Hub : Genes

Cdk2ap2

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 NAcc mRNA stability Cdk2ap2 0.04 0.03 1.8e-04 0.03 0.03 0.03 0.03 2.0e-05 5.0e-05 5.1e-05 4.3e-05
2 Brain mRNA stability Cdk2ap2 0.04 0.03 4.5e-03 0.02 0.01 0.01 0.01 2.8e-03 8.1e-02 6.2e-02 1.3e-02
3 Liver gene expression Cdk2ap2 0.05 0.04 2.7e-03 0.01 0.02 0.02 0.01 3.3e-02 3.1e-03 2.9e-03 7.4e-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 3
Bone: apparent density0.71.22.5-0.7-0.7-1.6
Area under the delay curve0.20.30.80.1-0.1-0.9
BMI with tail2.58.617.5-2.1-2.0-4.2
BMI without tail1.75.27.2-2.1-2.1-2.7
Body weight3.013.314.0-3.7-3.5-3.7
Weight adjusted by age0.71.01.8-1.3-1.0-0.5
Bone surface2.95.37.6-2.1-2.0-2.8
Bone volume0.91.63.2-0.9-0.9-1.8
Breakpoint value in progressive ratio session2.53.03.3-1.8-1.8-1.6
Number of licking bursts0.00.00.0-0.1-0.10.1
Context. condit. distance diff. score0.81.01.61.21.30.4
Locomotion velocity, session 10.00.00.0-0.00.0-0.2
Locomotion distance, session 10.91.12.6-0.6-0.6-1.6
Locomotion velocity, session 21.92.33.0-1.7-1.7-1.0
Locomotion distance, session 21.11.62.2-1.2-1.1-1.5
Locomotion velocity, session 30.60.72.00.10.1-1.4
Locomotion distance, session 30.20.20.50.00.1-0.7
Stereotopy head waving bouts, day 30.30.30.40.60.5-0.6
Stereotopy head waving duration, day 30.70.81.31.21.00.2
Locomotion velocity, session 70.50.51.5-0.00.0-1.2
Locomotion distance, session 70.50.60.8-0.7-0.7-0.9
Stereotopy head waving bouts, day 70.20.20.30.50.5-0.4
Stereotopy head waving duration, day 70.50.61.3-0.5-0.6-1.1
Locomotion velocity, session 81.21.52.1-1.5-1.4-0.6
Locomotion distance, session 80.20.20.40.50.6-0.2
Degree of sensitization distance0.50.50.6-0.6-0.7-0.8
Degree of sensitization stereotypy0.10.20.3-0.3-0.3-0.6
Conditioned locomotion1.72.03.0-1.7-1.70.1
Cocaine response after cond. corrected0.10.10.10.40.3-0.0
Cocaine response after cond. not corrected0.10.10.10.30.3-0.2
Cocaine response before conditioning0.00.00.1-0.2-0.20.0
Saline control response2.63.44.7-2.2-2.2-0.9
Bone: connectivity density2.74.25.3-1.9-1.9-2.3
Bone: cortical apparent density0.30.40.6-0.7-0.7-0.1
Bone: cortical area0.40.60.9-1.0-0.90.5
Bone: cortical porosity0.00.00.1-0.1-0.2-0.3
Bone: cortical porosity0.30.30.4-0.6-0.7-0.4
Bone: cortical thickness3.45.78.5-2.9-2.90.2
Bone: cortical thickness1.51.82.7-1.6-1.70.2
Bone: cortical tissue density0.40.60.9-0.9-0.9-0.2
Condit. Reinf. active minus inactive responses0.20.30.7-0.3-0.2-0.8
Condit. Reinf. active-inactive response ratio0.10.10.20.10.2-0.5
Condit. Reinf. active responses0.00.00.1-0.00.1-0.3
Condit. Reinf. inactive responses0.10.20.20.30.40.4
Incentive salience index mean0.20.20.4-0.4-0.3-0.7
Condit. Reinf. lever presses0.00.10.1-0.2-0.20.3
Condit. Reinf. active minus inactive responses0.50.70.90.80.7-0.9
Condit. Reinf. active-inactive response ratio1.31.52.41.51.4-0.0
Condit. Reinf. active responses0.50.72.00.20.1-1.4
Condit. Reinf. inactive responses1.11.42.1-1.0-1.0-1.5
Condit. Reinf. lever presses0.91.22.0-0.9-0.9-1.4
Condit. Reinf. lever reinforcers received0.70.92.7-0.1-0.1-1.7
Conditioned reinforcement - actives0.30.40.90.50.50.9
Conditioned reinforcement - inactives2.33.34.02.02.01.4
Conditioned locomotion8.210.712.83.43.62.8
Patch foraging indifference point 0 sec0.20.30.60.80.60.2
Patch foraging indifference point AUC0.71.01.3-1.1-0.9-0.9
Delay disc. indifference point, 0s delay0.91.02.90.30.0-1.7
Delay disc. indifference point, 16s delay0.91.01.41.21.20.4
Delay disc. indifference point, 2s delay0.30.30.40.60.6-0.2
Delay disc. indifference point, 24s delay0.10.10.40.0-0.30.6
Delay disc. indifference point, 4s delay0.40.41.1-0.3-0.1-1.1
Delay disc. indifference point, 8s delay0.10.10.20.0-0.4-0.4
Indifference point function ln k3.35.86.72.62.32.3
Indifference point function log k3.35.86.72.62.32.3
Patch foraging total patch changes 0 sec0.10.10.20.40.30.3
Patch foraging total patch changes 12 sec2.53.33.4-1.8-1.8-1.8
Patch foraging total patch changes 18 sec0.40.61.2-0.6-0.5-1.1
Patch foraging total patch changes 24 sec0.50.80.9-1.0-0.9-0.8
Patch foraging total patch changes 6 sec1.42.14.0-1.0-1.1-2.0
Patch foraging time to switch 0 sec1.02.12.8-1.3-1.3-1.7
Patch foraging water rate 0 sec3.26.88.52.42.42.9
Patch foraging water rate 12 sec4.79.710.23.13.13.2
Patch foraging water rate 18 sec1.62.43.41.41.41.8
Patch foraging water rate 24 sec2.43.45.31.61.52.3
Patch foraging water rate 6 sec2.02.95.41.31.32.3
Seeking ratio, delayed vs. immediate footshock0.00.00.0-0.1-0.0-0.2
Distance traveled before self-admin0.30.41.1-0.0-0.1-1.0
Distance traveled after self-admin0.00.00.0-0.1-0.10.2
Extensor digitorum longus weight6.525.634.2-5.9-5.7-3.2
Bone: elastic displacement0.30.31.00.0-0.11.0
Bone: elastic work1.51.92.9-1.7-1.7-0.2
Bone: endosteal estimation1.12.43.71.81.9-0.1
Bone: endosteal perimeter2.34.97.32.72.7-0.3
Epididymis fat weight4.415.017.14.14.13.3
Delta time in closed arm before/after self-admin1.41.31.8-1.3-1.2-0.9
Delta time in open arm before/after self-admin0.00.00.10.20.0-0.2
Diff in mean of infusions in LGA sessions0.60.71.1-1.0-1.00.0
Delay discount exponential model param0.20.20.60.10.10.8
Extinction: sum of active levers before priming1.51.62.5-1.3-1.6-0.7
Active lever presses in extinction session 61.41.41.8-1.3-1.2-0.9
Bone: final force1.11.82.4-1.6-1.4-0.9
Bone: final moment1.11.82.4-1.5-1.4-1.0
Food consumed during 24 hour testing period0.60.91.90.60.61.4
Glucose1.52.33.71.81.9-0.1
Heart weight0.20.30.40.60.6-0.5
Delay discount hyperbolic model param0.20.20.6-0.00.00.8
Intermittent access intake day 1-15 change2.75.66.82.22.32.6
Intermittent access intake escalation2.45.06.42.02.12.5
Intermittent access intake escalation 22.93.33.71.81.91.8
Intermitt. access day 1 inactive lever presses0.00.10.10.30.00.3
Intermitt. access day 15 inactive lever presses1.12.22.41.51.41.5
Intermitt. access escalation Index2.23.13.71.71.91.6
Intermittent access day 1 total infusions0.71.21.81.41.2-0.4
Intermittent access day 15 total infusions4.66.98.62.92.92.0
Intermittent access terminal intake (last 3 days)3.44.56.22.52.51.1
Intermittent access total infusions1.82.23.31.81.80.4
Intermittent access day 1 locomotion0.60.80.90.90.9-0.8
Intermittent access day 15 total locomotion3.05.47.62.62.71.5
Intermittent access total locomotion5.46.49.62.93.11.2
Intermittent access standard deviation0.61.21.51.01.21.1
Left kidney weight1.04.56.32.42.51.2
Right kidney weight0.83.84.01.92.01.9
Cocaine induced anxiety0.00.00.10.30.10.1
Post-drug Anxiety0.20.20.5-0.4-0.7-0.1
Baseline Anxiety0.40.40.7-0.8-0.8-0.2
Tail length0.62.33.6-1.9-1.80.2
Length with tail1.88.012.2-3.5-3.2-1.1
Length without tail1.85.78.3-2.9-2.7-1.2
Times rat made contact with spout0.40.50.5-0.7-0.7-0.6
Lifetime Intake1.01.21.81.41.30.0
Liver weight, left0.81.42.80.80.81.7
Liver weight, right1.42.43.01.51.51.7
Locomotor activity1.01.62.51.11.01.6
Locomotor testing distance1.01.82.51.31.21.6
Locomotor testing rearing0.51.11.51.21.20.5
Locomotion in novel chamber6.17.79.43.12.92.4
Locomotion in novel chamber post-restriction3.04.95.22.32.22.1
Fecal boli incidents, locomotor time 10.10.10.20.10.20.5
Change in fecal boli incidents, locomotor task0.10.10.1-0.2-0.3-0.4
Time >=10cm from walls, locomotor time 11.01.01.61.31.2-0.3
Bouts of movement, locomotor time 10.50.61.0-1.0-0.8-0.4
Total resting periods, locomotor time 10.10.20.3-0.6-0.4-0.1
Rest time, locomotor task time 12.02.52.61.61.61.5
Distance moved, locomotor task time 10.20.30.6-0.3-0.4-0.8
Vertical activity count, locomotor time 10.30.71.11.10.90.3
Time >=10cm from walls, locomotor time 20.20.20.40.30.40.7
Bouts of movement, locomotor time 20.30.50.6-0.7-0.8-0.7
Total resting periods, locomotor time 20.10.20.5-0.4-0.4-0.7
Rest time, locomotor task time 21.41.82.81.61.7-0.1
Distance moved, locomotor task time 20.70.81.2-1.0-1.10.4
Vertical activity count, locomotor time 20.70.92.6-0.2-0.31.6
Light reinforcement 10.51.21.41.01.21.1
Light reinforcement 21.93.03.91.92.01.2
Bone: marrow area1.12.53.81.92.0-0.1
Bone: maximum diameter0.20.30.60.40.50.8
Bone: maximum force1.83.15.0-1.5-1.4-2.2
Bone: maximum moment1.73.04.8-1.5-1.4-2.2
Mean time between licks in bursts0.30.80.9-0.9-0.9-0.7
Mean num. licks in bursts0.00.10.2-0.0-0.1-0.5
Cd content in liver1.71.92.51.61.50.9
Co content in liver0.50.61.30.50.51.1
Cu content in liver0.00.10.10.20.1-0.3
Fe content in liver0.20.30.5-0.4-0.4-0.7
K content in liver0.60.61.0-0.6-0.6-1.0
Mg content in liver0.30.30.50.70.70.1
Mn content in liver2.32.53.0-1.7-1.7-1.3
Na content in liver0.30.30.8-0.00.00.9
Rb content in liver0.80.91.41.21.2-0.1
Se content in liver0.10.20.30.50.5-0.1
Sr content in liver1.61.42.1-1.5-1.4-0.1
Zn content in liver0.30.30.5-0.7-0.70.1
Bone: minimum diameter0.71.31.81.31.3-0.7
Time in familiar zone, hab. session 10.40.40.60.70.7-0.3
Time in novel zone, hab. session 10.20.20.5-0.2-0.20.7
Total zone transitions, hab. session 10.40.50.7-0.9-0.8-0.3
Total locomotion distance, hab. session 10.40.50.60.80.80.5
Locomotion velocity, hab. session 10.10.10.10.30.30.3
Time in familiar zone, hab. session 20.40.40.8-0.9-0.70.1
Time in novel zone, hab. session 20.20.20.30.30.2-0.5
Total zone transitions, hab. session 22.22.86.0-1.1-1.0-2.5
Total locomotion distance, hab. session 20.30.31.00.10.1-1.0
Locomotion velocity, hab. session 20.30.30.70.40.4-0.8
Novel to familiar place preference ratio0.00.00.1-0.2-0.2-0.3
Novelty place preference0.00.00.00.10.2-0.0
Time in novel zone, NPP test0.00.00.00.10.1-0.0
Total zone transitions, NPP test1.42.03.4-1.2-1.1-1.8
Total locomotion distance, NPP test0.30.41.00.10.2-1.0
Locomotion velocity, NPP test0.20.30.80.20.2-0.9
Intraocular pressure0.50.70.90.70.71.0
Delta distance traveled before/after self-admin0.60.61.7-0.2-0.21.3
Delta ambulatory time before/after self-admin0.40.41.1-0.3-0.31.1
Parametrial fat weight2.45.68.22.72.91.0
Pavlov. Cond. lever latency0.30.40.40.70.60.6
Pavlov. Cond. magazine entry latency0.10.10.10.20.3-0.4
Pavlov. Cond. change in total contacts0.30.30.50.70.7-0.0
Pavlov. Cond. index score0.00.00.10.10.30.2
Pavlov. Cond. latency score0.00.00.00.00.2-0.0
Pavlov. Cond. lever contacts0.10.10.2-0.3-0.1-0.5
Pavlov. Cond. magazine entry number0.10.20.4-0.2-0.3-0.6
Pavlov. Cond. intertrial magazine entries0.20.30.50.40.30.7
Pavlov. Cond. lever-magazine prob. diff.0.00.00.00.10.20.0
Pavlov. Cond. response bias0.10.20.40.20.30.6
Pavlov. Cond. lever latency0.10.10.30.10.1-0.5
Pavlov. Cond. magazine entry latency3.23.94.1-2.0-2.0-1.9
Pavlov. Cond. change in total contacts0.20.30.6-0.4-0.4-0.7
Pavlov. Cond. index score0.60.81.0-1.0-1.0-0.8
Pavlov. Cond. latency score0.50.60.8-0.9-0.8-0.6
Pavlov. Cond. lever contacts0.10.10.2-0.2-0.20.4
Pavlov. Cond. magazine entry number4.15.05.22.32.22.2
Pavlov. Cond. intertrial magazine entries1.32.02.41.61.51.1
Pavlov. Cond. lever-magazine prob. diff.1.01.31.5-1.2-1.2-1.0
Pavlov. Cond. response bias0.60.91.0-1.0-1.0-0.8
Time in closed arm before self-admin0.50.61.00.91.00.1
Time in closed arm after self-admin0.00.00.0-0.10.2-0.1
Time in open arm before self-admin0.60.60.8-0.9-0.90.6
Time in open arm after self-admin0.40.40.7-0.7-0.8-0.4
Bone: periosteal estimation0.10.20.40.50.60.2
Bone: periosteal perimeter0.10.20.30.50.5-0.5
Bone: post-yield work2.03.08.10.60.7-2.8
Progressive ratio test 1 active lever presses0.10.20.50.20.1-0.7
Progressive ratio test 1 breakpoint0.10.20.50.10.0-0.7
Progressive ratio test 1 inactive lever presses0.10.10.30.20.1-0.5
Progressive ratio test 2 active lever presses1.21.42.31.51.40.1
Progressive ratio test 2 breakpoint1.21.42.21.51.40.2
Progressive ratio test 2 inactive lever presses4.77.69.83.13.11.9
Incentive Sensitization - Responses0.10.20.5-0.1-0.1-0.7
Incentive Sensitization - Breakpoint0.10.10.30.10.2-0.6
Sum of active levers in priming session hrs 5-60.80.82.3-0.0-0.01.5
Progressive ratio1.32.04.1-0.9-1.0-2.0
Food seeking constrained by brief footshock0.10.10.2-0.4-0.50.1
Seeking ratio, punishment vs. effort1.42.04.30.91.02.1
Retroperitoneal fat weight8.034.141.16.46.44.5
Reaction time number correct0.20.40.7-0.8-0.7-0.0
Reaction time mean minus median1.64.14.6-1.9-2.0-2.2
Reaction time mean minus median AUC1.23.03.5-1.8-1.9-1.6
Reaction time num false alarms0.20.30.6-0.3-0.30.8
Reaction time num false alarms AUC0.50.71.1-1.0-1.10.3
Reaction time trials correct on left0.20.40.7-0.8-0.7-0.0
Reaction time trials on left0.30.50.9-0.9-0.8-0.0
Reaction time mean0.00.00.0-0.1-0.1-0.2
Reaction time mean AUC0.00.00.10.10.0-0.2
Median of all reaction times0.10.10.20.40.50.2
Reaction time omissions2.53.64.3-2.1-2.0-1.5
Reaction time false alarm rate0.10.20.2-0.3-0.40.4
Reaction time premature initiation rate3.24.45.3-2.2-2.3-1.8
Reaction time premature initiations3.36.07.7-2.7-2.8-1.7
Std. dev. reaction times0.71.31.4-1.0-1.2-1.2
Reaction time trials completed0.30.50.9-0.9-0.8-0.0
Reaction time trials AUC0.20.40.7-0.8-0.7-0.0
Run reversals in cocaine runway, females1.01.01.4-1.0-0.9-1.2
Run reversals in cocaine runway, males0.40.41.0-0.3-0.31.0
Latency to leave start box in cocaine runway0.20.30.30.50.5-0.5
Latency to leave start box in cocaine runway, F0.00.00.10.10.2-0.2
Latency to leave start box in cocaine runway, M0.10.10.20.20.1-0.5
Std. dev. time between licks in bursts0.50.71.0-1.0-1.00.3
Total sessions with >9 infusions0.30.40.9-0.2-0.4-1.0
Short access day 1 total inactive lever presses1.62.22.41.61.51.4
Short access day 10 total inactive lever presses0.00.00.10.1-0.00.3
Short access day 1 total infusions0.81.01.81.31.00.4
Short access day 10 total infusions0.50.72.00.20.1-1.4
Short access total infusions0.30.31.00.20.0-1.0
Short access day 1 locomotion0.60.71.11.11.00.1
Short access day 10 total locomotion0.30.50.70.70.8-0.7
Short access total locomotion0.50.60.91.01.0-0.3
One hour access (0.3 mA shock)3.84.46.42.52.40.9
Compulsive drug intake2.02.44.1-1.7-2.0-0.3
One hour access (shock baseline)4.77.210.13.23.21.2
Social response proportion0.91.01.5-0.9-0.9-1.2
Social responses0.81.01.3-1.0-0.9-1.2
Social time1.01.42.4-1.0-0.9-1.5
Soleus weight4.412.914.23.73.83.3
Bone: stiffness1.01.62.8-1.0-0.9-1.7
Tibialis anterior weight6.823.233.8-5.8-5.6-2.0
Time to tail flick, vehicle, before self-admin0.10.10.2-0.5-0.40.1
Time to tail flick, vehicle, after self-admin2.53.46.8-1.2-1.4-2.6
Time to tail flick, test, before self-admin0.60.60.90.50.8-1.0
Time to tail flick, test, after self-admin0.20.20.4-0.30.10.6
Delta time to tail flick, vehicle, before/after SA3.23.17.7-0.9-0.9-2.8
Delta time to tail flick, test, before/after SA1.61.63.2-1.0-0.81.8
Tibia length0.20.61.1-0.7-0.51.1
Ambulatory time before self-admin0.30.41.20.1-0.0-1.1
Ambulatory time after self-admin0.40.50.80.90.80.2
Bone: tissue strength0.10.10.20.30.4-0.2
Total heroin consumption4.45.25.9-2.3-2.4-2.1
Bone: trabecular number0.91.53.2-0.8-0.8-1.8
Bone: trabecular spacing0.20.30.40.60.70.2
Bone: trabecular thickness0.10.20.30.50.5-0.1
Bone: trabecular tissue density6.69.79.93.13.13.1
Water consumed over 24 hours0.60.81.2-1.0-1.1-0.5
Number of responses in last shaping day0.30.30.7-0.2-0.3-0.8