Hub : Genes

Nefl

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 Nefl 0.03 0.04 1.3e-03 0.01 0.03 0.02 0.02 9.1e-03 6.9e-04 3.8e-03 4.4e-03
2 IL mRNA stability Nefl 0.16 0.15 9.6e-03 0.03 0.02 0 0.02 5.8e-02 1.3e-01 2.5e-01 1.3e-01

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 density1.62.72.71.6-1.6
Area under the delay curve0.10.10.1-0.40.3
BMI with tail0.31.01.1-1.10.9
BMI without tail0.00.00.00.0-0.1
Body weight0.62.62.8-1.71.6
Weight adjusted by age1.42.22.3-1.51.4
Bone surface0.81.51.51.2-1.2
Bone volume0.91.51.51.2-1.2
Breakpoint value in progressive ratio session0.10.10.1-0.30.3
Number of licking bursts0.00.00.0-0.10.0
Context. condit. distance diff. score1.01.21.31.0-1.1
Locomotion velocity, session 10.20.20.3-0.50.3
Locomotion distance, session 10.00.00.0-0.10.0
Locomotion velocity, session 20.00.00.00.00.1
Locomotion distance, session 20.00.00.0-0.0-0.0
Locomotion velocity, session 30.70.80.8-0.90.9
Locomotion distance, session 30.10.10.2-0.10.4
Stereotopy head waving bouts, day 30.60.70.8-0.90.8
Stereotopy head waving duration, day 32.02.42.7-1.61.4
Locomotion velocity, session 74.04.44.52.1-2.1
Locomotion distance, session 74.15.15.42.2-2.3
Stereotopy head waving bouts, day 71.71.92.2-1.31.5
Stereotopy head waving duration, day 72.42.93.2-1.61.8
Locomotion velocity, session 80.00.00.0-0.10.1
Locomotion distance, session 80.60.80.90.9-0.9
Degree of sensitization distance7.98.19.42.6-3.1
Degree of sensitization stereotypy1.31.51.8-1.11.3
Conditioned locomotion0.00.00.00.10.2
Cocaine response after cond. corrected0.40.50.6-0.70.8
Cocaine response after cond. not corrected0.30.40.4-0.50.6
Cocaine response before conditioning0.30.30.30.6-0.6
Saline control response0.30.40.40.6-0.7
Bone: connectivity density2.84.44.62.1-2.1
Bone: cortical apparent density0.10.10.10.3-0.3
Bone: cortical area0.00.00.00.1-0.1
Bone: cortical porosity1.51.61.7-1.21.3
Bone: cortical porosity0.90.91.0-1.01.0
Bone: cortical thickness0.00.00.00.00.1
Bone: cortical thickness0.00.00.00.10.0
Bone: cortical tissue density0.10.10.10.3-0.4
Condit. Reinf. active minus inactive responses0.60.70.8-0.90.8
Condit. Reinf. active-inactive response ratio2.62.82.9-1.71.6
Condit. Reinf. active responses0.00.00.0-0.20.0
Condit. Reinf. inactive responses2.63.23.31.8-1.8
Incentive salience index mean1.01.31.4-1.21.1
Condit. Reinf. lever presses0.50.70.8-0.90.9
Condit. Reinf. active minus inactive responses0.40.50.60.7-0.7
Condit. Reinf. active-inactive response ratio0.00.00.0-0.10.1
Condit. Reinf. active responses1.01.41.41.2-1.2
Condit. Reinf. inactive responses1.92.42.51.6-1.6
Condit. Reinf. lever presses0.10.20.20.4-0.4
Condit. Reinf. lever reinforcers received0.81.21.31.0-1.1
Conditioned reinforcement - actives1.11.81.81.3-1.4
Conditioned reinforcement - inactives3.55.15.32.2-2.3
Conditioned locomotion0.10.20.20.4-0.4
Patch foraging indifference point 0 sec2.03.84.01.9-2.0
Patch foraging indifference point AUC0.30.50.5-0.70.7
Delay disc. indifference point, 0s delay0.20.30.40.4-0.6
Delay disc. indifference point, 16s delay0.30.30.30.6-0.6
Delay disc. indifference point, 2s delay1.31.51.6-1.31.2
Delay disc. indifference point, 24s delay0.20.20.2-0.50.4
Delay disc. indifference point, 4s delay1.81.92.0-1.41.4
Delay disc. indifference point, 8s delay0.00.00.0-0.0-0.0
Indifference point function ln k0.00.10.10.2-0.3
Indifference point function log k0.00.10.10.2-0.3
Patch foraging total patch changes 0 sec1.52.93.11.6-1.8
Patch foraging total patch changes 12 sec0.60.80.80.9-0.9
Patch foraging total patch changes 18 sec1.01.61.71.3-1.2
Patch foraging total patch changes 24 sec0.00.00.0-0.10.0
Patch foraging total patch changes 6 sec0.40.50.70.6-0.8
Patch foraging time to switch 0 sec0.50.91.11.1-0.9
Patch foraging water rate 0 sec0.30.70.8-0.90.8
Patch foraging water rate 12 sec0.51.01.0-1.01.0
Patch foraging water rate 18 sec2.33.63.9-2.01.8
Patch foraging water rate 24 sec0.10.10.2-0.40.2
Patch foraging water rate 6 sec2.33.43.6-1.91.8
Seeking ratio, delayed vs. immediate footshock0.50.60.70.9-0.6
Distance traveled before self-admin0.60.80.8-0.90.9
Distance traveled after self-admin2.63.23.4-1.81.7
Extensor digitorum longus weight13.051.251.4-7.27.1
Bone: elastic displacement0.30.30.40.6-0.5
Bone: elastic work0.20.20.30.5-0.5
Bone: endosteal estimation0.00.00.0-0.1-0.1
Bone: endosteal perimeter0.00.00.0-0.1-0.1
Epididymis fat weight0.82.83.11.6-1.8
Delta time in closed arm before/after self-admin3.02.82.91.7-1.6
Delta time in open arm before/after self-admin0.00.00.0-0.10.1
Diff in mean of infusions in LGA sessions0.40.50.6-0.80.7
Delay discount exponential model param0.40.50.50.7-0.7
Extinction: sum of active levers before priming2.12.32.71.4-1.6
Active lever presses in extinction session 60.20.20.20.5-0.5
Bone: final force0.00.00.1-0.30.1
Bone: final moment0.00.00.0-0.2-0.0
Food consumed during 24 hour testing period0.40.60.70.7-0.9
Glucose0.00.00.10.1-0.2
Heart weight0.81.21.41.0-1.2
Delay discount hyperbolic model param0.50.60.70.8-0.7
Intermittent access intake day 1-15 change1.83.73.71.9-1.9
Intermittent access intake escalation1.93.93.92.0-2.0
Intermittent access intake escalation 21.61.92.01.3-1.4
Intermitt. access day 1 inactive lever presses0.00.00.00.1-0.2
Intermitt. access day 15 inactive lever presses0.00.00.10.2-0.2
Intermitt. access escalation Index0.00.10.1-0.20.2
Intermittent access day 1 total infusions0.00.00.00.0-0.0
Intermittent access day 15 total infusions1.82.62.71.6-1.6
Intermittent access terminal intake (last 3 days)1.11.51.51.2-1.2
Intermittent access total infusions1.21.41.41.2-1.2
Intermittent access day 1 locomotion0.00.00.00.1-0.1
Intermittent access day 15 total locomotion0.20.40.40.6-0.6
Intermittent access total locomotion0.10.10.10.3-0.4
Intermittent access standard deviation0.20.40.40.6-0.6
Left kidney weight0.00.10.1-0.30.3
Right kidney weight0.00.00.0-0.20.1
Cocaine induced anxiety0.00.00.0-0.1-0.0
Post-drug Anxiety0.70.70.80.9-0.8
Baseline Anxiety0.30.40.40.7-0.5
Tail length0.41.61.61.3-1.2
Length with tail0.10.20.2-0.50.5
Length without tail2.27.17.2-2.72.7
Times rat made contact with spout0.70.80.90.8-1.0
Lifetime Intake0.70.80.80.9-0.9
Liver weight, left1.62.62.9-1.71.5
Liver weight, right0.61.01.0-1.01.0
Locomotor activity1.52.42.4-1.51.6
Locomotor testing distance0.00.10.10.3-0.3
Locomotor testing rearing0.20.30.30.6-0.5
Locomotion in novel chamber0.60.81.00.8-1.0
Locomotion in novel chamber post-restriction0.91.41.6-1.11.3
Fecal boli incidents, locomotor time 10.60.91.0-1.00.8
Change in fecal boli incidents, locomotor task0.30.30.4-0.50.6
Time >=10cm from walls, locomotor time 11.31.41.51.2-1.2
Bouts of movement, locomotor time 15.15.85.9-2.42.4
Total resting periods, locomotor time 15.05.65.8-2.42.3
Rest time, locomotor task time 12.02.62.6-1.61.6
Distance moved, locomotor task time 11.82.72.81.7-1.6
Vertical activity count, locomotor time 10.30.60.80.9-0.7
Time >=10cm from walls, locomotor time 20.30.40.5-0.70.6
Bouts of movement, locomotor time 23.04.75.0-2.22.1
Total resting periods, locomotor time 22.95.05.3-2.32.2
Rest time, locomotor task time 20.91.21.2-1.11.1
Distance moved, locomotor task time 22.53.03.01.7-1.7
Vertical activity count, locomotor time 20.20.30.30.6-0.5
Light reinforcement 12.05.05.12.3-2.2
Light reinforcement 20.91.41.51.2-1.2
Bone: marrow area0.00.00.10.0-0.3
Bone: maximum diameter0.20.40.5-0.70.6
Bone: maximum force0.10.30.3-0.60.4
Bone: maximum moment0.10.10.2-0.40.2
Mean time between licks in bursts1.02.52.51.6-1.6
Mean num. licks in bursts0.30.50.50.7-0.7
Cd content in liver1.31.51.5-1.21.2
Co content in liver4.95.65.9-2.42.3
Cu content in liver0.50.60.6-0.80.8
Fe content in liver1.82.22.21.5-1.5
K content in liver0.90.91.11.0-0.8
Mg content in liver2.02.12.41.5-1.3
Mn content in liver2.52.82.81.6-1.7
Na content in liver1.31.41.4-1.21.2
Rb content in liver0.00.00.00.2-0.1
Se content in liver0.91.01.11.1-1.0
Sr content in liver0.00.00.00.0-0.1
Zn content in liver0.10.10.10.3-0.3
Bone: minimum diameter0.00.10.1-0.30.1
Time in familiar zone, hab. session 10.00.00.0-0.10.1
Time in novel zone, hab. session 11.31.31.4-1.21.1
Total zone transitions, hab. session 10.20.30.4-0.60.4
Total locomotion distance, hab. session 10.00.00.0-0.0-0.1
Locomotion velocity, hab. session 10.10.10.10.3-0.4
Time in familiar zone, hab. session 21.61.71.9-1.41.2
Time in novel zone, hab. session 20.50.50.60.8-0.7
Total zone transitions, hab. session 21.92.42.4-1.51.6
Total locomotion distance, hab. session 20.50.70.8-0.80.9
Locomotion velocity, hab. session 20.91.31.3-1.11.2
Novel to familiar place preference ratio1.01.11.41.2-0.9
Novelty place preference0.80.81.01.0-0.8
Time in novel zone, NPP test0.30.30.50.7-0.5
Total zone transitions, NPP test0.10.10.10.3-0.3
Total locomotion distance, NPP test2.23.03.11.7-1.7
Locomotion velocity, NPP test2.13.03.01.7-1.7
Intraocular pressure0.60.91.10.9-1.0
Delta distance traveled before/after self-admin3.33.53.7-1.91.8
Delta ambulatory time before/after self-admin2.93.63.8-1.91.8
Parametrial fat weight2.25.15.22.3-2.2
Pavlov. Cond. lever latency0.00.00.00.1-0.2
Pavlov. Cond. magazine entry latency0.10.10.20.3-0.5
Pavlov. Cond. change in total contacts1.31.41.5-1.21.2
Pavlov. Cond. index score0.10.10.1-0.30.3
Pavlov. Cond. latency score0.00.00.0-0.20.2
Pavlov. Cond. lever contacts0.00.00.00.00.1
Pavlov. Cond. magazine entry number0.20.30.30.6-0.4
Pavlov. Cond. intertrial magazine entries0.10.10.10.3-0.3
Pavlov. Cond. lever-magazine prob. diff.0.20.20.2-0.50.5
Pavlov. Cond. response bias0.10.10.2-0.40.3
Pavlov. Cond. lever latency0.50.70.80.8-0.9
Pavlov. Cond. magazine entry latency0.00.00.00.2-0.2
Pavlov. Cond. change in total contacts1.22.02.1-1.41.4
Pavlov. Cond. index score0.50.60.6-0.80.8
Pavlov. Cond. latency score0.30.40.4-0.60.6
Pavlov. Cond. lever contacts0.30.40.4-0.60.6
Pavlov. Cond. magazine entry number0.00.00.0-0.10.0
Pavlov. Cond. intertrial magazine entries5.88.79.02.9-3.0
Pavlov. Cond. lever-magazine prob. diff.0.60.80.8-0.90.9
Pavlov. Cond. response bias0.40.50.6-0.70.7
Time in closed arm before self-admin1.11.41.6-1.21.2
Time in closed arm after self-admin0.00.00.0-0.00.2
Time in open arm before self-admin0.00.00.0-0.20.2
Time in open arm after self-admin0.00.00.00.1-0.2
Bone: periosteal estimation0.00.00.0-0.0-0.1
Bone: periosteal perimeter0.00.00.0-0.1-0.0
Bone: post-yield work0.20.30.40.5-0.6
Progressive ratio test 1 active lever presses0.00.10.1-0.20.2
Progressive ratio test 1 breakpoint0.10.10.1-0.30.3
Progressive ratio test 1 inactive lever presses1.01.41.51.1-1.2
Progressive ratio test 2 active lever presses0.00.00.00.1-0.2
Progressive ratio test 2 breakpoint0.00.00.00.1-0.1
Progressive ratio test 2 inactive lever presses0.30.40.40.6-0.6
Incentive Sensitization - Responses0.20.30.30.5-0.5
Incentive Sensitization - Breakpoint0.30.40.40.6-0.7
Sum of active levers in priming session hrs 5-60.00.00.00.1-0.2
Progressive ratio0.10.20.2-0.30.5
Food seeking constrained by brief footshock1.92.42.5-1.61.5
Seeking ratio, punishment vs. effort0.30.50.6-0.80.6
Retroperitoneal fat weight0.20.60.70.7-0.9
Reaction time number correct0.40.81.0-1.00.8
Reaction time mean minus median0.10.30.3-0.60.5
Reaction time mean minus median AUC0.10.30.3-0.50.5
Reaction time num false alarms0.00.00.0-0.1-0.2
Reaction time num false alarms AUC0.00.00.0-0.0-0.2
Reaction time trials correct on left0.40.81.0-1.00.8
Reaction time trials on left0.30.60.8-0.90.6
Reaction time mean0.30.50.5-0.70.7
Reaction time mean AUC0.50.80.8-0.90.9
Median of all reaction times0.30.40.4-0.70.6
Reaction time omissions1.72.52.51.6-1.6
Reaction time false alarm rate0.20.30.30.5-0.6
Reaction time premature initiation rate1.72.42.4-1.51.6
Reaction time premature initiations1.93.43.6-1.91.8
Std. dev. reaction times0.20.40.4-0.60.6
Reaction time trials completed0.30.60.8-0.90.6
Reaction time trials AUC0.30.50.7-0.80.6
Run reversals in cocaine runway, females3.03.03.11.8-1.7
Run reversals in cocaine runway, males1.81.81.9-1.41.3
Latency to leave start box in cocaine runway0.80.91.1-0.91.0
Latency to leave start box in cocaine runway, F2.32.63.0-1.51.7
Latency to leave start box in cocaine runway, M0.20.10.20.3-0.4
Std. dev. time between licks in bursts1.72.42.61.5-1.6
Total sessions with >9 infusions0.00.00.0-0.20.1
Short access day 1 total inactive lever presses0.10.10.20.4-0.3
Short access day 10 total inactive lever presses0.10.20.20.5-0.4
Short access day 1 total infusions0.10.10.2-0.30.4
Short access day 10 total infusions0.30.30.3-0.60.6
Short access total infusions0.00.00.0-0.20.2
Short access day 1 locomotion0.91.11.1-1.01.1
Short access day 10 total locomotion0.00.00.00.2-0.1
Short access total locomotion0.10.10.1-0.30.3
One hour access (0.3 mA shock)0.70.80.90.9-0.9
Compulsive drug intake0.50.60.60.8-0.7
One hour access (shock baseline)0.00.00.00.0-0.1
Social response proportion0.20.30.3-0.50.5
Social responses1.21.51.71.2-1.3
Social time0.10.20.30.5-0.4
Soleus weight1.13.43.5-1.91.8
Bone: stiffness0.50.80.9-1.00.8
Tibialis anterior weight8.528.729.0-5.45.3
Time to tail flick, vehicle, before self-admin1.11.11.11.1-1.1
Time to tail flick, vehicle, after self-admin1.62.12.4-1.41.5
Time to tail flick, test, before self-admin3.33.43.71.8-1.9
Time to tail flick, test, after self-admin2.02.12.31.5-1.3
Delta time to tail flick, vehicle, before/after SA0.50.50.6-0.60.8
Delta time to tail flick, test, before/after SA0.00.00.00.00.2
Tibia length1.13.13.31.8-1.7
Ambulatory time before self-admin0.20.30.3-0.50.5
Ambulatory time after self-admin5.46.46.6-2.62.5
Bone: tissue strength0.10.10.10.4-0.4
Total heroin consumption0.60.70.7-0.80.8
Bone: trabecular number2.54.24.32.1-2.0
Bone: trabecular spacing2.33.13.2-1.81.8
Bone: trabecular thickness1.11.41.41.2-1.2
Bone: trabecular tissue density1.32.02.2-1.51.3
Water consumed over 24 hours1.01.31.6-1.31.0
Number of responses in last shaping day0.60.70.7-0.80.8