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 XM_039086671.1 0.08 0.07 1.7e-04 0.01 0.01 -0 -0 5.9e-02 5.7e-02 6.5e-01 4.3e-01
2 PL alternative TSS NM_019326.2 0.07 0.07 1.4e-04 0.01 0.01 -0 0 7.0e-02 3.2e-02 4.7e-01 3.5e-01
3 PL isoform ratio NM_019326.2 0.05 0.06 2.6e-03 0.02 0.01 0.01 0.01 1.8e-03 8.4e-03 5.1e-02 1.3e-02
4 PL isoform ratio XM_039086671.1 0.04 0.05 3.2e-03 0.02 0.01 0 0.01 2.3e-03 1.5e-02 7.7e-02 1.7e-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 density1.73.03.61.9-1.9-1.51.5
Area under the delay curve0.50.60.91.0-1.0-0.50.5
BMI with tail3.211.212.5-3.23.13.5-3.5
BMI without tail2.06.26.6-2.62.52.4-2.4
Body weight8.637.641.2-6.46.45.9-5.9
Weight adjusted by age0.20.40.4-0.50.50.7-0.7
Bone surface0.00.10.1-0.20.20.4-0.4
Bone volume0.00.10.10.0-0.10.3-0.3
Breakpoint value in progressive ratio session0.80.91.9-1.31.40.1-0.1
Number of licking bursts0.10.20.20.4-0.40.4-0.4
Context. condit. distance diff. score0.30.30.4-0.60.60.5-0.5
Locomotion velocity, session 10.91.01.2-1.11.10.9-0.9
Locomotion distance, session 14.25.36.2-2.52.52.1-2.1
Locomotion velocity, session 20.20.20.5-0.70.70.1-0.1
Locomotion distance, session 20.81.11.5-1.21.20.9-0.9
Locomotion velocity, session 30.10.10.1-0.10.1-0.40.4
Locomotion distance, session 30.40.40.5-0.70.70.6-0.6
Stereotopy head waving bouts, day 33.84.44.92.2-2.2-2.02.0
Stereotopy head waving duration, day 30.40.50.70.8-0.8-0.50.5
Locomotion velocity, session 71.71.82.1-1.31.21.5-1.5
Locomotion distance, session 70.40.50.7-0.60.60.8-0.8
Stereotopy head waving bouts, day 70.91.01.61.3-1.3-0.60.6
Stereotopy head waving duration, day 70.30.40.60.8-0.8-0.40.4
Locomotion velocity, session 86.98.29.2-3.03.02.7-2.7
Locomotion distance, session 81.72.42.7-1.71.61.4-1.4
Degree of sensitization distance0.50.50.5-0.60.70.7-0.7
Degree of sensitization stereotypy0.91.01.81.3-1.4-0.50.5
Conditioned locomotion0.50.50.70.6-0.6-0.80.8
Cocaine response after cond. corrected0.60.71.51.1-1.20.2-0.2
Cocaine response after cond. not corrected0.80.91.91.3-1.40.3-0.3
Cocaine response before conditioning0.10.20.30.5-0.6-0.20.2
Saline control response0.60.81.4-0.50.41.2-1.2
Bone: connectivity density2.94.55.12.3-2.3-2.02.0
Bone: cortical apparent density8.311.412.53.2-3.2-3.53.5
Bone: cortical area0.10.10.20.4-0.4-0.30.3
Bone: cortical porosity0.20.20.40.6-0.60.1-0.1
Bone: cortical porosity0.20.20.30.4-0.50.5-0.5
Bone: cortical thickness1.62.63.11.7-1.7-1.51.5
Bone: cortical thickness5.46.36.62.6-2.6-2.52.5
Bone: cortical tissue density8.311.412.43.2-3.2-3.53.5
Condit. Reinf. active minus inactive responses1.31.52.01.0-1.0-1.41.4
Condit. Reinf. active-inactive response ratio2.22.43.11.3-1.2-1.81.8
Condit. Reinf. active responses1.31.61.91.1-1.1-1.41.4
Condit. Reinf. inactive responses0.10.10.30.5-0.5-0.00.0
Incentive salience index mean2.22.73.21.5-1.5-1.81.8
Condit. Reinf. lever presses1.21.71.81.3-1.3-1.31.3
Condit. Reinf. active minus inactive responses0.50.70.70.8-0.8-0.80.8
Condit. Reinf. active-inactive response ratio0.30.40.40.6-0.6-0.60.6
Condit. Reinf. active responses0.60.90.90.9-1.0-0.90.9
Condit. Reinf. inactive responses0.91.21.41.2-1.2-1.01.0
Condit. Reinf. lever presses0.00.00.00.2-0.2-0.20.2
Condit. Reinf. lever reinforcers received0.91.21.31.0-1.0-1.21.2
Conditioned reinforcement - actives0.10.20.30.6-0.6-0.20.2
Conditioned reinforcement - inactives0.20.20.40.3-0.2-0.60.6
Conditioned locomotion0.70.91.41.2-1.2-0.70.7
Patch foraging indifference point 0 sec2.03.74.21.8-1.8-2.12.1
Patch foraging indifference point AUC0.00.00.10.0-0.00.3-0.3
Delay disc. indifference point, 0s delay2.22.42.51.6-1.6-1.51.5
Delay disc. indifference point, 16s delay0.91.01.21.1-1.0-1.01.0
Delay disc. indifference point, 2s delay0.91.01.71.2-1.3-0.60.6
Delay disc. indifference point, 24s delay0.10.10.10.2-0.20.3-0.3
Delay disc. indifference point, 4s delay0.70.80.90.9-0.9-0.80.8
Delay disc. indifference point, 8s delay0.20.20.40.6-0.6-0.20.2
Indifference point function ln k0.10.10.20.3-0.2-0.40.4
Indifference point function log k0.10.10.20.3-0.2-0.40.4
Patch foraging total patch changes 0 sec1.32.52.91.5-1.4-1.71.7
Patch foraging total patch changes 12 sec3.95.15.82.4-2.4-2.12.1
Patch foraging total patch changes 18 sec0.30.50.50.7-0.7-0.70.7
Patch foraging total patch changes 24 sec1.11.82.61.6-1.6-1.01.0
Patch foraging total patch changes 6 sec1.72.62.81.5-1.5-1.71.7
Patch foraging time to switch 0 sec0.00.10.20.2-0.2-0.40.4
Patch foraging water rate 0 sec0.00.00.10.2-0.1-0.30.3
Patch foraging water rate 12 sec0.10.10.2-0.50.50.0-0.0
Patch foraging water rate 18 sec0.20.30.50.7-0.7-0.40.4
Patch foraging water rate 24 sec0.30.50.60.6-0.6-0.80.8
Patch foraging water rate 6 sec1.01.51.61.2-1.2-1.31.3
Seeking ratio, delayed vs. immediate footshock0.20.20.4-0.10.2-0.60.6
Distance traveled before self-admin0.20.20.4-0.60.6-0.20.2
Distance traveled after self-admin0.81.01.6-1.31.30.6-0.6
Extensor digitorum longus weight8.533.436.5-6.06.05.5-5.5
Bone: elastic displacement0.00.00.00.2-0.2-0.00.0
Bone: elastic work0.00.00.0-0.0-0.0-0.10.1
Bone: endosteal estimation2.96.56.6-2.62.52.5-2.5
Bone: endosteal perimeter2.14.45.5-2.32.31.9-1.9
Epididymis fat weight0.31.01.1-1.01.01.1-1.1
Delta time in closed arm before/after self-admin5.04.64.6-2.12.12.2-2.2
Delta time in open arm before/after self-admin0.00.00.00.1-0.10.1-0.1
Diff in mean of infusions in LGA sessions0.20.20.4-0.60.60.2-0.2
Delay discount exponential model param0.30.30.6-0.70.70.3-0.3
Extinction: sum of active levers before priming1.41.51.9-1.11.11.4-1.4
Active lever presses in extinction session 60.00.00.0-0.20.20.1-0.1
Bone: final force0.30.50.90.9-1.0-0.20.2
Bone: final moment0.20.30.70.8-0.8-0.00.0
Food consumed during 24 hour testing period1.01.31.4-1.11.11.2-1.2
Glucose0.30.50.90.3-0.40.9-0.9
Heart weight3.14.96.1-2.52.51.9-1.9
Delay discount hyperbolic model param0.20.20.4-0.60.70.3-0.3
Intermittent access intake day 1-15 change0.10.10.2-0.50.50.0-0.0
Intermittent access intake escalation0.10.10.2-0.50.50.1-0.1
Intermittent access intake escalation 20.50.60.8-0.90.90.6-0.6
Intermitt. access day 1 inactive lever presses0.31.21.80.8-0.8-1.41.4
Intermitt. access day 15 inactive lever presses1.02.12.21.4-1.4-1.51.5
Intermitt. access escalation Index1.42.02.6-1.21.21.6-1.6
Intermittent access day 1 total infusions0.00.00.1-0.00.0-0.20.2
Intermittent access day 15 total infusions0.10.10.2-0.50.5-0.00.0
Intermittent access terminal intake (last 3 days)0.10.10.20.00.0-0.40.4
Intermittent access total infusions0.10.10.1-0.30.3-0.20.2
Intermittent access day 1 locomotion0.10.10.20.3-0.3-0.50.5
Intermittent access day 15 total locomotion0.20.40.40.6-0.6-0.60.6
Intermittent access total locomotion1.11.31.31.1-1.1-1.11.1
Intermittent access standard deviation0.61.22.00.6-0.5-1.41.4
Left kidney weight0.52.44.1-2.02.00.9-0.9
Right kidney weight0.10.30.5-0.70.70.2-0.2
Cocaine induced anxiety3.65.15.5-2.32.32.2-2.2
Post-drug Anxiety1.11.21.2-1.11.11.1-1.1
Baseline Anxiety2.42.73.92.0-2.0-1.31.3
Tail length0.72.64.6-2.12.10.9-0.9
Length with tail3.515.020.6-4.54.53.1-3.1
Length without tail3.611.713.0-3.63.63.2-3.2
Times rat made contact with spout0.60.71.11.0-1.0-0.60.6
Lifetime Intake0.10.10.2-0.10.2-0.40.4
Liver weight, left0.40.60.7-0.70.70.8-0.8
Liver weight, right0.50.91.00.9-0.9-1.01.0
Locomotor activity0.10.20.50.6-0.7-0.10.1
Locomotor testing distance1.62.84.02.0-2.0-1.31.3
Locomotor testing rearing5.110.410.43.2-3.2-3.23.2
Locomotion in novel chamber4.65.96.32.5-2.5-2.32.3
Locomotion in novel chamber post-restriction0.00.00.10.2-0.20.2-0.2
Fecal boli incidents, locomotor time 10.20.30.3-0.50.50.6-0.6
Change in fecal boli incidents, locomotor task0.10.10.20.4-0.40.0-0.0
Time >=10cm from walls, locomotor time 10.60.70.91.0-0.9-0.70.7
Bouts of movement, locomotor time 10.50.60.6-0.80.80.7-0.7
Total resting periods, locomotor time 11.11.21.2-1.11.11.1-1.1
Rest time, locomotor task time 10.00.00.0-0.10.10.1-0.1
Distance moved, locomotor task time 10.00.00.00.1-0.10.1-0.1
Vertical activity count, locomotor time 10.30.71.0-0.70.61.0-1.0
Time >=10cm from walls, locomotor time 20.71.11.71.3-1.3-0.70.7
Bouts of movement, locomotor time 20.50.91.30.7-0.6-1.11.1
Total resting periods, locomotor time 20.30.61.00.4-0.4-1.01.0
Rest time, locomotor task time 20.81.11.3-1.11.10.9-0.9
Distance moved, locomotor task time 20.10.20.3-0.20.20.6-0.6
Vertical activity count, locomotor time 20.40.50.8-0.50.50.9-0.9
Light reinforcement 11.33.23.31.8-1.8-1.81.8
Light reinforcement 20.10.20.40.5-0.6-0.10.1
Bone: marrow area2.86.06.2-2.52.52.4-2.4
Bone: maximum diameter0.00.00.0-0.10.1-0.00.0
Bone: maximum force0.10.20.4-0.30.20.6-0.6
Bone: maximum moment0.20.30.5-0.40.30.7-0.7
Mean time between licks in bursts1.12.62.9-1.71.71.5-1.5
Mean num. licks in bursts0.20.30.50.4-0.3-0.70.7
Cd content in liver1.31.41.9-1.41.41.0-1.0
Co content in liver1.01.22.0-1.41.40.7-0.7
Cu content in liver0.20.30.4-0.40.4-0.60.6
Fe content in liver2.63.23.3-1.81.81.8-1.8
K content in liver0.90.91.30.7-0.6-1.11.1
Mg content in liver1.71.82.51.1-1.0-1.61.6
Mn content in liver2.02.23.41.0-0.9-1.91.9
Na content in liver0.10.10.20.1-0.10.4-0.4
Rb content in liver1.92.22.21.5-1.5-1.51.5
Se content in liver7.79.111.12.7-2.6-3.33.3
Sr content in liver0.30.30.4-0.40.5-0.60.6
Zn content in liver3.53.84.71.7-1.7-2.22.2
Bone: minimum diameter0.81.51.6-1.31.21.2-1.2
Time in familiar zone, hab. session 10.20.20.4-0.0-0.00.6-0.6
Time in novel zone, hab. session 11.51.51.61.3-1.2-1.21.2
Total zone transitions, hab. session 11.82.53.3-1.81.81.3-1.3
Total locomotion distance, hab. session 10.00.00.0-0.20.2-0.10.1
Locomotion velocity, hab. session 10.30.40.8-0.90.90.3-0.3
Time in familiar zone, hab. session 20.10.10.20.4-0.5-0.10.1
Time in novel zone, hab. session 20.30.30.40.5-0.4-0.70.7
Total zone transitions, hab. session 21.21.51.7-1.21.21.3-1.3
Total locomotion distance, hab. session 20.50.60.8-0.70.70.9-0.9
Locomotion velocity, hab. session 20.81.11.1-1.01.01.1-1.1
Novel to familiar place preference ratio0.50.50.8-0.90.90.5-0.5
Novelty place preference0.20.20.4-0.60.60.2-0.2
Time in novel zone, NPP test0.00.00.0-0.20.20.1-0.1
Total zone transitions, NPP test1.11.61.9-1.11.11.4-1.4
Total locomotion distance, NPP test0.20.30.5-0.30.30.7-0.7
Locomotion velocity, NPP test0.50.70.8-0.90.80.8-0.8
Intraocular pressure2.02.82.9-1.71.71.7-1.7
Delta distance traveled before/after self-admin0.90.91.0-0.90.91.0-1.0
Delta ambulatory time before/after self-admin1.11.32.0-0.80.81.4-1.4
Parametrial fat weight0.10.30.40.6-0.6-0.40.4
Pavlov. Cond. lever latency1.41.82.5-1.51.61.1-1.1
Pavlov. Cond. magazine entry latency8.611.112.53.5-3.5-3.13.1
Pavlov. Cond. change in total contacts11.312.012.33.5-3.5-3.43.4
Pavlov. Cond. index score7.08.810.83.2-3.3-2.72.7
Pavlov. Cond. latency score5.16.48.22.8-2.9-2.22.2
Pavlov. Cond. lever contacts2.02.33.11.7-1.8-1.31.3
Pavlov. Cond. magazine entry number12.916.218.8-4.34.33.7-3.7
Pavlov. Cond. intertrial magazine entries0.81.01.3-1.11.10.8-0.8
Pavlov. Cond. lever-magazine prob. diff.8.610.712.73.5-3.6-3.03.0
Pavlov. Cond. response bias9.712.013.53.7-3.7-3.23.2
Pavlov. Cond. lever latency0.10.20.3-0.50.60.3-0.3
Pavlov. Cond. magazine entry latency0.20.20.4-0.30.30.6-0.6
Pavlov. Cond. change in total contacts0.60.91.10.9-0.9-1.11.1
Pavlov. Cond. index score0.00.00.10.3-0.30.1-0.1
Pavlov. Cond. latency score0.00.00.10.2-0.20.1-0.1
Pavlov. Cond. lever contacts0.10.20.40.6-0.6-0.20.2
Pavlov. Cond. magazine entry number0.00.00.1-0.30.3-0.10.1
Pavlov. Cond. intertrial magazine entries0.50.81.4-1.11.20.5-0.5
Pavlov. Cond. lever-magazine prob. diff.0.00.00.00.1-0.10.2-0.2
Pavlov. Cond. response bias0.30.50.80.8-0.9-0.50.5
Time in closed arm before self-admin2.83.64.11.8-1.7-2.02.0
Time in closed arm after self-admin0.10.10.1-0.20.2-0.40.4
Time in open arm before self-admin2.22.43.1-1.81.81.3-1.3
Time in open arm after self-admin0.40.50.5-0.70.70.7-0.7
Bone: periosteal estimation0.51.01.1-1.00.91.1-1.1
Bone: periosteal perimeter1.52.62.6-1.61.61.6-1.6
Bone: post-yield work1.11.61.6-1.31.21.2-1.2
Progressive ratio test 1 active lever presses0.10.10.20.4-0.4-0.20.2
Progressive ratio test 1 breakpoint0.10.10.10.4-0.4-0.10.1
Progressive ratio test 1 inactive lever presses0.10.10.20.2-0.2-0.50.5
Progressive ratio test 2 active lever presses0.60.70.90.7-0.7-1.01.0
Progressive ratio test 2 breakpoint0.70.81.00.8-0.8-1.01.0
Progressive ratio test 2 inactive lever presses0.10.10.2-0.10.1-0.40.4
Incentive Sensitization - Responses0.91.31.61.0-1.0-1.31.3
Incentive Sensitization - Breakpoint0.91.11.50.9-0.9-1.21.2
Sum of active levers in priming session hrs 5-60.00.00.10.2-0.20.2-0.2
Progressive ratio0.00.00.0-0.20.2-0.20.2
Food seeking constrained by brief footshock0.30.40.40.6-0.7-0.60.6
Seeking ratio, punishment vs. effort0.10.20.30.5-0.6-0.10.1
Retroperitoneal fat weight0.10.30.40.5-0.5-0.60.6
Reaction time number correct0.91.81.9-1.41.41.3-1.3
Reaction time mean minus median0.10.20.4-0.30.30.6-0.6
Reaction time mean minus median AUC0.00.10.20.4-0.40.3-0.3
Reaction time num false alarms0.20.20.40.6-0.6-0.30.3
Reaction time num false alarms AUC0.10.10.20.4-0.4-0.10.1
Reaction time trials correct on left0.91.81.9-1.41.41.3-1.3
Reaction time trials on left0.91.71.8-1.41.31.2-1.2
Reaction time mean0.40.60.80.6-0.6-0.90.9
Reaction time mean AUC0.30.50.70.6-0.5-0.90.9
Median of all reaction times1.21.72.21.1-1.1-1.51.5
Reaction time omissions0.30.40.50.7-0.7-0.60.6
Reaction time false alarm rate0.70.91.31.1-1.1-0.80.8
Reaction time premature initiation rate0.10.20.20.4-0.4-0.50.5
Reaction time premature initiations0.20.30.3-0.60.60.5-0.5
Std. dev. reaction times0.00.00.00.2-0.2-0.00.0
Reaction time trials completed0.91.71.8-1.41.31.2-1.2
Reaction time trials AUC0.81.41.5-1.21.21.2-1.2
Run reversals in cocaine runway, females1.21.21.4-1.11.21.0-1.0
Run reversals in cocaine runway, males0.10.10.20.5-0.5-0.20.2
Latency to leave start box in cocaine runway1.82.02.9-1.71.71.1-1.1
Latency to leave start box in cocaine runway, F2.93.34.0-2.02.01.6-1.6
Latency to leave start box in cocaine runway, M0.30.30.60.00.0-0.80.8
Std. dev. time between licks in bursts0.20.30.3-0.50.50.5-0.5
Total sessions with >9 infusions0.20.20.30.2-0.2-0.60.6
Short access day 1 total inactive lever presses1.31.72.11.1-1.1-1.51.5
Short access day 10 total inactive lever presses0.10.30.5-0.70.70.3-0.3
Short access day 1 total infusions0.40.61.00.4-0.4-1.01.0
Short access day 10 total infusions0.30.40.50.5-0.5-0.70.7
Short access total infusions0.20.20.40.1-0.1-0.60.6
Short access day 1 locomotion1.11.41.71.0-1.0-1.31.3
Short access day 10 total locomotion1.32.43.21.8-1.8-1.31.3
Short access total locomotion0.30.40.50.5-0.5-0.70.7
One hour access (0.3 mA shock)0.20.30.4-0.40.40.6-0.6
Compulsive drug intake0.10.10.20.4-0.40.2-0.2
One hour access (shock baseline)0.10.10.3-0.50.5-0.00.0
Social response proportion0.10.20.3-0.20.10.6-0.6
Social responses0.10.10.2-0.0-0.00.4-0.4
Social time0.70.91.6-0.50.51.3-1.3
Soleus weight0.20.61.00.4-0.51.0-1.0
Bone: stiffness0.00.10.1-0.20.10.3-0.3
Tibialis anterior weight1.75.96.3-2.42.32.5-2.5
Time to tail flick, vehicle, before self-admin0.10.10.10.2-0.20.3-0.3
Time to tail flick, vehicle, after self-admin0.10.10.10.1-0.10.4-0.4
Time to tail flick, test, before self-admin1.21.31.8-0.90.91.4-1.4
Time to tail flick, test, after self-admin0.00.00.00.1-0.10.0-0.0
Delta time to tail flick, vehicle, before/after SA0.10.10.20.4-0.40.1-0.1
Delta time to tail flick, test, before/after SA2.52.52.91.5-1.5-1.71.7
Tibia length2.36.38.4-2.12.02.9-2.9
Ambulatory time before self-admin0.20.30.6-0.70.8-0.20.2
Ambulatory time after self-admin2.52.93.7-1.91.91.5-1.5
Bone: tissue strength0.90.91.3-0.80.81.1-1.1
Total heroin consumption0.91.01.50.7-0.8-1.21.2
Bone: trabecular number4.26.98.62.9-2.9-2.32.3
Bone: trabecular spacing2.93.94.7-1.81.72.2-2.2
Bone: trabecular thickness0.10.10.10.2-0.2-0.30.3
Bone: trabecular tissue density0.40.61.10.5-0.4-1.01.0
Water consumed over 24 hours0.20.30.5-0.40.30.7-0.7
Number of responses in last shaping day0.30.30.60.3-0.2-0.80.8