Sptlc3

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 Sptlc3 0.07 0.05 1.3e-05 0.03 0.06 0.05 0.05 4.4e-04 4.1e-06 8.1e-06 1.2e-05
2 Eye gene expression Sptlc3 0.49 0.17 8.1e-04 0.01 0.1 0 0.05 2.0e-01 1.4e-02 3.2e-01 6.9e-02
3 PL gene expression Sptlc3 0.06 0.03 1.1e-07 0.05 0.06 0.06 0.05 1.9e-06 2.2e-07 4.0e-07 1.8e-06

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 density1.11.93.6-0.51.3-1.9
Area under the delay curve0.50.61.31.10.70.0
BMI with tail3.010.223.3-4.8-1.4-2.3
BMI without tail2.67.818.3-4.3-1.5-1.7
Body weight4.519.644.9-6.7-2.1-3.1
Weight adjusted by age0.30.40.7-0.8-0.70.1
Bone surface2.03.66.10.62.5-2.1
Bone volume1.42.43.70.11.9-1.9
Breakpoint value in progressive ratio session0.30.41.0-1.0-0.4-0.3
Number of licking bursts0.60.91.8-0.6-1.30.7
Context. condit. distance diff. score0.10.10.2-0.40.1-0.4
Locomotion velocity, session 10.40.50.70.80.9-0.2
Locomotion distance, session 13.34.16.62.22.6-0.9
Locomotion velocity, session 21.01.22.41.61.10.1
Locomotion distance, session 22.43.46.52.51.90.1
Locomotion velocity, session 30.40.51.01.00.7-0.1
Locomotion distance, session 30.00.00.00.0-0.0-0.0
Stereotopy head waving bouts, day 30.50.51.1-0.30.6-1.0
Stereotopy head waving duration, day 30.20.30.5-0.20.5-0.7
Locomotion velocity, session 70.60.71.20.6-0.71.1
Locomotion distance, session 70.10.10.1-0.4-0.3-0.1
Stereotopy head waving bouts, day 70.20.20.4-0.60.0-0.5
Stereotopy head waving duration, day 70.50.50.90.11.0-0.8
Locomotion velocity, session 80.40.51.11.00.50.2
Locomotion distance, session 80.71.01.61.31.2-0.3
Degree of sensitization distance0.20.20.40.10.6-0.6
Degree of sensitization stereotypy0.10.10.2-0.5-0.2-0.1
Conditioned locomotion1.31.43.4-1.8-0.5-0.9
Cocaine response after cond. corrected0.30.30.60.3-0.60.8
Cocaine response after cond. not corrected0.10.20.30.5-0.10.5
Cocaine response before conditioning0.81.01.70.71.3-0.8
Saline control response0.00.00.0-0.20.0-0.0
Bone: connectivity density2.94.57.10.12.5-2.7
Bone: cortical apparent density2.12.85.0-1.5-2.21.1
Bone: cortical area4.46.711.9-3.5-2.80.4
Bone: cortical porosity1.31.42.8-0.90.8-1.7
Bone: cortical porosity1.11.11.8-1.30.1-1.3
Bone: cortical thickness9.115.127.5-5.2-4.20.4
Bone: cortical thickness3.54.17.1-2.7-2.3-0.0
Bone: cortical tissue density2.02.74.8-1.3-2.21.2
Condit. Reinf. active minus inactive responses0.60.71.3-0.80.4-1.1
Condit. Reinf. active-inactive response ratio0.30.30.5-0.7-0.1-0.6
Condit. Reinf. active responses0.00.00.0-0.00.1-0.0
Condit. Reinf. inactive responses0.40.50.80.90.10.7
Incentive salience index mean0.50.71.20.71.1-0.6
Condit. Reinf. lever presses1.11.63.31.81.20.4
Condit. Reinf. active minus inactive responses0.00.00.10.30.20.1
Condit. Reinf. active-inactive response ratio0.10.10.10.40.00.4
Condit. Reinf. active responses0.00.00.10.10.20.0
Condit. Reinf. inactive responses0.00.00.10.10.3-0.0
Condit. Reinf. lever presses1.82.54.31.72.1-0.6
Condit. Reinf. lever reinforcers received0.10.20.30.50.50.2
Conditioned reinforcement - actives1.11.83.11.01.8-1.1
Conditioned reinforcement - inactives0.20.30.60.40.8-0.4
Conditioned locomotion0.60.81.61.30.90.1
Patch foraging indifference point 0 sec1.01.94.12.01.10.6
Patch foraging indifference point AUC4.15.910.42.4-1.23.2
Delay disc. indifference point, 0s delay0.10.10.10.30.2-0.2
Delay disc. indifference point, 16s delay1.01.12.71.60.70.5
Delay disc. indifference point, 2s delay1.71.92.81.71.7-0.5
Delay disc. indifference point, 24s delay0.10.10.20.40.4-0.0
Delay disc. indifference point, 4s delay0.10.10.30.60.20.0
Delay disc. indifference point, 8s delay0.20.20.30.20.6-0.5
Indifference point function ln k2.84.98.6-2.31.0-2.9
Indifference point function log k2.84.98.6-2.31.0-2.9
Patch foraging total patch changes 0 sec1.12.14.72.21.00.9
Patch foraging total patch changes 12 sec1.52.03.92.00.41.4
Patch foraging total patch changes 18 sec4.77.213.23.60.12.9
Patch foraging total patch changes 24 sec2.84.89.23.00.22.3
Patch foraging total patch changes 6 sec2.94.47.32.4-0.62.7
Patch foraging time to switch 0 sec1.63.25.2-2.00.6-2.3
Patch foraging water rate 0 sec2.04.36.82.4-0.72.6
Patch foraging water rate 12 sec0.61.32.31.2-0.61.5
Patch foraging water rate 18 sec1.52.44.10.3-1.72.0
Patch foraging water rate 24 sec3.75.29.30.8-2.43.1
Patch foraging water rate 6 sec1.72.54.7-0.8-2.21.5
Seeking ratio, delayed vs. immediate footshock0.91.12.1-0.80.7-1.5
Distance traveled before self-admin0.20.20.30.1-0.60.5
Distance traveled after self-admin1.72.13.7-1.0-1.91.3
Extensor digitorum longus weight0.00.10.1-0.20.2-0.3
Bone: elastic displacement1.21.42.5-0.9-1.60.9
Bone: elastic work2.63.47.3-2.7-1.7-0.3
Bone: endosteal estimation2.65.710.11.73.2-2.0
Bone: endosteal perimeter1.53.25.61.62.4-1.2
Epididymis fat weight4.114.126.8-5.2-0.3-3.9
Delta time in closed arm before/after self-admin0.00.00.0-0.2-0.2-0.0
Delta time in open arm before/after self-admin1.11.12.3-1.5-1.0-0.1
Diff in mean of infusions in LGA sessions0.10.10.20.50.00.3
Delay discount exponential model param0.40.51.1-1.1-0.6-0.1
Extinction: sum of active levers before priming0.40.40.90.4-0.60.9
Active lever presses in extinction session 61.21.22.0-1.40.1-1.2
Bone: final force2.94.68.6-2.9-2.20.1
Bone: final moment2.43.87.7-2.8-1.9-0.1
Food consumed during 24 hour testing period4.36.09.6-0.32.9-3.1
Glucose0.50.81.4-1.2-0.0-1.0
Heart weight0.71.12.8-1.7-0.3-0.7
Delay discount hyperbolic model param0.40.51.0-1.0-0.70.0
Intermittent access intake day 1-15 change1.94.06.10.32.5-2.4
Intermittent access intake escalation2.44.97.40.22.7-2.7
Intermittent access intake escalation 24.85.59.30.83.0-2.6
Intermitt. access day 1 inactive lever presses0.51.93.11.21.8-1.1
Intermitt. access day 15 inactive lever presses0.81.63.2-0.51.2-1.8
Intermitt. access escalation Index0.10.20.4-0.7-0.2-0.2
Intermittent access day 1 total infusions0.91.42.6-1.6-0.1-1.3
Intermittent access day 15 total infusions2.53.77.1-1.51.4-2.7
Intermittent access terminal intake (last 3 days)2.53.26.3-1.31.4-2.5
Intermittent access total infusions1.82.13.9-1.30.9-2.0
Intermittent access day 1 locomotion0.50.71.3-0.60.6-1.2
Intermittent access day 15 total locomotion0.71.32.1-0.11.3-1.5
Intermittent access total locomotion0.60.71.1-0.01.0-1.1
Intermittent access standard deviation1.83.75.90.52.4-2.2
Left kidney weight0.31.32.7-1.7-0.9-0.5
Right kidney weight0.00.20.4-0.7-0.3-0.3
Cocaine induced anxiety0.30.40.80.60.9-0.5
Post-drug Anxiety0.10.10.1-0.10.3-0.4
Baseline Anxiety0.80.91.6-0.9-1.30.6
Tail length0.72.55.9-2.4-1.0-0.8
Length with tail1.35.812.4-3.5-0.6-2.2
Length without tail1.85.99.8-2.71.0-3.1
Times rat made contact with spout0.70.81.30.61.2-0.7
Lifetime Intake1.21.42.7-1.00.8-1.6
Liver weight, left1.42.34.3-2.1-1.60.2
Liver weight, right2.13.76.1-2.5-2.20.4
Locomotor activity0.91.32.51.11.6-0.7
Locomotor testing distance1.22.13.21.71.8-0.4
Locomotor testing rearing1.42.95.92.41.70.2
Locomotion in novel chamber1.92.54.2-1.5-2.01.0
Locomotion in novel chamber post-restriction0.00.10.1-0.3-0.30.1
Fecal boli incidents, locomotor time 10.00.00.1-0.0-0.20.3
Change in fecal boli incidents, locomotor task0.40.40.9-0.9-0.6-0.2
Time >=10cm from walls, locomotor time 10.10.10.2-0.20.4-0.5
Bouts of movement, locomotor time 10.60.71.30.8-0.51.1
Total resting periods, locomotor time 10.60.61.10.9-0.31.0
Rest time, locomotor task time 11.11.42.30.11.5-1.4
Distance moved, locomotor task time 11.72.64.1-0.2-2.01.9
Vertical activity count, locomotor time 10.00.00.1-0.20.0-0.3
Time >=10cm from walls, locomotor time 21.42.03.7-1.30.8-1.9
Bouts of movement, locomotor time 20.20.40.6-0.0-0.80.7
Total resting periods, locomotor time 20.20.40.6-0.1-0.80.8
Rest time, locomotor task time 20.40.50.9-0.0-0.91.0
Distance moved, locomotor task time 20.70.91.41.01.2-0.6
Vertical activity count, locomotor time 21.62.24.20.82.1-1.4
Light reinforcement 11.22.84.51.72.1-1.0
Light reinforcement 20.60.91.40.41.2-1.0
Bone: marrow area2.55.49.51.73.1-1.9
Bone: maximum diameter0.10.20.4-0.7-0.5-0.1
Bone: maximum force2.13.78.2-2.9-1.7-0.4
Bone: maximum moment1.73.07.1-2.7-1.3-0.7
Mean time between licks in bursts1.43.45.5-2.0-2.30.8
Mean num. licks in bursts1.21.83.40.51.8-1.3
Cd content in liver0.50.61.3-1.1-0.6-0.3
Co content in liver0.60.71.20.2-0.91.1
Cu content in liver0.20.20.40.60.40.1
Fe content in liver2.02.54.10.32.0-1.8
K content in liver1.41.32.71.60.41.1
Mg content in liver0.60.60.9-0.1-0.90.9
Mn content in liver2.93.26.01.7-0.92.5
Na content in liver2.93.15.41.82.3-0.8
Rb content in liver1.41.63.4-1.8-1.2-0.3
Se content in liver0.91.12.4-1.5-0.9-0.2
Sr content in liver1.41.22.41.61.00.2
Zn content in liver1.51.73.1-1.8-0.0-1.4
Bone: minimum diameter0.40.81.7-1.3-0.1-0.8
Time in familiar zone, hab. session 11.71.62.80.71.7-1.2
Time in novel zone, hab. session 10.80.81.30.2-0.91.1
Total zone transitions, hab. session 10.10.10.30.50.3-0.0
Total locomotion distance, hab. session 10.50.71.71.30.30.6
Locomotion velocity, hab. session 10.30.50.70.8-0.20.8
Time in familiar zone, hab. session 21.51.52.70.61.6-1.2
Time in novel zone, hab. session 20.70.71.2-0.5-1.10.8
Total zone transitions, hab. session 20.81.01.80.71.3-0.8
Total locomotion distance, hab. session 22.12.85.22.31.8-0.0
Locomotion velocity, hab. session 21.72.35.02.21.30.5
Novel to familiar place preference ratio0.00.00.1-0.1-0.30.0
Novelty place preference0.20.20.5-0.5-0.70.2
Time in novel zone, NPP test0.20.20.4-0.6-0.60.1
Total zone transitions, NPP test0.71.01.51.21.2-0.2
Total locomotion distance, NPP test2.53.47.02.71.80.2
Locomotion velocity, NPP test2.43.37.42.71.50.6
Intraocular pressure0.40.51.0-0.8-1.00.1
Delta distance traveled before/after self-admin0.80.91.2-0.5-1.11.1
Delta ambulatory time before/after self-admin0.60.71.0-0.5-1.00.9
Parametrial fat weight1.94.68.3-2.90.1-2.3
Pavlov. Cond. lever latency0.91.12.3-1.5-0.8-0.6
Pavlov. Cond. magazine entry latency0.50.71.1-1.00.2-0.9
Pavlov. Cond. change in total contacts0.80.81.50.1-1.01.2
Pavlov. Cond. index score0.10.10.20.30.4-0.1
Pavlov. Cond. latency score0.20.20.40.60.40.2
Pavlov. Cond. lever contacts0.60.81.61.30.70.5
Pavlov. Cond. magazine entry number0.40.51.21.10.30.4
Pavlov. Cond. intertrial magazine entries0.30.40.80.5-0.40.9
Pavlov. Cond. lever-magazine prob. diff.0.10.10.30.30.6-0.2
Pavlov. Cond. response bias0.20.30.4-0.60.3-0.6
Pavlov. Cond. lever latency0.91.31.9-0.1-1.41.4
Pavlov. Cond. magazine entry latency1.82.23.81.22.0-1.1
Pavlov. Cond. change in total contacts0.10.10.20.40.5-0.2
Pavlov. Cond. index score0.91.22.10.61.4-1.1
Pavlov. Cond. latency score0.70.91.60.61.3-0.9
Pavlov. Cond. lever contacts1.41.93.10.31.8-1.6
Pavlov. Cond. magazine entry number0.50.61.0-0.3-1.00.8
Pavlov. Cond. intertrial magazine entries0.10.20.50.20.7-0.3
Pavlov. Cond. lever-magazine prob. diff.0.81.01.70.51.3-1.0
Pavlov. Cond. response bias0.81.11.90.21.4-1.2
Time in closed arm before self-admin0.20.20.4-0.40.2-0.6
Time in closed arm after self-admin0.30.40.7-0.8-0.60.0
Time in open arm before self-admin0.30.30.60.80.50.1
Time in open arm after self-admin0.50.60.9-0.4-1.00.8
Bone: periosteal estimation0.30.61.0-0.90.3-1.0
Bone: periosteal perimeter0.00.00.1-0.20.1-0.2
Bone: post-yield work1.21.73.1-0.51.3-1.8
Progressive ratio test 1 active lever presses0.10.20.3-0.40.0-0.5
Progressive ratio test 1 breakpoint0.10.10.2-0.40.0-0.5
Progressive ratio test 1 inactive lever presses0.60.91.30.81.2-0.7
Progressive ratio test 2 active lever presses0.50.61.10.31.1-0.8
Progressive ratio test 2 breakpoint0.60.71.20.31.1-0.9
Progressive ratio test 2 inactive lever presses1.32.23.80.92.0-1.4
Incentive Sensitization - Responses0.50.71.11.01.0-0.2
Incentive Sensitization - Breakpoint0.60.71.21.01.1-0.2
Sum of active levers in priming session hrs 5-60.30.20.4-0.4-0.70.4
Progressive ratio0.10.20.4-0.7-0.3-0.2
Food seeking constrained by brief footshock1.11.43.31.80.70.6
Seeking ratio, punishment vs. effort0.71.02.21.50.80.2
Retroperitoneal fat weight4.017.338.1-6.2-1.4-3.4
Reaction time number correct0.61.11.7-0.0-1.21.3
Reaction time mean minus median0.20.61.2-0.50.6-1.1
Reaction time mean minus median AUC0.00.10.20.00.3-0.4
Reaction time num false alarms0.10.20.40.6-0.00.4
Reaction time num false alarms AUC0.40.60.91.0-0.20.9
Reaction time trials correct on left0.61.11.7-0.0-1.21.3
Reaction time trials on left0.61.21.90.0-1.31.4
Reaction time mean0.20.30.7-0.20.5-0.8
Reaction time mean AUC0.20.30.7-0.20.5-0.8
Median of all reaction times0.30.40.60.00.7-0.8
Reaction time omissions0.10.20.40.1-0.50.6
Reaction time false alarm rate0.20.30.80.90.40.2
Reaction time premature initiation rate0.10.20.4-0.30.1-0.6
Reaction time premature initiations0.10.20.5-0.2-0.70.4
Std. dev. reaction times0.20.30.7-0.40.4-0.9
Reaction time trials completed0.61.21.90.0-1.31.4
Reaction time trials AUC0.61.21.9-0.1-1.31.4
Run reversals in cocaine runway, females0.20.20.4-0.30.4-0.7
Run reversals in cocaine runway, males0.10.10.2-0.2-0.30.5
Latency to leave start box in cocaine runway3.94.49.9-3.1-0.8-1.6
Latency to leave start box in cocaine runway, F3.54.07.8-2.8-0.1-2.1
Latency to leave start box in cocaine runway, M2.01.83.1-1.8-1.50.2
Std. dev. time between licks in bursts0.30.40.8-0.1-0.90.6
Total sessions with >9 infusions0.30.30.6-0.10.6-0.8
Short access day 1 total inactive lever presses2.63.46.2-0.61.9-2.5
Short access day 10 total inactive lever presses2.15.08.20.82.9-2.5
Short access day 1 total infusions0.30.40.70.40.8-0.6
Short access day 10 total infusions0.30.40.50.40.7-0.6
Short access total infusions0.60.71.5-0.50.7-1.2
Short access day 1 locomotion0.00.00.00.20.00.1
Short access day 10 total locomotion0.81.62.81.71.3-0.0
Short access total locomotion0.60.71.51.20.80.1
One hour access (0.3 mA shock)1.01.22.10.71.5-0.9
Compulsive drug intake0.40.50.91.00.20.6
One hour access (shock baseline)0.60.91.6-0.21.0-1.3
Social response proportion0.30.30.7-0.9-0.1-0.5
Social responses0.10.10.20.3-0.20.5
Social time0.30.50.70.20.8-0.8
Soleus weight0.10.40.60.7-0.30.8
Bone: stiffness1.72.75.5-2.3-1.6-0.1
Tibialis anterior weight0.20.61.1-1.10.1-0.8
Time to tail flick, vehicle, before self-admin2.32.43.8-2.0-1.80.4
Time to tail flick, vehicle, after self-admin0.40.50.9-0.80.2-0.9
Time to tail flick, test, before self-admin1.01.11.70.31.3-1.2
Time to tail flick, test, after self-admin2.52.64.4-0.31.8-2.1
Delta time to tail flick, vehicle, before/after SA0.90.81.40.91.2-0.6
Delta time to tail flick, test, before/after SA0.20.20.30.00.6-0.4
Tibia length3.59.622.2-4.7-2.0-1.5
Ambulatory time before self-admin0.00.10.2-0.1-0.40.1
Ambulatory time after self-admin1.82.13.6-1.2-1.91.1
Bone: tissue strength0.10.10.10.10.4-0.2
Total heroin consumption0.00.10.1-0.3-0.20.1
Bone: trabecular number1.52.55.0-0.71.4-2.2
Bone: trabecular spacing2.43.24.8-0.5-2.22.1
Bone: trabecular thickness0.60.81.3-1.00.2-1.1
Bone: trabecular tissue density0.20.30.5-0.2-0.70.6
Water consumed over 24 hours0.71.02.00.61.4-0.8
Number of responses in last shaping day0.10.10.20.20.4-0.3