Traf4

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 Liver gene expression Traf4 0.34 0.19 0.0e+00 0.15 0.17 0.17 0.17 1.4e-16 5.7e-19 8.5e-19 9.3e-19
2 PL gene expression Traf4 0.03 0.03 8.4e-03 0.01 0.01 0 0.01 1.4e-02 2.5e-02 8.5e-02 2.4e-02
3 Brain gene expression Traf4 0.03 0.03 1.1e-03 0.02 0.02 0.02 0.02 3.1e-03 1.1e-02 3.0e-03 8.4e-03

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 density2.13.84.3-1.92.11.8
Area under the delay curve1.52.23.31.1-1.8-1.5
BMI with tail1.86.26.9-2.62.52.3
BMI without tail1.15.66.4-2.52.32.3
Body weight2.410.712.8-3.63.32.9
Weight adjusted by age0.00.10.1-0.30.10.3
Bone surface1.53.03.1-1.71.81.7
Bone volume1.32.62.7-1.61.61.5
Breakpoint value in progressive ratio session0.20.30.4-0.60.60.5
Number of licking bursts0.10.40.60.7-0.8-0.4
Context. condit. distance diff. score0.50.70.7-0.90.80.8
Locomotion velocity, session 11.92.12.5-1.61.41.3
Locomotion distance, session 10.10.20.3-0.60.40.2
Locomotion velocity, session 20.00.00.1-0.10.20.1
Locomotion distance, session 21.31.82.0-1.31.31.4
Locomotion velocity, session 33.03.44.22.1-1.9-1.6
Locomotion distance, session 30.40.40.40.7-0.7-0.6
Stereotopy head waving bouts, day 30.00.00.1-0.00.20.3
Stereotopy head waving duration, day 30.40.50.90.9-0.6-0.4
Locomotion velocity, session 70.30.30.5-0.40.70.6
Locomotion distance, session 70.40.50.6-0.70.80.7
Stereotopy head waving bouts, day 70.60.70.8-0.70.90.9
Stereotopy head waving duration, day 70.30.40.5-0.40.70.6
Locomotion velocity, session 80.00.00.1-0.20.10.3
Locomotion distance, session 80.81.21.2-1.11.11.1
Degree of sensitization distance2.93.13.3-1.81.81.7
Degree of sensitization stereotypy0.60.70.7-0.80.80.8
Conditioned locomotion1.51.72.51.6-1.3-1.0
Cocaine response after cond. corrected1.42.12.5-1.41.41.6
Cocaine response after cond. not corrected1.92.73.1-1.61.61.8
Cocaine response before conditioning0.20.20.3-0.50.50.3
Saline control response0.00.00.0-0.0-0.00.0
Bone: connectivity density3.86.06.6-2.52.62.3
Bone: cortical apparent density0.40.60.80.9-0.7-0.6
Bone: cortical area1.42.22.31.5-1.5-1.4
Bone: cortical porosity0.30.30.5-0.60.70.4
Bone: cortical porosity0.10.10.2-0.40.50.2
Bone: cortical thickness2.74.55.22.3-2.0-2.0
Bone: cortical thickness0.10.10.10.2-0.1-0.3
Bone: cortical tissue density0.20.30.50.7-0.5-0.4
Condit. Reinf. active minus inactive responses0.70.70.91.0-0.9-0.7
Condit. Reinf. active-inactive response ratio0.20.20.20.4-0.5-0.4
Condit. Reinf. active responses0.00.00.00.2-0.10.0
Condit. Reinf. inactive responses0.30.40.5-0.60.70.7
Incentive salience index mean0.20.30.40.6-0.5-0.3
Condit. Reinf. lever presses0.10.20.3-0.30.50.6
Condit. Reinf. active minus inactive responses0.30.50.80.9-0.6-0.5
Condit. Reinf. active-inactive response ratio0.40.60.90.9-0.8-0.6
Condit. Reinf. active responses0.20.30.50.7-0.5-0.4
Condit. Reinf. inactive responses0.00.00.0-0.00.20.0
Condit. Reinf. lever presses2.43.53.61.9-1.8-1.9
Condit. Reinf. lever reinforcers received0.50.60.91.0-0.7-0.7
Conditioned reinforcement - actives0.10.60.9-0.80.90.4
Conditioned reinforcement - inactives0.10.20.3-0.50.60.1
Conditioned locomotion0.40.60.8-0.90.60.8
Patch foraging indifference point 0 sec0.30.81.01.0-0.7-1.0
Patch foraging indifference point AUC1.02.53.31.8-1.6-1.2
Delay disc. indifference point, 0s delay0.80.91.10.7-1.0-1.1
Delay disc. indifference point, 16s delay1.21.72.90.8-1.7-1.3
Delay disc. indifference point, 2s delay2.83.24.11.6-1.7-2.0
Delay disc. indifference point, 24s delay0.50.71.0-0.90.61.0
Delay disc. indifference point, 4s delay0.30.30.50.3-0.7-0.7
Delay disc. indifference point, 8s delay0.60.91.70.8-1.3-0.7
Indifference point function ln k0.20.60.9-0.90.90.3
Indifference point function log k0.20.60.9-0.90.90.3
Patch foraging total patch changes 0 sec0.20.60.80.9-0.6-0.9
Patch foraging total patch changes 12 sec0.20.20.30.5-0.4-0.5
Patch foraging total patch changes 18 sec1.12.63.11.8-1.6-1.5
Patch foraging total patch changes 24 sec0.82.93.92.0-1.7-1.4
Patch foraging total patch changes 6 sec2.54.25.22.3-2.0-1.8
Patch foraging time to switch 0 sec0.62.52.8-1.71.51.6
Patch foraging water rate 0 sec0.93.23.81.8-1.6-1.9
Patch foraging water rate 12 sec0.10.20.5-0.40.70.1
Patch foraging water rate 18 sec0.30.60.8-0.90.80.6
Patch foraging water rate 24 sec0.30.40.60.4-0.6-0.8
Patch foraging water rate 6 sec1.21.82.41.3-1.2-1.6
Seeking ratio, delayed vs. immediate footshock1.52.12.91.5-1.7-1.1
Distance traveled before self-admin1.63.44.92.2-1.3-1.9
Distance traveled after self-admin0.00.00.10.3-0.2-0.1
Extensor digitorum longus weight0.73.03.3-1.81.51.8
Bone: elastic displacement2.83.53.71.9-1.8-1.9
Bone: elastic work9.011.812.13.5-3.3-3.5
Bone: endosteal estimation0.00.00.1-0.2-0.2-0.3
Bone: endosteal perimeter0.00.00.1-0.3-0.10.1
Epididymis fat weight5.226.230.6-5.55.24.6
Delta time in closed arm before/after self-admin2.82.63.11.8-1.5-1.6
Delta time in open arm before/after self-admin5.36.27.0-2.72.22.6
Diff in mean of infusions in LGA sessions0.50.80.9-0.90.90.9
Delay discount exponential model param1.11.62.3-0.91.51.2
Extinction: sum of active levers before priming0.60.91.0-1.01.00.8
Active lever presses in extinction session 60.20.20.5-0.30.70.2
Bone: final force0.30.50.60.6-0.7-0.8
Bone: final moment0.40.60.70.7-0.8-0.9
Food consumed during 24 hour testing period0.30.60.90.6-0.6-1.0
Glucose1.32.12.51.5-1.6-1.2
Heart weight1.11.82.1-1.51.41.1
Delay discount hyperbolic model param1.72.12.8-1.11.71.5
Intermittent access intake day 1-15 change0.00.20.4-0.30.60.3
Intermittent access intake escalation0.10.30.5-0.50.70.5
Intermittent access intake escalation 20.00.10.10.3-0.3-0.2
Intermitt. access day 1 inactive lever presses0.00.20.20.3-0.5-0.5
Intermitt. access day 15 inactive lever presses0.10.71.00.8-0.7-1.0
Intermitt. access escalation Index0.41.21.6-1.30.91.0
Intermittent access day 1 total infusions0.10.20.4-0.60.30.3
Intermittent access day 15 total infusions0.71.61.8-1.31.21.2
Intermittent access terminal intake (last 3 days)0.91.61.9-1.41.21.2
Intermittent access total infusions0.60.70.8-0.80.80.9
Intermittent access day 1 locomotion0.00.10.1-0.3-0.10.4
Intermittent access day 15 total locomotion0.20.60.8-0.90.80.7
Intermittent access total locomotion0.70.81.0-1.00.80.9
Intermittent access standard deviation0.00.00.0-0.20.10.1
Left kidney weight0.00.10.2-0.40.20.2
Right kidney weight0.10.60.8-0.90.70.6
Cocaine induced anxiety0.10.30.40.4-0.6-0.6
Post-drug Anxiety0.20.20.3-0.30.50.5
Baseline Anxiety0.30.60.8-0.50.90.8
Tail length0.21.31.9-1.40.91.0
Length with tail0.41.93.0-1.71.31.0
Length without tail0.21.01.6-1.31.00.6
Times rat made contact with spout0.10.10.20.3-0.4-0.4
Lifetime Intake0.81.01.1-1.01.01.0
Liver weight, left4.78.19.1-3.02.82.7
Liver weight, right3.56.27.1-2.72.52.3
Locomotor activity0.00.00.10.1-0.3-0.2
Locomotor testing distance0.00.10.10.3-0.4-0.1
Locomotor testing rearing0.00.10.10.4-0.3-0.2
Locomotion in novel chamber1.82.53.11.7-1.8-1.1
Locomotion in novel chamber post-restriction0.10.20.6-0.1-0.10.7
Fecal boli incidents, locomotor time 10.82.02.5-1.41.31.6
Change in fecal boli incidents, locomotor task0.10.10.20.2-0.4-0.4
Time >=10cm from walls, locomotor time 10.00.00.1-0.2-0.00.0
Bouts of movement, locomotor time 10.50.60.70.7-0.9-0.7
Total resting periods, locomotor time 10.20.20.20.4-0.5-0.4
Rest time, locomotor task time 10.20.30.4-0.30.50.7
Distance moved, locomotor task time 10.10.40.70.5-0.5-0.8
Vertical activity count, locomotor time 10.00.10.10.1-0.3-0.4
Time >=10cm from walls, locomotor time 20.31.01.6-1.31.00.5
Bouts of movement, locomotor time 20.20.71.10.7-0.7-1.0
Total resting periods, locomotor time 20.10.20.30.4-0.4-0.6
Rest time, locomotor task time 20.00.10.10.30.00.3
Distance moved, locomotor task time 20.10.20.20.3-0.5-0.5
Vertical activity count, locomotor time 20.10.30.50.2-0.7-0.6
Light reinforcement 10.00.00.00.1-0.1-0.1
Light reinforcement 20.30.71.00.7-0.8-1.0
Bone: marrow area0.00.10.1-0.1-0.2-0.3
Bone: maximum diameter0.30.70.80.7-0.9-0.8
Bone: maximum force0.50.91.00.9-1.0-1.0
Bone: maximum moment0.61.11.30.9-1.1-1.1
Mean time between licks in bursts0.10.71.0-1.00.80.8
Mean num. licks in bursts0.10.30.4-0.70.70.3
Cd content in liver0.70.81.10.9-1.0-0.8
Co content in liver0.30.30.60.6-0.8-0.1
Cu content in liver1.72.02.21.5-1.4-1.4
Fe content in liver1.92.32.6-1.61.41.6
K content in liver0.10.10.2-0.40.20.4
Mg content in liver0.70.81.00.9-1.0-0.8
Mn content in liver0.20.20.30.5-0.5-0.4
Na content in liver0.10.10.2-0.4-0.00.4
Rb content in liver0.10.10.2-0.40.20.3
Se content in liver0.60.80.80.9-0.9-0.8
Sr content in liver0.50.40.4-0.60.70.6
Zn content in liver0.20.30.4-0.60.50.4
Bone: minimum diameter0.10.10.20.4-0.4-0.3
Time in familiar zone, hab. session 10.20.20.30.5-0.5-0.4
Time in novel zone, hab. session 10.10.10.1-0.30.30.3
Total zone transitions, hab. session 10.00.00.10.1-0.3-0.2
Total locomotion distance, hab. session 10.10.20.20.3-0.3-0.5
Locomotion velocity, hab. session 10.40.50.70.7-0.7-0.8
Time in familiar zone, hab. session 20.20.20.20.5-0.3-0.5
Time in novel zone, hab. session 20.10.10.20.3-0.4-0.3
Total zone transitions, hab. session 20.30.40.6-0.60.60.8
Total locomotion distance, hab. session 20.10.10.10.4-0.2-0.2
Locomotion velocity, hab. session 20.10.10.10.4-0.3-0.2
Novel to familiar place preference ratio0.70.91.0-1.01.00.8
Novelty place preference0.91.21.3-1.11.11.0
Time in novel zone, NPP test1.01.21.4-1.21.21.0
Total zone transitions, NPP test0.00.00.0-0.10.10.1
Total locomotion distance, NPP test0.91.21.31.1-1.1-1.1
Locomotion velocity, NPP test1.01.51.61.3-1.2-1.2
Intraocular pressure0.81.41.71.3-1.0-1.2
Delta distance traveled before/after self-admin2.32.63.4-1.91.31.6
Delta ambulatory time before/after self-admin1.12.02.9-1.70.91.5
Parametrial fat weight5.713.414.4-3.83.63.6
Pavlov. Cond. lever latency0.00.00.0-0.10.1-0.0
Pavlov. Cond. magazine entry latency0.00.00.1-0.20.10.2
Pavlov. Cond. change in total contacts0.20.20.40.6-0.5-0.2
Pavlov. Cond. index score0.00.00.00.1-0.10.1
Pavlov. Cond. latency score0.00.00.0-0.00.00.2
Pavlov. Cond. lever contacts0.00.00.0-0.0-0.00.2
Pavlov. Cond. magazine entry number0.10.10.2-0.40.40.2
Pavlov. Cond. intertrial magazine entries0.20.20.30.6-0.4-0.5
Pavlov. Cond. lever-magazine prob. diff.0.00.00.10.2-0.2-0.0
Pavlov. Cond. response bias0.00.00.00.0-0.10.2
Pavlov. Cond. lever latency2.53.53.9-1.91.82.0
Pavlov. Cond. magazine entry latency0.20.30.40.4-0.6-0.6
Pavlov. Cond. change in total contacts0.92.12.41.4-1.4-1.6
Pavlov. Cond. index score2.03.23.31.7-1.8-1.8
Pavlov. Cond. latency score2.33.83.91.9-1.9-2.0
Pavlov. Cond. lever contacts1.32.02.21.4-1.3-1.5
Pavlov. Cond. magazine entry number0.00.00.1-0.10.20.2
Pavlov. Cond. intertrial magazine entries0.30.60.7-0.70.80.8
Pavlov. Cond. lever-magazine prob. diff.1.62.42.51.5-1.6-1.6
Pavlov. Cond. response bias1.21.61.91.2-1.2-1.4
Time in closed arm before self-admin1.32.32.6-1.51.51.6
Time in closed arm after self-admin0.40.40.50.7-0.7-0.6
Time in open arm before self-admin2.12.63.21.6-1.4-1.8
Time in open arm after self-admin0.80.91.1-1.10.80.9
Bone: periosteal estimation0.40.91.00.8-1.0-1.0
Bone: periosteal perimeter0.30.50.70.6-0.9-0.7
Bone: post-yield work0.20.40.6-0.70.40.8
Progressive ratio test 1 active lever presses0.10.20.30.5-0.4-0.4
Progressive ratio test 1 breakpoint0.20.30.40.6-0.5-0.5
Progressive ratio test 1 inactive lever presses0.61.72.11.2-1.2-1.4
Progressive ratio test 2 active lever presses0.10.20.30.6-0.3-0.5
Progressive ratio test 2 breakpoint0.10.20.30.6-0.3-0.4
Progressive ratio test 2 inactive lever presses0.00.10.20.30.0-0.4
Incentive Sensitization - Responses0.00.00.0-0.00.1-0.1
Incentive Sensitization - Breakpoint0.00.00.0-0.10.2-0.1
Sum of active levers in priming session hrs 5-61.41.31.5-1.21.01.2
Progressive ratio0.00.10.2-0.00.40.1
Food seeking constrained by brief footshock0.10.10.1-0.30.40.0
Seeking ratio, punishment vs. effort0.00.10.20.1-0.5-0.2
Retroperitoneal fat weight0.52.32.8-1.71.51.4
Reaction time number correct0.31.11.3-1.21.10.9
Reaction time mean minus median0.10.30.4-0.50.70.6
Reaction time mean minus median AUC0.42.52.8-1.51.61.7
Reaction time num false alarms4.88.28.72.8-2.8-2.9
Reaction time num false alarms AUC3.78.49.02.9-2.8-3.0
Reaction time trials correct on left0.31.11.3-1.21.10.9
Reaction time trials on left0.31.21.4-1.21.20.9
Reaction time mean0.40.80.9-0.91.00.9
Reaction time mean AUC0.30.70.7-0.80.80.8
Median of all reaction times0.30.50.6-0.70.70.7
Reaction time omissions1.21.92.0-1.41.41.3
Reaction time false alarm rate6.18.58.52.9-2.9-2.9
Reaction time premature initiation rate0.20.30.3-0.60.40.5
Reaction time premature initiations0.20.60.7-0.80.70.7
Std. dev. reaction times0.41.21.3-1.11.11.0
Reaction time trials completed0.31.21.4-1.21.20.9
Reaction time trials AUC0.31.01.1-1.01.10.8
Run reversals in cocaine runway, females0.10.20.3-0.30.3-0.5
Run reversals in cocaine runway, males0.10.10.1-0.3-0.10.3
Latency to leave start box in cocaine runway0.50.71.10.9-0.3-1.0
Latency to leave start box in cocaine runway, F0.10.10.30.4-0.1-0.5
Latency to leave start box in cocaine runway, M0.30.30.40.60.0-0.6
Std. dev. time between licks in bursts0.00.00.0-0.2-0.10.1
Total sessions with >9 infusions0.40.50.7-0.80.60.7
Short access day 1 total inactive lever presses2.44.85.7-2.42.22.0
Short access day 10 total inactive lever presses0.00.00.10.0-0.30.1
Short access day 1 total infusions0.51.01.1-1.00.91.0
Short access day 10 total infusions0.30.50.7-0.80.60.7
Short access total infusions0.30.40.4-0.70.50.6
Short access day 1 locomotion0.00.00.0-0.0-0.10.1
Short access day 10 total locomotion0.20.81.40.7-1.2-0.8
Short access total locomotion0.40.61.10.5-1.0-0.6
One hour access (0.3 mA shock)0.00.00.0-0.0-0.2-0.2
Compulsive drug intake0.71.01.1-1.10.91.1
One hour access (shock baseline)0.00.10.10.2-0.2-0.3
Social response proportion2.22.73.3-1.81.51.6
Social responses2.12.72.9-1.71.61.6
Social time1.62.53.6-1.51.31.9
Soleus weight2.26.57.2-2.62.42.7
Bone: stiffness1.73.03.4-1.81.81.6
Tibialis anterior weight2.69.09.5-3.13.02.9
Time to tail flick, vehicle, before self-admin0.10.10.2-0.40.50.3
Time to tail flick, vehicle, after self-admin0.10.20.40.6-0.3-0.4
Time to tail flick, test, before self-admin0.10.10.1-0.00.40.3
Time to tail flick, test, after self-admin0.40.50.80.9-0.5-0.5
Delta time to tail flick, vehicle, before/after SA0.40.40.50.7-0.6-0.6
Delta time to tail flick, test, before/after SA0.50.60.70.8-0.8-0.7
Tibia length0.00.10.20.2-0.4-0.2
Ambulatory time before self-admin0.51.52.01.4-0.7-1.4
Ambulatory time after self-admin0.00.00.0-0.1-0.00.1
Bone: tissue strength1.51.61.71.3-1.3-1.2
Total heroin consumption2.63.03.9-1.72.01.5
Bone: trabecular number2.64.95.5-2.22.32.1
Bone: trabecular spacing0.20.30.40.6-0.6-0.5
Bone: trabecular thickness0.00.00.00.1-0.0-0.2
Bone: trabecular tissue density1.01.81.91.4-1.4-1.3
Water consumed over 24 hours0.10.10.20.2-0.3-0.5
Number of responses in last shaping day0.81.11.71.3-1.1-0.6