content in liver0.00.00.00.00.0