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 0.06 0.04 2.2e-05 0.01 0.03 0.02 0.03 1.4e-02 4.9e-04 7.6e-03 2.1e-03
2 Eye gene expression Sptlc3 0.52 0.17 6.6e-04 0.01 0.1 0 0.05 1.9e-01 1.5e-02 3.3e-01 6.2e-02
3 PL gene expression Sptlc3 0.06 0.03 1.9e-07 0.03 0.05 0.05 0.04 4.0e-04 3.5e-06 8.6e-06 1.7e-05

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 density1.32.14.2-0.81.2-2.1
Area under the delay curve0.40.40.80.90.7-0.1
BMI with tail2.47.717.6-4.2-1.0-2.1
BMI without tail2.04.210.0-3.2-0.7-1.5
Body weight3.815.937.0-6.1-2.4-2.3
Weight adjusted by age0.40.41.1-1.0-0.4-0.3
Bone surface2.03.55.60.32.4-2.2
Bone volume1.42.34.1-0.41.6-2.0
Breakpoint value in progressive ratio session0.91.02.5-1.6-0.6-0.4
Number of licking bursts0.70.81.8-0.4-1.30.6
Context. condit. distance diff. score0.10.20.3-0.50.1-0.4
Locomotion velocity, session 10.40.40.70.70.8-0.1
Locomotion distance, session 13.13.96.42.22.5-0.7
Locomotion velocity, session 21.11.22.51.61.10.2
Locomotion distance, session 22.53.56.72.61.90.1
Locomotion velocity, session 30.40.51.11.10.6-0.1
Locomotion distance, session 30.00.00.00.1-0.1-0.0
Stereotopy head waving bouts, day 30.50.51.1-0.40.6-1.1
Stereotopy head waving duration, day 30.20.30.5-0.30.4-0.7
Locomotion velocity, session 70.50.50.70.6-0.60.9
Locomotion distance, session 70.10.10.1-0.3-0.3-0.1
Stereotopy head waving bouts, day 70.10.10.1-0.30.1-0.3
Stereotopy head waving duration, day 70.50.61.00.11.0-0.9
Locomotion velocity, session 80.40.41.01.00.50.3
Locomotion distance, session 80.60.91.51.21.1-0.2
Degree of sensitization distance0.20.20.30.10.6-0.6
Degree of sensitization stereotypy0.10.10.2-0.4-0.1-0.2
Conditioned locomotion0.91.12.5-1.6-0.7-0.5
Cocaine response after cond. corrected0.30.30.50.3-0.60.7
Cocaine response after cond. not corrected0.20.20.30.5-0.10.5
Cocaine response before conditioning0.80.91.80.71.3-0.7
Saline control response0.00.00.0-0.10.2-0.1
Bone: connectivity density2.94.57.7-0.22.4-2.8
Bone: cortical apparent density2.33.05.4-1.6-2.31.1
Bone: cortical area4.66.912.4-3.5-2.90.3
Bone: cortical porosity1.51.73.1-1.00.9-1.8
Bone: cortical porosity1.41.52.5-1.60.1-1.4
Bone: cortical thickness9.515.528.7-5.4-4.20.3
Bone: cortical thickness4.04.67.3-2.7-2.50.1
Bone: cortical tissue density2.12.74.9-1.4-2.21.2
Condit. Reinf. active minus inactive responses0.70.81.4-0.80.5-1.2
Condit. Reinf. active-inactive response ratio0.30.30.5-0.7-0.1-0.7
Condit. Reinf. active responses0.00.00.00.00.1-0.1
Condit. Reinf. inactive responses0.40.50.91.00.10.8
Incentive salience index mean0.60.71.30.71.2-0.6
Condit. Reinf. lever presses1.21.63.31.81.10.5
Condit. Reinf. active minus inactive responses0.10.10.30.50.20.3
Condit. Reinf. active-inactive response ratio0.10.10.30.50.10.3
Condit. Reinf. active responses0.10.10.20.40.20.2
Condit. Reinf. inactive responses0.00.00.10.20.10.2
Condit. Reinf. lever presses1.92.64.41.72.1-0.6
Condit. Reinf. lever reinforcers received0.20.30.60.70.50.3
Conditioned reinforcement - actives1.31.32.21.51.30.0
Conditioned reinforcement - inactives0.70.81.61.30.90.4
Conditioned locomotion1.11.43.01.70.90.5
Patch foraging indifference point 0 sec1.11.73.92.00.90.5
Patch foraging indifference point AUC5.36.110.62.5-1.33.3
Delay disc. indifference point, 0s delay0.10.10.20.00.4-0.4
Delay disc. indifference point, 16s delay1.01.02.41.60.60.4
Delay disc. indifference point, 2s delay1.71.92.81.61.7-0.6
Delay disc. indifference point, 24s delay0.10.10.20.50.30.0
Delay disc. indifference point, 4s delay0.10.10.20.40.3-0.2
Delay disc. indifference point, 8s delay0.20.20.30.10.6-0.5
Indifference point function ln k3.14.47.7-2.10.9-2.8
Indifference point function log k3.14.47.7-2.10.9-2.8
Patch foraging total patch changes 0 sec1.32.04.72.20.80.9
Patch foraging total patch changes 12 sec1.52.03.71.90.31.5
Patch foraging total patch changes 18 sec5.67.212.93.6-0.12.9
Patch foraging total patch changes 24 sec4.04.99.03.00.02.4
Patch foraging total patch changes 6 sec3.04.47.02.4-0.82.7
Patch foraging time to switch 0 sec2.13.24.7-2.10.6-2.2
Patch foraging water rate 0 sec2.74.46.42.5-0.82.5
Patch foraging water rate 12 sec1.01.52.31.3-0.71.5
Patch foraging water rate 18 sec1.72.23.40.3-1.81.9
Patch foraging water rate 24 sec3.85.28.80.9-2.53.0
Patch foraging water rate 6 sec1.82.65.0-0.8-2.21.5
Seeking ratio, delayed vs. immediate footshock1.01.22.3-0.80.8-1.5
Distance traveled before self-admin0.10.10.30.60.10.3
Distance traveled after self-admin3.03.45.7-0.9-2.41.9
Extensor digitorum longus weight0.00.10.1-0.10.3-0.3
Bone: elastic displacement1.21.42.5-1.0-1.60.8
Bone: elastic work2.73.47.6-2.8-1.6-0.4
Bone: endosteal estimation2.65.710.21.73.2-2.0
Bone: endosteal perimeter1.63.46.01.62.5-1.2
Epididymis fat weight3.88.919.4-4.4-0.9-2.5
Delta time in closed arm before/after self-admin0.20.20.40.1-0.60.5
Delta time in open arm before/after self-admin1.21.12.2-1.5-1.1-0.1
Diff in mean of infusions in LGA sessions0.00.00.10.1-0.30.2
Delay discount exponential model param0.30.40.7-0.9-0.60.0
Extinction: sum of active levers before priming0.30.30.6-0.3-0.70.6
Active lever presses in extinction session 61.41.32.9-1.7-0.1-1.1
Bone: final force2.94.79.5-3.1-2.2-0.2
Bone: final moment2.43.98.4-2.9-1.8-0.4
Food consumed during 24 hour testing period5.16.19.7-0.32.9-3.1
Glucose0.50.81.2-1.10.1-1.0
Heart weight1.21.73.9-2.0-1.0-0.5
Delay discount hyperbolic model param0.40.50.9-1.0-0.70.1
Intermittent access intake day 1-15 change3.73.76.30.32.5-2.2
Intermittent access intake escalation5.04.98.80.63.0-2.4
Intermittent access intake escalation 26.06.010.40.43.2-2.7
Intermitt. access day 1 inactive lever presses0.40.40.91.00.40.2
Intermitt. access day 15 inactive lever presses0.80.91.8-0.70.6-1.4
Intermitt. access escalation Index0.60.51.1-1.1-0.2-0.6
Intermittent access day 1 total infusions0.50.61.2-1.1-0.4-0.5
Intermittent access day 15 total infusions1.82.13.6-0.51.6-1.9
Intermittent access terminal intake (last 3 days)1.51.62.8-0.51.3-1.7
Intermittent access total infusions0.91.01.7-0.70.8-1.3
Intermittent access day 1 locomotion0.20.20.4-0.40.2-0.6
Intermittent access day 15 total locomotion1.11.22.30.51.5-1.0
Intermittent access total locomotion0.40.40.80.30.9-0.6
Intermittent access standard deviation5.05.39.91.43.2-2.0
Left kidney weight0.41.02.0-1.4-1.0-0.3
Right kidney weight0.51.52.2-1.5-1.50.1
Cocaine induced anxiety1.21.32.01.41.4-0.3
Post-drug Anxiety0.10.10.20.40.40.0
Baseline Anxiety1.71.83.4-1.8-1.5-0.1
Tail length0.82.35.2-2.3-1.3-0.4
Length with tail1.55.512.5-3.5-1.8-0.9
Length without tail0.71.53.4-1.8-0.6-0.9
Times rat made contact with spout0.60.71.20.61.1-0.7
Lifetime Intake0.40.51.0-0.50.6-1.0
Liver weight, left0.40.61.4-1.2-0.0-0.7
Liver weight, right1.83.14.7-1.9-2.20.8
Locomotor activity0.91.42.61.11.6-0.6
Locomotor testing distance1.32.23.61.71.9-0.4
Locomotor testing rearing1.92.95.82.41.70.2
Locomotion in novel chamber2.22.74.5-1.7-2.10.9
Locomotion in novel chamber post-restriction0.00.00.0-0.2-0.20.2
Fecal boli incidents, locomotor time 10.10.10.10.2-0.20.3
Change in fecal boli incidents, locomotor task0.50.40.9-0.9-0.5-0.4
Time >=10cm from walls, locomotor time 10.10.10.3-0.10.5-0.3
Bouts of movement, locomotor time 10.70.81.40.8-0.51.2
Total resting periods, locomotor time 10.60.71.20.9-0.31.1
Rest time, locomotor task time 11.31.42.40.51.6-1.3
Distance moved, locomotor task time 12.52.74.1-0.1-2.02.0
Vertical activity count, locomotor time 10.00.00.1-0.20.1-0.3
Time >=10cm from walls, locomotor time 21.92.13.4-1.31.1-1.8
Bouts of movement, locomotor time 20.30.30.5-0.1-0.70.6
Total resting periods, locomotor time 20.30.30.6-0.1-0.80.6
Rest time, locomotor task time 20.40.50.80.1-0.90.8
Distance moved, locomotor task time 20.70.81.40.91.2-0.4
Vertical activity count, locomotor time 21.92.14.30.82.1-1.1
Light reinforcement 11.22.33.71.51.9-0.9
Light reinforcement 20.60.81.30.21.1-1.0
Bone: marrow area2.55.59.81.73.1-1.9
Bone: maximum diameter0.20.30.6-0.8-0.6-0.0
Bone: maximum force2.23.88.8-3.0-1.5-0.6
Bone: maximum moment1.83.27.5-2.7-1.0-1.0
Mean time between licks in bursts2.53.56.0-1.8-2.51.1
Mean num. licks in bursts1.41.73.40.41.8-1.2
Cd content in liver2.12.33.6-1.80.5-1.9
Co content in liver0.20.20.30.6-0.00.6
Cu content in liver0.10.10.20.50.30.1
Fe content in liver0.70.81.60.51.3-0.7
K content in liver1.41.42.91.70.51.0
Mg content in liver0.10.10.20.4-0.00.4
Mn content in liver3.23.66.91.6-1.22.6
Na content in liver2.12.23.31.81.8-0.2
Rb content in liver1.62.04.0-2.0-1.4-0.2
Se content in liver0.70.91.5-1.2-1.1-0.0
Sr content in liver1.91.72.71.51.6-0.4
Zn content in liver1.21.42.2-1.20.6-1.5
Bone: minimum diameter0.50.91.7-1.30.0-0.9
Time in familiar zone, hab. session 11.51.42.50.71.6-1.1
Time in novel zone, hab. session 10.70.71.10.2-0.91.0
Total zone transitions, hab. session 10.10.10.30.50.3-0.0
Total locomotion distance, hab. session 10.50.81.71.30.20.7
Locomotion velocity, hab. session 10.40.50.80.8-0.30.9
Time in familiar zone, hab. session 21.51.62.80.71.7-1.2
Time in novel zone, hab. session 20.70.71.3-0.6-1.10.7
Total zone transitions, hab. session 20.70.91.80.71.3-0.7
Total locomotion distance, hab. session 22.02.75.02.21.70.1
Locomotion velocity, hab. session 21.72.35.02.21.20.6
Novel to familiar place preference ratio0.00.00.1-0.2-0.30.0
Novelty place preference0.20.20.5-0.5-0.70.2
Time in novel zone, NPP test0.20.20.4-0.6-0.60.0
Total zone transitions, NPP test0.70.91.41.21.2-0.0
Total locomotion distance, NPP test2.43.36.72.61.70.4
Locomotion velocity, NPP test2.33.27.12.71.40.8
Intraocular pressure0.30.50.9-0.7-1.0-0.0
Delta distance traveled before/after self-admin2.52.64.3-0.8-2.11.7
Delta ambulatory time before/after self-admin2.02.13.7-0.7-1.91.5
Parametrial fat weight1.52.96.9-2.6-0.8-1.0
Pavlov. Cond. lever latency0.70.91.9-1.4-0.9-0.4
Pavlov. Cond. magazine entry latency0.40.50.8-0.80.3-0.9
Pavlov. Cond. change in total contacts0.60.71.10.1-0.91.1
Pavlov. Cond. index score0.10.10.30.30.5-0.1
Pavlov. Cond. latency score0.20.20.40.70.50.2
Pavlov. Cond. lever contacts0.70.91.81.30.80.5
Pavlov. Cond. magazine entry number0.50.61.31.10.20.7
Pavlov. Cond. intertrial magazine entries0.30.40.80.5-0.40.9
Pavlov. Cond. lever-magazine prob. diff.0.20.20.50.30.7-0.3
Pavlov. Cond. response bias0.20.20.3-0.20.5-0.5
Pavlov. Cond. lever latency1.31.72.9-0.0-1.51.7
Pavlov. Cond. magazine entry latency1.82.13.61.11.9-1.2
Pavlov. Cond. change in total contacts0.10.10.20.30.5-0.3
Pavlov. Cond. index score1.01.32.10.41.4-1.3
Pavlov. Cond. latency score0.81.01.50.51.2-1.1
Pavlov. Cond. lever contacts1.31.83.00.41.7-1.4
Pavlov. Cond. magazine entry number0.50.61.0-0.2-1.00.9
Pavlov. Cond. intertrial magazine entries0.20.20.50.20.7-0.2
Pavlov. Cond. lever-magazine prob. diff.0.81.11.70.31.3-1.2
Pavlov. Cond. response bias0.91.21.90.41.4-1.2
Time in closed arm before self-admin0.20.20.3-0.10.5-0.6
Time in closed arm after self-admin0.10.10.3-0.3-0.60.2
Time in open arm before self-admin0.40.40.80.90.30.6
Time in open arm after self-admin1.11.21.9-0.4-1.41.3
Bone: periosteal estimation0.30.71.1-1.10.2-1.0
Bone: periosteal perimeter0.10.10.2-0.50.0-0.2
Bone: post-yield work1.82.43.9-0.51.8-2.0
Progressive ratio test 1 active lever presses0.00.00.0-0.00.2-0.2
Progressive ratio test 1 breakpoint0.00.00.00.10.2-0.1
Progressive ratio test 1 inactive lever presses0.50.50.80.70.9-0.5
Progressive ratio test 2 active lever presses0.40.51.00.31.0-0.6
Progressive ratio test 2 breakpoint0.10.20.3-0.00.6-0.3
Progressive ratio test 2 inactive lever presses2.93.36.30.92.5-1.7
Incentive Sensitization - Responses0.30.30.80.30.9-0.3
Incentive Sensitization - Breakpoint0.40.40.90.40.9-0.2
Sum of active levers in priming session hrs 5-60.00.00.0-0.1-0.20.1
Progressive ratio0.10.10.20.1-0.20.4
Food seeking constrained by brief footshock1.31.73.81.90.41.0
Seeking ratio, punishment vs. effort0.70.82.01.40.70.2
Retroperitoneal fat weight3.912.929.6-5.4-1.6-2.5
Reaction time number correct0.91.32.00.1-1.31.4
Reaction time mean minus median0.50.61.3-0.50.6-1.2
Reaction time mean minus median AUC0.10.10.20.00.3-0.5
Reaction time num false alarms0.10.10.20.50.10.3
Reaction time num false alarms AUC0.30.50.70.8-0.10.8
Reaction time trials correct on left0.91.32.00.1-1.31.4
Reaction time trials on left1.01.42.20.1-1.41.5
Reaction time mean0.20.30.7-0.20.5-0.8
Reaction time mean AUC0.20.30.7-0.30.4-0.8
Median of all reaction times0.20.20.40.00.5-0.7
Reaction time omissions0.20.20.40.5-0.30.7
Reaction time false alarm rate0.20.20.50.70.50.1
Reaction time premature initiation rate0.10.20.5-0.30.1-0.7
Reaction time premature initiations0.20.30.6-0.0-0.80.4
Std. dev. reaction times0.30.40.8-0.40.3-0.9
Reaction time trials completed1.01.42.20.1-1.41.5
Reaction time trials AUC0.91.32.00.0-1.41.4
Run reversals in cocaine runway, females0.40.40.7-0.40.6-0.8
Run reversals in cocaine runway, males0.30.30.5-0.2-0.50.7
Latency to leave start box in cocaine runway4.54.910.8-3.3-0.7-1.8
Latency to leave start box in cocaine runway, F4.85.210.3-3.2-0.1-2.3
Latency to leave start box in cocaine runway, M0.80.81.1-1.1-1.10.2
Std. dev. time between licks in bursts0.30.30.7-0.1-0.90.5
Total sessions with >9 infusions0.70.71.30.21.1-0.9
Short access day 1 total inactive lever presses1.82.03.6-0.71.4-1.9
Short access day 10 total inactive lever presses0.50.60.90.40.9-0.8
Short access day 1 total infusions0.30.30.40.10.6-0.6
Short access day 10 total infusions0.00.00.10.3-0.10.2
Short access total infusions0.10.10.2-0.30.0-0.4
Short access day 1 locomotion0.20.20.30.1-0.50.6
Short access day 10 total locomotion1.51.63.51.91.10.4
Short access total locomotion1.21.22.81.70.50.8
One hour access (0.3 mA shock)1.51.73.21.21.8-0.8
Compulsive drug intake0.20.20.40.5-0.10.6
One hour access (shock baseline)1.01.22.00.41.4-1.2
Social response proportion0.30.40.7-0.8-0.3-0.5
Social responses0.10.10.20.3-0.30.4
Social time0.50.71.00.11.0-1.0
Soleus weight0.10.30.40.6-0.30.7
Bone: stiffness1.72.65.5-2.4-1.5-0.2
Tibialis anterior weight0.20.81.1-1.10.5-1.0
Time to tail flick, vehicle, before self-admin2.52.64.1-2.0-1.80.6
Time to tail flick, vehicle, after self-admin0.00.00.0-0.00.1-0.2
Time to tail flick, test, before self-admin2.52.54.2-0.41.7-2.0
Time to tail flick, test, after self-admin3.94.06.9-0.62.2-2.6
Delta time to tail flick, vehicle, before/after SA1.11.11.91.41.2-0.3
Delta time to tail flick, test, before/after SA0.40.30.70.50.8-0.4
Tibia length3.49.522.6-4.7-1.8-1.7
Ambulatory time before self-admin0.00.00.10.30.2-0.0
Ambulatory time after self-admin2.62.95.1-0.9-2.31.6
Bone: tissue strength0.10.10.20.00.5-0.3
Total heroin consumption0.20.20.3-0.6-0.50.3
Bone: trabecular number1.62.65.1-0.91.3-2.3
Bone: trabecular spacing2.73.55.2-0.3-2.32.3
Bone: trabecular thickness1.01.22.1-1.40.1-1.3
Bone: trabecular tissue density0.20.30.4-0.3-0.70.6
Water consumed over 24 hours1.11.32.10.31.5-1.3
Number of responses in last shaping day0.91.01.50.21.2-1.1