Neurod2

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 alternative TSS NM_019326.2 0.08 0.07 8.3e-05 0 0.02 0 0 7.6e-02 5.0e-03 1.5e-01 1.2e-01
2 PL alternative TSS XM_039086671.1 0.09 0.07 8.8e-05 0 0.02 0 0 7.7e-02 5.0e-03 1.1e-01 9.6e-02
3 PL isoform ratio NM_019326.2 0.34 0.15 9.7e-03 0 0.01 0 0 9.1e-02 2.0e-02 1.5e-01 1.8e-01
4 PL isoform ratio XM_039086671.1 0.34 0.15 7.8e-03 0.01 0.01 0 0 7.3e-02 1.5e-02 1.0e-01 9.5e-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 density1.42.34.1-2.02.0-0.80.7
Area under the delay curve0.30.30.6-0.80.8-0.10.0
BMI with tail2.68.49.13.0-3.02.8-2.8
BMI without tail0.10.20.40.4-0.4-0.60.5
Body weight6.025.032.85.7-5.74.4-4.0
Weight adjusted by age0.30.40.40.6-0.60.6-0.6
Bone surface0.20.30.50.2-0.20.7-0.7
Bone volume0.20.40.8-0.10.10.8-0.9
Breakpoint value in progressive ratio session0.50.50.90.9-0.9-0.30.4
Number of licking bursts0.20.30.4-0.50.40.5-0.7
Context. condit. distance diff. score0.20.20.30.6-0.5-0.20.4
Locomotion velocity, session 10.60.61.01.0-1.00.5-0.5
Locomotion distance, session 14.15.36.52.5-2.62.1-2.0
Locomotion velocity, session 20.20.20.40.6-0.6-0.20.3
Locomotion distance, session 21.11.51.81.3-1.31.2-1.2
Locomotion velocity, session 30.30.30.70.1-0.1-0.80.8
Locomotion distance, session 30.20.20.40.7-0.7-0.10.1
Stereotopy head waving bouts, day 32.73.25.0-2.22.2-1.21.1
Stereotopy head waving duration, day 30.20.20.5-0.70.70.2-0.2
Locomotion velocity, session 71.51.71.81.3-1.31.3-1.3
Locomotion distance, session 70.60.71.10.6-0.61.0-1.0
Stereotopy head waving bouts, day 70.50.51.0-1.01.0-0.40.3
Stereotopy head waving duration, day 70.20.30.4-0.60.6-0.40.4
Locomotion velocity, session 85.26.29.43.1-3.01.9-1.6
Locomotion distance, session 81.31.92.71.6-1.61.0-1.0
Degree of sensitization distance0.90.91.40.8-0.71.2-1.1
Degree of sensitization stereotypy0.70.71.5-1.21.2-0.20.1
Conditioned locomotion0.30.30.4-0.50.5-0.60.6
Cocaine response after cond. corrected1.41.62.3-1.11.11.3-1.5
Cocaine response after cond. not corrected2.02.33.0-1.41.31.5-1.7
Cocaine response before conditioning0.30.40.8-0.90.9-0.10.1
Saline control response0.70.92.0-0.0-0.01.3-1.4
Bone: connectivity density2.33.55.5-2.32.3-1.41.2
Bone: cortical apparent density6.07.910.8-3.33.3-2.32.2
Bone: cortical area0.10.20.2-0.50.5-0.30.2
Bone: cortical porosity0.50.51.0-0.50.40.9-1.0
Bone: cortical porosity0.70.71.5-0.40.41.1-1.2
Bone: cortical thickness1.82.93.5-1.91.9-1.61.5
Bone: cortical thickness5.26.07.9-2.82.8-2.12.0
Bone: cortical tissue density5.97.810.8-3.33.3-2.32.1
Condit. Reinf. active minus inactive responses1.41.62.0-1.11.1-1.41.4
Condit. Reinf. active-inactive response ratio2.52.73.7-1.31.4-1.91.9
Condit. Reinf. active responses1.21.51.5-1.21.2-1.21.2
Condit. Reinf. inactive responses0.20.20.3-0.60.60.3-0.4
Incentive salience index mean1.82.22.5-1.61.6-1.41.3
Condit. Reinf. lever presses0.60.81.4-1.21.2-0.50.4
Condit. Reinf. active minus inactive responses0.50.60.7-0.80.8-0.70.7
Condit. Reinf. active-inactive response ratio0.20.20.3-0.50.5-0.40.3
Condit. Reinf. active responses0.50.71.2-1.11.0-0.50.4
Condit. Reinf. inactive responses0.81.02.0-1.41.4-0.1-0.0
Condit. Reinf. lever presses0.10.10.2-0.30.3-0.40.4
Condit. Reinf. lever reinforcers received0.70.91.3-1.11.1-0.80.7
Conditioned reinforcement - actives0.60.61.0-1.01.00.4-0.4
Conditioned reinforcement - inactives1.82.02.2-1.41.4-1.51.5
Conditioned locomotion0.50.61.0-1.01.0-0.50.4
Patch foraging indifference point 0 sec1.93.03.6-1.91.9-1.61.5
Patch foraging indifference point AUC0.20.30.60.1-0.10.7-0.7
Delay disc. indifference point, 0s delay1.41.51.8-1.21.2-1.31.2
Delay disc. indifference point, 16s delay1.01.01.3-1.11.1-0.90.9
Delay disc. indifference point, 2s delay1.01.11.5-1.21.20.8-1.0
Delay disc. indifference point, 24s delay0.10.10.1-0.30.30.4-0.4
Delay disc. indifference point, 4s delay0.80.91.3-0.80.8-1.10.9
Delay disc. indifference point, 8s delay0.20.20.3-0.60.60.2-0.3
Indifference point function ln k0.60.81.5-0.30.3-1.21.2
Indifference point function log k0.60.81.5-0.30.3-1.21.2
Patch foraging total patch changes 0 sec1.52.42.6-1.61.6-1.51.5
Patch foraging total patch changes 12 sec2.63.36.5-2.52.5-0.50.4
Patch foraging total patch changes 18 sec0.40.61.0-1.01.0-0.40.3
Patch foraging total patch changes 24 sec2.02.43.3-1.81.8-1.31.1
Patch foraging total patch changes 6 sec1.62.33.3-1.81.8-1.21.1
Patch foraging time to switch 0 sec0.10.20.3-0.30.3-0.60.5
Patch foraging water rate 0 sec0.00.00.00.0-0.0-0.20.2
Patch foraging water rate 12 sec0.40.61.10.4-0.4-1.01.1
Patch foraging water rate 18 sec0.20.30.4-0.60.6-0.50.4
Patch foraging water rate 24 sec0.30.40.5-0.60.6-0.70.7
Patch foraging water rate 6 sec0.60.91.4-1.21.2-0.70.6
Seeking ratio, delayed vs. immediate footshock1.41.63.0-0.50.5-1.71.7
Distance traveled before self-admin0.30.40.40.6-0.7-0.60.5
Distance traveled after self-admin2.42.72.91.6-1.61.7-1.5
Extensor digitorum longus weight5.120.134.65.9-5.82.7-2.3
Bone: elastic displacement0.10.10.3-0.10.1-0.50.5
Bone: elastic work0.00.10.10.0-0.10.3-0.3
Bone: endosteal estimation3.16.77.42.7-2.72.5-2.4
Bone: endosteal perimeter1.63.44.72.2-2.21.5-1.4
Epididymis fat weight0.92.13.31.1-1.11.8-1.7
Delta time in closed arm before/after self-admin2.32.24.22.1-2.10.4-0.4
Delta time in open arm before/after self-admin0.00.00.0-0.20.20.0-0.0
Diff in mean of infusions in LGA sessions0.40.50.60.7-0.70.8-0.6
Delay discount exponential model param0.10.10.30.5-0.5-0.00.1
Extinction: sum of active levers before priming1.51.51.61.2-1.31.2-1.2
Active lever presses in extinction session 60.00.00.0-0.20.1-0.1-0.2
Bone: final force0.81.32.0-0.90.81.3-1.4
Bone: final moment0.81.32.3-0.70.71.4-1.5
Food consumed during 24 hour testing period0.91.01.31.1-1.10.9-0.9
Glucose0.30.40.6-0.60.50.6-0.8
Heart weight2.43.45.82.4-2.41.0-0.9
Delay discount hyperbolic model param0.20.20.40.7-0.60.00.1
Intermittent access intake day 1-15 change0.10.10.2-0.40.4-0.10.2
Intermittent access intake escalation0.20.20.3-0.30.3-0.50.6
Intermittent access intake escalation 20.10.10.20.3-0.3-0.50.4
Intermitt. access day 1 inactive lever presses0.40.50.9-0.90.9-0.10.2
Intermitt. access day 15 inactive lever presses7.98.613.8-2.22.2-3.73.4
Intermitt. access escalation Index1.31.21.51.0-1.01.2-1.1
Intermittent access day 1 total infusions0.10.10.1-0.30.30.3-0.3
Intermittent access day 15 total infusions0.20.20.3-0.50.5-0.30.3
Intermittent access terminal intake (last 3 days)0.20.20.4-0.60.60.10.0
Intermittent access total infusions0.10.10.2-0.10.10.4-0.3
Intermittent access day 1 locomotion0.20.20.3-0.60.6-0.40.4
Intermittent access day 15 total locomotion0.60.61.0-0.70.7-1.00.8
Intermittent access total locomotion1.11.31.8-1.01.0-1.31.2
Intermittent access standard deviation1.51.62.4-0.90.9-1.51.6
Left kidney weight0.82.34.42.1-2.0-0.40.6
Right kidney weight0.20.71.11.0-1.10.6-0.5
Cocaine induced anxiety2.93.33.81.9-1.91.7-1.7
Post-drug Anxiety0.40.40.70.4-0.40.8-0.8
Baseline Anxiety3.13.33.9-1.92.0-1.71.6
Tail length0.51.61.81.2-1.2-1.31.4
Length with tail2.48.716.04.0-4.01.4-1.1
Length without tail5.111.213.43.6-3.73.2-2.9
Times rat made contact with spout0.50.61.1-1.11.0-0.40.2
Lifetime Intake0.00.10.1-0.10.10.4-0.2
Liver weight, left0.10.20.30.2-0.2-0.50.5
Liver weight, right0.20.30.4-0.40.4-0.60.6
Locomotor activity0.20.30.5-0.70.60.4-0.5
Locomotor testing distance1.42.34.1-2.02.0-0.80.6
Locomotor testing rearing6.710.411.6-3.43.4-3.22.9
Locomotion in novel chamber10.212.519.9-2.82.8-4.53.8
Locomotion in novel chamber post-restriction0.50.71.1-0.60.50.9-1.1
Fecal boli incidents, locomotor time 10.10.10.30.5-0.5-0.0-0.1
Change in fecal boli incidents, locomotor task0.30.30.6-0.10.10.8-0.7
Time >=10cm from walls, locomotor time 10.60.61.1-1.01.0-0.30.3
Bouts of movement, locomotor time 11.01.11.60.9-0.91.3-1.1
Total resting periods, locomotor time 12.22.43.71.2-1.21.9-1.8
Rest time, locomotor task time 10.40.40.90.1-0.11.0-0.9
Distance moved, locomotor task time 10.10.10.2-0.40.40.2-0.2
Vertical activity count, locomotor time 10.10.10.20.4-0.4-0.20.1
Time >=10cm from walls, locomotor time 21.92.02.2-1.41.5-1.51.3
Bouts of movement, locomotor time 21.51.62.9-0.60.6-1.71.7
Total resting periods, locomotor time 21.61.73.2-0.40.4-1.81.8
Rest time, locomotor task time 20.60.71.41.2-1.2-0.20.2
Distance moved, locomotor task time 20.30.30.70.1-0.10.8-0.8
Vertical activity count, locomotor time 20.20.30.40.4-0.40.6-0.6
Light reinforcement 11.52.64.1-2.02.0-1.21.0
Light reinforcement 20.40.60.8-0.60.60.8-0.9
Bone: marrow area2.86.27.02.6-2.62.4-2.3
Bone: maximum diameter0.00.00.0-0.10.10.0-0.1
Bone: maximum force0.71.22.40.2-0.21.5-1.5
Bone: maximum moment0.71.22.40.3-0.31.5-1.6
Mean time between licks in bursts1.21.72.31.5-1.51.0-1.0
Mean num. licks in bursts0.20.30.5-0.30.3-0.70.7
Cd content in liver0.10.10.1-0.20.20.4-0.4
Co content in liver0.40.40.90.9-0.90.10.1
Cu content in liver0.20.20.30.5-0.5-0.40.5
Fe content in liver1.21.42.11.4-1.50.8-0.8
K content in liver0.70.70.8-0.90.9-0.80.7
Mg content in liver2.72.84.0-1.21.3-2.02.0
Mn content in liver2.32.63.1-1.41.4-1.81.8
Na content in liver0.50.61.2-0.20.21.0-1.1
Rb content in liver1.21.41.8-1.31.3-1.11.0
Se content in liver3.74.55.4-2.32.3-1.91.9
Sr content in liver0.60.51.2-0.00.1-1.01.1
Zn content in liver2.02.22.6-1.61.6-1.41.3
Bone: minimum diameter0.81.51.61.2-1.21.3-1.2
Time in familiar zone, hab. session 10.60.61.4-0.20.11.0-1.2
Time in novel zone, hab. session 12.12.02.5-1.21.3-1.51.6
Total zone transitions, hab. session 11.11.62.81.7-1.70.7-0.5
Total locomotion distance, hab. session 10.00.00.00.1-0.1-0.10.1
Locomotion velocity, hab. session 10.20.30.70.8-0.80.2-0.1
Time in familiar zone, hab. session 20.10.20.2-0.40.40.3-0.4
Time in novel zone, hab. session 20.80.81.3-0.50.6-1.11.1
Total zone transitions, hab. session 21.01.21.31.1-1.21.1-1.1
Total locomotion distance, hab. session 20.60.71.00.7-0.71.0-1.0
Locomotion velocity, hab. session 20.81.11.21.0-1.01.1-1.1
Novel to familiar place preference ratio0.60.60.70.9-0.8-0.60.8
Novelty place preference0.60.61.10.6-0.5-0.91.0
Time in novel zone, NPP test0.60.61.30.1-0.0-1.01.1
Total zone transitions, NPP test1.62.23.21.1-1.11.8-1.8
Total locomotion distance, NPP test0.60.81.60.3-0.31.2-1.2
Locomotion velocity, NPP test0.91.31.80.9-0.91.3-1.3
Intraocular pressure1.21.72.61.6-1.61.0-0.9
Delta distance traveled before/after self-admin1.21.31.61.1-1.11.3-1.1
Delta ambulatory time before/after self-admin2.52.75.40.8-0.82.3-2.1
Parametrial fat weight0.20.40.9-0.90.90.1-0.1
Pavlov. Cond. lever latency1.11.32.81.7-1.60.10.1
Pavlov. Cond. magazine entry latency5.97.613.3-3.73.6-1.61.3
Pavlov. Cond. change in total contacts8.59.111.6-3.43.4-2.72.5
Pavlov. Cond. index score4.25.310.1-3.23.1-1.00.7
Pavlov. Cond. latency score3.03.97.6-2.72.7-0.70.4
Pavlov. Cond. lever contacts0.91.02.2-1.51.4-0.1-0.2
Pavlov. Cond. magazine entry number7.99.917.04.1-4.11.9-1.5
Pavlov. Cond. intertrial magazine entries0.60.71.41.2-1.1-0.10.2
Pavlov. Cond. lever-magazine prob. diff.5.26.411.7-3.43.4-1.31.0
Pavlov. Cond. response bias6.07.212.3-3.53.5-1.71.4
Pavlov. Cond. lever latency0.10.10.20.5-0.50.3-0.2
Pavlov. Cond. magazine entry latency0.10.20.20.3-0.40.4-0.5
Pavlov. Cond. change in total contacts0.60.80.9-0.90.9-0.90.8
Pavlov. Cond. index score0.00.10.1-0.30.30.1-0.2
Pavlov. Cond. latency score0.00.00.1-0.20.10.2-0.3
Pavlov. Cond. lever contacts0.20.30.7-0.80.80.0-0.2
Pavlov. Cond. magazine entry number0.00.00.00.1-0.1-0.10.2
Pavlov. Cond. intertrial magazine entries0.60.81.01.0-0.9-0.60.9
Pavlov. Cond. lever-magazine prob. diff.0.00.00.1-0.10.10.1-0.2
Pavlov. Cond. response bias0.30.51.0-1.00.9-0.30.1
Time in closed arm before self-admin0.91.02.0-1.41.40.00.1
Time in closed arm after self-admin0.40.40.80.4-0.4-0.80.9
Time in open arm before self-admin1.71.83.61.9-1.9-0.30.3
Time in open arm after self-admin0.40.40.80.9-0.9-0.10.1
Bone: periosteal estimation0.61.21.60.9-1.01.2-1.3
Bone: periosteal perimeter1.11.92.01.4-1.41.4-1.4
Bone: post-yield work1.31.71.91.4-1.41.3-1.2
Progressive ratio test 1 active lever presses0.70.71.3-1.11.10.2-0.2
Progressive ratio test 1 breakpoint0.80.91.1-1.01.00.8-0.8
Progressive ratio test 1 inactive lever presses1.01.11.5-1.21.2-0.90.9
Progressive ratio test 2 active lever presses1.31.41.6-1.31.3-1.21.1
Progressive ratio test 2 breakpoint0.80.91.3-1.21.2-0.70.7
Progressive ratio test 2 inactive lever presses1.82.14.3-0.50.5-2.11.9
Incentive Sensitization - Responses1.81.82.4-1.21.2-1.61.4
Incentive Sensitization - Breakpoint2.02.02.9-1.21.2-1.71.5
Sum of active levers in priming session hrs 5-60.10.10.2-0.50.50.1-0.1
Progressive ratio0.00.00.10.0-0.00.1-0.2
Food seeking constrained by brief footshock1.21.53.0-0.40.31.7-1.6
Seeking ratio, punishment vs. effort0.10.10.2-0.40.40.2-0.2
Retroperitoneal fat weight0.41.42.30.7-0.71.5-1.4
Reaction time number correct0.71.01.81.3-1.30.5-0.6
Reaction time mean minus median0.00.10.10.3-0.30.1-0.1
Reaction time mean minus median AUC0.10.10.1-0.40.4-0.30.2
Reaction time num false alarms0.20.30.5-0.70.60.3-0.5
Reaction time num false alarms AUC0.30.40.6-0.50.50.6-0.7
Reaction time trials correct on left0.71.01.81.3-1.30.5-0.6
Reaction time trials on left0.71.01.71.3-1.30.6-0.6
Reaction time mean1.31.93.4-0.60.6-1.81.8
Reaction time mean AUC1.31.83.3-0.50.6-1.81.8
Median of all reaction times2.63.65.8-1.21.2-2.42.4
Reaction time omissions0.40.51.1-1.01.00.1-0.1
Reaction time false alarm rate0.50.71.2-1.11.10.3-0.4
Reaction time premature initiation rate0.40.61.1-0.50.51.0-0.9
Reaction time premature initiations0.60.91.70.5-0.51.3-1.2
Std. dev. reaction times0.00.10.1-0.10.2-0.30.3
Reaction time trials completed0.71.01.71.3-1.30.6-0.6
Reaction time trials AUC0.50.71.31.1-1.20.3-0.4
Run reversals in cocaine runway, females1.11.12.01.4-1.4-0.40.6
Run reversals in cocaine runway, males2.72.65.5-0.70.7-2.32.0
Latency to leave start box in cocaine runway1.41.52.91.7-1.70.2-0.2
Latency to leave start box in cocaine runway, F1.61.83.01.7-1.70.8-0.7
Latency to leave start box in cocaine runway, M2.42.34.8-0.10.1-2.22.1
Std. dev. time between licks in bursts0.10.20.30.5-0.50.3-0.3
Total sessions with >9 infusions0.50.51.1-1.01.0-0.00.1
Short access day 1 total inactive lever presses1.21.41.8-1.41.3-1.00.9
Short access day 10 total inactive lever presses0.30.40.50.7-0.70.6-0.4
Short access day 1 total infusions0.30.30.4-0.60.6-0.40.5
Short access day 10 total infusions0.10.10.2-0.40.40.0-0.0
Short access total infusions0.10.10.2-0.20.20.4-0.3
Short access day 1 locomotion2.42.63.7-1.91.9-1.31.2
Short access day 10 total locomotion1.31.42.0-1.41.4-1.00.8
Short access total locomotion0.30.30.6-0.70.80.00.1
One hour access (0.3 mA shock)0.30.30.8-0.10.10.9-0.7
Compulsive drug intake0.80.81.90.1-0.01.4-1.1
One hour access (shock baseline)0.10.10.2-0.30.2-0.50.4
Social response proportion0.20.20.50.2-0.20.7-0.7
Social responses0.40.51.0-0.0-0.00.9-1.0
Social time1.01.32.30.6-0.61.4-1.5
Soleus weight0.41.32.8-0.40.31.4-1.7
Bone: stiffness0.40.71.40.0-0.11.2-1.2
Tibialis anterior weight1.03.35.52.3-2.41.1-1.0
Time to tail flick, vehicle, before self-admin0.30.30.7-0.20.10.8-0.8
Time to tail flick, vehicle, after self-admin0.00.00.0-0.20.2-0.0-0.1
Time to tail flick, test, before self-admin2.12.13.11.2-1.21.8-1.6
Time to tail flick, test, after self-admin0.10.10.4-0.10.00.4-0.6
Delta time to tail flick, vehicle, before/after SA0.30.30.6-0.30.20.7-0.8
Delta time to tail flick, test, before/after SA3.02.73.8-1.51.5-2.01.6
Tibia length2.46.88.52.2-2.32.9-2.9
Ambulatory time before self-admin0.70.71.10.7-0.7-1.11.0
Ambulatory time after self-admin4.34.85.42.1-2.22.3-2.1
Bone: tissue strength0.70.70.80.7-0.70.9-0.9
Total heroin consumption0.40.50.8-0.60.5-0.90.7
Bone: trabecular number2.74.27.9-2.82.8-0.90.7
Bone: trabecular spacing2.73.54.41.6-1.72.1-2.1
Bone: trabecular thickness0.10.10.2-0.30.3-0.40.4
Bone: trabecular tissue density1.21.73.1-0.60.7-1.71.8
Water consumed over 24 hours0.20.20.40.2-0.20.6-0.6
Number of responses in last shaping day1.01.12.0-0.40.4-1.41.4