Hub : Genes

Alpl

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 Adipose gene expression Alpl 0.08 0.05 2.6e-13 0.12 0.12 0.12 0.12 2.8e-13 2.5e-13 8.7e-13 3.0e-13
2 Brain gene expression Alpl 0.07 0.05 4.6e-09 0.09 0.08 0.08 0.09 5.5e-09 4.5e-08 7.5e-08 2.6e-08
3 Liver gene expression Alpl 0.16 0.09 0.0e+00 0.22 0.24 0.24 0.24 2.3e-24 1.6e-26 7.5e-27 2.5e-26

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 density0.10.10.2-0.30.10.4
Area under the delay curve0.60.60.6-0.80.70.8
BMI with tail0.00.10.20.1-0.50.2
BMI without tail0.30.70.80.8-0.9-0.8
Body weight2.08.59.72.9-3.1-2.7
Weight adjusted by age0.91.01.31.1-0.8-1.1
Bone surface0.00.00.0-0.1-0.10.0
Bone volume0.00.00.0-0.20.10.2
Breakpoint value in progressive ratio session1.41.51.81.3-1.2-1.1
Number of licking bursts0.00.00.00.10.0-0.1
Context. condit. distance diff. score0.70.91.30.9-1.1-0.7
Locomotion velocity, session 11.82.02.2-1.51.31.4
Locomotion distance, session 12.43.13.3-1.81.81.7
Locomotion velocity, session 24.04.75.7-2.22.41.8
Locomotion distance, session 20.91.21.5-1.21.10.9
Locomotion velocity, session 31.51.72.0-1.31.21.4
Locomotion distance, session 30.40.50.60.7-0.7-0.6
Stereotopy head waving bouts, day 31.11.31.7-1.31.01.1
Stereotopy head waving duration, day 30.50.60.8-0.90.70.7
Locomotion velocity, session 72.22.42.61.6-1.6-1.5
Locomotion distance, session 70.30.40.60.6-0.8-0.5
Stereotopy head waving bouts, day 70.10.10.20.1-0.5-0.3
Stereotopy head waving duration, day 70.20.20.30.3-0.4-0.6
Locomotion velocity, session 81.01.11.3-1.21.10.9
Locomotion distance, session 80.00.00.1-0.1-0.20.1
Degree of sensitization distance0.30.30.3-0.50.60.5
Degree of sensitization stereotypy1.61.72.01.2-1.4-1.3
Conditioned locomotion1.72.02.2-1.41.31.5
Cocaine response after cond. corrected0.10.10.3-0.20.30.5
Cocaine response after cond. not corrected0.00.00.00.1-0.20.1
Cocaine response before conditioning1.72.02.31.3-1.4-1.5
Saline control response0.10.10.1-0.20.30.4
Bone: connectivity density0.10.10.20.3-0.5-0.3
Bone: cortical apparent density2.33.03.41.9-1.6-1.7
Bone: cortical area0.71.11.21.1-1.1-1.0
Bone: cortical porosity0.70.71.0-0.91.00.6
Bone: cortical porosity1.51.61.9-1.31.41.0
Bone: cortical thickness0.50.80.91.0-0.9-0.8
Bone: cortical thickness0.30.40.7-0.40.80.6
Bone: cortical tissue density2.02.63.11.8-1.5-1.6
Condit. Reinf. active minus inactive responses0.20.20.3-0.60.50.5
Condit. Reinf. active-inactive response ratio0.00.00.1-0.20.30.1
Condit. Reinf. active responses0.10.10.2-0.40.40.0
Condit. Reinf. inactive responses0.10.10.1-0.30.2-0.2
Incentive salience index mean0.10.10.2-0.40.40.2
Condit. Reinf. lever presses0.10.10.2-0.00.4-0.2
Condit. Reinf. active minus inactive responses0.20.20.2-0.50.50.4
Condit. Reinf. active-inactive response ratio1.01.01.0-1.01.01.0
Condit. Reinf. active responses0.00.00.10.2-0.1-0.3
Condit. Reinf. inactive responses1.11.31.81.1-0.9-1.4
Condit. Reinf. lever presses0.40.50.7-0.80.80.4
Condit. Reinf. lever reinforcers received0.00.00.10.1-0.1-0.3
Conditioned reinforcement - actives0.30.30.40.5-0.6-0.6
Conditioned reinforcement - inactives0.30.30.60.4-0.8-0.4
Conditioned locomotion1.21.51.51.2-1.2-1.2
Patch foraging indifference point 0 sec0.10.10.10.2-0.4-0.3
Patch foraging indifference point AUC1.01.21.51.2-1.0-1.1
Delay disc. indifference point, 0s delay1.61.71.9-1.31.21.4
Delay disc. indifference point, 16s delay0.00.00.0-0.00.10.0
Delay disc. indifference point, 2s delay0.20.30.4-0.50.40.6
Delay disc. indifference point, 24s delay0.00.00.1-0.10.3-0.0
Delay disc. indifference point, 4s delay0.50.50.7-0.80.60.8
Delay disc. indifference point, 8s delay0.50.50.5-0.70.70.7
Indifference point function ln k4.46.17.0-2.62.52.2
Indifference point function log k4.46.17.0-2.62.52.2
Patch foraging total patch changes 0 sec0.00.00.00.0-0.1-0.1
Patch foraging total patch changes 12 sec1.82.32.61.5-1.5-1.6
Patch foraging total patch changes 18 sec1.21.51.61.2-1.3-1.2
Patch foraging total patch changes 24 sec1.01.21.51.1-1.2-0.9
Patch foraging total patch changes 6 sec2.94.34.92.1-2.2-1.9
Patch foraging time to switch 0 sec1.32.02.41.4-1.6-1.3
Patch foraging water rate 0 sec2.03.33.4-1.81.81.8
Patch foraging water rate 12 sec2.03.13.3-1.81.71.8
Patch foraging water rate 18 sec1.21.72.3-1.41.50.9
Patch foraging water rate 24 sec2.23.13.9-2.01.71.6
Patch foraging water rate 6 sec3.45.05.4-2.32.32.1
Seeking ratio, delayed vs. immediate footshock0.20.20.3-0.40.20.6
Distance traveled before self-admin7.17.58.42.9-2.7-2.6
Distance traveled after self-admin2.73.03.31.8-1.8-1.6
Extensor digitorum longus weight0.20.91.2-1.00.71.1
Bone: elastic displacement0.10.10.2-0.20.40.2
Bone: elastic work0.00.00.10.10.30.1
Bone: endosteal estimation0.30.70.80.8-0.8-0.9
Bone: endosteal perimeter0.10.10.2-0.40.20.4
Epididymis fat weight0.00.00.1-0.1-0.00.4
Delta time in closed arm before/after self-admin0.00.00.1-0.20.2-0.2
Delta time in open arm before/after self-admin0.40.40.80.4-0.9-0.3
Diff in mean of infusions in LGA sessions0.00.00.0-0.00.20.1
Delay discount exponential model param0.40.50.50.7-0.6-0.7
Extinction: sum of active levers before priming0.60.60.80.8-0.9-0.7
Active lever presses in extinction session 60.30.30.50.5-0.7-0.4
Bone: final force1.11.82.31.5-1.1-1.4
Bone: final moment0.81.31.61.3-1.0-1.1
Food consumed during 24 hour testing period1.11.41.81.1-1.3-1.0
Glucose3.45.15.92.3-2.4-2.0
Heart weight1.52.12.51.5-1.6-1.3
Delay discount hyperbolic model param0.50.50.60.7-0.6-0.8
Intermittent access intake day 1-15 change0.30.30.4-0.60.50.6
Intermittent access intake escalation0.20.20.2-0.40.40.5
Intermittent access intake escalation 20.20.20.3-0.50.60.4
Intermitt. access day 1 inactive lever presses4.24.44.62.1-2.2-2.0
Intermitt. access day 15 inactive lever presses1.71.82.11.4-1.1-1.5
Intermitt. access escalation Index0.10.10.10.3-0.40.0
Intermittent access day 1 total infusions5.56.36.52.5-2.5-2.5
Intermittent access day 15 total infusions2.73.03.31.7-1.8-1.7
Intermittent access terminal intake (last 3 days)1.92.12.11.5-1.4-1.4
Intermittent access total infusions3.23.53.61.9-1.9-1.8
Intermittent access day 1 locomotion0.00.00.10.2-0.3-0.1
Intermittent access day 15 total locomotion0.10.10.1-0.30.10.3
Intermittent access total locomotion0.10.20.20.4-0.4-0.4
Intermittent access standard deviation1.41.41.51.2-1.2-1.2
Left kidney weight9.627.128.85.3-5.4-5.0
Right kidney weight5.214.715.83.8-4.0-3.7
Cocaine induced anxiety0.10.10.20.3-0.3-0.5
Post-drug Anxiety1.92.12.3-1.51.51.3
Baseline Anxiety4.34.65.1-2.12.02.3
Tail length1.95.97.12.4-2.2-2.7
Length with tail2.910.811.13.3-3.2-3.3
Length without tail1.43.03.51.8-1.9-1.5
Times rat made contact with spout0.30.30.40.6-0.5-0.5
Lifetime Intake2.62.93.11.7-1.7-1.7
Liver weight, left3.45.46.82.2-2.1-2.6
Liver weight, right2.74.45.42.0-1.9-2.3
Locomotor activity1.11.71.91.2-1.3-1.4
Locomotor testing distance0.50.91.00.8-1.0-1.0
Locomotor testing rearing0.61.01.30.9-0.9-1.1
Locomotion in novel chamber0.30.30.80.3-0.90.1
Locomotion in novel chamber post-restriction0.00.10.10.1-0.4-0.0
Fecal boli incidents, locomotor time 14.75.25.62.4-2.3-2.1
Change in fecal boli incidents, locomotor task5.75.45.7-2.32.42.3
Time >=10cm from walls, locomotor time 12.62.63.11.8-1.6-1.4
Bouts of movement, locomotor time 10.10.10.1-0.3-0.10.3
Total resting periods, locomotor time 10.00.00.0-0.1-0.20.2
Rest time, locomotor task time 10.91.01.80.8-1.3-0.7
Distance moved, locomotor task time 10.70.80.9-0.81.00.8
Vertical activity count, locomotor time 11.41.51.7-1.21.31.1
Time >=10cm from walls, locomotor time 21.51.62.21.5-1.3-1.0
Bouts of movement, locomotor time 20.10.10.2-0.20.20.4
Total resting periods, locomotor time 20.10.10.3-0.30.30.5
Rest time, locomotor task time 21.11.21.91.0-1.4-0.9
Distance moved, locomotor task time 20.00.00.0-0.10.20.1
Vertical activity count, locomotor time 20.50.50.7-0.60.90.6
Light reinforcement 10.20.40.60.7-0.2-0.8
Light reinforcement 20.10.10.2-0.10.40.1
Bone: marrow area0.30.70.80.8-0.8-0.9
Bone: maximum diameter0.30.60.60.8-0.8-0.7
Bone: maximum force0.71.11.41.2-0.9-1.1
Bone: maximum moment0.40.70.80.9-0.7-0.9
Mean time between licks in bursts0.60.91.0-1.01.00.9
Mean num. licks in bursts0.30.30.50.5-0.7-0.5
Cd content in liver0.40.40.60.7-0.8-0.4
Co content in liver0.10.10.1-0.40.10.2
Cu content in liver0.00.00.10.2-0.2-0.3
Fe content in liver0.60.81.1-0.91.10.7
K content in liver0.10.10.1-0.30.30.1
Mg content in liver0.10.10.10.3-0.3-0.3
Mn content in liver0.10.10.20.2-0.2-0.4
Na content in liver0.10.10.2-0.10.5-0.1
Rb content in liver1.82.32.41.5-1.5-1.5
Se content in liver0.10.20.2-0.40.30.5
Sr content in liver1.81.72.2-1.51.11.3
Zn content in liver3.03.43.91.7-2.0-1.8
Bone: minimum diameter1.22.22.61.3-1.6-1.5
Time in familiar zone, hab. session 11.41.31.51.2-1.1-1.1
Time in novel zone, hab. session 10.00.00.1-0.20.10.2
Total zone transitions, hab. session 10.10.10.2-0.40.40.2
Total locomotion distance, hab. session 10.10.20.3-0.60.30.2
Locomotion velocity, hab. session 10.40.60.8-0.90.80.4
Time in familiar zone, hab. session 20.20.20.30.5-0.3-0.5
Time in novel zone, hab. session 20.50.50.6-0.80.50.8
Total zone transitions, hab. session 21.62.12.2-1.41.51.4
Total locomotion distance, hab. session 22.02.63.2-1.71.81.4
Locomotion velocity, hab. session 21.52.02.4-1.51.61.2
Novel to familiar place preference ratio1.11.21.41.1-1.2-1.0
Novelty place preference1.71.71.81.3-1.3-1.3
Time in novel zone, NPP test1.92.02.21.4-1.5-1.3
Total zone transitions, NPP test1.31.92.1-1.41.51.2
Total locomotion distance, NPP test1.11.62.0-1.31.41.0
Locomotion velocity, NPP test1.72.43.0-1.61.71.2
Intraocular pressure0.00.10.10.2-0.1-0.3
Delta distance traveled before/after self-admin0.10.20.2-0.50.10.5
Delta ambulatory time before/after self-admin0.30.40.5-0.70.30.7
Parametrial fat weight0.10.10.3-0.30.50.2
Pavlov. Cond. lever latency1.41.72.41.3-1.5-1.1
Pavlov. Cond. magazine entry latency0.00.00.10.0-0.30.1
Pavlov. Cond. change in total contacts1.51.61.8-1.31.31.2
Pavlov. Cond. index score0.30.30.3-0.60.60.6
Pavlov. Cond. latency score0.50.60.7-0.70.80.7
Pavlov. Cond. lever contacts2.83.34.1-1.82.01.6
Pavlov. Cond. magazine entry number0.40.50.7-0.70.80.6
Pavlov. Cond. intertrial magazine entries2.53.03.3-1.71.81.6
Pavlov. Cond. lever-magazine prob. diff.0.50.60.6-0.80.80.8
Pavlov. Cond. response bias0.20.30.3-0.60.50.5
Pavlov. Cond. lever latency0.10.10.20.4-0.4-0.1
Pavlov. Cond. magazine entry latency1.72.02.3-1.51.51.2
Pavlov. Cond. change in total contacts0.10.20.3-0.50.60.1
Pavlov. Cond. index score0.91.11.4-1.21.10.9
Pavlov. Cond. latency score1.11.41.7-1.31.21.0
Pavlov. Cond. lever contacts0.00.00.0-0.10.1-0.2
Pavlov. Cond. magazine entry number0.20.20.30.5-0.3-0.4
Pavlov. Cond. intertrial magazine entries0.20.20.30.4-0.4-0.5
Pavlov. Cond. lever-magazine prob. diff.1.01.31.6-1.31.11.0
Pavlov. Cond. response bias0.20.30.4-0.60.60.3
Time in closed arm before self-admin5.25.86.72.6-2.3-2.4
Time in closed arm after self-admin1.51.52.01.2-1.1-1.4
Time in open arm before self-admin1.41.51.6-1.21.31.2
Time in open arm after self-admin0.50.50.6-0.80.60.8
Bone: periosteal estimation0.61.21.21.1-1.1-1.1
Bone: periosteal perimeter0.30.40.70.6-0.8-0.6
Bone: post-yield work0.00.00.10.1-0.0-0.2
Progressive ratio test 1 active lever presses1.31.31.41.2-1.1-1.2
Progressive ratio test 1 breakpoint1.01.11.11.0-1.0-1.0
Progressive ratio test 1 inactive lever presses1.11.21.61.1-1.0-1.3
Progressive ratio test 2 active lever presses3.23.43.81.9-1.7-1.9
Progressive ratio test 2 breakpoint3.53.94.42.0-1.8-2.1
Progressive ratio test 2 inactive lever presses4.85.56.02.3-2.4-2.3
Incentive Sensitization - Responses4.24.24.72.1-1.9-2.2
Incentive Sensitization - Breakpoint4.04.14.52.1-1.9-2.1
Sum of active levers in priming session hrs 5-60.30.30.30.6-0.6-0.4
Progressive ratio0.30.40.50.6-0.7-0.6
Food seeking constrained by brief footshock2.43.03.51.6-1.9-1.7
Seeking ratio, punishment vs. effort0.00.00.10.2-0.1-0.3
Retroperitoneal fat weight0.41.31.8-1.11.01.3
Reaction time number correct0.81.11.3-1.11.01.0
Reaction time mean minus median1.01.41.91.2-1.4-0.9
Reaction time mean minus median AUC2.43.13.91.8-2.0-1.5
Reaction time num false alarms0.00.10.10.2-0.3-0.2
Reaction time num false alarms AUC0.00.00.1-0.20.00.2
Reaction time trials correct on left0.81.11.3-1.11.01.0
Reaction time trials on left0.81.11.3-1.11.01.1
Reaction time mean0.30.40.60.5-0.8-0.4
Reaction time mean AUC0.00.10.10.1-0.4-0.0
Median of all reaction times0.00.00.00.0-0.20.0
Reaction time omissions0.00.00.0-0.1-0.2-0.0
Reaction time false alarm rate0.10.10.20.3-0.4-0.2
Reaction time premature initiation rate1.11.51.9-1.21.11.4
Reaction time premature initiations1.92.73.1-1.71.51.8
Std. dev. reaction times0.40.61.10.7-1.1-0.5
Reaction time trials completed0.81.11.3-1.11.01.1
Reaction time trials AUC0.50.70.9-0.90.70.8
Run reversals in cocaine runway, females0.50.50.60.7-0.8-0.7
Run reversals in cocaine runway, males2.82.73.61.7-1.9-1.3
Latency to leave start box in cocaine runway0.50.60.7-0.70.80.8
Latency to leave start box in cocaine runway, F0.10.10.2-0.30.30.4
Latency to leave start box in cocaine runway, M1.71.61.8-1.31.31.2
Std. dev. time between licks in bursts0.10.10.1-0.30.20.3
Total sessions with >9 infusions0.80.91.10.9-0.9-1.0
Short access day 1 total inactive lever presses0.10.10.1-0.40.20.4
Short access day 10 total inactive lever presses1.61.82.51.3-1.6-1.1
Short access day 1 total infusions2.12.22.31.5-1.5-1.4
Short access day 10 total infusions2.32.62.81.7-1.6-1.6
Short access total infusions1.61.71.81.3-1.3-1.3
Short access day 1 locomotion0.10.10.1-0.20.20.3
Short access day 10 total locomotion0.60.71.20.8-1.1-0.6
Short access total locomotion0.10.10.20.4-0.4-0.3
One hour access (0.3 mA shock)1.92.22.41.5-1.5-1.5
Compulsive drug intake1.31.31.61.1-1.0-1.3
One hour access (shock baseline)0.40.50.60.8-0.8-0.6
Social response proportion0.00.00.0-0.00.0-0.1
Social responses0.10.10.20.3-0.4-0.3
Social time0.30.40.4-0.60.60.6
Soleus weight0.30.91.1-0.90.91.1
Bone: stiffness0.91.41.51.1-1.1-1.2
Tibialis anterior weight0.10.20.3-0.40.40.5
Time to tail flick, vehicle, before self-admin1.91.92.2-1.31.41.5
Time to tail flick, vehicle, after self-admin0.10.10.20.20.1-0.5
Time to tail flick, test, before self-admin0.00.00.0-0.1-0.20.1
Time to tail flick, test, after self-admin0.40.50.50.6-0.7-0.7
Delta time to tail flick, vehicle, before/after SA1.41.42.01.1-1.0-1.4
Delta time to tail flick, test, before/after SA0.10.10.2-0.10.40.0
Tibia length0.41.01.11.1-0.9-1.0
Ambulatory time before self-admin4.95.15.62.4-2.1-2.2
Ambulatory time after self-admin2.42.63.01.6-1.7-1.5
Bone: tissue strength0.00.00.0-0.10.1-0.2
Total heroin consumption1.31.61.81.4-1.3-1.1
Bone: trabecular number0.30.50.7-0.70.50.8
Bone: trabecular spacing0.00.00.0-0.10.20.1
Bone: trabecular thickness1.01.21.31.1-1.1-1.0
Bone: trabecular tissue density0.50.80.90.9-0.7-0.9
Water consumed over 24 hours0.00.00.0-0.10.20.2
Number of responses in last shaping day0.10.10.20.4-0.2-0.4