Tlcd1

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 PL gene expression Tlcd1 0.03 0.02 8.1e-04 0.01 0.03 0.02 0.02 7.7e-03 6.3e-04 3.7e-03 2.4e-03
2 Brain gene expression Tlcd1 0.05 0.04 2.3e-05 0.04 0.04 0.05 0.04 5.6e-05 4.6e-05 3.3e-05 6.8e-05
3 Liver gene expression Tlcd1 0.27 0.29 3.1e-03 0.01 0.01 0.01 0.01 1.4e-02 1.5e-02 3.5e-02 1.5e-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
Bone: apparent density2.13.93.92.0-1.9-2.0
Area under the delay curve1.62.43.0-1.61.31.7
BMI with tail1.75.96.22.5-2.5-2.3
BMI without tail1.26.36.72.6-2.4-2.6
Body weight2.510.811.73.4-3.1-3.3
Weight adjusted by age0.10.20.30.4-0.6-0.5
Bone surface1.53.03.11.7-1.8-1.7
Bone volume1.32.62.61.6-1.6-1.6
Breakpoint value in progressive ratio session0.40.71.00.9-0.6-1.0
Number of licking bursts0.10.40.4-0.60.60.6
Context. condit. distance diff. score0.60.70.80.8-0.9-0.8
Locomotion velocity, session 12.02.22.41.6-1.4-1.5
Locomotion distance, session 10.20.20.30.6-0.2-0.5
Locomotion velocity, session 20.00.00.10.2-0.1-0.2
Locomotion distance, session 21.31.82.01.3-1.4-1.3
Locomotion velocity, session 33.13.53.8-2.01.81.9
Locomotion distance, session 30.40.50.5-0.70.70.7
Stereotopy head waving bouts, day 30.00.00.00.1-0.2-0.2
Stereotopy head waving duration, day 30.30.40.5-0.70.70.5
Locomotion velocity, session 70.30.40.50.6-0.5-0.7
Locomotion distance, session 70.50.60.70.8-0.6-0.8
Stereotopy head waving bouts, day 70.60.70.90.8-1.0-0.8
Stereotopy head waving duration, day 70.30.40.40.5-0.6-0.6
Locomotion velocity, session 80.00.00.00.1-0.2-0.1
Locomotion distance, session 80.91.21.41.1-1.2-1.1
Degree of sensitization distance3.13.43.61.9-1.8-1.9
Degree of sensitization stereotypy0.70.70.90.8-0.9-0.8
Conditioned locomotion1.51.71.8-1.31.31.3
Cocaine response after cond. corrected1.32.02.41.4-1.5-1.3
Cocaine response after cond. not corrected1.82.63.11.6-1.8-1.5
Cocaine response before conditioning0.20.20.30.5-0.4-0.5
Saline control response0.00.00.0-0.0-0.0-0.1
Bone: connectivity density3.96.26.32.5-2.5-2.5
Bone: cortical apparent density0.40.60.8-0.80.90.7
Bone: cortical area1.42.32.5-1.51.61.5
Bone: cortical porosity0.20.30.30.6-0.4-0.6
Bone: cortical porosity0.10.10.10.4-0.3-0.3
Bone: cortical thickness2.94.85.2-2.22.32.1
Bone: cortical thickness0.00.00.0-0.10.20.1
Bone: cortical tissue density0.20.40.5-0.60.70.5
Condit. Reinf. active minus inactive responses0.60.70.8-0.90.90.8
Condit. Reinf. active-inactive response ratio0.20.20.2-0.40.40.4
Condit. Reinf. active responses0.00.00.0-0.10.10.1
Condit. Reinf. inactive responses0.30.40.40.6-0.6-0.6
Incentive salience index mean0.20.30.3-0.60.40.6
Condit. Reinf. lever presses0.10.20.30.3-0.6-0.3
Condit. Reinf. active minus inactive responses0.20.30.5-0.60.70.3
Condit. Reinf. active-inactive response ratio0.30.50.7-0.80.80.6
Condit. Reinf. active responses0.10.20.3-0.40.50.2
Condit. Reinf. inactive responses0.00.00.10.2-0.1-0.2
Condit. Reinf. lever presses2.33.33.5-1.91.81.8
Condit. Reinf. lever reinforcers received0.30.50.6-0.70.80.5
Conditioned reinforcement - actives0.10.40.40.6-0.7-0.6
Conditioned reinforcement - inactives0.00.10.10.4-0.3-0.3
Conditioned locomotion0.30.40.80.5-0.9-0.4
Patch foraging indifference point 0 sec0.20.70.9-0.80.90.7
Patch foraging indifference point AUC1.22.83.1-1.81.51.7
Delay disc. indifference point, 0s delay1.01.21.3-1.01.11.1
Delay disc. indifference point, 16s delay1.21.82.4-1.31.11.5
Delay disc. indifference point, 2s delay2.73.03.0-1.71.71.7
Delay disc. indifference point, 24s delay0.50.81.00.8-1.0-0.8
Delay disc. indifference point, 4s delay0.30.30.3-0.50.60.6
Delay disc. indifference point, 8s delay0.61.11.6-1.10.61.3
Indifference point function ln k0.20.71.01.0-0.6-1.0
Indifference point function log k0.20.71.01.0-0.6-1.0
Patch foraging total patch changes 0 sec0.20.50.7-0.70.80.5
Patch foraging total patch changes 12 sec0.20.20.3-0.50.50.5
Patch foraging total patch changes 18 sec1.02.42.7-1.51.61.5
Patch foraging total patch changes 24 sec0.82.83.1-1.81.61.6
Patch foraging total patch changes 6 sec2.84.85.2-2.32.12.2
Patch foraging time to switch 0 sec0.62.42.91.6-1.7-1.3
Patch foraging water rate 0 sec0.83.03.6-1.71.91.5
Patch foraging water rate 12 sec0.10.30.50.6-0.2-0.7
Patch foraging water rate 18 sec0.30.70.80.8-0.7-0.9
Patch foraging water rate 24 sec0.20.30.5-0.50.70.5
Patch foraging water rate 6 sec1.11.62.3-1.21.51.1
Seeking ratio, delayed vs. immediate footshock1.62.32.6-1.61.41.6
Distance traveled before self-admin2.24.84.9-2.22.22.2
Distance traveled after self-admin0.10.10.1-0.30.30.4
Extensor digitorum longus weight0.83.23.81.7-1.9-1.7
Bone: elastic displacement2.83.53.5-1.91.91.9
Bone: elastic work8.811.612.9-3.33.63.3
Bone: endosteal estimation0.00.00.0-0.10.00.2
Bone: endosteal perimeter0.00.00.00.1-0.10.0
Epididymis fat weight5.326.727.95.3-5.1-5.1
Delta time in closed arm before/after self-admin2.92.72.8-1.71.61.6
Delta time in open arm before/after self-admin5.16.06.52.5-2.6-2.3
Diff in mean of infusions in LGA sessions0.40.70.70.8-0.8-0.8
Delay discount exponential model param1.21.62.01.3-1.1-1.4
Extinction: sum of active levers before priming0.71.11.31.1-0.9-1.2
Active lever presses in extinction session 60.30.30.60.6-0.3-0.8
Bone: final force0.40.60.6-0.70.80.8
Bone: final moment0.40.70.8-0.80.90.8
Food consumed during 24 hour testing period0.10.30.6-0.40.80.3
Glucose1.32.12.4-1.51.31.5
Heart weight1.62.52.91.7-1.4-1.7
Delay discount hyperbolic model param1.62.12.41.5-1.3-1.6
Intermittent access intake day 1-15 change0.00.10.20.2-0.4-0.2
Intermittent access intake escalation0.00.20.30.3-0.6-0.3
Intermittent access intake escalation 20.10.10.2-0.40.20.4
Intermitt. access day 1 inactive lever presses0.00.10.2-0.40.30.4
Intermitt. access day 15 inactive lever presses0.10.70.7-0.80.80.8
Intermitt. access escalation Index0.31.01.21.0-1.1-0.8
Intermittent access day 1 total infusions0.10.20.30.3-0.5-0.2
Intermittent access day 15 total infusions0.51.31.91.0-1.4-1.0
Intermittent access terminal intake (last 3 days)0.71.31.71.1-1.3-1.0
Intermittent access total infusions0.40.50.90.5-1.0-0.4
Intermittent access day 1 locomotion0.00.00.10.1-0.30.0
Intermittent access day 15 total locomotion0.10.60.80.7-0.9-0.7
Intermittent access total locomotion0.60.71.10.7-1.0-0.7
Intermittent access standard deviation0.00.00.0-0.1-0.20.2
Left kidney weight0.00.20.20.5-0.3-0.4
Right kidney weight0.10.70.80.8-0.7-0.9
Cocaine induced anxiety0.10.20.2-0.40.50.5
Post-drug Anxiety0.20.20.30.5-0.4-0.5
Baseline Anxiety0.30.50.60.7-0.6-0.8
Tail length0.31.61.91.4-1.1-1.3
Length with tail0.52.22.61.6-1.3-1.5
Length without tail0.20.91.01.0-0.9-0.9
Times rat made contact with spout0.00.00.1-0.10.30.1
Lifetime Intake0.50.61.10.7-1.1-0.5
Liver weight, left5.08.69.12.9-3.0-2.9
Liver weight, right3.96.87.02.7-2.5-2.6
Locomotor activity0.00.00.0-0.20.2-0.0
Locomotor testing distance0.00.10.1-0.30.20.1
Locomotor testing rearing0.00.00.0-0.20.20.1
Locomotion in novel chamber2.33.13.8-1.91.41.9
Locomotion in novel chamber post-restriction0.00.00.10.0-0.3-0.0
Fecal boli incidents, locomotor time 10.92.42.51.5-1.5-1.6
Change in fecal boli incidents, locomotor task0.20.20.3-0.50.30.6
Time >=10cm from walls, locomotor time 10.00.00.00.2-0.2-0.2
Bouts of movement, locomotor time 10.50.60.6-0.70.80.8
Total resting periods, locomotor time 10.10.10.2-0.30.40.3
Rest time, locomotor task time 10.20.30.30.5-0.5-0.6
Distance moved, locomotor task time 10.20.50.6-0.70.70.8
Vertical activity count, locomotor time 10.00.20.3-0.40.30.6
Time >=10cm from walls, locomotor time 20.41.11.21.0-1.1-1.0
Bouts of movement, locomotor time 20.20.50.8-0.60.90.6
Total resting periods, locomotor time 20.00.10.3-0.30.50.2
Rest time, locomotor task time 20.00.00.10.1-0.1-0.4
Distance moved, locomotor task time 20.40.50.8-0.70.50.9
Vertical activity count, locomotor time 20.30.81.4-0.80.51.2
Light reinforcement 10.00.00.1-0.20.00.2
Light reinforcement 20.30.60.7-0.80.70.9
Bone: marrow area0.00.00.0-0.10.10.2
Bone: maximum diameter0.40.70.8-0.80.80.9
Bone: maximum force0.51.01.1-1.01.01.0
Bone: maximum moment0.71.21.3-1.11.11.1
Mean time between licks in bursts0.10.80.90.9-0.9-0.8
Mean num. licks in bursts0.20.40.40.7-0.6-0.6
Cd content in liver0.80.91.0-1.00.91.0
Co content in liver0.20.30.4-0.60.30.6
Cu content in liver1.61.92.3-1.31.51.2
Fe content in liver2.12.62.91.6-1.7-1.6
K content in liver0.10.10.10.3-0.3-0.3
Mg content in liver0.60.70.8-0.80.90.7
Mn content in liver0.20.20.2-0.50.40.4
Na content in liver0.00.00.10.1-0.20.1
Rb content in liver0.10.10.10.3-0.3-0.2
Se content in liver0.60.70.8-0.80.90.7
Sr content in liver0.50.40.40.7-0.6-0.7
Zn content in liver0.30.40.40.7-0.5-0.7
Bone: minimum diameter0.10.10.1-0.40.30.4
Time in familiar zone, hab. session 10.30.40.4-0.60.50.6
Time in novel zone, hab. session 10.20.20.20.4-0.4-0.5
Total zone transitions, hab. session 10.00.10.1-0.20.10.3
Total locomotion distance, hab. session 10.10.10.2-0.30.40.3
Locomotion velocity, hab. session 10.30.50.5-0.70.70.7
Time in familiar zone, hab. session 20.10.10.2-0.40.40.3
Time in novel zone, hab. session 20.20.20.2-0.40.40.5
Total zone transitions, hab. session 20.30.40.50.6-0.7-0.6
Total locomotion distance, hab. session 20.00.00.1-0.20.20.2
Locomotion velocity, hab. session 20.10.10.1-0.30.20.2
Novel to familiar place preference ratio0.70.90.91.0-0.9-0.9
Novelty place preference0.91.21.21.1-1.1-1.1
Time in novel zone, NPP test1.01.31.31.1-1.1-1.1
Total zone transitions, NPP test0.00.00.00.1-0.2-0.1
Total locomotion distance, NPP test0.81.11.2-1.11.01.0
Locomotion velocity, NPP test0.91.41.4-1.21.11.2
Intraocular pressure1.01.61.6-1.31.31.3
Delta distance traveled before/after self-admin3.03.33.41.8-1.7-1.8
Delta ambulatory time before/after self-admin1.52.62.71.6-1.6-1.6
Parametrial fat weight6.314.815.13.9-3.8-3.9
Pavlov. Cond. lever latency0.00.00.00.20.0-0.2
Pavlov. Cond. magazine entry latency0.00.00.00.1-0.2-0.1
Pavlov. Cond. change in total contacts0.30.30.4-0.60.30.6
Pavlov. Cond. index score0.00.00.0-0.2-0.10.2
Pavlov. Cond. latency score0.00.00.0-0.0-0.20.1
Pavlov. Cond. lever contacts0.00.00.1-0.1-0.30.2
Pavlov. Cond. magazine entry number0.10.20.20.4-0.3-0.5
Pavlov. Cond. intertrial magazine entries0.20.30.3-0.50.60.4
Pavlov. Cond. lever-magazine prob. diff.0.10.10.1-0.30.00.4
Pavlov. Cond. response bias0.00.00.0-0.1-0.10.2
Pavlov. Cond. lever latency2.53.53.61.9-1.9-1.8
Pavlov. Cond. magazine entry latency0.20.30.3-0.50.50.6
Pavlov. Cond. change in total contacts0.92.12.2-1.51.51.4
Pavlov. Cond. index score2.03.13.2-1.81.71.8
Pavlov. Cond. latency score2.23.63.7-1.91.91.9
Pavlov. Cond. lever contacts1.31.91.9-1.41.41.4
Pavlov. Cond. magazine entry number0.00.00.10.2-0.1-0.2
Pavlov. Cond. intertrial magazine entries0.30.70.80.8-0.8-0.9
Pavlov. Cond. lever-magazine prob. diff.1.52.32.4-1.51.51.6
Pavlov. Cond. response bias1.21.61.7-1.31.31.3
Time in closed arm before self-admin0.91.62.11.3-1.5-1.1
Time in closed arm after self-admin0.91.01.5-1.00.71.2
Time in open arm before self-admin1.51.82.5-1.31.61.1
Time in open arm after self-admin1.01.11.21.1-1.0-1.1
Bone: periosteal estimation0.40.90.9-0.90.91.0
Bone: periosteal perimeter0.30.60.7-0.70.70.8
Bone: post-yield work0.20.40.60.6-0.8-0.5
Progressive ratio test 1 active lever presses0.30.60.8-0.80.50.9
Progressive ratio test 1 breakpoint0.40.70.9-0.90.60.9
Progressive ratio test 1 inactive lever presses0.92.42.9-1.61.41.7
Progressive ratio test 2 active lever presses0.20.30.4-0.60.50.7
Progressive ratio test 2 breakpoint0.20.30.4-0.60.40.6
Progressive ratio test 2 inactive lever presses0.10.20.2-0.40.40.4
Incentive Sensitization - Responses0.00.00.00.1-0.1-0.2
Incentive Sensitization - Breakpoint0.00.00.10.2-0.1-0.2
Sum of active levers in priming session hrs 5-61.61.51.71.3-1.1-1.3
Progressive ratio0.00.10.20.3-0.1-0.4
Food seeking constrained by brief footshock0.10.10.10.3-0.2-0.3
Seeking ratio, punishment vs. effort0.10.20.3-0.40.20.6
Retroperitoneal fat weight0.52.02.11.5-1.4-1.4
Reaction time number correct0.31.21.31.2-1.0-1.1
Reaction time mean minus median0.00.30.30.6-0.5-0.6
Reaction time mean minus median AUC0.32.32.61.5-1.6-1.4
Reaction time num false alarms4.67.98.5-2.82.92.7
Reaction time num false alarms AUC3.58.18.9-2.83.02.7
Reaction time trials correct on left0.31.21.31.2-1.0-1.1
Reaction time trials on left0.31.21.41.2-1.0-1.1
Reaction time mean0.40.91.11.0-0.9-1.0
Reaction time mean AUC0.30.70.80.9-0.8-0.8
Median of all reaction times0.40.60.80.9-0.7-0.8
Reaction time omissions1.11.82.11.3-1.4-1.2
Reaction time false alarm rate5.98.28.5-2.92.92.7
Reaction time premature initiation rate0.10.20.20.4-0.5-0.4
Reaction time premature initiations0.20.50.60.7-0.7-0.7
Std. dev. reaction times0.41.21.21.1-1.1-1.1
Reaction time trials completed0.31.21.41.2-1.0-1.1
Reaction time trials AUC0.31.01.11.1-0.9-1.0
Run reversals in cocaine runway, females0.00.10.10.30.2-0.2
Run reversals in cocaine runway, males0.10.10.20.2-0.5-0.2
Latency to leave start box in cocaine runway0.20.30.8-0.40.90.2
Latency to leave start box in cocaine runway, F0.00.10.2-0.00.4-0.2
Latency to leave start box in cocaine runway, M0.10.10.3-0.30.50.1
Std. dev. time between licks in bursts0.00.00.00.1-0.10.0
Total sessions with >9 infusions0.20.20.50.4-0.7-0.2
Short access day 1 total inactive lever presses2.14.25.12.0-2.3-1.8
Short access day 10 total inactive lever presses0.00.00.0-0.1-0.00.2
Short access day 1 total infusions0.30.51.00.7-1.0-0.5
Short access day 10 total infusions0.20.30.60.5-0.8-0.3
Short access total infusions0.10.20.40.2-0.60.0
Short access day 1 locomotion0.00.10.1-0.20.00.4
Short access day 10 total locomotion0.20.60.7-0.80.70.8
Short access total locomotion0.40.60.8-0.80.60.9
One hour access (0.3 mA shock)0.10.10.1-0.3-0.10.3
Compulsive drug intake0.81.11.31.0-1.2-1.0
One hour access (shock baseline)0.10.10.2-0.40.20.4
Social response proportion1.92.42.81.6-1.7-1.4
Social responses2.02.62.61.6-1.6-1.6
Social time1.32.13.21.3-1.8-1.1
Soleus weight2.36.77.22.6-2.7-2.5
Bone: stiffness1.62.93.11.7-1.8-1.7
Tibialis anterior weight2.89.59.83.1-3.1-3.0
Time to tail flick, vehicle, before self-admin0.00.00.10.2-0.3-0.0
Time to tail flick, vehicle, after self-admin0.30.50.6-0.70.70.8
Time to tail flick, test, before self-admin0.00.00.00.1-0.2-0.1
Time to tail flick, test, after self-admin0.20.20.3-0.40.60.2
Delta time to tail flick, vehicle, before/after SA0.30.30.4-0.50.60.4
Delta time to tail flick, test, before/after SA0.40.40.5-0.70.70.6
Tibia length0.00.10.1-0.30.20.3
Ambulatory time before self-admin0.82.62.9-1.61.51.7
Ambulatory time after self-admin0.00.00.0-0.00.00.0
Bone: tissue strength1.81.91.9-1.31.41.4
Total heroin consumption3.84.55.72.2-1.8-2.4
Bone: trabecular number2.75.25.32.3-2.2-2.3
Bone: trabecular spacing0.30.40.4-0.60.60.7
Bone: trabecular thickness0.00.00.0-0.00.10.1
Bone: trabecular tissue density1.12.02.2-1.41.51.4
Water consumed over 24 hours0.00.10.1-0.10.30.2
Number of responses in last shaping day1.11.41.5-1.21.21.2