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 2.1e-11
2 NAcc gene expression Yif1a 0.04 0.03 3.1e-05 0.03 0.03 0.03 0.03 1.0e-04 3.5e-05 3.9e-05 9.4e-05
3 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
Bone: apparent density2.23.85.9-0.8-2.4-2.2
Area under the delay curve0.30.40.60.4-0.7-0.8
BMI with tail4.916.825.2-2.2-4.5-5.0
BMI without tail2.37.010.0-1.7-2.9-3.2
Body weight2.711.813.5-3.5-3.7-3.1
Weight adjusted by age0.81.23.0-1.7-0.8-0.3
Bone surface4.99.013.8-2.8-3.7-2.3
Bone volume2.64.67.6-1.5-2.8-2.0
Breakpoint value in progressive ratio session2.53.04.9-2.2-1.8-0.9
Number of licking bursts0.20.30.5-0.5-0.7-0.2
Context. condit. distance diff. score1.11.42.71.61.2-0.0
Locomotion velocity, session 10.10.20.30.20.50.4
Locomotion distance, session 11.62.03.3-0.4-1.6-1.8
Locomotion velocity, session 22.32.72.8-1.7-1.7-1.6
Locomotion distance, session 21.21.72.3-0.8-1.5-1.5
Locomotion velocity, session 30.20.30.50.3-0.4-0.7
Locomotion distance, session 30.00.00.10.00.00.3
Stereotopy head waving bouts, day 30.60.81.31.20.1-1.0
Stereotopy head waving duration, day 30.60.71.61.30.2-0.6
Locomotion velocity, session 71.11.23.20.3-0.5-1.8
Locomotion distance, session 70.40.61.5-0.1-0.4-1.2
Stereotopy head waving bouts, day 70.20.20.40.0-0.6-0.6
Stereotopy head waving duration, day 71.31.52.4-1.0-1.6-1.1
Locomotion velocity, session 80.40.51.3-1.1-0.50.0
Locomotion distance, session 80.30.40.70.70.1-0.9
Degree of sensitization distance0.80.82.0-0.2-0.6-1.4
Degree of sensitization stereotypy0.70.71.0-1.0-1.0-0.6
Conditioned locomotion0.91.12.7-1.6-0.6-0.3
Cocaine response after cond. corrected0.70.81.31.01.10.3
Cocaine response after cond. not corrected0.40.50.80.90.80.2
Cocaine response before conditioning0.40.51.0-0.7-1.0-0.2
Saline control response2.43.34.5-2.1-2.1-0.9
Bone: connectivity density4.57.010.3-2.0-3.2-2.6
Bone: cortical apparent density0.10.20.3-0.50.30.3
Bone: cortical area0.30.41.1-1.0-0.5-0.0
Bone: cortical porosity0.40.40.9-0.2-0.9-0.6
Bone: cortical porosity0.60.71.2-0.6-1.1-0.7
Bone: cortical thickness1.42.36.5-2.5-0.40.5
Bone: cortical thickness0.30.30.8-0.90.20.4
Bone: cortical tissue density0.20.20.5-0.70.30.3
Condit. Reinf. active minus inactive responses0.50.50.6-0.6-0.8-0.7
Condit. Reinf. active-inactive response ratio0.10.10.2-0.3-0.4-0.2
Condit. Reinf. active responses0.40.40.7-0.6-0.6-0.8
Condit. Reinf. inactive responses0.20.20.5-0.1-0.1-0.7
Incentive salience index mean0.91.21.8-0.7-1.0-1.4
Condit. Reinf. lever presses0.60.91.5-0.8-0.7-1.2
Condit. Reinf. active minus inactive responses0.20.20.30.5-0.5-0.2
Condit. Reinf. active-inactive response ratio0.40.41.31.10.10.1
Condit. Reinf. active responses0.60.92.1-0.0-1.4-0.8
Condit. Reinf. inactive responses1.31.62.9-0.9-1.7-1.1
Condit. Reinf. lever presses1.72.33.9-1.5-2.0-0.9
Condit. Reinf. lever reinforcers received0.71.02.4-0.3-1.6-0.7
Conditioned reinforcement - actives0.10.20.60.00.40.8
Conditioned reinforcement - inactives1.72.42.91.71.41.6
Conditioned locomotion5.97.610.83.32.82.0
Patch foraging indifference point 0 sec0.10.10.30.5-0.3-0.1
Patch foraging indifference point AUC1.21.74.1-2.0-1.0-0.1
Delay disc. indifference point, 0s delay0.60.61.11.1-0.2-0.8
Delay disc. indifference point, 16s delay0.20.30.80.9-0.1-0.1
Delay disc. indifference point, 2s delay0.10.20.40.6-0.2-0.2
Delay disc. indifference point, 24s delay0.10.10.20.10.40.3
Delay disc. indifference point, 4s delay0.30.30.50.5-0.4-0.7
Delay disc. indifference point, 8s delay0.20.20.30.3-0.4-0.6
Indifference point function ln k4.68.115.13.92.91.0
Indifference point function log k4.68.115.13.92.91.0
Patch foraging total patch changes 0 sec0.00.10.20.50.10.2
Patch foraging total patch changes 12 sec3.44.56.1-2.5-2.3-1.4
Patch foraging total patch changes 18 sec0.60.91.3-1.0-1.1-0.7
Patch foraging total patch changes 24 sec0.61.02.1-1.5-0.9-0.2
Patch foraging total patch changes 6 sec1.11.62.4-1.3-1.6-0.9
Patch foraging time to switch 0 sec2.95.97.7-1.9-2.8-2.6
Patch foraging water rate 0 sec4.69.712.42.93.52.9
Patch foraging water rate 12 sec7.616.018.64.34.33.3
Patch foraging water rate 18 sec3.24.96.92.62.21.7
Patch foraging water rate 24 sec5.88.110.92.83.32.3
Patch foraging water rate 6 sec5.58.010.52.93.22.3
Seeking ratio, delayed vs. immediate footshock0.30.40.70.2-0.7-0.8
Distance traveled before self-admin0.60.81.2-0.6-1.1-0.9
Distance traveled after self-admin0.10.20.2-0.4-0.5-0.2
Extensor digitorum longus weight5.119.936.2-6.0-3.9-2.9
Bone: elastic displacement2.12.43.60.91.91.7
Bone: elastic work0.30.41.2-1.10.10.1
Bone: endosteal estimation0.81.83.51.9-0.3-1.4
Bone: endosteal perimeter0.92.03.92.0-0.5-1.3
Epididymis fat weight2.48.214.93.92.81.4
Delta time in closed arm before/after self-admin0.20.20.5-0.7-0.1-0.4
Delta time in open arm before/after self-admin0.10.10.2-0.5-0.20.3
Diff in mean of infusions in LGA sessions0.50.61.4-1.2-0.50.1
Delay discount exponential model param0.30.30.4-0.20.60.6
Extinction: sum of active levers before priming3.23.54.1-1.8-2.0-1.8
Active lever presses in extinction session 61.71.73.7-1.9-1.2-0.0
Bone: final force1.42.22.9-1.7-1.6-1.1
Bone: final moment1.32.02.5-1.6-1.5-1.1
Food consumed during 24 hour testing period0.60.82.00.00.51.4
Glucose1.32.15.02.20.1-1.1
Heart weight1.11.63.01.2-0.6-1.7
Delay discount hyperbolic model param0.30.30.4-0.30.60.7
Intermittent access intake day 1-15 change0.91.82.21.21.51.4
Intermittent access intake escalation0.81.72.11.01.51.4
Intermittent access intake escalation 21.61.82.41.11.51.4
Intermitt. access day 1 inactive lever presses0.00.10.10.10.40.3
Intermitt. access day 15 inactive lever presses0.30.61.11.00.60.6
Intermitt. access escalation Index1.72.45.82.41.10.0
Intermittent access day 1 total infusions0.81.32.51.6-0.5-1.1
Intermittent access day 15 total infusions1.72.65.32.31.30.9
Intermittent access terminal intake (last 3 days)1.21.63.82.00.80.5
Intermittent access total infusions0.80.92.61.60.1-0.3
Intermittent access day 1 locomotion0.50.71.51.2-0.2-0.7
Intermittent access day 15 total locomotion1.01.84.02.00.90.7
Intermittent access total locomotion1.92.36.32.50.70.2
Intermittent access standard deviation0.71.51.81.11.31.2
Left kidney weight0.52.44.92.21.50.0
Right kidney weight0.52.33.01.71.71.0
Cocaine induced anxiety0.00.00.1-0.3-0.20.0
Post-drug Anxiety0.40.40.8-0.9-0.6-0.2
Baseline Anxiety0.00.00.1-0.4-0.10.1
Tail length0.20.81.6-1.30.20.8
Length with tail0.73.07.9-2.8-1.00.1
Length without tail0.72.35.7-2.4-1.00.2
Times rat made contact with spout0.60.71.0-0.7-1.0-0.8
Lifetime Intake0.50.71.81.3-0.1-0.4
Liver weight, left1.01.62.41.31.60.7
Liver weight, right1.42.43.71.91.70.8
Locomotor activity2.53.94.42.02.11.8
Locomotor testing distance2.54.55.32.22.31.8
Locomotor testing rearing1.32.54.02.01.41.3
Locomotion in novel chamber3.74.78.42.92.01.3
Locomotion in novel chamber post-restriction1.72.75.22.31.50.9
Fecal boli incidents, locomotor time 10.10.10.2-0.20.10.4
Change in fecal boli incidents, locomotor task0.20.20.50.2-0.4-0.7
Time >=10cm from walls, locomotor time 10.50.60.70.8-0.6-0.9
Bouts of movement, locomotor time 10.80.92.0-1.4-0.80.1
Total resting periods, locomotor time 10.60.61.3-1.1-0.70.0
Rest time, locomotor task time 11.62.12.51.61.41.3
Distance moved, locomotor task time 10.81.21.8-0.5-1.2-1.3
Vertical activity count, locomotor time 10.20.40.70.90.60.1
Time >=10cm from walls, locomotor time 20.00.00.00.1-0.1-0.2
Bouts of movement, locomotor time 20.40.71.3-1.1-0.8-0.3
Total resting periods, locomotor time 20.30.50.7-0.9-0.7-0.3
Rest time, locomotor task time 21.51.93.01.71.40.9
Distance moved, locomotor task time 20.60.81.6-1.3-0.8-0.4
Vertical activity count, locomotor time 20.50.71.0-0.11.01.0
Light reinforcement 10.10.20.20.50.40.5
Light reinforcement 20.61.01.11.10.91.0
Bone: marrow area0.92.03.81.9-0.3-1.4
Bone: maximum diameter0.00.00.0-0.0-0.20.2
Bone: maximum force3.05.47.3-2.1-2.7-2.1
Bone: maximum moment2.84.96.8-2.0-2.6-2.1
Mean time between licks in bursts0.00.00.0-0.1-0.2-0.1
Mean num. licks in bursts0.10.10.20.40.2-0.2
Cd content in liver0.90.91.51.20.70.9
Co content in liver2.73.15.21.32.31.5
Cu content in liver0.20.30.60.1-0.5-0.8
Fe content in liver0.10.10.1-0.30.10.4
K content in liver1.11.11.6-0.8-1.0-1.3
Mg content in liver0.20.20.30.6-0.1-0.4
Mn content in liver2.73.06.1-2.5-1.6-0.4
Na content in liver0.20.20.5-0.20.40.7
Rb content in liver0.60.72.01.40.4-0.1
Se content in liver0.00.00.10.3-0.10.2
Sr content in liver1.31.12.8-1.7-0.40.6
Zn content in liver0.40.40.6-0.6-0.5-0.8
Bone: minimum diameter1.32.44.31.5-0.9-2.1
Time in familiar zone, hab. session 10.20.20.30.5-0.2-0.6
Time in novel zone, hab. session 10.60.60.90.40.91.0
Total zone transitions, hab. session 10.81.11.2-1.0-1.1-1.0
Total locomotion distance, hab. session 10.30.40.70.80.2-0.8
Locomotion velocity, hab. session 10.20.30.80.3-0.1-0.9
Time in familiar zone, hab. session 20.20.20.2-0.30.40.5
Time in novel zone, hab. session 20.40.50.70.1-0.8-0.9
Total zone transitions, hab. session 24.15.28.2-1.0-2.9-2.5
Total locomotion distance, hab. session 21.21.53.10.3-1.2-1.8
Locomotion velocity, hab. session 21.01.42.80.5-1.1-1.7
Novel to familiar place preference ratio1.11.21.5-1.2-1.2-0.8
Novelty place preference0.60.70.9-0.8-0.9-0.7
Time in novel zone, NPP test0.50.50.7-0.7-0.8-0.6
Total zone transitions, NPP test2.33.34.4-1.4-2.1-1.9
Total locomotion distance, NPP test0.70.92.30.2-0.6-1.5
Locomotion velocity, NPP test0.60.92.30.1-0.6-1.5
Intraocular pressure1.52.13.20.61.71.8
Delta distance traveled before/after self-admin0.20.30.40.10.70.6
Delta ambulatory time before/after self-admin0.10.20.30.00.50.5
Parametrial fat weight1.63.87.92.81.80.4
Pavlov. Cond. lever latency0.30.40.60.50.60.8
Pavlov. Cond. magazine entry latency0.81.11.8-0.3-1.1-1.3
Pavlov. Cond. change in total contacts0.20.30.4-0.2-0.6-0.6
Pavlov. Cond. index score0.10.10.2-0.2-0.4-0.4
Pavlov. Cond. latency score0.20.20.4-0.1-0.4-0.6
Pavlov. Cond. lever contacts0.20.30.6-0.1-0.4-0.8
Pavlov. Cond. magazine entry number0.10.10.10.40.30.0
Pavlov. Cond. intertrial magazine entries0.40.50.70.50.70.9
Pavlov. Cond. lever-magazine prob. diff.0.30.30.5-0.3-0.6-0.7
Pavlov. Cond. response bias0.00.00.1-0.3-0.2-0.1
Pavlov. Cond. lever latency0.20.30.60.70.50.0
Pavlov. Cond. magazine entry latency4.85.87.5-2.5-2.7-1.9
Pavlov. Cond. change in total contacts1.42.33.6-1.6-1.9-0.9
Pavlov. Cond. index score2.23.04.0-1.9-2.0-1.2
Pavlov. Cond. latency score1.92.53.2-1.7-1.8-1.1
Pavlov. Cond. lever contacts0.30.40.7-0.8-0.7-0.0
Pavlov. Cond. magazine entry number6.27.79.93.13.11.8
Pavlov. Cond. intertrial magazine entries0.81.31.61.31.10.9
Pavlov. Cond. lever-magazine prob. diff.2.73.74.8-2.1-2.2-1.3
Pavlov. Cond. response bias1.82.43.2-1.7-1.8-1.0
Time in closed arm before self-admin0.20.20.70.8-0.1-0.1
Time in closed arm after self-admin0.10.10.10.30.2-0.3
Time in open arm before self-admin0.20.20.50.30.70.1
Time in open arm after self-admin0.10.10.1-0.30.10.3
Bone: periosteal estimation0.20.30.60.4-0.4-0.8
Bone: periosteal perimeter0.40.61.0-0.0-1.0-1.0
Bone: post-yield work6.18.915.2-0.5-3.4-3.9
Progressive ratio test 1 active lever presses0.00.00.00.1-0.2-0.0
Progressive ratio test 1 breakpoint0.00.00.00.0-0.2-0.0
Progressive ratio test 1 inactive lever presses0.00.00.10.1-0.10.2
Progressive ratio test 2 active lever presses0.60.71.61.20.50.5
Progressive ratio test 2 breakpoint0.60.71.51.20.50.6
Progressive ratio test 2 inactive lever presses2.64.38.93.01.61.2
Incentive Sensitization - Responses0.20.30.6-0.2-0.8-0.6
Incentive Sensitization - Breakpoint0.10.20.30.0-0.6-0.5
Sum of active levers in priming session hrs 5-61.91.73.1-1.30.61.8
Progressive ratio2.74.26.0-0.9-2.4-2.4
Food seeking constrained by brief footshock0.10.10.2-0.5-0.3-0.1
Seeking ratio, punishment vs. effort2.23.24.71.22.21.8
Retroperitoneal fat weight6.025.449.87.14.72.0
Reaction time number correct0.20.40.9-0.30.41.0
Reaction time mean minus median1.53.87.3-2.7-1.8-0.9
Reaction time mean minus median AUC0.71.74.4-2.1-0.9-0.0
Reaction time num false alarms0.40.51.20.61.10.3
Reaction time num false alarms AUC0.10.10.3-0.20.5-0.0
Reaction time trials correct on left0.20.40.9-0.30.41.0
Reaction time trials on left0.20.41.0-0.40.41.0
Reaction time mean0.00.10.1-0.4-0.20.1
Reaction time mean AUC0.00.00.1-0.3-0.30.0
Median of all reaction times0.00.10.10.40.10.2
Reaction time omissions1.52.24.8-2.2-1.2-0.5
Reaction time false alarm rate0.10.20.30.20.6-0.3
Reaction time premature initiation rate1.21.63.3-1.8-1.1-0.5
Reaction time premature initiations1.11.94.8-2.2-1.00.1
Std. dev. reaction times0.61.12.4-1.5-1.0-0.2
Reaction time trials completed0.20.41.0-0.40.41.0
Reaction time trials AUC0.20.30.8-0.30.40.9
Run reversals in cocaine runway, females1.61.63.3-0.4-1.1-1.8
Run reversals in cocaine runway, males2.12.13.20.11.81.7
Latency to leave start box in cocaine runway0.60.71.40.3-0.8-1.2
Latency to leave start box in cocaine runway, F0.40.50.90.3-0.6-1.0
Latency to leave start box in cocaine runway, M0.20.20.3-0.3-0.5-0.5
Std. dev. time between licks in bursts0.20.30.60.20.80.3
Total sessions with >9 infusions0.80.91.4-0.2-1.2-1.2
Short access day 1 total inactive lever presses1.21.63.31.81.00.5
Short access day 10 total inactive lever presses0.10.20.30.40.50.3
Short access day 1 total infusions0.50.71.71.30.1-0.6
Short access day 10 total infusions1.82.34.00.2-1.7-2.0
Short access total infusions0.70.81.50.3-0.9-1.2
Short access day 1 locomotion0.20.20.70.8-0.0-0.2
Short access day 10 total locomotion0.20.40.60.8-0.2-0.7
Short access total locomotion0.30.41.01.0-0.1-0.5
One hour access (0.3 mA shock)2.73.15.62.41.61.1
Compulsive drug intake0.50.61.7-1.3-0.10.1
One hour access (shock baseline)2.33.57.12.71.51.0
Social response proportion0.50.61.2-0.8-1.1-0.1
Social responses0.10.20.2-0.5-0.30.4
Social time0.20.30.4-0.6-0.20.6
Soleus weight3.510.216.44.13.41.6
Bone: stiffness2.84.66.7-1.9-2.6-1.8
Tibialis anterior weight5.017.041.4-6.4-3.0-0.9
Time to tail flick, vehicle, before self-admin0.50.50.8-0.4-0.8-0.9
Time to tail flick, vehicle, after self-admin2.02.74.7-0.9-1.6-2.2
Time to tail flick, test, before self-admin0.90.91.71.3-0.0-1.0
Time to tail flick, test, after self-admin0.00.00.1-0.2-0.00.3
Delta time to tail flick, vehicle, before/after SA1.00.91.1-0.7-1.0-1.0
Delta time to tail flick, test, before/after SA1.92.03.5-1.50.61.9
Tibia length0.41.02.1-1.5-0.50.9
Ambulatory time before self-admin0.50.81.4-0.7-1.2-0.7
Ambulatory time after self-admin0.10.10.20.3-0.4-0.4
Bone: tissue strength0.10.10.20.1-0.4-0.4
Total heroin consumption3.03.56.2-2.5-1.9-1.0
Bone: trabecular number2.33.96.3-1.2-2.5-1.9
Bone: trabecular spacing0.70.91.31.01.10.7
Bone: trabecular thickness0.40.50.60.5-0.8-0.8
Bone: trabecular tissue density3.95.77.82.52.81.7
Water consumed over 24 hours0.50.71.2-1.1-1.0-0.0
Number of responses in last shaping day0.10.10.1-0.10.30.3