Trim54

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 BLA mRNA stability Trim54 0.08 0.09 2.6e-03 0.05 0.04 0.02 0.04 1.2e-03 3.4e-03 4.0e-02 3.0e-03
2 Brain gene expression Trim54 0.12 0.1 3.7e-09 0.07 0.09 0.07 0.07 5.0e-07 1.5e-08 1.7e-07 2.2e-07
3 PL gene expression Trim54 0.06 0.07 5.4e-05 0.04 0.04 0.04 0.04 4.6e-05 1.1e-05 1.3e-05 2.0e-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 density4.58.39.73.1-2.8-2.7
Area under the delay curve0.10.20.30.6-0.1-0.5
BMI with tail0.31.11.2-1.11.11.0
BMI without tail0.42.22.3-1.51.41.5
Body weight2.410.511.5-3.43.33.1
Weight adjusted by age0.00.10.10.3-0.4-0.3
Bone surface2.44.76.12.5-2.1-1.9
Bone volume2.44.76.02.4-2.1-1.9
Breakpoint value in progressive ratio session0.61.01.40.9-0.9-1.2
Number of licking bursts0.00.00.10.3-0.0-0.1
Context. condit. distance diff. score0.00.00.0-0.0-0.0-0.0
Locomotion velocity, session 10.00.00.10.10.10.3
Locomotion distance, session 11.72.23.01.7-1.4-1.3
Locomotion velocity, session 20.20.30.3-0.50.60.5
Locomotion distance, session 20.00.00.00.2-0.00.1
Locomotion velocity, session 30.80.91.00.9-1.0-1.0
Locomotion distance, session 30.80.91.01.0-0.9-0.9
Stereotopy head waving bouts, day 32.12.52.61.5-1.6-1.6
Stereotopy head waving duration, day 30.20.20.30.3-0.5-0.5
Locomotion velocity, session 71.21.41.71.3-1.2-1.0
Locomotion distance, session 70.10.10.10.4-0.2-0.0
Stereotopy head waving bouts, day 70.00.00.00.1-0.1-0.1
Stereotopy head waving duration, day 70.30.40.50.5-0.6-0.7
Locomotion velocity, session 80.20.30.40.5-0.6-0.4
Locomotion distance, session 80.30.40.50.7-0.7-0.5
Degree of sensitization distance0.80.91.0-0.90.91.0
Degree of sensitization stereotypy0.20.20.2-0.50.50.4
Conditioned locomotion3.13.63.71.9-1.9-1.9
Cocaine response after cond. corrected0.50.70.80.9-0.7-0.8
Cocaine response after cond. not corrected1.31.92.31.5-1.2-1.3
Cocaine response before conditioning1.62.02.21.5-1.4-1.3
Saline control response0.60.91.01.0-1.0-0.9
Bone: connectivity density4.57.38.32.9-2.6-2.6
Bone: cortical apparent density0.40.60.90.9-0.7-0.8
Bone: cortical area0.50.81.11.0-0.9-0.8
Bone: cortical porosity1.21.31.51.1-1.2-1.1
Bone: cortical porosity1.31.41.61.2-1.3-1.2
Bone: cortical thickness0.00.00.00.10.10.2
Bone: cortical thickness1.31.61.81.3-1.3-1.2
Bone: cortical tissue density0.30.40.60.8-0.6-0.6
Condit. Reinf. active minus inactive responses0.70.70.9-0.81.00.8
Condit. Reinf. active-inactive response ratio0.80.81.0-0.91.00.8
Condit. Reinf. active responses0.10.20.20.5-0.3-0.4
Condit. Reinf. inactive responses1.62.02.41.6-1.4-1.3
Incentive salience index mean0.00.00.00.20.0-0.1
Condit. Reinf. lever presses0.60.91.21.1-0.9-0.9
Condit. Reinf. active minus inactive responses3.14.85.42.0-2.2-2.3
Condit. Reinf. active-inactive response ratio0.71.11.30.9-1.1-1.1
Condit. Reinf. active responses3.24.55.02.1-2.1-2.2
Condit. Reinf. inactive responses1.42.12.31.5-1.4-1.5
Condit. Reinf. lever presses1.92.73.01.6-1.6-1.7
Condit. Reinf. lever reinforcers received2.94.14.52.0-2.0-2.1
Conditioned reinforcement - actives0.41.62.30.8-1.5-1.4
Conditioned reinforcement - inactives1.74.75.92.4-2.1-1.9
Conditioned locomotion0.10.10.30.0-0.6-0.3
Patch foraging indifference point 0 sec0.20.70.7-0.80.80.8
Patch foraging indifference point AUC0.71.71.91.4-1.4-1.1
Delay disc. indifference point, 0s delay2.83.13.9-1.62.01.7
Delay disc. indifference point, 16s delay0.10.20.20.4-0.1-0.5
Delay disc. indifference point, 2s delay0.10.20.2-0.30.40.4
Delay disc. indifference point, 24s delay0.81.21.91.1-0.8-1.4
Delay disc. indifference point, 4s delay0.00.00.10.3-0.0-0.1
Delay disc. indifference point, 8s delay0.00.10.20.3-0.0-0.4
Indifference point function ln k0.00.00.00.1-0.2-0.1
Indifference point function log k0.00.00.00.1-0.2-0.1
Patch foraging total patch changes 0 sec0.20.60.6-0.70.80.8
Patch foraging total patch changes 12 sec1.01.31.4-1.11.21.2
Patch foraging total patch changes 18 sec0.00.10.2-0.30.30.4
Patch foraging total patch changes 24 sec0.41.41.6-1.21.01.3
Patch foraging total patch changes 6 sec0.10.10.2-0.30.40.4
Patch foraging time to switch 0 sec0.00.00.1-0.20.2-0.0
Patch foraging water rate 0 sec0.00.00.00.1-0.2-0.0
Patch foraging water rate 12 sec0.52.12.4-1.51.41.4
Patch foraging water rate 18 sec0.30.70.7-0.80.80.8
Patch foraging water rate 24 sec2.33.24.2-2.01.81.5
Patch foraging water rate 6 sec1.11.71.7-1.31.31.3
Seeking ratio, delayed vs. immediate footshock0.00.00.1-0.00.00.4
Distance traveled before self-admin0.00.00.0-0.20.10.2
Distance traveled after self-admin1.62.73.0-1.71.61.6
Extensor digitorum longus weight4.517.918.14.2-4.2-4.3
Bone: elastic displacement0.60.70.90.7-0.8-1.0
Bone: elastic work0.91.11.31.0-1.0-1.2
Bone: endosteal estimation0.61.41.41.2-1.2-1.1
Bone: endosteal perimeter0.20.50.50.7-0.7-0.7
Epididymis fat weight11.859.465.1-8.17.77.4
Delta time in closed arm before/after self-admin0.00.00.00.0-0.1-0.1
Delta time in open arm before/after self-admin0.10.10.20.3-0.4-0.4
Diff in mean of infusions in LGA sessions0.00.00.00.2-0.1-0.1
Delay discount exponential model param0.40.50.7-0.80.50.8
Extinction: sum of active levers before priming0.20.30.50.4-0.5-0.7
Active lever presses in extinction session 60.50.50.70.5-0.8-0.8
Bone: final force0.10.10.10.4-0.4-0.3
Bone: final moment0.10.20.20.5-0.4-0.3
Food consumed during 24 hour testing period0.10.20.30.5-0.5-0.4
Glucose0.20.40.5-0.60.60.7
Heart weight2.94.65.5-1.92.12.3
Delay discount hyperbolic model param0.20.30.5-0.70.30.6
Intermittent access intake day 1-15 change0.00.10.1-0.3-0.3-0.1
Intermittent access intake escalation0.00.10.3-0.6-0.00.2
Intermittent access intake escalation 20.00.00.1-0.1-0.10.3
Intermitt. access day 1 inactive lever presses0.11.82.21.5-1.4-1.2
Intermitt. access day 15 inactive lever presses1.58.19.93.1-3.0-2.4
Intermitt. access escalation Index0.20.50.7-0.70.60.8
Intermittent access day 1 total infusions1.85.45.72.4-2.3-2.3
Intermittent access day 15 total infusions0.81.92.41.2-1.6-1.3
Intermittent access terminal intake (last 3 days)1.62.73.31.5-1.8-1.6
Intermittent access total infusions2.02.42.81.3-1.7-1.7
Intermittent access day 1 locomotion1.32.32.51.5-1.5-1.6
Intermittent access day 15 total locomotion0.10.30.40.5-0.6-0.5
Intermittent access total locomotion0.30.30.40.4-0.6-0.6
Intermittent access standard deviation0.31.71.81.3-1.3-1.2
Left kidney weight0.00.00.1-0.20.20.1
Right kidney weight0.32.02.5-1.41.61.3
Cocaine induced anxiety0.10.30.30.6-0.6-0.4
Post-drug Anxiety1.21.41.5-1.11.21.2
Baseline Anxiety2.33.94.2-2.02.01.9
Tail length0.31.82.0-1.41.31.4
Length with tail2.08.79.8-3.12.92.8
Length without tail0.42.22.6-1.61.51.4
Times rat made contact with spout1.92.22.31.5-1.4-1.5
Lifetime Intake2.22.73.11.4-1.8-1.7
Liver weight, left3.86.56.6-2.52.62.5
Liver weight, right10.117.618.1-4.34.24.2
Locomotor activity0.20.30.6-0.50.80.5
Locomotor testing distance0.10.20.40.4-0.3-0.6
Locomotor testing rearing0.31.01.50.7-1.0-1.2
Locomotion in novel chamber0.40.51.3-1.10.40.4
Locomotion in novel chamber post-restriction1.64.85.3-2.32.32.0
Fecal boli incidents, locomotor time 10.10.30.30.4-0.6-0.5
Change in fecal boli incidents, locomotor task4.24.44.6-2.12.12.0
Time >=10cm from walls, locomotor time 10.10.10.2-0.40.40.1
Bouts of movement, locomotor time 11.41.92.01.3-1.4-1.4
Total resting periods, locomotor time 11.92.22.41.5-1.5-1.5
Rest time, locomotor task time 10.00.10.1-0.30.20.3
Distance moved, locomotor task time 10.41.21.4-1.21.21.0
Vertical activity count, locomotor time 10.10.60.8-0.90.80.6
Time >=10cm from walls, locomotor time 20.10.20.30.4-0.5-0.4
Bouts of movement, locomotor time 20.00.10.2-0.40.20.3
Total resting periods, locomotor time 20.00.00.0-0.0-0.10.0
Rest time, locomotor task time 21.11.82.31.5-1.2-1.2
Distance moved, locomotor task time 21.01.31.6-1.31.11.1
Vertical activity count, locomotor time 20.30.81.2-1.10.70.8
Light reinforcement 11.67.38.83.0-2.7-2.5
Light reinforcement 22.24.96.32.5-2.2-1.9
Bone: marrow area0.51.31.41.2-1.2-1.1
Bone: maximum diameter1.02.02.21.5-1.4-1.3
Bone: maximum force0.10.20.30.5-0.5-0.4
Bone: maximum moment0.20.30.40.6-0.6-0.5
Mean time between licks in bursts0.63.83.9-1.92.01.9
Mean num. licks in bursts0.10.20.20.4-0.5-0.5
Cd content in liver0.00.00.00.0-0.0-0.0
Co content in liver5.96.97.22.7-2.6-2.6
Cu content in liver0.10.10.10.3-0.3-0.3
Fe content in liver0.91.11.31.0-1.1-1.1
K content in liver0.40.40.60.8-0.6-0.4
Mg content in liver0.40.40.70.8-0.6-0.5
Mn content in liver0.10.10.10.3-0.2-0.2
Na content in liver0.50.60.60.8-0.8-0.7
Rb content in liver0.00.00.00.1-0.0-0.1
Se content in liver0.10.10.1-0.40.30.3
Sr content in liver0.20.10.2-0.40.40.4
Zn content in liver0.81.01.1-1.01.01.0
Bone: minimum diameter0.00.10.1-0.10.20.3
Time in familiar zone, hab. session 10.60.70.8-0.80.80.9
Time in novel zone, hab. session 10.50.50.8-0.90.70.6
Total zone transitions, hab. session 10.10.20.20.5-0.4-0.3
Total locomotion distance, hab. session 10.20.30.40.6-0.5-0.4
Locomotion velocity, hab. session 11.01.51.91.4-1.2-1.1
Time in familiar zone, hab. session 20.00.00.00.0-0.1-0.0
Time in novel zone, hab. session 20.50.50.6-0.80.80.6
Total zone transitions, hab. session 20.10.10.20.4-0.2-0.3
Total locomotion distance, hab. session 20.20.20.40.6-0.4-0.3
Locomotion velocity, hab. session 20.40.50.70.9-0.6-0.6
Novel to familiar place preference ratio0.81.11.2-1.01.11.0
Novelty place preference1.41.71.9-1.31.41.3
Time in novel zone, NPP test1.62.02.1-1.41.51.3
Total zone transitions, NPP test1.52.22.51.6-1.4-1.4
Total locomotion distance, NPP test2.02.83.11.8-1.6-1.6
Locomotion velocity, NPP test3.34.65.22.3-2.1-2.1
Intraocular pressure5.28.49.3-2.93.02.7
Delta distance traveled before/after self-admin1.71.92.1-1.41.31.4
Delta ambulatory time before/after self-admin0.10.20.3-0.50.40.5
Parametrial fat weight11.928.030.3-5.15.35.5
Pavlov. Cond. lever latency1.82.32.9-1.71.51.4
Pavlov. Cond. magazine entry latency0.10.10.20.4-0.3-0.2
Pavlov. Cond. change in total contacts0.00.10.10.3-0.2-0.1
Pavlov. Cond. index score0.81.01.41.2-0.9-0.8
Pavlov. Cond. latency score0.81.01.41.2-0.9-0.8
Pavlov. Cond. lever contacts1.21.51.91.4-1.1-1.1
Pavlov. Cond. magazine entry number0.50.60.9-1.00.70.6
Pavlov. Cond. intertrial magazine entries1.21.51.71.2-1.2-1.3
Pavlov. Cond. lever-magazine prob. diff.1.41.82.31.5-1.3-1.2
Pavlov. Cond. response bias1.41.82.31.5-1.3-1.2
Pavlov. Cond. lever latency1.42.02.1-1.41.41.4
Pavlov. Cond. magazine entry latency0.20.30.40.6-0.6-0.4
Pavlov. Cond. change in total contacts0.41.01.11.0-1.0-1.1
Pavlov. Cond. index score1.01.51.61.2-1.3-1.2
Pavlov. Cond. latency score1.01.51.71.2-1.3-1.2
Pavlov. Cond. lever contacts0.91.41.51.1-1.2-1.2
Pavlov. Cond. magazine entry number0.10.20.2-0.40.50.4
Pavlov. Cond. intertrial magazine entries2.55.55.9-2.42.42.2
Pavlov. Cond. lever-magazine prob. diff.0.61.01.11.0-1.0-1.0
Pavlov. Cond. response bias1.62.22.31.4-1.5-1.5
Time in closed arm before self-admin0.50.91.0-0.91.01.0
Time in closed arm after self-admin1.21.41.7-1.31.21.1
Time in open arm before self-admin0.10.10.10.3-0.2-0.3
Time in open arm after self-admin1.51.61.81.3-1.3-1.2
Bone: periosteal estimation0.92.12.41.5-1.4-1.3
Bone: periosteal perimeter0.40.70.80.9-0.8-0.8
Bone: post-yield work0.71.31.51.0-1.2-1.2
Progressive ratio test 1 active lever presses1.01.81.81.3-1.3-1.3
Progressive ratio test 1 breakpoint1.01.81.81.3-1.3-1.4
Progressive ratio test 1 inactive lever presses1.54.04.81.9-2.2-1.9
Progressive ratio test 2 active lever presses0.10.20.30.2-0.6-0.5
Progressive ratio test 2 breakpoint0.10.10.20.1-0.5-0.4
Progressive ratio test 2 inactive lever presses0.61.82.51.2-1.6-1.2
Incentive Sensitization - Responses0.00.10.1-0.0-0.4-0.2
Incentive Sensitization - Breakpoint0.00.00.1-0.1-0.3-0.1
Sum of active levers in priming session hrs 5-60.70.71.31.1-0.6-0.7
Progressive ratio0.00.00.1-0.20.10.2
Food seeking constrained by brief footshock3.54.44.92.0-2.2-2.1
Seeking ratio, punishment vs. effort0.30.60.80.9-0.7-0.8
Retroperitoneal fat weight21.796.998.1-9.99.99.8
Reaction time number correct0.30.91.21.1-0.9-0.9
Reaction time mean minus median0.00.00.0-0.0-0.00.0
Reaction time mean minus median AUC0.00.10.1-0.20.30.3
Reaction time num false alarms0.00.00.10.30.1-0.0
Reaction time num false alarms AUC0.00.00.10.30.1-0.1
Reaction time trials correct on left0.30.91.21.1-0.9-0.9
Reaction time trials on left0.31.01.31.1-0.9-0.9
Reaction time mean0.81.71.9-1.21.31.4
Reaction time mean AUC0.61.41.6-1.01.21.2
Median of all reaction times1.21.92.2-1.21.41.5
Reaction time omissions0.10.10.20.4-0.3-0.2
Reaction time false alarm rate0.10.20.3-0.20.50.4
Reaction time premature initiation rate0.10.20.2-0.40.50.4
Reaction time premature initiations0.00.00.10.2-0.1-0.1
Std. dev. reaction times0.10.40.5-0.50.70.7
Reaction time trials completed0.31.01.31.1-0.9-0.9
Reaction time trials AUC0.41.21.51.2-1.1-1.0
Run reversals in cocaine runway, females0.00.00.1-0.20.20.1
Run reversals in cocaine runway, males0.10.10.2-0.1-0.1-0.4
Latency to leave start box in cocaine runway0.40.60.70.7-0.8-0.7
Latency to leave start box in cocaine runway, F0.20.30.40.6-0.5-0.5
Latency to leave start box in cocaine runway, M0.00.00.1-0.1-0.3-0.1
Std. dev. time between licks in bursts0.10.10.2-0.10.30.4
Total sessions with >9 infusions0.60.71.00.5-1.0-0.9
Short access day 1 total inactive lever presses5.010.011.93.5-3.2-2.8
Short access day 10 total inactive lever presses0.74.65.52.3-2.1-2.0
Short access day 1 total infusions2.24.45.41.9-2.3-2.1
Short access day 10 total infusions1.62.62.71.6-1.6-1.6
Short access total infusions0.91.21.60.9-1.3-1.1
Short access day 1 locomotion1.83.03.71.5-1.9-1.8
Short access day 10 total locomotion0.62.32.81.7-1.5-1.4
Short access total locomotion0.10.20.20.3-0.5-0.4
One hour access (0.3 mA shock)1.01.11.50.9-1.2-1.0
Compulsive drug intake0.60.91.2-0.81.10.9
One hour access (shock baseline)0.82.12.71.2-1.6-1.5
Social response proportion0.30.40.4-0.60.60.6
Social responses0.10.10.2-0.10.30.4
Social time0.30.50.8-0.60.50.9
Soleus weight4.713.914.63.8-3.6-3.7
Bone: stiffness0.00.00.00.1-0.2-0.1
Tibialis anterior weight3.712.913.43.7-3.5-3.6
Time to tail flick, vehicle, before self-admin1.01.31.8-1.31.01.0
Time to tail flick, vehicle, after self-admin2.44.95.5-2.42.22.1
Time to tail flick, test, before self-admin0.10.10.10.3-0.2-0.3
Time to tail flick, test, after self-admin0.10.10.10.4-0.3-0.3
Delta time to tail flick, vehicle, before/after SA0.10.10.1-0.20.30.3
Delta time to tail flick, test, before/after SA1.21.51.71.3-1.3-1.1
Tibia length2.77.68.2-2.72.72.9
Ambulatory time before self-admin0.00.00.00.0-0.00.0
Ambulatory time after self-admin1.11.71.9-1.41.21.3
Bone: tissue strength0.91.01.1-1.01.00.9
Total heroin consumption3.13.74.12.0-1.8-1.9
Bone: trabecular number3.36.17.42.7-2.4-2.3
Bone: trabecular spacing2.94.34.9-2.22.11.9
Bone: trabecular thickness0.71.01.31.1-1.0-0.9
Bone: trabecular tissue density0.20.40.50.6-0.7-0.6
Water consumed over 24 hours0.30.60.80.9-0.7-0.7
Number of responses in last shaping day0.10.10.2-0.0-0.5-0.3