Hub : Genes

Npc1l1

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 Npc1l1 0.05 0.04 8.7e-03 0.01 0.02 0.01 0.01 3.1e-02 6.1e-03 2.5e-02 3.2e-02
2 NAcc gene expression Npc1l1 0.04 0.03 2.3e-03 0.01 0.02 0.02 0.01 4.0e-02 9.7e-04 5.6e-04 1.9e-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
Bone: apparent density0.00.00.0-0.2-0.1
Area under the delay curve1.11.72.0-1.21.4
BMI with tail0.00.10.20.20.5
BMI without tail0.00.20.3-0.20.5
Body weight0.41.52.9-0.41.7
Weight adjusted by age0.10.30.4-0.40.6
Bone surface0.10.10.20.4-0.2
Bone volume0.00.10.10.3-0.2
Breakpoint value in progressive ratio session0.00.10.20.10.4
Number of licking bursts0.10.40.90.00.9
Context. condit. distance diff. score0.70.81.50.3-1.2
Locomotion velocity, session 10.40.40.60.5-0.8
Locomotion distance, session 12.32.94.4-2.11.2
Locomotion velocity, session 22.22.72.81.6-1.7
Locomotion distance, session 20.20.30.5-0.7-0.2
Locomotion velocity, session 30.20.20.4-0.60.0
Locomotion distance, session 30.10.10.20.30.4
Stereotopy head waving bouts, day 30.10.10.2-0.4-0.0
Stereotopy head waving duration, day 30.20.30.5-0.2-0.7
Locomotion velocity, session 70.10.10.10.4-0.3
Locomotion distance, session 70.20.30.40.3-0.7
Stereotopy head waving bouts, day 70.00.00.00.1-0.1
Stereotopy head waving duration, day 70.10.10.1-0.40.3
Locomotion velocity, session 81.31.62.60.8-1.6
Locomotion distance, session 80.91.42.7-0.2-1.6
Degree of sensitization distance1.41.52.80.3-1.7
Degree of sensitization stereotypy0.00.00.00.00.1
Conditioned locomotion2.52.93.8-1.91.4
Cocaine response after cond. corrected0.50.71.4-0.01.2
Cocaine response after cond. not corrected0.81.12.1-0.31.5
Cocaine response before conditioning0.20.20.4-0.70.2
Saline control response0.30.40.60.4-0.7
Bone: connectivity density0.00.10.10.0-0.3
Bone: cortical apparent density0.00.10.10.40.1
Bone: cortical area0.61.01.9-0.41.4
Bone: cortical porosity0.00.00.00.2-0.1
Bone: cortical porosity0.10.10.2-0.40.1
Bone: cortical thickness0.81.42.2-0.71.5
Bone: cortical thickness1.31.62.5-1.60.8
Bone: cortical tissue density0.10.10.20.5-0.0
Condit. Reinf. active minus inactive responses0.91.01.51.2-0.7
Condit. Reinf. active-inactive response ratio4.24.54.72.2-2.1
Condit. Reinf. active responses0.10.10.30.5-0.1
Condit. Reinf. inactive responses1.11.41.8-1.01.3
Incentive salience index mean0.10.10.20.40.3
Condit. Reinf. lever presses1.52.32.8-1.31.7
Condit. Reinf. active minus inactive responses0.10.10.1-0.3-0.3
Condit. Reinf. active-inactive response ratio0.10.20.2-0.50.3
Condit. Reinf. active responses0.10.10.2-0.2-0.4
Condit. Reinf. inactive responses0.30.50.90.4-1.0
Condit. Reinf. lever presses0.10.10.1-0.4-0.2
Condit. Reinf. lever reinforcers received0.10.10.1-0.3-0.3
Conditioned reinforcement - actives0.10.20.40.1-0.6
Conditioned reinforcement - inactives0.00.00.00.1-0.1
Conditioned locomotion0.10.20.4-0.1-0.6
Patch foraging indifference point 0 sec0.92.43.92.0-0.9
Patch foraging indifference point AUC0.20.50.60.6-0.8
Delay disc. indifference point, 0s delay0.60.71.0-0.61.0
Delay disc. indifference point, 16s delay0.00.10.1-0.10.3
Delay disc. indifference point, 2s delay3.23.64.5-1.62.1
Delay disc. indifference point, 24s delay0.20.30.6-0.30.8
Delay disc. indifference point, 4s delay2.32.42.7-1.51.6
Delay disc. indifference point, 8s delay1.01.61.7-1.31.2
Indifference point function ln k0.41.21.4-1.01.2
Indifference point function log k0.41.21.4-1.01.2
Patch foraging total patch changes 0 sec1.03.04.82.2-1.1
Patch foraging total patch changes 12 sec2.02.63.61.9-1.3
Patch foraging total patch changes 18 sec1.84.25.42.3-1.7
Patch foraging total patch changes 24 sec1.55.16.41.9-2.5
Patch foraging total patch changes 6 sec1.62.74.32.1-1.0
Patch foraging time to switch 0 sec0.10.30.5-0.70.2
Patch foraging water rate 0 sec0.41.52.91.7-0.4
Patch foraging water rate 12 sec0.00.10.10.30.1
Patch foraging water rate 18 sec1.73.83.8-1.92.0
Patch foraging water rate 24 sec0.00.00.00.2-0.0
Patch foraging water rate 6 sec0.81.11.6-0.81.2
Seeking ratio, delayed vs. immediate footshock0.71.11.8-1.30.6
Distance traveled before self-admin0.10.10.20.50.1
Distance traveled after self-admin0.20.40.4-0.60.6
Extensor digitorum longus weight0.31.21.60.91.3
Bone: elastic displacement0.00.10.10.1-0.3
Bone: elastic work0.40.50.7-0.60.8
Bone: endosteal estimation0.00.00.0-0.0-0.0
Bone: endosteal perimeter0.41.01.3-0.81.1
Epididymis fat weight0.00.20.50.00.7
Delta time in closed arm before/after self-admin2.01.93.6-1.90.3
Delta time in open arm before/after self-admin1.31.63.21.80.1
Diff in mean of infusions in LGA sessions0.20.40.7-0.80.4
Delay discount exponential model param1.21.61.81.2-1.3
Extinction: sum of active levers before priming0.30.50.80.4-0.9
Active lever presses in extinction session 61.41.41.5-1.21.1
Bone: final force0.20.30.50.7-0.3
Bone: final moment0.20.30.50.7-0.2
Food consumed during 24 hour testing period0.71.32.31.5-0.6
Glucose14.422.934.05.8-3.4
Heart weight1.93.13.81.9-1.6
Delay discount hyperbolic model param1.62.12.41.3-1.5
Intermittent access intake day 1-15 change0.42.32.61.4-1.6
Intermittent access intake escalation0.31.92.21.2-1.5
Intermittent access intake escalation 21.01.61.61.3-1.3
Intermitt. access day 1 inactive lever presses0.00.30.5-0.70.1
Intermitt. access day 15 inactive lever presses0.10.81.51.2-0.2
Intermitt. access escalation Index0.92.72.81.6-1.7
Intermittent access day 1 total infusions0.41.11.4-1.20.9
Intermittent access day 15 total infusions0.10.40.40.6-0.6
Intermittent access terminal intake (last 3 days)0.61.01.01.0-1.0
Intermittent access total infusions0.00.00.00.1-0.1
Intermittent access day 1 locomotion0.81.42.6-1.60.5
Intermittent access day 15 total locomotion0.00.00.1-0.3-0.1
Intermittent access total locomotion0.10.10.2-0.50.0
Intermittent access standard deviation0.20.91.40.6-1.2
Left kidney weight0.32.42.8-1.41.7
Right kidney weight0.43.03.6-1.61.9
Cocaine induced anxiety0.20.50.91.00.2
Post-drug Anxiety0.20.20.30.50.4
Baseline Anxiety0.30.50.9-0.90.4
Tail length0.31.73.3-0.31.8
Length with tail0.41.83.5-0.31.9
Length without tail0.10.50.9-0.21.0
Times rat made contact with spout7.68.79.53.1-2.8
Lifetime Intake0.00.00.0-0.00.1
Liver weight, left0.50.81.3-1.10.6
Liver weight, right0.81.52.3-1.50.8
Locomotor activity1.21.92.91.7-0.9
Locomotor testing distance0.10.20.4-0.10.6
Locomotor testing rearing0.20.81.61.2-0.2
Locomotion in novel chamber0.40.51.0-1.00.2
Locomotion in novel chamber post-restriction0.20.61.1-1.1-0.1
Fecal boli incidents, locomotor time 10.00.10.2-0.20.4
Change in fecal boli incidents, locomotor task1.41.51.61.2-1.2
Time >=10cm from walls, locomotor time 10.00.00.1-0.1-0.3
Bouts of movement, locomotor time 11.01.31.51.2-1.0
Total resting periods, locomotor time 11.01.11.31.0-1.1
Rest time, locomotor task time 10.20.30.50.1-0.7
Distance moved, locomotor task time 10.00.10.2-0.20.4
Vertical activity count, locomotor time 10.00.00.10.10.3
Time >=10cm from walls, locomotor time 20.51.42.1-1.40.8
Bouts of movement, locomotor time 21.13.64.0-2.01.8
Total resting periods, locomotor time 20.62.32.6-1.61.4
Rest time, locomotor task time 20.61.01.10.9-1.0
Distance moved, locomotor task time 20.10.20.3-0.60.1
Vertical activity count, locomotor time 20.20.40.6-0.80.5
Light reinforcement 10.00.20.2-0.50.5
Light reinforcement 22.04.55.3-2.31.9
Bone: marrow area0.00.00.0-0.10.0
Bone: maximum diameter0.20.50.50.70.7
Bone: maximum force0.00.00.00.10.2
Bone: maximum moment0.00.10.10.00.3
Mean time between licks in bursts0.10.50.90.9-0.3
Mean num. licks in bursts1.95.26.81.9-2.6
Cd content in liver0.50.61.11.0-0.2
Co content in liver0.10.10.10.40.1
Cu content in liver0.40.40.70.9-0.4
Fe content in liver0.30.40.8-0.9-0.2
K content in liver3.43.34.5-1.52.1
Mg content in liver0.30.40.7-0.30.8
Mn content in liver0.91.01.4-0.81.2
Na content in liver0.30.30.6-0.00.8
Rb content in liver0.20.30.40.40.6
Se content in liver0.80.91.5-0.61.2
Sr content in liver0.50.50.90.21.0
Zn content in liver1.21.41.7-1.11.3
Bone: minimum diameter0.20.30.3-0.50.5
Time in familiar zone, hab. session 10.00.00.0-0.2-0.1
Time in novel zone, hab. session 10.20.30.50.7-0.3
Total zone transitions, hab. session 10.00.00.0-0.2-0.0
Total locomotion distance, hab. session 10.91.31.8-1.40.9
Locomotion velocity, hab. session 10.60.91.3-1.20.6
Time in familiar zone, hab. session 20.30.30.6-0.2-0.8
Time in novel zone, hab. session 20.50.51.01.00.2
Total zone transitions, hab. session 20.70.91.1-0.91.1
Total locomotion distance, hab. session 20.40.60.7-0.80.7
Locomotion velocity, hab. session 21.11.41.5-1.21.1
Novel to familiar place preference ratio0.20.30.50.7-0.4
Novelty place preference0.30.40.70.8-0.5
Time in novel zone, NPP test0.60.71.01.0-0.6
Total zone transitions, NPP test1.31.92.8-1.71.0
Total locomotion distance, NPP test2.12.94.0-2.01.4
Locomotion velocity, NPP test2.23.14.2-2.01.4
Intraocular pressure0.10.10.10.4-0.2
Delta distance traveled before/after self-admin0.60.71.4-1.20.1
Delta ambulatory time before/after self-admin0.40.61.2-1.10.2
Parametrial fat weight0.71.62.51.6-0.8
Pavlov. Cond. lever latency0.50.60.90.9-0.5
Pavlov. Cond. magazine entry latency0.10.10.2-0.4-0.3
Pavlov. Cond. change in total contacts0.10.10.10.30.4
Pavlov. Cond. index score0.30.40.8-0.90.2
Pavlov. Cond. latency score0.40.50.9-0.90.3
Pavlov. Cond. lever contacts0.50.50.9-1.00.4
Pavlov. Cond. magazine entry number0.20.20.4-0.10.6
Pavlov. Cond. intertrial magazine entries3.54.24.5-2.12.0
Pavlov. Cond. lever-magazine prob. diff.0.40.51.0-1.00.2
Pavlov. Cond. response bias0.20.20.4-0.60.3
Pavlov. Cond. lever latency2.23.15.1-1.02.3
Pavlov. Cond. magazine entry latency0.10.10.20.1-0.4
Pavlov. Cond. change in total contacts0.10.20.30.1-0.6
Pavlov. Cond. index score0.50.81.50.4-1.2
Pavlov. Cond. latency score0.30.50.90.1-1.0
Pavlov. Cond. lever contacts1.82.74.60.9-2.1
Pavlov. Cond. magazine entry number1.52.02.3-1.31.5
Pavlov. Cond. intertrial magazine entries0.00.00.1-0.10.3
Pavlov. Cond. lever-magazine prob. diff.0.60.91.60.4-1.3
Pavlov. Cond. response bias2.02.84.41.1-2.1
Time in closed arm before self-admin0.00.00.1-0.10.2
Time in closed arm after self-admin0.80.91.8-1.3-0.1
Time in open arm before self-admin0.30.30.6-0.8-0.1
Time in open arm after self-admin0.40.50.90.9-0.3
Bone: periosteal estimation0.10.40.6-0.30.8
Bone: periosteal perimeter0.91.72.5-0.91.6
Bone: post-yield work0.00.00.1-0.2-0.0
Progressive ratio test 1 active lever presses0.20.40.5-0.70.6
Progressive ratio test 1 breakpoint0.20.40.5-0.70.6
Progressive ratio test 1 inactive lever presses0.92.33.9-0.82.0
Progressive ratio test 2 active lever presses0.00.00.00.1-0.2
Progressive ratio test 2 breakpoint0.00.00.10.2-0.2
Progressive ratio test 2 inactive lever presses0.00.10.2-0.40.1
Incentive Sensitization - Responses0.10.20.20.3-0.5
Incentive Sensitization - Breakpoint0.10.30.30.4-0.6
Sum of active levers in priming session hrs 5-61.00.91.6-0.51.3
Progressive ratio0.20.40.6-0.80.5
Food seeking constrained by brief footshock3.24.05.3-1.72.3
Seeking ratio, punishment vs. effort0.41.01.5-0.71.2
Retroperitoneal fat weight0.10.30.50.70.1
Reaction time number correct0.20.70.91.0-0.7
Reaction time mean minus median0.52.94.31.2-2.1
Reaction time mean minus median AUC0.31.92.81.0-1.7
Reaction time num false alarms0.61.01.7-0.51.3
Reaction time num false alarms AUC0.81.72.6-0.91.6
Reaction time trials correct on left0.20.70.91.0-0.7
Reaction time trials on left0.20.70.91.0-0.7
Reaction time mean0.10.20.4-0.1-0.6
Reaction time mean AUC0.10.20.3-0.4-0.5
Median of all reaction times0.10.10.3-0.5-0.1
Reaction time omissions0.30.50.90.2-1.0
Reaction time false alarm rate1.92.63.3-1.31.8
Reaction time premature initiation rate0.40.71.3-1.1-0.0
Reaction time premature initiations0.00.10.2-0.3-0.4
Std. dev. reaction times0.41.32.20.7-1.5
Reaction time trials completed0.20.70.91.0-0.7
Reaction time trials AUC0.20.60.80.9-0.6
Run reversals in cocaine runway, females0.70.81.3-1.10.5
Run reversals in cocaine runway, males0.10.10.10.3-0.2
Latency to leave start box in cocaine runway0.40.61.0-0.41.0
Latency to leave start box in cocaine runway, F1.41.73.1-0.51.8
Latency to leave start box in cocaine runway, M0.20.20.4-0.1-0.6
Std. dev. time between licks in bursts0.00.10.10.3-0.3
Total sessions with >9 infusions0.10.20.3-0.6-0.2
Short access day 1 total inactive lever presses0.30.51.00.21.0
Short access day 10 total inactive lever presses0.00.20.3-0.20.6
Short access day 1 total infusions0.20.30.6-0.8-0.0
Short access day 10 total infusions0.20.30.6-0.80.2
Short access total infusions0.10.10.1-0.30.3
Short access day 1 locomotion0.91.52.8-1.70.4
Short access day 10 total locomotion0.51.93.7-1.90.2
Short access total locomotion0.40.61.3-1.1-0.1
One hour access (0.3 mA shock)0.00.00.1-0.30.1
Compulsive drug intake0.10.10.2-0.40.1
One hour access (shock baseline)0.00.00.00.1-0.2
Social response proportion0.10.20.4-0.10.6
Social responses0.40.50.91.0-0.3
Social time0.10.20.40.6-0.2
Soleus weight1.33.85.7-1.42.4
Bone: stiffness0.00.10.10.0-0.3
Tibialis anterior weight0.10.40.70.80.2
Time to tail flick, vehicle, before self-admin1.21.41.9-1.41.0
Time to tail flick, vehicle, after self-admin0.20.40.7-0.80.5
Time to tail flick, test, before self-admin0.40.40.80.9-0.2
Time to tail flick, test, after self-admin1.61.72.7-0.81.6
Delta time to tail flick, vehicle, before/after SA0.10.10.1-0.40.2
Delta time to tail flick, test, before/after SA0.20.30.4-0.60.4
Tibia length1.23.23.4-1.81.8
Ambulatory time before self-admin0.00.10.10.30.4
Ambulatory time after self-admin0.30.50.6-0.80.7
Bone: tissue strength2.22.32.61.6-1.4
Total heroin consumption0.00.00.00.1-0.1
Bone: trabecular number0.00.00.0-0.00.0
Bone: trabecular spacing0.10.10.20.10.4
Bone: trabecular thickness0.60.91.7-1.30.2
Bone: trabecular tissue density0.71.32.10.7-1.5
Water consumed over 24 hours1.02.03.01.7-1.0
Number of responses in last shaping day0.40.50.7-0.80.5