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 4.3e-02 2.9e-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 density4.88.39.7-3.1-2.8-2.7
Area under the delay curve0.20.20.3-0.6-0.1-0.5
BMI with tail0.31.11.21.11.11.0
BMI without tail0.72.22.31.51.41.5
Body weight2.410.511.53.43.33.1
Weight adjusted by age0.10.10.1-0.3-0.4-0.3
Bone surface2.64.76.1-2.5-2.1-1.9
Bone volume2.64.76.0-2.4-2.1-1.9
Breakpoint value in progressive ratio session0.81.01.4-0.9-0.9-1.2
Number of licking bursts0.00.00.1-0.3-0.0-0.1
Context. condit. distance diff. score0.00.00.00.0-0.0-0.0
Locomotion velocity, session 10.00.00.1-0.10.10.3
Locomotion distance, session 11.72.23.0-1.7-1.4-1.3
Locomotion velocity, session 20.20.30.30.50.60.5
Locomotion distance, session 20.00.00.0-0.2-0.00.1
Locomotion velocity, session 30.80.91.0-0.9-1.0-1.0
Locomotion distance, session 30.80.91.0-1.0-0.9-0.9
Stereotopy head waving bouts, day 32.12.52.6-1.5-1.6-1.6
Stereotopy head waving duration, day 30.20.20.3-0.3-0.5-0.5
Locomotion velocity, session 71.21.41.7-1.3-1.2-1.0
Locomotion distance, session 70.10.10.1-0.4-0.2-0.0
Stereotopy head waving bouts, day 70.00.00.0-0.1-0.1-0.1
Stereotopy head waving duration, day 70.30.40.5-0.5-0.6-0.7
Locomotion velocity, session 80.20.30.4-0.5-0.6-0.4
Locomotion distance, session 80.30.40.5-0.7-0.7-0.5
Degree of sensitization distance0.90.91.00.90.91.0
Degree of sensitization stereotypy0.20.20.20.50.50.4
Conditioned locomotion3.13.63.7-1.9-1.9-1.9
Cocaine response after cond. corrected0.60.70.8-0.9-0.7-0.8
Cocaine response after cond. not corrected1.61.92.3-1.5-1.2-1.3
Cocaine response before conditioning1.62.02.2-1.5-1.4-1.3
Saline control response0.70.91.0-1.0-1.0-0.9
Bone: connectivity density4.67.38.3-2.9-2.6-2.6
Bone: cortical apparent density0.50.60.9-0.9-0.7-0.8
Bone: cortical area0.50.81.1-1.0-0.9-0.8
Bone: cortical porosity1.21.31.5-1.1-1.2-1.1
Bone: cortical porosity1.31.41.6-1.2-1.3-1.2
Bone: cortical thickness0.00.00.0-0.10.10.2
Bone: cortical thickness1.41.61.8-1.3-1.3-1.2
Bone: cortical tissue density0.30.40.6-0.8-0.6-0.6
Condit. Reinf. active minus inactive responses0.70.70.90.81.00.8
Condit. Reinf. active-inactive response ratio0.80.81.00.91.00.8
Condit. Reinf. active responses0.10.20.2-0.5-0.3-0.4
Condit. Reinf. inactive responses1.72.02.4-1.6-1.4-1.3
Incentive salience index mean0.00.00.0-0.20.0-0.1
Condit. Reinf. lever presses0.70.91.2-1.1-0.9-0.9
Condit. Reinf. active minus inactive responses3.74.85.4-2.0-2.2-2.3
Condit. Reinf. active-inactive response ratio0.91.11.3-0.9-1.1-1.1
Condit. Reinf. active responses3.24.55.0-2.1-2.1-2.2
Condit. Reinf. inactive responses1.62.12.3-1.5-1.4-1.5
Condit. Reinf. lever presses2.02.73.0-1.6-1.6-1.7
Condit. Reinf. lever reinforcers received3.04.14.5-2.0-2.0-2.1
Conditioned reinforcement - actives1.01.62.3-0.8-1.5-1.4
Conditioned reinforcement - inactives3.24.75.9-2.4-2.1-1.9
Conditioned locomotion0.10.10.3-0.0-0.6-0.3
Patch foraging indifference point 0 sec0.40.70.70.80.80.8
Patch foraging indifference point AUC1.21.71.9-1.4-1.4-1.1
Delay disc. indifference point, 0s delay2.83.13.91.62.01.7
Delay disc. indifference point, 16s delay0.10.20.2-0.4-0.1-0.5
Delay disc. indifference point, 2s delay0.10.20.20.30.40.4
Delay disc. indifference point, 24s delay1.11.21.9-1.1-0.8-1.4
Delay disc. indifference point, 4s delay0.00.00.1-0.3-0.0-0.1
Delay disc. indifference point, 8s delay0.10.10.2-0.3-0.0-0.4
Indifference point function ln k0.00.00.0-0.1-0.2-0.1
Indifference point function log k0.00.00.0-0.1-0.2-0.1
Patch foraging total patch changes 0 sec0.30.60.60.70.80.8
Patch foraging total patch changes 12 sec1.01.31.41.11.21.2
Patch foraging total patch changes 18 sec0.10.10.20.30.30.4
Patch foraging total patch changes 24 sec0.81.41.61.21.01.3
Patch foraging total patch changes 6 sec0.10.10.20.30.40.4
Patch foraging time to switch 0 sec0.00.00.10.20.2-0.0
Patch foraging water rate 0 sec0.00.00.0-0.1-0.2-0.0
Patch foraging water rate 12 sec1.02.12.41.51.41.4
Patch foraging water rate 18 sec0.40.70.70.80.80.8
Patch foraging water rate 24 sec2.33.24.22.01.81.5
Patch foraging water rate 6 sec1.11.71.71.31.31.3
Seeking ratio, delayed vs. immediate footshock0.00.00.10.00.00.4
Distance traveled before self-admin0.00.00.00.20.10.2
Distance traveled after self-admin2.22.73.01.71.61.6
Extensor digitorum longus weight4.617.918.1-4.2-4.2-4.3
Bone: elastic displacement0.60.70.9-0.7-0.8-1.0
Bone: elastic work0.91.11.3-1.0-1.0-1.2
Bone: endosteal estimation0.61.41.4-1.2-1.2-1.1
Bone: endosteal perimeter0.20.50.5-0.7-0.7-0.7
Epididymis fat weight17.459.465.18.17.77.4
Delta time in closed arm before/after self-admin0.00.00.0-0.0-0.1-0.1
Delta time in open arm before/after self-admin0.10.10.2-0.3-0.4-0.4
Diff in mean of infusions in LGA sessions0.00.00.0-0.2-0.1-0.1
Delay discount exponential model param0.50.50.70.80.50.8
Extinction: sum of active levers before priming0.30.30.5-0.4-0.5-0.7
Active lever presses in extinction session 60.50.50.7-0.5-0.8-0.8
Bone: final force0.10.10.1-0.4-0.4-0.3
Bone: final moment0.10.20.2-0.5-0.4-0.3
Food consumed during 24 hour testing period0.20.20.3-0.5-0.5-0.4
Glucose0.20.40.50.60.60.7
Heart weight3.04.65.51.92.12.3
Delay discount hyperbolic model param0.30.30.50.70.30.6
Intermittent access intake day 1-15 change0.00.10.10.3-0.3-0.1
Intermittent access intake escalation0.10.10.30.6-0.00.2
Intermittent access intake escalation 20.00.00.10.1-0.10.3
Intermitt. access day 1 inactive lever presses0.51.82.2-1.5-1.4-1.2
Intermitt. access day 15 inactive lever presses4.08.19.9-3.1-3.0-2.4
Intermitt. access escalation Index0.30.50.70.70.60.8
Intermittent access day 1 total infusions3.45.45.7-2.4-2.3-2.3
Intermittent access day 15 total infusions1.31.92.4-1.2-1.6-1.3
Intermittent access terminal intake (last 3 days)2.12.73.3-1.5-1.8-1.6
Intermittent access total infusions2.02.42.8-1.3-1.7-1.7
Intermittent access day 1 locomotion1.82.32.5-1.5-1.5-1.6
Intermittent access day 15 total locomotion0.20.30.4-0.5-0.6-0.5
Intermittent access total locomotion0.30.30.4-0.4-0.6-0.6
Intermittent access standard deviation0.81.71.8-1.3-1.3-1.2
Left kidney weight0.00.00.10.20.20.1
Right kidney weight0.42.02.51.41.61.3
Cocaine induced anxiety0.20.30.3-0.6-0.6-0.4
Post-drug Anxiety1.31.41.51.11.21.2
Baseline Anxiety3.33.94.22.02.01.9
Tail length0.51.82.01.41.31.4
Length with tail2.08.79.83.12.92.8
Length without tail0.72.22.61.61.51.4
Times rat made contact with spout1.92.22.3-1.5-1.4-1.5
Lifetime Intake2.22.73.1-1.4-1.8-1.7
Liver weight, left3.96.56.62.52.62.5
Liver weight, right10.117.618.14.34.24.2
Locomotor activity0.20.30.60.50.80.5
Locomotor testing distance0.10.20.4-0.4-0.3-0.6
Locomotor testing rearing0.51.01.5-0.7-1.0-1.2
Locomotion in novel chamber0.40.51.31.10.40.4
Locomotion in novel chamber post-restriction2.94.85.32.32.32.0
Fecal boli incidents, locomotor time 10.20.30.3-0.4-0.6-0.5
Change in fecal boli incidents, locomotor task4.54.44.62.12.12.0
Time >=10cm from walls, locomotor time 10.10.10.20.40.40.1
Bouts of movement, locomotor time 11.61.92.0-1.3-1.4-1.4
Total resting periods, locomotor time 12.02.22.4-1.5-1.5-1.5
Rest time, locomotor task time 10.10.10.10.30.20.3
Distance moved, locomotor task time 10.81.21.41.21.21.0
Vertical activity count, locomotor time 10.20.60.80.90.80.6
Time >=10cm from walls, locomotor time 20.10.20.3-0.4-0.5-0.4
Bouts of movement, locomotor time 20.10.10.20.40.20.3
Total resting periods, locomotor time 20.00.00.00.0-0.10.0
Rest time, locomotor task time 21.41.82.3-1.5-1.2-1.2
Distance moved, locomotor task time 21.11.31.61.31.11.1
Vertical activity count, locomotor time 20.60.81.21.10.70.8
Light reinforcement 13.07.38.8-3.0-2.7-2.5
Light reinforcement 23.24.96.3-2.5-2.2-1.9
Bone: marrow area0.61.31.4-1.2-1.2-1.1
Bone: maximum diameter1.12.02.2-1.5-1.4-1.3
Bone: maximum force0.10.20.3-0.5-0.5-0.4
Bone: maximum moment0.20.30.4-0.6-0.6-0.5
Mean time between licks in bursts1.53.83.91.92.01.9
Mean num. licks in bursts0.10.20.2-0.4-0.5-0.5
Cd content in liver0.00.00.0-0.0-0.0-0.0
Co content in liver5.96.97.2-2.7-2.6-2.6
Cu content in liver0.10.10.1-0.3-0.3-0.3
Fe content in liver0.91.11.3-1.0-1.1-1.1
K content in liver0.40.40.6-0.8-0.6-0.4
Mg content in liver0.40.40.7-0.8-0.6-0.5
Mn content in liver0.10.10.1-0.3-0.2-0.2
Na content in liver0.50.60.6-0.8-0.8-0.7
Rb content in liver0.00.00.0-0.1-0.0-0.1
Se content in liver0.10.10.10.40.30.3
Sr content in liver0.20.10.20.40.40.4
Zn content in liver0.91.01.11.01.01.0
Bone: minimum diameter0.00.10.10.10.20.3
Time in familiar zone, hab. session 10.70.70.80.80.80.9
Time in novel zone, hab. session 10.50.50.80.90.70.6
Total zone transitions, hab. session 10.10.20.2-0.5-0.4-0.3
Total locomotion distance, hab. session 10.20.30.4-0.6-0.5-0.4
Locomotion velocity, hab. session 11.11.51.9-1.4-1.2-1.1
Time in familiar zone, hab. session 20.00.00.0-0.0-0.1-0.0
Time in novel zone, hab. session 20.50.50.60.80.80.6
Total zone transitions, hab. session 20.10.10.2-0.4-0.2-0.3
Total locomotion distance, hab. session 20.20.20.4-0.6-0.4-0.3
Locomotion velocity, hab. session 20.40.50.7-0.9-0.6-0.6
Novel to familiar place preference ratio1.01.11.21.01.11.0
Novelty place preference1.61.71.91.31.41.3
Time in novel zone, NPP test1.92.02.11.41.51.3
Total zone transitions, NPP test1.52.22.5-1.6-1.4-1.4
Total locomotion distance, NPP test2.02.83.1-1.8-1.6-1.6
Locomotion velocity, NPP test3.34.65.2-2.3-2.1-2.1
Intraocular pressure5.88.49.32.93.02.7
Delta distance traveled before/after self-admin1.81.92.11.41.31.4
Delta ambulatory time before/after self-admin0.20.20.30.50.40.5
Parametrial fat weight11.928.030.35.15.35.5
Pavlov. Cond. lever latency1.82.32.91.71.51.4
Pavlov. Cond. magazine entry latency0.10.10.2-0.4-0.3-0.2
Pavlov. Cond. change in total contacts0.00.10.1-0.3-0.2-0.1
Pavlov. Cond. index score0.81.01.4-1.2-0.9-0.8
Pavlov. Cond. latency score0.81.01.4-1.2-0.9-0.8
Pavlov. Cond. lever contacts1.21.51.9-1.4-1.1-1.1
Pavlov. Cond. magazine entry number0.50.60.91.00.70.6
Pavlov. Cond. intertrial magazine entries1.31.51.7-1.2-1.2-1.3
Pavlov. Cond. lever-magazine prob. diff.1.51.82.3-1.5-1.3-1.2
Pavlov. Cond. response bias1.41.82.3-1.5-1.3-1.2
Pavlov. Cond. lever latency1.42.02.11.41.41.4
Pavlov. Cond. magazine entry latency0.30.30.4-0.6-0.6-0.4
Pavlov. Cond. change in total contacts0.61.01.1-1.0-1.0-1.1
Pavlov. Cond. index score1.11.51.6-1.2-1.3-1.2
Pavlov. Cond. latency score1.21.51.7-1.2-1.3-1.2
Pavlov. Cond. lever contacts1.01.41.5-1.1-1.2-1.2
Pavlov. Cond. magazine entry number0.10.20.20.40.50.4
Pavlov. Cond. intertrial magazine entries3.65.55.92.42.42.2
Pavlov. Cond. lever-magazine prob. diff.0.71.01.1-1.0-1.0-1.0
Pavlov. Cond. response bias1.62.22.3-1.4-1.5-1.5
Time in closed arm before self-admin0.70.91.00.91.01.0
Time in closed arm after self-admin1.31.41.71.31.21.1
Time in open arm before self-admin0.10.10.1-0.3-0.2-0.3
Time in open arm after self-admin1.51.61.8-1.3-1.3-1.2
Bone: periosteal estimation1.02.12.4-1.5-1.4-1.3
Bone: periosteal perimeter0.40.70.8-0.9-0.8-0.8
Bone: post-yield work0.91.31.5-1.0-1.2-1.2
Progressive ratio test 1 active lever presses1.41.81.8-1.3-1.3-1.3
Progressive ratio test 1 breakpoint1.51.81.8-1.3-1.3-1.4
Progressive ratio test 1 inactive lever presses2.84.04.8-1.9-2.2-1.9
Progressive ratio test 2 active lever presses0.20.20.3-0.2-0.6-0.5
Progressive ratio test 2 breakpoint0.10.10.2-0.1-0.5-0.4
Progressive ratio test 2 inactive lever presses1.11.82.5-1.2-1.6-1.2
Incentive Sensitization - Responses0.00.10.10.0-0.4-0.2
Incentive Sensitization - Breakpoint0.00.00.10.1-0.3-0.1
Sum of active levers in priming session hrs 5-60.80.71.3-1.1-0.6-0.7
Progressive ratio0.00.00.10.20.10.2
Food seeking constrained by brief footshock3.64.44.9-2.0-2.2-2.1
Seeking ratio, punishment vs. effort0.40.60.8-0.9-0.7-0.8
Retroperitoneal fat weight22.796.998.19.99.99.8
Reaction time number correct0.50.91.2-1.1-0.9-0.9
Reaction time mean minus median0.00.00.00.0-0.00.0
Reaction time mean minus median AUC0.00.10.10.20.30.3
Reaction time num false alarms0.00.00.1-0.30.1-0.0
Reaction time num false alarms AUC0.00.00.1-0.30.1-0.1
Reaction time trials correct on left0.50.91.2-1.1-0.9-0.9
Reaction time trials on left0.51.01.3-1.1-0.9-0.9
Reaction time mean1.11.71.91.21.31.4
Reaction time mean AUC0.81.41.61.01.21.2
Median of all reaction times1.41.92.21.21.41.5
Reaction time omissions0.10.10.2-0.4-0.3-0.2
Reaction time false alarm rate0.10.20.30.20.50.4
Reaction time premature initiation rate0.10.20.20.40.50.4
Reaction time premature initiations0.00.00.1-0.2-0.1-0.1
Std. dev. reaction times0.20.40.50.50.70.7
Reaction time trials completed0.51.01.3-1.1-0.9-0.9
Reaction time trials AUC0.71.21.5-1.2-1.1-1.0
Run reversals in cocaine runway, females0.00.00.10.20.20.1
Run reversals in cocaine runway, males0.10.10.20.1-0.1-0.4
Latency to leave start box in cocaine runway0.50.60.7-0.7-0.8-0.7
Latency to leave start box in cocaine runway, F0.30.30.4-0.6-0.5-0.5
Latency to leave start box in cocaine runway, M0.00.00.10.1-0.3-0.1
Std. dev. time between licks in bursts0.10.10.20.10.30.4
Total sessions with >9 infusions0.60.71.0-0.5-1.0-0.9
Short access day 1 total inactive lever presses7.610.011.9-3.5-3.2-2.8
Short access day 10 total inactive lever presses1.94.65.5-2.3-2.1-2.0
Short access day 1 total infusions3.34.45.4-1.9-2.3-2.1
Short access day 10 total infusions2.02.62.7-1.6-1.6-1.6
Short access total infusions0.91.21.6-0.9-1.3-1.1
Short access day 1 locomotion2.43.03.7-1.5-1.9-1.8
Short access day 10 total locomotion1.22.32.8-1.7-1.5-1.4
Short access total locomotion0.10.20.2-0.3-0.5-0.4
One hour access (0.3 mA shock)1.01.11.5-0.9-1.2-1.0
Compulsive drug intake0.70.91.20.81.10.9
One hour access (shock baseline)1.42.12.7-1.2-1.6-1.5
Social response proportion0.30.40.40.60.60.6
Social responses0.10.10.20.10.30.4
Social time0.30.50.80.60.50.9
Soleus weight4.713.914.6-3.8-3.6-3.7
Bone: stiffness0.00.00.0-0.1-0.2-0.1
Tibialis anterior weight3.812.913.4-3.7-3.5-3.6
Time to tail flick, vehicle, before self-admin1.21.31.81.31.01.0
Time to tail flick, vehicle, after self-admin3.74.95.52.42.22.1
Time to tail flick, test, before self-admin0.10.10.1-0.3-0.2-0.3
Time to tail flick, test, after self-admin0.10.10.1-0.4-0.3-0.3
Delta time to tail flick, vehicle, before/after SA0.10.10.10.20.30.3
Delta time to tail flick, test, before/after SA1.51.51.7-1.3-1.3-1.1
Tibia length2.77.68.22.72.72.9
Ambulatory time before self-admin0.00.00.0-0.0-0.00.0
Ambulatory time after self-admin1.51.71.91.41.21.3
Bone: tissue strength0.91.01.11.01.00.9
Total heroin consumption3.13.74.1-2.0-1.8-1.9
Bone: trabecular number3.76.17.4-2.7-2.4-2.3
Bone: trabecular spacing3.24.34.92.22.11.9
Bone: trabecular thickness0.81.01.3-1.1-1.0-0.9
Bone: trabecular tissue density0.30.40.5-0.6-0.7-0.6
Water consumed over 24 hours0.50.60.8-0.9-0.7-0.7
Number of responses in last shaping day0.10.10.20.0-0.5-0.3