Hub : Genes

Tbc1d12

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 Tbc1d12 0.04 0.03 2.3e-03 0.01 0.01 0 0.01 1.4e-02 1.1e-02 2.9e-01 2.1e-02
2 Liver gene expression Tbc1d12 0.03 0.02 2.7e-03 0.02 0.02 0.02 0.02 3.3e-03 4.5e-03 6.6e-03 4.6e-03
3 Brain gene expression Tbc1d12 0.06 0.04 2.3e-04 0.03 0.03 0.04 0.03 3.4e-04 5.2e-04 3.0e-04 5.2e-04
4 Brain intron excision ratio chr1_246092240_246094394 0.04 0.03 8.6e-03 0.02 0.01 0.01 0.01 7.9e-03 1.3e-02 1.3e-02 3.5e-02

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 4
Bone: apparent density2.34.26.51.8-2.52.5-1.0
Area under the delay curve0.71.01.9-1.40.5-1.0-1.0
BMI with tail0.31.01.81.3-0.70.4-1.2
BMI without tail0.00.20.40.40.5-0.6-0.1
Body weight0.10.61.21.1-0.10.60.8
Weight adjusted by age0.00.10.30.20.0-0.5-0.5
Bone surface2.34.46.22.2-2.42.5-1.0
Bone volume2.24.46.52.2-2.42.5-0.4
Breakpoint value in progressive ratio session0.20.30.7-0.90.2-0.1-0.5
Number of licking bursts0.51.53.1-1.80.9-1.3-0.4
Context. condit. distance diff. score1.41.72.41.0-1.51.6-1.0
Locomotion velocity, session 12.02.25.2-2.30.9-1.5-0.7
Locomotion distance, session 10.71.02.4-1.50.7-0.90.1
Locomotion velocity, session 21.41.74.2-0.6-1.11.0-2.0
Locomotion distance, session 20.20.30.5-0.7-0.30.2-0.7
Locomotion velocity, session 30.30.40.90.3-0.71.00.0
Locomotion distance, session 30.70.91.40.6-0.61.21.2
Stereotopy head waving bouts, day 30.00.10.1-0.3-0.30.1-0.1
Stereotopy head waving duration, day 30.20.30.8-0.4-0.50.1-0.9
Locomotion velocity, session 72.42.74.31.5-2.02.1-0.0
Locomotion distance, session 72.02.64.21.8-1.82.00.0
Stereotopy head waving bouts, day 70.50.62.1-1.50.0-0.2-0.4
Stereotopy head waving duration, day 70.20.30.9-1.0-0.2-0.0-0.3
Locomotion velocity, session 80.40.50.8-0.0-0.80.8-0.9
Locomotion distance, session 81.42.13.90.3-1.51.5-2.0
Degree of sensitization distance0.70.72.50.2-0.50.2-1.6
Degree of sensitization stereotypy0.70.82.8-1.70.4-0.50.0
Conditioned locomotion0.50.61.21.1-0.20.30.9
Cocaine response after cond. corrected0.10.10.2-0.30.3-0.4-0.3
Cocaine response after cond. not corrected0.10.10.2-0.50.2-0.2-0.5
Cocaine response before conditioning0.20.20.7-0.80.20.1-0.4
Saline control response1.72.34.0-2.01.5-1.60.7
Bone: connectivity density3.55.68.22.4-2.92.6-1.3
Bone: cortical apparent density0.50.81.7-1.30.5-1.0-0.5
Bone: cortical area0.71.11.71.2-0.71.30.9
Bone: cortical porosity1.21.42.70.3-1.31.0-1.6
Bone: cortical porosity1.21.31.80.5-1.31.2-1.3
Bone: cortical thickness1.01.62.0-1.31.4-1.01.4
Bone: cortical thickness1.92.34.4-2.11.5-1.50.6
Bone: cortical tissue density0.50.91.7-1.30.5-1.0-0.7
Condit. Reinf. active minus inactive responses0.00.10.2-0.4-0.10.00.0
Condit. Reinf. active-inactive response ratio0.00.00.1-0.20.0-0.1-0.0
Condit. Reinf. active responses0.10.10.2-0.30.1-0.10.4
Condit. Reinf. inactive responses0.10.10.2-0.30.1-0.30.4
Incentive salience index mean0.30.40.7-0.80.8-0.60.3
Condit. Reinf. lever presses1.21.83.3-1.31.8-1.50.3
Condit. Reinf. active minus inactive responses1.72.64.22.1-1.81.7-0.1
Condit. Reinf. active-inactive response ratio0.91.52.41.5-1.41.2-0.6
Condit. Reinf. active responses0.81.11.71.3-0.50.91.3
Condit. Reinf. inactive responses1.32.05.3-0.61.3-0.72.3
Condit. Reinf. lever presses0.20.30.5-0.60.6-0.30.7
Condit. Reinf. lever reinforcers received0.50.61.50.8-0.20.61.2
Conditioned reinforcement - actives0.10.51.5-0.6-0.30.6-1.2
Conditioned reinforcement - inactives0.51.31.9-0.5-1.21.4-1.3
Conditioned locomotion0.10.10.4-0.60.3-0.2-0.1
Patch foraging indifference point 0 sec0.30.81.2-0.81.1-0.71.0
Patch foraging indifference point AUC2.04.88.6-2.92.2-2.40.3
Delay disc. indifference point, 0s delay1.11.22.30.6-1.30.8-1.5
Delay disc. indifference point, 16s delay0.60.91.6-1.30.9-1.0-0.4
Delay disc. indifference point, 2s delay0.30.31.0-0.3-0.5-0.3-1.0
Delay disc. indifference point, 24s delay1.21.93.8-1.91.3-1.3-0.6
Delay disc. indifference point, 4s delay0.70.81.4-1.10.3-0.7-1.2
Delay disc. indifference point, 8s delay1.62.64.8-2.21.4-1.9-0.4
Indifference point function ln k1.75.18.42.9-2.42.50.1
Indifference point function log k1.75.18.42.9-2.42.50.1
Patch foraging total patch changes 0 sec0.30.91.5-0.71.1-0.71.2
Patch foraging total patch changes 12 sec4.15.58.6-2.92.5-2.50.7
Patch foraging total patch changes 18 sec0.51.32.8-1.71.0-1.2-0.1
Patch foraging total patch changes 24 sec0.20.81.3-1.11.1-0.80.4
Patch foraging total patch changes 6 sec3.15.39.1-3.02.5-2.30.6
Patch foraging time to switch 0 sec0.41.51.9-1.11.1-1.4-1.3
Patch foraging water rate 0 sec0.51.92.81.4-1.51.70.8
Patch foraging water rate 12 sec0.20.91.30.9-1.01.10.9
Patch foraging water rate 18 sec0.81.73.31.1-1.51.80.4
Patch foraging water rate 24 sec0.60.81.21.0-1.01.10.2
Patch foraging water rate 6 sec0.10.20.30.3-0.40.40.6
Seeking ratio, delayed vs. immediate footshock0.10.20.5-0.20.7-0.20.5
Distance traveled before self-admin0.30.61.10.4-1.00.9-0.7
Distance traveled after self-admin0.91.63.01.0-1.71.5-0.6
Extensor digitorum longus weight0.21.01.61.1-1.31.10.0
Bone: elastic displacement0.10.10.30.2-0.1-0.6-0.3
Bone: elastic work0.30.40.70.5-0.80.5-0.5
Bone: endosteal estimation3.58.411.43.3-3.23.4-0.9
Bone: endosteal perimeter3.48.310.73.2-3.13.3-1.5
Epididymis fat weight0.42.05.42.3-1.10.90.9
Delta time in closed arm before/after self-admin0.80.71.6-0.20.9-0.71.3
Delta time in open arm before/after self-admin2.22.66.30.6-1.41.3-2.5
Diff in mean of infusions in LGA sessions0.81.52.11.1-1.51.4-0.9
Delay discount exponential model param0.81.12.01.4-0.51.01.0
Extinction: sum of active levers before priming0.00.00.10.10.30.00.1
Active lever presses in extinction session 64.64.69.21.0-2.31.8-3.0
Bone: final force0.10.20.40.20.10.60.6
Bone: final moment0.20.30.50.40.10.60.7
Food consumed during 24 hour testing period0.20.30.6-0.80.6-0.20.5
Glucose0.10.20.30.6-0.10.40.6
Heart weight0.91.43.80.61.0-0.72.0
Delay discount hyperbolic model param0.60.81.51.2-0.40.91.0
Intermittent access intake day 1-15 change0.42.33.41.4-1.61.8-1.1
Intermittent access intake escalation0.63.55.21.7-2.02.3-1.3
Intermittent access intake escalation 23.25.37.01.8-2.52.6-2.2
Intermitt. access day 1 inactive lever presses0.00.10.30.3-0.60.3-0.0
Intermitt. access day 15 inactive lever presses0.10.40.60.7-0.80.80.1
Intermitt. access escalation Index0.20.70.80.9-0.90.90.7
Intermittent access day 1 total infusions0.10.20.3-0.1-0.60.5-0.6
Intermittent access day 15 total infusions0.92.24.01.5-1.52.0-0.7
Intermittent access terminal intake (last 3 days)1.22.03.41.0-1.61.8-1.2
Intermittent access total infusions0.50.71.10.5-0.91.0-0.7
Intermittent access day 1 locomotion0.10.20.40.6-0.20.4-0.4
Intermittent access day 15 total locomotion0.10.41.1-0.7-0.0-0.0-1.0
Intermittent access total locomotion0.50.61.9-0.2-0.50.4-1.4
Intermittent access standard deviation0.63.14.21.1-1.62.1-2.1
Left kidney weight0.10.61.1-0.51.0-0.50.9
Right kidney weight0.42.74.2-1.22.1-1.51.7
Cocaine induced anxiety0.61.72.31.4-1.51.3-0.9
Post-drug Anxiety0.60.71.71.1-0.0-0.21.3
Baseline Anxiety1.83.08.2-0.11.5-1.22.9
Tail length0.10.41.50.30.20.31.2
Length with tail0.10.62.1-0.30.40.51.5
Length without tail0.10.61.90.2-0.71.40.2
Times rat made contact with spout0.30.40.9-0.1-1.00.7-0.4
Lifetime Intake0.30.30.40.4-0.70.7-0.6
Liver weight, left0.10.20.6-0.10.8-0.50.4
Liver weight, right0.40.61.30.9-0.71.1-0.2
Locomotor activity0.10.10.2-0.0-0.30.50.4
Locomotor testing distance0.00.10.2-0.2-0.30.50.2
Locomotor testing rearing0.31.11.60.8-1.21.3-0.9
Locomotion in novel chamber2.73.64.72.2-2.22.0-1.0
Locomotion in novel chamber post-restriction0.10.20.3-0.50.5-0.20.3
Fecal boli incidents, locomotor time 10.41.11.90.2-1.41.2-1.1
Change in fecal boli incidents, locomotor task0.91.02.2-0.51.5-1.10.2
Time >=10cm from walls, locomotor time 10.20.20.7-0.30.20.8-0.1
Bouts of movement, locomotor time 10.40.51.1-1.00.3-0.7-0.6
Total resting periods, locomotor time 10.70.82.1-1.50.4-0.7-0.7
Rest time, locomotor task time 10.20.30.6-0.8-0.3-0.1-0.6
Distance moved, locomotor task time 10.30.92.50.51.0-0.21.6
Vertical activity count, locomotor time 10.10.61.70.30.9-0.21.3
Time >=10cm from walls, locomotor time 20.10.30.6-0.4-0.30.8-0.4
Bouts of movement, locomotor time 20.82.65.4-2.31.0-1.5-1.3
Total resting periods, locomotor time 20.72.86.0-2.41.0-1.4-1.5
Rest time, locomotor task time 20.40.71.8-1.30.1-0.4-1.0
Distance moved, locomotor task time 20.81.12.11.3-0.20.71.5
Vertical activity count, locomotor time 20.10.20.40.60.00.40.3
Light reinforcement 10.10.40.6-0.70.4-0.80.5
Light reinforcement 20.71.53.1-1.80.8-1.5-0.4
Bone: marrow area3.68.711.73.3-3.33.4-1.0
Bone: maximum diameter4.48.912.93.3-3.43.6-0.7
Bone: maximum force0.40.81.60.8-1.01.3-0.3
Bone: maximum moment0.50.91.51.0-0.91.2-0.2
Mean time between licks in bursts0.10.40.60.10.8-0.50.8
Mean num. licks in bursts1.02.63.81.9-1.71.9-0.1
Cd content in liver1.21.32.1-1.31.1-1.40.5
Co content in liver2.22.67.2-0.41.3-1.22.7
Cu content in liver3.94.68.2-2.92.1-2.4-0.3
Fe content in liver2.22.84.4-1.91.8-2.10.2
K content in liver1.31.34.5-0.80.1-0.1-2.1
Mg content in liver1.31.55.0-0.80.1-0.2-2.2
Mn content in liver3.03.35.1-2.31.1-1.5-2.2
Na content in liver1.11.32.1-1.41.0-1.1-0.9
Rb content in liver0.10.10.30.1-0.60.4-0.2
Se content in liver16.419.429.6-5.44.6-5.20.0
Sr content in liver0.40.30.6-0.80.6-0.60.3
Zn content in liver1.51.73.0-1.71.2-1.5-0.4
Bone: minimum diameter5.310.216.24.0-3.33.80.0
Time in familiar zone, hab. session 10.10.10.20.5-0.40.10.3
Time in novel zone, hab. session 10.10.20.4-0.70.4-0.1-0.1
Total zone transitions, hab. session 10.00.10.2-0.4-0.20.2-0.1
Total locomotion distance, hab. session 11.01.43.1-1.81.0-1.10.2
Locomotion velocity, hab. session 12.02.85.2-2.31.6-1.60.8
Time in familiar zone, hab. session 20.70.72.20.00.5-0.71.5
Time in novel zone, hab. session 20.10.10.1-0.3-0.10.3-0.3
Total zone transitions, hab. session 20.50.60.8-0.90.9-0.70.5
Total locomotion distance, hab. session 21.01.31.6-1.31.2-1.20.7
Locomotion velocity, hab. session 21.01.32.0-1.41.2-1.20.6
Novel to familiar place preference ratio4.05.29.90.8-2.52.0-3.2
Novelty place preference4.05.29.20.9-2.52.1-3.0
Time in novel zone, NPP test4.15.08.10.9-2.62.2-2.8
Total zone transitions, NPP test0.61.01.2-1.01.1-0.81.0
Total locomotion distance, NPP test1.92.64.8-2.21.6-1.50.8
Locomotion velocity, NPP test1.72.44.2-2.11.6-1.50.7
Intraocular pressure0.30.51.0-0.50.7-1.0-0.1
Delta distance traveled before/after self-admin1.11.21.91.4-1.21.2-0.3
Delta ambulatory time before/after self-admin1.22.03.21.8-1.51.6-0.2
Parametrial fat weight0.81.83.4-0.81.4-1.01.8
Pavlov. Cond. lever latency0.10.10.30.3-0.1-0.20.6
Pavlov. Cond. magazine entry latency0.71.01.3-0.91.1-0.71.0
Pavlov. Cond. change in total contacts0.00.00.0-0.20.20.10.1
Pavlov. Cond. index score0.40.50.9-1.00.8-0.50.3
Pavlov. Cond. latency score0.30.30.6-0.80.7-0.40.3
Pavlov. Cond. lever contacts0.30.40.7-0.70.8-0.5-0.1
Pavlov. Cond. magazine entry number0.20.20.60.2-0.60.2-0.8
Pavlov. Cond. intertrial magazine entries0.20.20.5-0.40.2-0.2-0.7
Pavlov. Cond. lever-magazine prob. diff.0.40.50.8-0.90.8-0.50.3
Pavlov. Cond. response bias0.20.20.5-0.50.7-0.30.3
Pavlov. Cond. lever latency1.01.51.81.3-1.20.9-1.3
Pavlov. Cond. magazine entry latency0.20.20.4-0.60.4-0.20.6
Pavlov. Cond. change in total contacts0.20.60.8-0.60.9-0.60.9
Pavlov. Cond. index score0.50.91.3-1.20.9-0.61.0
Pavlov. Cond. latency score0.40.71.1-1.10.7-0.50.9
Pavlov. Cond. lever contacts1.21.82.3-1.31.4-1.11.5
Pavlov. Cond. magazine entry number1.52.02.61.6-1.41.1-1.4
Pavlov. Cond. intertrial magazine entries0.51.21.71.3-1.20.9-0.7
Pavlov. Cond. lever-magazine prob. diff.0.50.71.3-1.10.8-0.50.8
Pavlov. Cond. response bias1.11.51.9-1.31.3-0.91.4
Time in closed arm before self-admin0.50.91.40.2-1.20.9-1.2
Time in closed arm after self-admin0.30.41.0-0.10.4-0.61.0
Time in open arm before self-admin0.40.51.10.30.3-0.81.1
Time in open arm after self-admin0.50.51.8-0.1-0.50.3-1.4
Bone: periosteal estimation2.35.48.12.7-2.52.8-0.5
Bone: periosteal perimeter2.34.66.62.5-2.32.6-0.5
Bone: post-yield work0.91.62.11.1-1.31.4-1.2
Progressive ratio test 1 active lever presses0.10.20.8-0.2-0.20.2-0.9
Progressive ratio test 1 breakpoint0.10.20.7-0.4-0.00.0-0.8
Progressive ratio test 1 inactive lever presses0.20.61.30.4-1.10.9-0.3
Progressive ratio test 2 active lever presses1.21.73.30.1-1.41.2-1.8
Progressive ratio test 2 breakpoint1.41.73.20.1-1.41.3-1.8
Progressive ratio test 2 inactive lever presses0.30.91.9-0.0-1.10.8-1.4
Incentive Sensitization - Responses0.92.53.50.3-1.81.8-1.9
Incentive Sensitization - Breakpoint1.02.23.00.2-1.71.7-1.7
Sum of active levers in priming session hrs 5-60.20.20.4-0.30.5-0.70.3
Progressive ratio0.20.71.70.20.7-0.71.3
Food seeking constrained by brief footshock0.20.20.5-0.70.5-0.10.2
Seeking ratio, punishment vs. effort0.20.30.9-0.90.10.1-0.7
Retroperitoneal fat weight0.21.02.90.30.7-0.71.7
Reaction time number correct1.03.75.51.9-2.32.0-1.3
Reaction time mean minus median0.10.51.20.7-0.20.61.1
Reaction time mean minus median AUC0.10.51.10.7-0.20.41.0
Reaction time num false alarms0.10.10.30.00.5-0.20.4
Reaction time num false alarms AUC0.10.20.40.10.6-0.20.5
Reaction time trials correct on left1.03.75.51.9-2.32.0-1.3
Reaction time trials on left1.03.55.31.9-2.32.0-1.2
Reaction time mean0.71.52.6-0.71.4-1.11.6
Reaction time mean AUC0.81.92.6-0.91.6-1.31.6
Median of all reaction times1.11.72.2-1.01.5-1.41.4
Reaction time omissions0.61.02.11.0-0.60.61.5
Reaction time false alarm rate1.01.42.6-0.81.6-1.11.0
Reaction time premature initiation rate0.50.81.8-0.70.9-0.21.3
Reaction time premature initiations0.20.50.90.3-0.40.80.9
Std. dev. reaction times0.41.34.40.30.7-0.12.1
Reaction time trials completed1.03.55.31.9-2.32.0-1.2
Reaction time trials AUC0.93.35.11.8-2.21.8-1.1
Run reversals in cocaine runway, females0.60.61.1-0.80.4-0.7-1.1
Run reversals in cocaine runway, males2.32.63.9-2.01.7-1.51.1
Latency to leave start box in cocaine runway1.72.45.12.3-1.51.30.7
Latency to leave start box in cocaine runway, F2.73.46.42.5-2.01.80.0
Latency to leave start box in cocaine runway, M0.30.20.50.7-0.2-0.10.6
Std. dev. time between licks in bursts1.22.33.9-1.11.9-2.00.5
Total sessions with >9 infusions0.40.40.9-0.40.8-1.00.2
Short access day 1 total inactive lever presses0.91.83.31.1-1.81.1-1.2
Short access day 10 total inactive lever presses0.00.10.2-0.2-0.40.30.4
Short access day 1 total infusions0.40.81.3-1.00.7-1.1-0.4
Short access day 10 total infusions0.71.21.6-1.11.2-1.30.8
Short access total infusions0.10.10.2-0.3-0.0-0.1-0.4
Short access day 1 locomotion0.20.30.80.2-0.0-0.5-0.9
Short access day 10 total locomotion0.10.30.6-0.70.5-0.4-0.6
Short access total locomotion0.10.20.5-0.40.4-0.7-0.4
One hour access (0.3 mA shock)2.83.34.91.0-2.02.2-1.8
Compulsive drug intake1.21.72.61.5-1.41.60.0
One hour access (shock baseline)0.10.20.6-0.0-0.20.4-0.8
Social response proportion2.93.75.31.7-1.91.7-2.3
Social responses0.81.11.41.1-0.81.1-1.2
Social time0.30.51.4-0.20.7-0.2-1.2
Soleus weight1.13.24.72.1-2.21.9-0.5
Bone: stiffness0.61.12.30.9-1.11.50.2
Tibialis anterior weight0.62.23.41.4-1.91.6-0.9
Time to tail flick, vehicle, before self-admin0.40.50.7-0.90.2-0.7-0.8
Time to tail flick, vehicle, after self-admin0.20.30.50.6-0.60.7-0.3
Time to tail flick, test, before self-admin0.80.91.30.6-0.91.0-1.1
Time to tail flick, test, after self-admin0.10.10.2-0.0-0.50.0-0.2
Delta time to tail flick, vehicle, before/after SA0.80.81.50.9-1.01.2-0.3
Delta time to tail flick, test, before/after SA0.20.20.4-0.60.2-0.60.2
Tibia length0.10.30.5-0.20.6-0.50.7
Ambulatory time before self-admin0.10.41.00.4-1.00.7-0.3
Ambulatory time after self-admin2.33.76.11.5-2.52.2-1.2
Bone: tissue strength0.10.10.40.6-0.10.30.1
Total heroin consumption0.10.10.2-0.50.1-0.0-0.4
Bone: trabecular number1.42.63.91.4-2.01.9-0.9
Bone: trabecular spacing1.11.72.4-0.81.5-1.31.4
Bone: trabecular thickness1.72.33.71.6-1.81.90.1
Bone: trabecular tissue density0.61.11.61.1-1.31.2-0.3
Water consumed over 24 hours0.40.81.2-0.2-1.11.0-1.1
Number of responses in last shaping day0.20.30.5-0.00.5-0.70.7