Yif1a

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 Adipose gene expression Yif1a 0.19 0.09 1.4e-14 0.1 0.1 0.1 0.1 1.5e-11 2.1e-11 3.3e-11 2.0e-11
2 NAcc gene expression Yif1a 0.04 0.03 3.1e-05 0.03 0.03 0.03 0.02 1.0e-04 3.5e-05 3.7e-05 1.1e-04
3 BLA gene expression Yif1a 0.11 0.11 8.4e-03 0.03 0.04 0.05 0.04 1.7e-02 4.1e-03 1.4e-03 2.1e-03
4 PL gene expression Yif1a 0.06 0.04 1.3e-04 0.05 0.04 0.04 0.04 5.1e-06 2.1e-05 2.4e-05 1.0e-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 4
Bone: apparent density1.83.35.90.8-2.41.32.2
Area under the delay curve0.20.30.6-0.4-0.70.10.8
BMI with tail4.616.025.22.2-4.53.75.0
BMI without tail1.58.011.01.7-2.93.33.2
Body weight2.912.916.23.5-3.74.03.1
Weight adjusted by age0.51.53.01.7-0.81.50.3
Bone surface3.97.713.82.8-3.71.92.3
Bone volume2.14.17.61.5-2.81.62.0
Breakpoint value in progressive ratio session1.42.54.92.2-1.81.10.9
Number of licking bursts0.10.20.50.5-0.70.10.2
Context. condit. distance diff. score1.01.32.7-1.61.2-1.00.0
Locomotion velocity, session 10.10.20.3-0.20.50.4-0.4
Locomotion distance, session 11.62.03.30.4-1.61.41.8
Locomotion velocity, session 23.23.87.31.7-1.72.71.6
Locomotion distance, session 21.92.75.50.8-1.52.31.5
Locomotion velocity, session 30.20.20.5-0.3-0.40.20.7
Locomotion distance, session 30.00.00.1-0.00.00.0-0.3
Stereotopy head waving bouts, day 30.50.61.3-1.20.10.31.0
Stereotopy head waving duration, day 30.40.51.6-1.30.2-0.30.6
Locomotion velocity, session 71.01.13.2-0.3-0.50.81.8
Locomotion distance, session 70.60.81.50.1-0.41.21.2
Stereotopy head waving bouts, day 70.20.30.4-0.0-0.6-0.60.6
Stereotopy head waving duration, day 70.91.22.41.0-1.60.11.1
Locomotion velocity, session 80.50.61.31.1-0.50.8-0.0
Locomotion distance, session 80.30.40.7-0.70.10.50.9
Degree of sensitization distance0.70.72.00.2-0.60.81.4
Degree of sensitization stereotypy0.50.61.01.0-1.0-0.20.6
Conditioned locomotion1.41.63.41.6-0.61.80.3
Cocaine response after cond. corrected0.81.22.4-1.01.1-1.5-0.3
Cocaine response after cond. not corrected0.71.02.7-0.90.8-1.6-0.2
Cocaine response before conditioning0.30.41.00.7-1.00.40.2
Saline control response2.43.34.52.1-2.11.80.9
Bone: connectivity density3.96.210.32.0-3.21.92.6
Bone: cortical apparent density0.10.10.30.50.30.0-0.3
Bone: cortical area0.30.51.11.0-0.50.90.0
Bone: cortical porosity0.60.71.30.2-0.91.20.6
Bone: cortical porosity1.21.33.30.6-1.11.80.7
Bone: cortical thickness1.62.66.52.5-0.41.9-0.5
Bone: cortical thickness0.80.92.70.90.21.6-0.4
Bone: cortical tissue density0.10.20.50.70.30.2-0.3
Condit. Reinf. active minus inactive responses0.30.40.60.6-0.8-0.00.7
Condit. Reinf. active-inactive response ratio0.20.30.70.3-0.4-0.90.2
Condit. Reinf. active responses0.30.40.70.6-0.60.50.8
Condit. Reinf. inactive responses0.30.41.10.1-0.11.00.7
Incentive salience index mean0.81.01.80.7-1.00.81.4
Condit. Reinf. lever presses0.60.91.50.8-0.70.81.2
Condit. Reinf. active minus inactive responses0.50.72.3-0.5-0.5-1.50.2
Condit. Reinf. active-inactive response ratio0.71.13.3-1.10.1-1.8-0.1
Condit. Reinf. active responses0.50.72.10.0-1.4-0.30.8
Condit. Reinf. inactive responses1.31.92.90.9-1.71.61.1
Condit. Reinf. lever presses1.42.13.91.5-2.01.10.9
Condit. Reinf. lever reinforcers received0.50.82.40.3-1.6-0.10.7
Conditioned reinforcement - actives0.00.20.6-0.00.40.0-0.8
Conditioned reinforcement - inactives0.92.42.9-1.71.4-1.5-1.6
Conditioned locomotion4.77.010.8-3.32.8-2.3-2.0
Patch foraging indifference point 0 sec0.00.10.3-0.5-0.3-0.10.1
Patch foraging indifference point AUC0.61.44.12.0-1.00.70.1
Delay disc. indifference point, 0s delay0.50.51.1-1.1-0.20.60.8
Delay disc. indifference point, 16s delay0.30.51.1-0.9-0.1-1.00.1
Delay disc. indifference point, 2s delay0.10.10.4-0.6-0.2-0.30.2
Delay disc. indifference point, 24s delay0.00.10.2-0.10.40.1-0.3
Delay disc. indifference point, 4s delay0.20.20.5-0.5-0.40.30.7
Delay disc. indifference point, 8s delay0.10.10.3-0.3-0.40.10.6
Indifference point function ln k2.26.815.1-3.92.9-1.7-1.0
Indifference point function log k2.26.815.1-3.92.9-1.7-1.0
Patch foraging total patch changes 0 sec0.00.10.2-0.50.10.1-0.2
Patch foraging total patch changes 12 sec3.44.66.12.5-2.32.21.4
Patch foraging total patch changes 18 sec0.30.71.31.0-1.10.50.7
Patch foraging total patch changes 24 sec0.30.92.11.5-0.90.80.2
Patch foraging total patch changes 6 sec0.81.42.41.3-1.60.80.9
Patch foraging time to switch 0 sec1.55.77.71.9-2.82.22.6
Patch foraging water rate 0 sec2.69.612.4-2.93.5-3.1-2.9
Patch foraging water rate 12 sec3.413.918.6-4.34.3-2.8-3.3
Patch foraging water rate 18 sec2.04.56.9-2.62.2-1.8-1.7
Patch foraging water rate 24 sec5.27.510.9-2.83.3-2.3-2.3
Patch foraging water rate 6 sec5.17.510.5-2.93.2-2.5-2.3
Seeking ratio, delayed vs. immediate footshock0.30.40.7-0.2-0.70.60.8
Distance traveled before self-admin0.30.71.20.6-1.10.70.9
Distance traveled after self-admin0.10.10.20.4-0.50.20.2
Extensor digitorum longus weight5.521.936.26.0-3.95.32.9
Bone: elastic displacement1.72.23.6-0.91.9-1.2-1.7
Bone: elastic work0.30.41.21.10.10.7-0.1
Bone: endosteal estimation0.61.43.5-1.9-0.3-0.41.4
Bone: endosteal perimeter0.82.13.9-2.0-0.5-1.61.3
Epididymis fat weight1.68.114.9-3.92.8-2.8-1.4
Delta time in closed arm before/after self-admin0.90.92.80.7-0.11.70.4
Delta time in open arm before/after self-admin0.10.10.20.5-0.2-0.4-0.3
Diff in mean of infusions in LGA sessions0.20.41.41.2-0.5-0.0-0.1
Delay discount exponential model param0.20.20.40.20.6-0.1-0.6
Extinction: sum of active levers before priming2.03.04.11.8-2.01.21.8
Active lever presses in extinction session 61.41.43.71.9-1.20.80.0
Bone: final force1.93.15.61.7-1.62.41.1
Bone: final moment1.82.95.51.6-1.52.31.1
Food consumed during 24 hour testing period0.30.72.0-0.00.5-0.6-1.4
Glucose1.22.05.0-2.20.1-1.31.1
Heart weight0.81.23.0-1.2-0.60.11.7
Delay discount hyperbolic model param0.20.20.40.30.6-0.1-0.7
Intermittent access intake day 1-15 change0.31.72.2-1.21.5-1.2-1.4
Intermittent access intake escalation0.31.72.1-1.01.5-1.2-1.4
Intermittent access intake escalation 21.11.92.4-1.11.5-1.5-1.4
Intermitt. access day 1 inactive lever presses0.00.62.1-0.10.4-1.4-0.3
Intermitt. access day 15 inactive lever presses0.31.54.1-1.00.6-2.0-0.6
Intermitt. access escalation Index0.62.05.8-2.41.1-0.9-0.0
Intermittent access day 1 total infusions0.31.02.5-1.6-0.5-0.11.1
Intermittent access day 15 total infusions1.02.55.3-2.31.3-1.6-0.9
Intermittent access terminal intake (last 3 days)1.01.83.8-2.00.8-1.5-0.5
Intermittent access total infusions0.70.82.6-1.60.1-0.70.3
Intermittent access day 1 locomotion0.30.51.5-1.2-0.2-0.50.7
Intermittent access day 15 total locomotion0.41.64.0-2.00.9-1.1-0.7
Intermittent access total locomotion1.72.06.3-2.50.7-1.1-0.2
Intermittent access standard deviation0.31.31.8-1.11.3-1.0-1.2
Left kidney weight0.21.94.9-2.21.50.6-0.0
Right kidney weight0.21.73.0-1.71.7-0.3-1.0
Cocaine induced anxiety0.00.00.10.3-0.20.2-0.0
Post-drug Anxiety0.30.40.80.9-0.60.40.2
Baseline Anxiety0.00.00.10.4-0.1-0.1-0.1
Tail length0.20.91.61.30.21.2-0.8
Length with tail0.73.17.92.8-1.01.9-0.1
Length without tail0.42.25.72.4-1.01.4-0.2
Times rat made contact with spout0.60.71.00.7-1.00.70.8
Lifetime Intake0.40.51.8-1.3-0.1-0.30.4
Liver weight, left0.71.22.4-1.31.6-0.0-0.7
Liver weight, right1.11.93.7-1.91.7-0.6-0.8
Locomotor activity2.13.24.4-2.02.1-1.1-1.8
Locomotor testing distance1.53.75.3-2.22.3-1.2-1.8
Locomotor testing rearing0.62.34.0-2.01.4-1.2-1.3
Locomotion in novel chamber3.24.38.4-2.92.0-1.7-1.3
Locomotion in novel chamber post-restriction0.82.55.2-2.31.5-1.4-0.9
Fecal boli incidents, locomotor time 10.10.20.70.20.1-0.8-0.4
Change in fecal boli incidents, locomotor task0.50.61.6-0.2-0.41.30.7
Time >=10cm from walls, locomotor time 10.30.40.7-0.8-0.6-0.10.9
Bouts of movement, locomotor time 10.50.72.01.4-0.8-0.3-0.1
Total resting periods, locomotor time 10.50.61.31.1-0.7-0.6-0.0
Rest time, locomotor task time 11.62.54.0-1.61.4-2.0-1.3
Distance moved, locomotor task time 10.41.21.80.5-1.21.01.3
Vertical activity count, locomotor time 10.00.30.7-0.90.60.4-0.1
Time >=10cm from walls, locomotor time 20.00.10.2-0.1-0.1-0.40.2
Bouts of movement, locomotor time 20.20.61.31.1-0.80.50.3
Total resting periods, locomotor time 20.10.40.70.9-0.70.20.3
Rest time, locomotor task time 21.11.83.0-1.71.4-1.3-0.9
Distance moved, locomotor task time 20.50.61.61.3-0.80.50.4
Vertical activity count, locomotor time 20.20.61.00.11.00.5-1.0
Light reinforcement 10.00.10.2-0.50.40.1-0.5
Light reinforcement 20.71.53.0-1.10.9-1.7-1.0
Bone: marrow area0.61.53.8-1.9-0.3-0.51.4
Bone: maximum diameter0.00.10.30.0-0.2-0.5-0.2
Bone: maximum force2.44.77.32.1-2.71.72.1
Bone: maximum moment2.34.46.82.0-2.61.72.1
Mean time between licks in bursts0.00.10.10.1-0.20.40.1
Mean num. licks in bursts0.00.10.2-0.40.20.10.2
Cd content in liver0.80.91.5-1.20.7-0.8-0.9
Co content in liver2.02.45.2-1.32.3-0.5-1.5
Cu content in liver0.40.40.8-0.1-0.50.90.8
Fe content in liver0.10.10.10.30.10.1-0.4
K content in liver1.11.11.60.8-1.01.11.3
Mg content in liver0.10.10.3-0.6-0.1-0.20.4
Mn content in liver2.02.26.12.5-1.6-0.00.4
Na content in liver0.30.30.70.20.4-0.8-0.7
Rb content in liver0.60.72.0-1.40.4-0.70.1
Se content in liver0.20.20.7-0.3-0.1-0.8-0.2
Sr content in liver1.10.92.81.7-0.40.6-0.6
Zn content in liver0.60.71.50.6-0.51.20.8
Bone: minimum diameter1.01.94.3-1.5-0.9-0.62.1
Time in familiar zone, hab. session 10.20.20.4-0.5-0.2-0.60.6
Time in novel zone, hab. session 10.40.50.9-0.40.9-0.2-1.0
Total zone transitions, hab. session 10.91.21.71.0-1.11.31.0
Total locomotion distance, hab. session 10.30.40.7-0.80.2-0.40.8
Locomotion velocity, hab. session 10.20.20.8-0.3-0.10.20.9
Time in familiar zone, hab. session 20.10.10.20.30.4-0.1-0.5
Time in novel zone, hab. session 20.30.40.7-0.1-0.80.40.9
Total zone transitions, hab. session 23.74.78.21.0-2.91.82.5
Total locomotion distance, hab. session 20.91.23.1-0.3-1.20.51.8
Locomotion velocity, hab. session 20.81.12.8-0.5-1.10.21.7
Novel to familiar place preference ratio0.70.91.51.2-1.2-0.00.8
Novelty place preference0.40.50.90.8-0.9-0.30.7
Time in novel zone, NPP test0.30.40.70.7-0.8-0.20.6
Total zone transitions, NPP test2.84.16.41.4-2.12.51.9
Total locomotion distance, NPP test0.81.12.3-0.2-0.61.31.5
Locomotion velocity, NPP test0.81.12.3-0.1-0.61.31.5
Intraocular pressure1.62.64.1-0.61.7-2.0-1.8
Delta distance traveled before/after self-admin0.20.20.4-0.10.7-0.3-0.6
Delta ambulatory time before/after self-admin0.10.10.3-0.00.50.1-0.5
Parametrial fat weight1.43.47.9-2.81.8-1.5-0.4
Pavlov. Cond. lever latency0.30.40.6-0.50.6-0.7-0.8
Pavlov. Cond. magazine entry latency0.60.81.80.3-1.10.41.3
Pavlov. Cond. change in total contacts0.30.30.40.2-0.6-0.60.6
Pavlov. Cond. index score0.10.10.20.2-0.4-0.00.4
Pavlov. Cond. latency score0.10.10.40.1-0.40.00.6
Pavlov. Cond. lever contacts0.30.30.60.1-0.40.60.8
Pavlov. Cond. magazine entry number0.00.10.1-0.40.30.1-0.0
Pavlov. Cond. intertrial magazine entries0.40.40.7-0.50.7-0.5-0.9
Pavlov. Cond. lever-magazine prob. diff.0.20.30.50.3-0.60.30.7
Pavlov. Cond. response bias0.00.00.10.3-0.20.10.1
Pavlov. Cond. lever latency0.30.41.0-0.70.5-1.0-0.0
Pavlov. Cond. magazine entry latency3.44.87.52.5-2.71.31.9
Pavlov. Cond. change in total contacts0.71.83.61.6-1.90.40.9
Pavlov. Cond. index score1.72.64.01.9-2.01.21.2
Pavlov. Cond. latency score1.42.23.21.7-1.81.11.1
Pavlov. Cond. lever contacts0.30.40.70.8-0.70.80.0
Pavlov. Cond. magazine entry number4.96.49.9-3.13.1-1.6-1.8
Pavlov. Cond. intertrial magazine entries0.51.21.6-1.31.1-1.0-0.9
Pavlov. Cond. lever-magazine prob. diff.2.03.14.82.1-2.21.31.3
Pavlov. Cond. response bias1.52.13.21.7-1.81.11.0
Time in closed arm before self-admin0.30.51.2-0.8-0.1-1.10.1
Time in closed arm after self-admin0.10.10.1-0.30.2-0.20.3
Time in open arm before self-admin0.30.30.6-0.30.70.8-0.1
Time in open arm after self-admin0.10.10.10.30.10.2-0.3
Bone: periosteal estimation0.10.30.6-0.4-0.40.30.8
Bone: periosteal perimeter0.30.51.00.0-1.0-0.41.0
Bone: post-yield work3.96.715.20.5-3.40.23.9
Progressive ratio test 1 active lever presses0.00.00.0-0.1-0.20.20.0
Progressive ratio test 1 breakpoint0.00.00.0-0.0-0.20.20.0
Progressive ratio test 1 inactive lever presses0.00.00.1-0.1-0.1-0.2-0.2
Progressive ratio test 2 active lever presses0.50.71.6-1.20.5-0.9-0.5
Progressive ratio test 2 breakpoint0.60.81.5-1.20.5-1.0-0.6
Progressive ratio test 2 inactive lever presses1.34.28.9-3.01.6-2.0-1.2
Incentive Sensitization - Responses0.10.30.60.2-0.80.10.6
Incentive Sensitization - Breakpoint0.10.10.3-0.0-0.6-0.20.5
Sum of active levers in priming session hrs 5-61.51.43.11.30.6-0.6-1.8
Progressive ratio1.44.36.00.9-2.42.12.4
Food seeking constrained by brief footshock0.20.20.50.5-0.30.70.1
Seeking ratio, punishment vs. effort1.32.94.7-1.22.2-1.4-1.8
Retroperitoneal fat weight5.624.949.8-7.14.7-4.8-2.0
Reaction time number correct0.10.30.90.30.4-0.2-1.0
Reaction time mean minus median0.53.27.32.7-1.81.10.9
Reaction time mean minus median AUC0.21.44.42.1-0.90.60.0
Reaction time num false alarms0.20.41.2-0.61.1-0.0-0.3
Reaction time num false alarms AUC0.00.10.30.20.50.30.0
Reaction time trials correct on left0.10.30.90.30.4-0.2-1.0
Reaction time trials on left0.10.31.00.40.4-0.2-1.0
Reaction time mean0.00.10.20.4-0.20.5-0.1
Reaction time mean AUC0.00.00.10.3-0.30.2-0.0
Median of all reaction times0.00.10.1-0.40.10.2-0.2
Reaction time omissions1.11.84.82.2-1.20.90.5
Reaction time false alarm rate0.10.10.3-0.20.60.10.3
Reaction time premature initiation rate1.11.83.31.8-1.11.50.5
Reaction time premature initiations0.61.94.82.2-1.01.4-0.1
Std. dev. reaction times0.31.02.41.5-1.00.80.2
Reaction time trials completed0.10.31.00.40.4-0.2-1.0
Reaction time trials AUC0.10.30.80.30.4-0.2-0.9
Run reversals in cocaine runway, females1.82.03.40.4-1.11.81.8
Run reversals in cocaine runway, males1.51.63.2-0.11.8-0.5-1.7
Latency to leave start box in cocaine runway0.40.61.4-0.3-0.8-0.31.2
Latency to leave start box in cocaine runway, F0.30.40.9-0.3-0.6-0.21.0
Latency to leave start box in cocaine runway, M0.20.20.30.3-0.5-0.20.5
Std. dev. time between licks in bursts0.30.51.3-0.20.81.1-0.3
Total sessions with >9 infusions0.91.11.50.2-1.21.21.2
Short access day 1 total inactive lever presses0.61.23.3-1.81.0-0.5-0.5
Short access day 10 total inactive lever presses0.10.72.1-0.40.5-1.5-0.3
Short access day 1 total infusions0.30.61.7-1.30.1-0.50.6
Short access day 10 total infusions1.22.14.0-0.2-1.71.22.0
Short access total infusions0.60.81.5-0.3-0.90.81.2
Short access day 1 locomotion0.20.40.8-0.8-0.0-0.90.2
Short access day 10 total locomotion0.10.30.6-0.8-0.20.00.7
Short access total locomotion0.20.31.0-1.0-0.1-0.30.5
One hour access (0.3 mA shock)3.44.06.5-2.41.6-2.6-1.1
Compulsive drug intake0.50.81.71.3-0.11.2-0.1
One hour access (shock baseline)1.74.37.1-2.71.5-2.6-1.0
Social response proportion0.40.51.20.8-1.1-0.40.1
Social responses0.10.10.20.5-0.30.0-0.4
Social time0.10.20.40.6-0.20.3-0.6
Soleus weight2.88.316.4-4.13.4-1.7-1.6
Bone: stiffness2.23.96.71.9-2.61.41.8
Tibialis anterior weight5.518.841.46.4-3.04.90.9
Time to tail flick, vehicle, before self-admin0.40.50.80.4-0.80.70.9
Time to tail flick, vehicle, after self-admin1.32.64.70.9-1.61.52.2
Time to tail flick, test, before self-admin0.60.71.7-1.3-0.00.11.0
Time to tail flick, test, after self-admin0.00.00.10.2-0.0-0.2-0.3
Delta time to tail flick, vehicle, before/after SA0.80.81.10.7-1.00.71.0
Delta time to tail flick, test, before/after SA1.21.53.51.50.6-0.4-1.9
Tibia length0.51.32.11.5-0.51.4-0.9
Ambulatory time before self-admin0.20.61.40.7-1.20.00.7
Ambulatory time after self-admin0.10.20.4-0.3-0.4-0.60.4
Bone: tissue strength0.10.10.2-0.1-0.4-0.10.4
Total heroin consumption2.42.96.22.5-1.91.01.0
Bone: trabecular number1.83.36.31.2-2.51.31.9
Bone: trabecular spacing0.50.71.3-1.01.10.0-0.7
Bone: trabecular thickness0.30.40.6-0.5-0.8-0.40.8
Bone: trabecular tissue density3.35.77.8-2.52.8-2.4-1.7
Water consumed over 24 hours0.40.71.21.1-1.00.70.0
Number of responses in last shaping day0.10.10.20.10.3-0.5-0.3