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 Brain gene expression Trim54 0.14 0.11 3.3e-10 0.1 0.07 0.09 0.1 6.3e-10 2.0e-07 1.2e-08 3.4e-09
2 PL gene expression Trim54 0.05 0.05 5.6e-05 0.03 0.04 0.04 0.04 1.0e-04 2.2e-05 6.6e-05 4.0e-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
Bone: apparent density5.69.310.43.2-2.9
Area under the delay curve0.00.10.1-0.3-0.2
BMI with tail0.62.02.5-1.61.2
BMI without tail0.20.50.7-0.80.6
Body weight1.77.27.6-2.62.8
Weight adjusted by age0.00.00.0-0.2-0.1
Bone surface2.95.16.32.5-2.0
Bone volume3.25.56.92.6-2.0
Breakpoint value in progressive ratio session1.71.92.21.5-1.3
Number of licking bursts0.00.00.00.1-0.0
Context. condit. distance diff. score0.00.00.00.10.1
Locomotion velocity, session 10.10.10.2-0.40.2
Locomotion distance, session 11.41.81.91.3-1.4
Locomotion velocity, session 20.20.30.3-0.50.5
Locomotion distance, session 20.00.00.0-0.00.0
Locomotion velocity, session 30.60.80.80.8-0.9
Locomotion distance, session 30.70.80.90.8-1.0
Stereotopy head waving bouts, day 31.72.02.41.2-1.6
Stereotopy head waving duration, day 30.10.10.20.2-0.5
Locomotion velocity, session 71.31.41.81.3-1.0
Locomotion distance, session 70.10.10.20.5-0.1
Stereotopy head waving bouts, day 70.20.20.3-0.60.1
Stereotopy head waving duration, day 70.30.30.50.4-0.7
Locomotion velocity, session 80.30.40.50.7-0.4
Locomotion distance, session 80.20.40.50.7-0.5
Degree of sensitization distance0.70.70.9-0.71.0
Degree of sensitization stereotypy0.40.40.6-0.80.4
Conditioned locomotion3.23.84.01.9-2.0
Cocaine response after cond. corrected0.60.60.80.7-0.9
Cocaine response after cond. not corrected1.51.61.81.2-1.3
Cocaine response before conditioning1.21.41.61.1-1.3
Saline control response0.71.01.11.1-0.9
Bone: connectivity density5.38.39.23.0-2.7
Bone: cortical apparent density0.30.40.40.7-0.6
Bone: cortical area0.40.71.11.1-0.5
Bone: cortical porosity2.12.32.71.6-1.3
Bone: cortical porosity1.71.82.21.5-1.2
Bone: cortical thickness0.00.10.10.10.4
Bone: cortical thickness1.51.71.91.4-1.3
Bone: cortical tissue density0.20.30.30.6-0.5
Condit. Reinf. active minus inactive responses0.80.81.0-1.00.8
Condit. Reinf. active-inactive response ratio0.70.70.8-0.90.8
Condit. Reinf. active responses0.10.10.10.1-0.4
Condit. Reinf. inactive responses1.21.41.71.0-1.3
Incentive salience index mean0.00.00.00.0-0.1
Condit. Reinf. lever presses0.40.50.60.7-0.8
Condit. Reinf. active minus inactive responses3.54.35.51.8-2.3
Condit. Reinf. active-inactive response ratio0.70.71.10.5-1.1
Condit. Reinf. active responses3.04.25.01.8-2.2
Condit. Reinf. inactive responses2.12.62.71.6-1.6
Condit. Reinf. lever presses1.72.22.91.3-1.7
Condit. Reinf. lever reinforcers received2.63.74.51.7-2.1
Conditioned reinforcement - actives1.81.82.41.5-1.1
Conditioned reinforcement - inactives2.93.33.41.8-1.8
Conditioned locomotion0.40.40.60.8-0.5
Patch foraging indifference point 0 sec0.20.30.5-0.30.7
Patch foraging indifference point AUC2.93.34.12.0-1.6
Delay disc. indifference point, 0s delay3.84.24.8-2.21.9
Delay disc. indifference point, 16s delay0.10.10.2-0.1-0.5
Delay disc. indifference point, 2s delay0.40.40.6-0.80.6
Delay disc. indifference point, 24s delay1.01.01.60.6-1.3
Delay disc. indifference point, 4s delay0.00.00.1-0.30.1
Delay disc. indifference point, 8s delay0.00.00.10.1-0.3
Indifference point function ln k0.00.00.0-0.20.1
Indifference point function log k0.00.00.0-0.20.1
Patch foraging total patch changes 0 sec0.10.20.4-0.10.6
Patch foraging total patch changes 12 sec0.50.61.1-0.51.0
Patch foraging total patch changes 18 sec0.10.10.20.40.1
Patch foraging total patch changes 24 sec0.60.81.1-0.71.0
Patch foraging total patch changes 6 sec0.00.00.00.00.2
Patch foraging time to switch 0 sec0.20.30.6-0.8-0.0
Patch foraging water rate 0 sec0.20.30.70.8-0.1
Patch foraging water rate 12 sec1.31.92.3-1.21.5
Patch foraging water rate 18 sec0.50.70.8-0.80.9
Patch foraging water rate 24 sec1.42.02.5-1.21.6
Patch foraging water rate 6 sec1.21.72.0-1.21.4
Seeking ratio, delayed vs. immediate footshock0.00.00.10.20.2
Distance traveled before self-admin0.00.00.1-0.3-0.0
Distance traveled after self-admin1.21.41.7-1.31.0
Extensor digitorum longus weight4.618.118.34.3-4.2
Bone: elastic displacement1.11.31.41.2-1.1
Bone: elastic work1.21.51.51.2-1.2
Bone: endosteal estimation0.51.21.51.2-0.9
Bone: endosteal perimeter0.20.40.60.8-0.5
Epididymis fat weight12.529.133.1-5.05.8
Delta time in closed arm before/after self-admin0.00.00.0-0.00.2
Delta time in open arm before/after self-admin0.30.30.40.5-0.6
Diff in mean of infusions in LGA sessions0.50.60.90.9-0.5
Delay discount exponential model param0.10.10.2-0.00.5
Extinction: sum of active levers before priming0.40.40.50.6-0.7
Active lever presses in extinction session 60.80.80.91.0-0.8
Bone: final force0.30.40.80.9-0.3
Bone: final moment0.30.50.90.9-0.4
Food consumed during 24 hour testing period0.10.10.10.3-0.3
Glucose0.20.40.4-0.60.6
Heart weight10.014.114.8-3.73.8
Delay discount hyperbolic model param0.10.10.2-0.00.4
Intermittent access intake day 1-15 change0.00.00.10.2-0.3
Intermittent access intake escalation0.00.00.0-0.1-0.0
Intermittent access intake escalation 20.50.50.6-0.80.6
Intermitt. access day 1 inactive lever presses0.30.40.60.8-0.3
Intermitt. access day 15 inactive lever presses8.89.711.13.3-2.9
Intermitt. access escalation Index0.50.40.7-0.80.5
Intermittent access day 1 total infusions5.36.16.12.5-2.5
Intermittent access day 15 total infusions2.12.32.51.5-1.6
Intermittent access terminal intake (last 3 days)1.81.92.11.3-1.4
Intermittent access total infusions2.32.52.61.6-1.6
Intermittent access day 1 locomotion2.32.42.51.6-1.5
Intermittent access day 15 total locomotion0.60.70.70.8-0.9
Intermittent access total locomotion0.40.40.50.7-0.6
Intermittent access standard deviation0.40.40.70.8-0.4
Left kidney weight0.00.00.00.00.2
Right kidney weight1.13.13.3-1.71.8
Cocaine induced anxiety0.50.50.80.9-0.6
Post-drug Anxiety1.01.11.2-1.11.1
Baseline Anxiety2.32.43.2-1.81.3
Tail length0.00.10.2-0.00.4
Length with tail1.03.85.1-1.62.3
Length without tail0.51.11.7-0.81.3
Times rat made contact with spout2.63.03.82.0-1.4
Lifetime Intake3.43.84.12.0-1.9
Liver weight, left1.42.32.3-1.51.5
Liver weight, right9.616.016.1-4.04.0
Locomotor activity0.30.40.5-0.70.6
Locomotor testing distance0.10.10.20.2-0.4
Locomotor testing rearing0.81.31.51.0-1.2
Locomotion in novel chamber0.50.71.0-0.61.0
Locomotion in novel chamber post-restriction1.92.32.4-1.51.5
Fecal boli incidents, locomotor time 10.40.40.60.8-0.5
Change in fecal boli incidents, locomotor task3.93.74.2-1.82.1
Time >=10cm from walls, locomotor time 10.00.00.0-0.10.1
Bouts of movement, locomotor time 12.12.32.41.5-1.6
Total resting periods, locomotor time 12.52.72.81.6-1.7
Rest time, locomotor task time 10.10.10.10.4-0.3
Distance moved, locomotor task time 11.92.02.9-1.71.1
Vertical activity count, locomotor time 11.01.01.5-1.20.7
Time >=10cm from walls, locomotor time 20.30.30.50.7-0.4
Bouts of movement, locomotor time 20.20.20.2-0.40.4
Total resting periods, locomotor time 20.00.00.0-0.10.1
Rest time, locomotor task time 21.01.21.60.9-1.2
Distance moved, locomotor task time 20.91.11.3-1.11.0
Vertical activity count, locomotor time 20.30.30.4-0.40.7
Light reinforcement 13.36.06.82.3-2.6
Light reinforcement 22.43.24.21.5-2.0
Bone: marrow area0.51.21.51.2-0.9
Bone: maximum diameter1.01.82.31.5-1.1
Bone: maximum force0.10.20.30.6-0.0
Bone: maximum moment0.10.20.40.7-0.2
Mean time between licks in bursts2.63.73.9-1.92.0
Mean num. licks in bursts0.40.50.70.8-0.5
Cd content in liver0.00.00.0-0.10.0
Co content in liver4.95.76.12.3-2.5
Cu content in liver0.00.00.00.1-0.2
Fe content in liver0.00.00.00.0-0.0
K content in liver0.30.30.4-0.70.4
Mg content in liver0.20.20.3-0.40.6
Mn content in liver0.60.70.70.8-0.8
Na content in liver0.20.30.40.4-0.6
Rb content in liver0.00.00.0-0.10.1
Se content in liver0.30.30.4-0.50.6
Sr content in liver0.30.30.5-0.70.4
Zn content in liver1.21.41.6-1.11.3
Bone: minimum diameter0.10.20.20.40.5
Time in familiar zone, hab. session 10.60.60.8-0.60.9
Time in novel zone, hab. session 10.40.40.5-0.70.6
Total zone transitions, hab. session 10.10.10.10.3-0.3
Total locomotion distance, hab. session 10.10.10.20.4-0.4
Locomotion velocity, hab. session 10.71.01.30.9-1.1
Time in familiar zone, hab. session 20.00.00.10.20.0
Time in novel zone, hab. session 20.50.50.7-0.80.6
Total zone transitions, hab. session 20.10.10.10.3-0.3
Total locomotion distance, hab. session 20.30.30.50.7-0.4
Locomotion velocity, hab. session 20.50.60.80.9-0.7
Novel to familiar place preference ratio1.61.62.2-1.51.0
Novelty place preference2.22.22.8-1.71.3
Time in novel zone, NPP test2.42.53.1-1.81.4
Total zone transitions, NPP test1.11.51.91.1-1.4
Total locomotion distance, NPP test1.72.32.71.4-1.6
Locomotion velocity, NPP test2.94.14.51.9-2.1
Intraocular pressure5.27.27.7-2.62.8
Delta distance traveled before/after self-admin1.51.61.7-1.31.3
Delta ambulatory time before/after self-admin0.30.30.3-0.60.5
Parametrial fat weight6.011.612.7-3.23.6
Pavlov. Cond. lever latency2.02.53.1-1.81.4
Pavlov. Cond. magazine entry latency0.00.00.10.3-0.1
Pavlov. Cond. change in total contacts0.00.00.10.3-0.1
Pavlov. Cond. index score0.81.01.31.2-0.8
Pavlov. Cond. latency score0.81.01.41.2-0.8
Pavlov. Cond. lever contacts1.21.41.71.3-1.0
Pavlov. Cond. magazine entry number0.50.60.8-0.90.7
Pavlov. Cond. intertrial magazine entries1.11.41.61.1-1.3
Pavlov. Cond. lever-magazine prob. diff.1.62.02.41.5-1.3
Pavlov. Cond. response bias1.51.92.11.4-1.3
Pavlov. Cond. lever latency1.31.82.3-1.11.5
Pavlov. Cond. magazine entry latency0.10.20.30.2-0.5
Pavlov. Cond. change in total contacts0.50.70.80.8-0.9
Pavlov. Cond. index score0.81.11.30.9-1.2
Pavlov. Cond. latency score0.81.01.30.9-1.1
Pavlov. Cond. lever contacts0.60.81.10.8-1.0
Pavlov. Cond. magazine entry number0.00.10.1-0.20.3
Pavlov. Cond. intertrial magazine entries3.24.24.2-2.02.0
Pavlov. Cond. lever-magazine prob. diff.0.60.70.90.8-0.9
Pavlov. Cond. response bias1.21.62.11.0-1.4
Time in closed arm before self-admin0.20.30.5-0.20.7
Time in closed arm after self-admin0.80.81.2-0.61.1
Time in open arm before self-admin0.10.10.2-0.40.0
Time in open arm after self-admin1.21.41.90.9-1.4
Bone: periosteal estimation0.81.62.31.5-1.0
Bone: periosteal perimeter0.30.40.70.8-0.4
Bone: post-yield work0.71.01.41.2-0.8
Progressive ratio test 1 active lever presses2.12.22.71.6-1.3
Progressive ratio test 1 breakpoint1.92.02.51.6-1.2
Progressive ratio test 1 inactive lever presses5.15.66.82.6-2.1
Progressive ratio test 2 active lever presses0.00.00.10.1-0.3
Progressive ratio test 2 breakpoint0.10.10.10.2-0.3
Progressive ratio test 2 inactive lever presses2.22.62.81.7-1.5
Incentive Sensitization - Responses0.30.30.6-0.80.3
Incentive Sensitization - Breakpoint0.60.61.1-1.00.5
Sum of active levers in priming session hrs 5-60.50.50.70.5-0.8
Progressive ratio0.20.30.50.7-0.2
Food seeking constrained by brief footshock5.66.98.02.8-2.4
Seeking ratio, punishment vs. effort0.40.40.60.5-0.8
Retroperitoneal fat weight20.366.871.7-7.98.5
Reaction time number correct0.60.81.01.0-0.8
Reaction time mean minus median0.00.10.10.3-0.0
Reaction time mean minus median AUC0.00.00.0-0.00.2
Reaction time num false alarms0.00.00.0-0.2-0.2
Reaction time num false alarms AUC0.00.00.0-0.1-0.2
Reaction time trials correct on left0.60.81.01.0-0.8
Reaction time trials on left0.70.91.11.0-0.9
Reaction time mean1.01.41.6-1.11.3
Reaction time mean AUC0.91.21.3-1.01.2
Median of all reaction times1.31.81.9-1.31.4
Reaction time omissions0.10.10.10.4-0.3
Reaction time false alarm rate0.10.20.3-0.60.3
Reaction time premature initiation rate0.30.40.6-0.80.5
Reaction time premature initiations0.00.00.0-0.20.0
Std. dev. reaction times0.20.30.4-0.30.7
Reaction time trials completed0.70.91.11.0-0.9
Reaction time trials AUC0.81.11.21.1-1.0
Run reversals in cocaine runway, females0.10.10.2-0.40.3
Run reversals in cocaine runway, males0.20.20.20.4-0.4
Latency to leave start box in cocaine runway0.40.50.60.6-0.7
Latency to leave start box in cocaine runway, F0.30.40.60.4-0.8
Latency to leave start box in cocaine runway, M1.00.91.21.1-0.8
Std. dev. time between licks in bursts0.20.30.3-0.50.5
Total sessions with >9 infusions3.43.74.52.1-1.7
Short access day 1 total inactive lever presses4.04.45.02.0-2.2
Short access day 10 total inactive lever presses0.91.01.00.9-1.0
Short access day 1 total infusions6.36.78.02.8-2.3
Short access day 10 total infusions4.24.74.82.2-2.1
Short access total infusions3.74.24.92.2-1.9
Short access day 1 locomotion8.38.810.03.2-2.8
Short access day 10 total locomotion0.70.80.80.9-0.9
Short access total locomotion0.70.80.91.0-0.8
One hour access (0.3 mA shock)1.82.12.21.5-1.4
Compulsive drug intake0.40.40.4-0.60.7
One hour access (shock baseline)1.82.12.21.4-1.5
Social response proportion0.20.20.3-0.10.6
Social responses0.00.10.10.10.3
Social time0.20.30.6-0.10.7
Soleus weight4.613.615.03.9-3.5
Bone: stiffness0.00.00.10.00.2
Tibialis anterior weight3.210.911.93.1-3.5
Time to tail flick, vehicle, before self-admin1.92.02.3-1.31.5
Time to tail flick, vehicle, after self-admin3.33.54.4-1.62.1
Time to tail flick, test, before self-admin0.60.60.60.7-0.8
Time to tail flick, test, after self-admin0.00.10.10.10.3
Delta time to tail flick, vehicle, before/after SA0.00.00.00.10.1
Delta time to tail flick, test, before/after SA0.40.30.40.7-0.5
Tibia length2.46.77.1-2.52.7
Ambulatory time before self-admin0.10.10.1-0.3-0.3
Ambulatory time after self-admin0.91.01.4-1.20.8
Bone: tissue strength0.80.80.9-0.80.9
Total heroin consumption2.83.33.31.8-1.8
Bone: trabecular number4.46.97.82.8-2.4
Bone: trabecular spacing4.55.97.6-2.82.0
Bone: trabecular thickness1.11.31.81.3-0.9
Bone: trabecular tissue density0.20.20.20.4-0.5
Water consumed over 24 hours1.41.61.91.4-1.2
Number of responses in last shaping day0.91.01.41.2-0.7