Sf1

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 isoform ratio XM_039080342.1 0.04 0.02 4.5e-04 0.03 0.04 0.02 0.03 3.9e-04 2.4e-04 8.6e-03 3.9e-04
2 RMTg alternative TSS XM_039080429.1 0.18 0.09 3.8e-04 0.12 0.1 0.06 0.1 5.0e-04 1.4e-03 1.2e-02 1.0e-03
3 RMTg gene expression Sf1 0.15 0.1 8.7e-03 0 0 -0.01 0 2.5e-01 3.3e-01 5.6e-01 2.7e-01
4 BLA alternative polyA XM_039080582.1 0.11 0.07 2.9e-03 0.01 0.02 0.02 0.02 1.1e-01 3.2e-02 3.0e-02 2.7e-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 4
Bone: apparent density0.50.81.70.4-0.6-0.9-1.3
Area under the delay curve0.10.10.30.2-0.3-0.40.5
BMI with tail2.06.48.32.6-2.9-2.1-2.5
BMI without tail1.32.75.42.0-2.3-1.0-0.7
Body weight2.18.715.53.8-3.90.5-2.1
Weight adjusted by age1.61.82.41.3-1.51.2-1.2
Bone surface2.54.310.41.7-1.90.5-3.2
Bone volume1.42.38.40.5-0.7-0.2-2.9
Breakpoint value in progressive ratio session1.92.12.31.4-1.51.4-1.4
Number of licking bursts0.10.20.30.3-0.30.4-0.5
Context. condit. distance diff. score1.11.31.8-1.11.1-1.40.9
Locomotion velocity, session 10.30.30.70.6-0.4-0.00.9
Locomotion distance, session 10.40.50.90.9-0.7-0.7-0.1
Locomotion velocity, session 21.51.73.31.8-1.70.4-0.7
Locomotion distance, session 20.40.61.41.2-1.0-0.30.1
Locomotion velocity, session 30.80.93.2-0.30.5-1.8-0.1
Locomotion distance, session 30.10.10.2-0.10.1-0.40.1
Stereotopy head waving bouts, day 31.11.34.5-0.40.6-2.10.1
Stereotopy head waving duration, day 30.70.92.1-0.80.9-1.40.0
Locomotion velocity, session 71.21.43.6-0.81.0-1.9-0.5
Locomotion distance, session 70.40.51.50.10.0-1.20.6
Stereotopy head waving bouts, day 70.60.71.2-0.80.8-0.5-1.1
Stereotopy head waving duration, day 70.60.72.10.5-0.60.4-1.4
Locomotion velocity, session 81.01.22.31.5-1.30.40.7
Locomotion distance, session 80.50.72.7-0.30.4-1.6-0.3
Degree of sensitization distance0.40.41.50.00.1-1.2-0.0
Degree of sensitization stereotypy0.60.62.2-0.00.00.5-1.5
Conditioned locomotion1.01.22.11.4-1.40.7-0.3
Cocaine response after cond. corrected0.91.01.7-0.70.6-1.31.3
Cocaine response after cond. not corrected0.70.81.7-0.60.4-1.31.1
Cocaine response before conditioning0.40.51.00.5-0.60.7-1.0
Saline control response2.73.66.52.5-2.51.2-0.2
Bone: connectivity density1.21.92.81.5-1.7-0.1-1.7
Bone: cortical apparent density0.60.82.10.6-0.61.50.7
Bone: cortical area0.40.61.80.6-0.60.4-1.3
Bone: cortical porosity0.00.10.10.1-0.1-0.3-0.3
Bone: cortical porosity0.30.30.50.7-0.70.1-0.3
Bone: cortical thickness2.33.85.12.3-2.22.20.4
Bone: cortical thickness1.41.72.11.3-1.21.11.5
Bone: cortical tissue density0.81.02.50.7-0.71.60.7
Condit. Reinf. active minus inactive responses0.10.10.20.4-0.50.20.1
Condit. Reinf. active-inactive response ratio0.20.20.40.2-0.30.70.4
Condit. Reinf. active responses0.10.10.2-0.00.0-0.5-0.4
Condit. Reinf. inactive responses0.80.91.9-0.50.6-1.4-1.0
Incentive salience index mean0.20.20.40.6-0.7-0.3-0.3
Condit. Reinf. lever presses0.30.41.00.4-0.5-0.6-1.0
Condit. Reinf. active minus inactive responses0.50.61.0-0.90.9-0.3-1.0
Condit. Reinf. active-inactive response ratio2.32.43.2-1.61.5-1.3-1.8
Condit. Reinf. active responses0.10.10.4-0.20.10.2-0.7
Condit. Reinf. inactive responses0.60.81.10.9-1.10.70.7
Condit. Reinf. lever presses1.21.74.20.9-0.81.0-2.1
Condit. Reinf. lever reinforcers received0.20.30.80.1-0.20.6-0.9
Conditioned reinforcement - actives1.01.01.9-1.01.0-0.1-1.4
Conditioned reinforcement - inactives4.55.110.5-3.22.9-1.0-0.6
Conditioned locomotion5.56.612.4-3.53.5-1.30.5
Patch foraging indifference point 0 sec0.10.20.5-0.30.7-0.3-0.0
Patch foraging indifference point AUC2.52.94.11.6-1.72.0-1.4
Delay disc. indifference point, 0s delay0.40.51.00.1-0.1-1.00.9
Delay disc. indifference point, 16s delay0.80.81.3-1.11.2-0.70.0
Delay disc. indifference point, 2s delay0.10.10.4-0.20.0-0.6-0.1
Delay disc. indifference point, 24s delay0.50.51.70.3-0.40.31.3
Delay disc. indifference point, 4s delay0.60.61.70.4-0.6-0.51.3
Delay disc. indifference point, 8s delay0.40.41.00.4-0.5-0.31.0
Indifference point function ln k5.47.58.6-2.52.8-2.92.8
Indifference point function log k5.47.58.6-2.52.8-2.92.8
Patch foraging total patch changes 0 sec0.10.10.2-0.10.5-0.00.5
Patch foraging total patch changes 12 sec2.63.34.62.1-2.11.8-1.2
Patch foraging total patch changes 18 sec0.40.51.20.5-0.50.4-1.1
Patch foraging total patch changes 24 sec1.62.02.71.7-1.51.6-0.5
Patch foraging total patch changes 6 sec0.40.61.41.2-0.90.3-0.0
Patch foraging time to switch 0 sec1.21.94.71.0-1.3-0.4-2.2
Patch foraging water rate 0 sec2.23.55.9-2.12.4-0.41.8
Patch foraging water rate 12 sec4.46.812.5-2.42.8-1.03.5
Patch foraging water rate 18 sec1.92.64.6-1.31.6-1.32.2
Patch foraging water rate 24 sec1.92.73.7-1.71.8-0.91.9
Patch foraging water rate 6 sec2.43.57.9-1.41.8-1.12.8
Seeking ratio, delayed vs. immediate footshock0.10.10.1-0.20.2-0.30.4
Distance traveled before self-admin0.60.72.10.3-0.40.6-1.4
Distance traveled after self-admin0.30.30.70.0-0.10.8-0.7
Extensor digitorum longus weight4.216.728.15.3-5.32.4-2.2
Bone: elastic displacement1.21.34.8-0.30.60.02.2
Bone: elastic work1.41.82.41.5-1.40.81.4
Bone: endosteal estimation1.94.29.9-1.51.5-3.1-1.6
Bone: endosteal perimeter2.85.89.0-2.12.0-3.0-2.4
Epididymis fat weight2.15.06.9-2.62.5-2.6-0.4
Delta time in closed arm before/after self-admin1.41.33.71.0-0.6-0.41.9
Delta time in open arm before/after self-admin0.80.71.8-0.40.01.0-1.3
Diff in mean of infusions in LGA sessions0.40.51.00.6-0.71.0-0.2
Delay discount exponential model param0.10.10.3-0.20.40.2-0.6
Extinction: sum of active levers before priming2.72.64.11.8-2.01.1-1.4
Active lever presses in extinction session 61.81.82.71.1-1.11.4-1.7
Bone: final force1.62.53.41.8-1.90.7-1.7
Bone: final moment1.42.23.01.7-1.70.6-1.6
Food consumed during 24 hour testing period0.30.41.2-0.20.11.1-0.5
Glucose2.03.05.3-1.81.8-2.3-0.4
Heart weight2.33.24.1-1.91.9-2.01.2
Delay discount hyperbolic model param0.20.20.3-0.30.40.2-0.6
Intermittent access intake day 1-15 change0.80.81.5-1.21.00.2-0.7
Intermittent access intake escalation0.70.71.4-1.21.00.0-0.7
Intermittent access intake escalation 20.60.60.7-0.80.60.7-0.8
Intermitt. access day 1 inactive lever presses1.81.93.5-1.91.9-0.8-0.0
Intermitt. access day 15 inactive lever presses2.83.05.6-2.42.2-0.9-0.9
Intermitt. access escalation Index2.22.02.9-1.21.2-1.71.5
Intermittent access day 1 total infusions6.37.313.1-2.92.8-3.6-0.6
Intermittent access day 15 total infusions7.78.713.8-3.73.5-2.9-0.8
Intermittent access terminal intake (last 3 days)6.67.310.5-3.22.9-2.9-1.5
Intermittent access total infusions6.16.79.1-3.02.8-3.0-1.2
Intermittent access day 1 locomotion4.54.711.3-1.92.0-3.40.3
Intermittent access day 15 total locomotion4.54.88.3-2.92.5-2.1-0.7
Intermittent access total locomotion7.58.612.7-3.33.0-3.6-1.3
Intermittent access standard deviation1.11.12.3-1.51.4-0.3-0.5
Left kidney weight0.51.52.6-1.61.4-0.9-0.6
Right kidney weight0.41.22.0-1.21.0-0.1-1.4
Cocaine induced anxiety0.20.31.0-0.20.0-0.1-1.0
Post-drug Anxiety1.21.43.80.7-0.70.8-2.0
Baseline Anxiety1.51.62.81.7-1.51.1-0.2
Tail length1.13.44.52.0-2.02.11.0
Length with tail1.45.38.22.9-2.72.3-0.5
Length without tail0.92.03.41.8-1.61.2-1.0
Times rat made contact with spout0.70.81.11.0-1.00.90.6
Lifetime Intake5.15.79.4-2.62.5-3.1-0.8
Liver weight, left0.10.10.2-0.20.2-0.5-0.2
Liver weight, right0.30.41.30.3-0.4-1.20.5
Locomotor activity1.22.05.5-0.91.0-0.62.4
Locomotor testing distance1.93.110.1-0.91.0-0.83.2
Locomotor testing rearing1.42.16.0-0.91.0-0.72.4
Locomotion in novel chamber4.45.49.1-3.02.9-1.9-0.9
Locomotion in novel chamber post-restriction2.32.74.5-2.12.1-1.40.2
Fecal boli incidents, locomotor time 11.11.34.6-0.50.20.2-2.2
Change in fecal boli incidents, locomotor task1.00.92.20.7-0.5-0.91.5
Time >=10cm from walls, locomotor time 13.03.04.7-1.41.2-2.2-2.0
Bouts of movement, locomotor time 11.71.86.00.8-0.72.4-0.4
Total resting periods, locomotor time 11.21.34.20.5-0.52.0-0.7
Rest time, locomotor task time 10.80.91.7-1.21.3-0.50.2
Distance moved, locomotor task time 10.20.20.40.3-0.6-0.6-0.3
Vertical activity count, locomotor time 10.80.81.2-1.10.9-0.90.6
Time >=10cm from walls, locomotor time 20.40.41.4-0.40.30.3-1.2
Bouts of movement, locomotor time 20.60.62.00.5-0.51.40.0
Total resting periods, locomotor time 20.30.31.20.3-0.21.1-0.0
Rest time, locomotor task time 21.82.13.5-1.71.9-1.40.3
Distance moved, locomotor task time 20.81.01.61.1-1.31.0-0.2
Vertical activity count, locomotor time 20.60.72.20.4-0.50.41.5
Light reinforcement 10.10.30.6-0.30.40.50.7
Light reinforcement 21.92.54.3-1.82.1-0.6-1.4
Bone: marrow area2.04.310.3-1.51.5-3.2-1.5
Bone: maximum diameter0.71.24.8-0.20.1-0.3-2.2
Bone: maximum force1.93.37.51.6-1.7-0.0-2.7
Bone: maximum moment1.62.86.41.5-1.6-0.1-2.5
Mean time between licks in bursts1.31.82.51.6-1.40.41.6
Mean num. licks in bursts0.20.20.9-0.00.10.01.0
Cd content in liver0.90.92.3-1.51.10.0-0.5
Co content in liver1.82.17.3-0.40.40.82.7
Cu content in liver0.20.20.40.4-0.60.5-0.2
Fe content in liver0.10.10.40.2-0.4-0.1-0.6
K content in liver1.21.22.01.2-1.4-0.6-0.9
Mg content in liver0.40.41.10.1-0.2-1.1-0.6
Mn content in liver1.41.63.01.1-1.01.0-1.7
Na content in liver0.70.71.10.8-0.70.7-1.0
Rb content in liver1.01.21.7-1.21.2-1.30.6
Se content in liver1.01.23.4-0.90.7-0.1-1.9
Sr content in liver2.72.44.71.5-1.52.2-0.6
Zn content in liver0.50.60.80.9-0.80.8-0.5
Bone: minimum diameter1.63.06.2-1.41.3-2.5-1.3
Time in familiar zone, hab. session 10.30.30.8-0.50.4-0.9-0.1
Time in novel zone, hab. session 10.50.51.70.20.00.21.3
Total zone transitions, hab. session 10.30.40.60.8-0.70.6-0.4
Total locomotion distance, hab. session 10.40.61.4-0.60.7-1.2-0.3
Locomotion velocity, hab. session 10.10.20.5-0.20.3-0.7-0.4
Time in familiar zone, hab. session 20.80.82.10.7-0.8-0.31.4
Time in novel zone, hab. session 20.20.20.6-0.20.20.3-0.8
Total zone transitions, hab. session 20.70.91.61.3-1.2-0.4-0.8
Total locomotion distance, hab. session 20.40.62.20.1-0.1-1.5-0.2
Locomotion velocity, hab. session 20.60.93.0-0.20.3-1.7-0.6
Novel to familiar place preference ratio1.21.23.70.3-0.50.9-1.9
Novelty place preference0.80.82.5-0.0-0.20.7-1.6
Time in novel zone, NPP test0.50.51.80.0-0.20.6-1.3
Total zone transitions, NPP test1.11.62.71.6-1.60.5-1.0
Total locomotion distance, NPP test0.10.20.60.3-0.2-0.8-0.2
Locomotion velocity, NPP test0.10.10.30.2-0.1-0.5-0.3
Intraocular pressure1.01.52.8-1.71.30.4-1.0
Delta distance traveled before/after self-admin0.30.31.10.1-0.10.11.0
Delta ambulatory time before/after self-admin0.40.51.70.3-0.20.21.3
Parametrial fat weight2.24.37.8-2.22.0-2.8-0.8
Pavlov. Cond. lever latency0.20.30.5-0.50.60.30.7
Pavlov. Cond. magazine entry latency0.20.30.80.2-0.4-0.1-0.9
Pavlov. Cond. change in total contacts0.50.62.0-0.50.30.2-1.4
Pavlov. Cond. index score0.20.20.50.2-0.40.3-0.7
Pavlov. Cond. latency score0.10.10.30.2-0.3-0.1-0.6
Pavlov. Cond. lever contacts0.10.10.10.2-0.3-0.4-0.1
Pavlov. Cond. magazine entry number0.40.50.9-0.10.3-1.00.9
Pavlov. Cond. intertrial magazine entries0.50.61.2-1.11.10.20.1
Pavlov. Cond. lever-magazine prob. diff.0.30.40.80.4-0.60.4-0.9
Pavlov. Cond. response bias0.10.20.40.0-0.20.5-0.6
Pavlov. Cond. lever latency0.50.62.4-0.30.2-0.21.5
Pavlov. Cond. magazine entry latency2.02.33.61.7-1.91.2-1.1
Pavlov. Cond. change in total contacts1.52.16.70.4-0.51.1-2.6
Pavlov. Cond. index score1.41.84.21.0-1.10.9-2.0
Pavlov. Cond. latency score1.21.54.00.9-1.00.6-2.0
Pavlov. Cond. lever contacts0.40.61.70.3-0.20.7-1.3
Pavlov. Cond. magazine entry number3.64.35.2-2.22.3-2.01.9
Pavlov. Cond. intertrial magazine entries0.60.81.3-1.11.0-1.00.2
Pavlov. Cond. lever-magazine prob. diff.1.72.13.91.3-1.41.1-2.0
Pavlov. Cond. response bias1.11.52.81.0-0.91.2-1.7
Time in closed arm before self-admin0.50.52.0-0.30.1-0.2-1.4
Time in closed arm after self-admin0.30.30.90.10.1-0.90.7
Time in open arm before self-admin1.81.97.50.3-0.2-0.22.7
Time in open arm after self-admin0.40.40.8-0.10.00.90.9
Bone: periosteal estimation1.02.04.3-0.70.6-1.7-2.1
Bone: periosteal perimeter0.71.13.5-0.30.2-0.9-1.9
Bone: post-yield work4.05.415.4-0.70.7-2.3-3.9
Progressive ratio test 1 active lever presses2.52.74.5-2.12.1-1.30.0
Progressive ratio test 1 breakpoint2.12.23.9-2.01.9-1.10.1
Progressive ratio test 1 inactive lever presses0.80.91.3-1.11.1-0.70.7
Progressive ratio test 2 active lever presses4.64.98.3-2.92.7-1.9-0.9
Progressive ratio test 2 breakpoint4.85.49.5-3.13.0-1.7-0.3
Progressive ratio test 2 inactive lever presses7.48.515.4-3.93.5-2.4-0.8
Incentive Sensitization - Responses1.01.01.5-1.21.0-0.7-1.0
Incentive Sensitization - Breakpoint1.21.22.0-1.41.2-0.8-1.0
Sum of active levers in priming session hrs 5-62.12.04.80.2-0.31.7-2.2
Progressive ratio1.51.73.31.3-1.4-0.4-1.8
Food seeking constrained by brief footshock0.50.71.20.8-0.80.11.1
Seeking ratio, punishment vs. effort1.82.17.4-0.70.80.02.7
Retroperitoneal fat weight4.113.519.5-4.44.4-3.90.1
Reaction time number correct0.20.30.60.8-0.60.70.1
Reaction time mean minus median2.12.75.51.2-1.51.2-2.3
Reaction time mean minus median AUC1.21.62.11.0-1.31.2-1.5
Reaction time num false alarms1.01.34.70.20.3-0.62.2
Reaction time num false alarms AUC0.81.13.60.8-0.5-0.11.9
Reaction time trials correct on left0.20.30.60.8-0.60.70.1
Reaction time trials on left0.30.40.70.8-0.60.80.1
Reaction time mean0.30.51.3-0.40.20.6-1.2
Reaction time mean AUC0.40.61.6-0.50.30.5-1.3
Median of all reaction times0.30.40.7-0.70.60.3-0.8
Reaction time omissions0.60.91.40.9-0.91.2-0.6
Reaction time false alarm rate0.60.92.90.20.1-0.71.7
Reaction time premature initiation rate3.34.46.92.6-2.51.61.4
Reaction time premature initiations4.56.39.63.1-2.92.31.4
Std. dev. reaction times0.71.02.40.4-0.61.0-1.5
Reaction time trials completed0.30.40.70.8-0.60.80.1
Reaction time trials AUC0.20.30.50.7-0.50.50.3
Run reversals in cocaine runway, females1.21.21.41.2-1.0-1.11.0
Run reversals in cocaine runway, males0.20.20.6-0.20.00.40.8
Latency to leave start box in cocaine runway0.40.41.0-0.30.4-1.0-0.7
Latency to leave start box in cocaine runway, F0.10.10.2-0.10.1-0.0-0.5
Latency to leave start box in cocaine runway, M0.50.51.4-0.20.4-1.2-0.5
Std. dev. time between licks in bursts0.81.03.40.6-0.4-0.31.8
Total sessions with >9 infusions2.42.66.2-1.41.5-2.50.3
Short access day 1 total inactive lever presses3.23.55.4-2.22.3-1.80.7
Short access day 10 total inactive lever presses2.42.73.9-1.61.8-1.12.0
Short access day 1 total infusions3.23.46.8-1.91.8-2.6-0.0
Short access day 10 total infusions3.43.89.3-1.61.6-3.0-0.8
Short access total infusions2.32.67.0-1.31.4-2.6-0.2
Short access day 1 locomotion2.72.96.8-1.51.5-2.60.4
Short access day 10 total locomotion1.92.14.8-1.41.3-2.20.2
Short access total locomotion2.02.04.9-1.21.3-2.20.4
One hour access (0.3 mA shock)8.19.515.5-3.93.9-2.7-0.0
Compulsive drug intake4.54.55.72.4-2.12.21.8
One hour access (shock baseline)9.410.918.3-4.34.0-2.7-1.6
Social response proportion0.70.70.90.7-1.00.7-0.9
Social responses0.30.40.80.7-0.90.60.0
Social time0.50.71.20.9-1.10.80.3
Soleus weight2.57.210.7-3.23.3-2.61.0
Bone: stiffness1.62.56.81.2-1.30.2-2.6
Tibialis anterior weight6.522.135.05.8-5.93.7-2.5
Time to tail flick, vehicle, before self-admin0.60.61.20.6-0.8-0.3-1.1
Time to tail flick, vehicle, after self-admin1.82.04.41.8-2.1-0.50.0
Time to tail flick, test, before self-admin1.21.24.0-0.50.5-2.00.5
Time to tail flick, test, after self-admin0.10.10.10.2-0.40.20.0
Delta time to tail flick, vehicle, before/after SA0.60.61.21.1-1.1-0.20.5
Delta time to tail flick, test, before/after SA2.22.06.40.9-0.92.5-0.3
Tibia length1.13.09.70.5-0.71.3-3.1
Ambulatory time before self-admin1.01.03.7-0.1-0.00.5-1.9
Ambulatory time after self-admin0.50.61.1-0.90.7-0.0-1.0
Bone: tissue strength0.20.20.6-0.30.40.0-0.8
Total heroin consumption3.74.36.52.4-2.61.9-1.1
Bone: trabecular number0.71.13.80.1-0.3-0.5-2.0
Bone: trabecular spacing0.50.72.60.10.10.11.6
Bone: trabecular thickness0.70.81.1-1.01.0-0.9-0.5
Bone: trabecular tissue density2.02.95.2-2.32.3-1.00.5
Water consumed over 24 hours1.21.43.01.1-1.21.70.5
Number of responses in last shaping day0.80.91.6-0.90.9-0.41.3