Ccnt1

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 Ccnt1 0.06 0.04 4.1e-08 0.06 0.07 0.06 0.06 2.9e-07 1.1e-07 1.1e-06 1.4e-07
2 Brain mRNA stability Ccnt1 0.05 0.03 1.0e-06 0.06 0.07 0.06 0.07 1.7e-06 5.5e-07 1.0e-06 9.3e-07
3 pVTA gene expression Ccnt1 0.07 0.05 4.3e-07 0.09 0.07 0.07 0.08 1.5e-07 1.3e-06 5.4e-06 9.8e-07
4 Liver gene expression Ccnt1 0.04 0.04 9.9e-03 0.01 0.01 0.01 0.01 6.2e-02 3.2e-02 3.5e-02 2.6e-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 density8.815.117.04.1-4.04.0-3.4
Area under the delay curve1.01.21.81.0-0.91.1-1.3
BMI with tail6.221.624.75.0-4.94.9-3.7
BMI without tail1.65.06.42.5-2.52.5-1.1
Body weight6.528.233.25.7-5.65.8-3.9
Weight adjusted by age2.23.44.72.0-2.22.10.6
Bone surface10.218.521.24.6-4.54.5-3.5
Bone volume7.914.216.24.0-3.94.0-3.1
Breakpoint value in progressive ratio session0.91.11.51.2-1.21.2-0.3
Number of licking bursts0.50.93.1-0.40.2-0.31.8
Context. condit. distance diff. score0.30.30.40.6-0.70.6-0.3
Locomotion velocity, session 11.01.11.4-1.01.0-1.01.2
Locomotion distance, session 12.43.04.4-2.02.1-1.9-0.1
Locomotion velocity, session 20.20.30.4-0.60.6-0.6-0.2
Locomotion distance, session 22.02.84.0-1.92.0-2.00.2
Locomotion velocity, session 33.13.54.8-2.12.2-2.10.6
Locomotion distance, session 34.04.35.9-2.42.4-2.30.7
Stereotopy head waving bouts, day 31.01.11.71.2-1.31.10.2
Stereotopy head waving duration, day 30.40.50.70.8-0.90.70.3
Locomotion velocity, session 70.10.10.2-0.30.3-0.10.5
Locomotion distance, session 71.11.41.6-1.21.2-1.11.2
Stereotopy head waving bouts, day 71.31.42.11.3-1.41.30.5
Stereotopy head waving duration, day 70.91.11.61.2-1.31.10.3
Locomotion velocity, session 80.10.10.40.1-0.10.2-0.6
Locomotion distance, session 81.01.52.1-1.31.4-1.4-0.2
Degree of sensitization distance0.50.60.80.8-0.90.90.3
Degree of sensitization stereotypy0.40.40.70.5-0.60.50.8
Conditioned locomotion0.70.82.90.2-0.30.11.7
Cocaine response after cond. corrected1.01.24.6-0.10.3-0.0-2.1
Cocaine response after cond. not corrected0.91.11.4-0.91.1-0.9-1.2
Cocaine response before conditioning4.75.76.8-2.32.2-2.42.6
Saline control response0.00.00.00.00.0-0.10.1
Bone: connectivity density6.19.510.23.2-3.03.1-3.0
Bone: cortical apparent density0.50.71.9-0.60.5-0.61.4
Bone: cortical area10.215.719.24.3-4.34.4-2.4
Bone: cortical porosity1.31.41.6-1.11.1-1.31.2
Bone: cortical porosity1.61.71.9-1.21.2-1.41.3
Bone: cortical thickness4.67.69.63.0-3.03.1-1.8
Bone: cortical thickness0.30.30.60.6-0.60.8-0.3
Bone: cortical tissue density0.60.92.1-0.70.6-0.71.4
Condit. Reinf. active minus inactive responses0.20.20.6-0.30.4-0.3-0.8
Condit. Reinf. active-inactive response ratio0.50.51.70.4-0.30.3-1.3
Condit. Reinf. active responses0.50.60.8-0.80.9-0.9-0.1
Condit. Reinf. inactive responses2.53.13.4-1.81.8-1.81.5
Incentive salience index mean0.10.20.60.2-0.10.2-0.8
Condit. Reinf. lever presses0.30.40.50.5-0.50.7-0.6
Condit. Reinf. active minus inactive responses0.10.20.6-0.20.1-0.20.7
Condit. Reinf. active-inactive response ratio0.30.40.4-0.60.6-0.60.6
Condit. Reinf. active responses0.30.40.7-0.60.5-0.60.8
Condit. Reinf. inactive responses0.70.91.3-0.90.8-1.01.1
Condit. Reinf. lever presses0.00.00.00.1-0.00.10.0
Condit. Reinf. lever reinforcers received0.50.80.8-0.90.8-0.90.9
Conditioned reinforcement - actives0.61.01.4-1.21.1-0.80.9
Conditioned reinforcement - inactives2.63.85.1-2.32.2-1.91.3
Conditioned locomotion0.50.62.1-0.50.3-0.41.5
Patch foraging indifference point 0 sec1.52.83.6-1.91.9-1.90.7
Patch foraging indifference point AUC0.91.21.5-1.11.0-1.21.1
Delay disc. indifference point, 0s delay0.91.01.51.2-1.21.0-0.3
Delay disc. indifference point, 16s delay0.91.01.31.0-1.11.1-0.7
Delay disc. indifference point, 2s delay0.91.01.31.1-1.11.1-0.5
Delay disc. indifference point, 24s delay1.01.11.41.1-1.11.2-0.6
Delay disc. indifference point, 4s delay0.90.92.70.6-0.50.6-1.6
Delay disc. indifference point, 8s delay2.53.04.01.6-1.51.7-2.0
Indifference point function ln k2.23.95.32.3-2.32.1-0.8
Indifference point function log k2.23.95.32.3-2.32.1-0.8
Patch foraging total patch changes 0 sec1.52.83.6-1.91.8-1.90.9
Patch foraging total patch changes 12 sec1.92.43.0-1.71.6-1.71.2
Patch foraging total patch changes 18 sec3.55.46.2-2.42.3-2.52.1
Patch foraging total patch changes 24 sec1.52.63.0-1.61.5-1.61.7
Patch foraging total patch changes 6 sec2.03.04.0-2.02.0-1.90.8
Patch foraging time to switch 0 sec1.53.13.9-2.01.9-1.71.3
Patch foraging water rate 0 sec2.34.86.22.5-2.52.3-1.3
Patch foraging water rate 12 sec2.04.25.62.4-2.42.2-0.9
Patch foraging water rate 18 sec0.30.50.70.7-0.80.8-0.4
Patch foraging water rate 24 sec2.43.34.82.1-2.22.0-0.2
Patch foraging water rate 6 sec3.55.16.82.6-2.62.5-0.9
Seeking ratio, delayed vs. immediate footshock0.70.93.20.4-0.20.5-1.8
Distance traveled before self-admin0.81.12.0-0.90.8-1.01.4
Distance traveled after self-admin0.20.30.4-0.50.6-0.70.1
Extensor digitorum longus weight4.015.619.94.2-4.44.5-2.3
Bone: elastic displacement4.24.95.6-2.42.4-2.41.6
Bone: elastic work0.00.00.1-0.10.1-0.10.4
Bone: endosteal estimation6.113.417.34.2-4.14.0-1.9
Bone: endosteal perimeter6.213.216.14.0-4.03.9-2.3
Epididymis fat weight0.72.42.81.7-1.61.7-1.1
Delta time in closed arm before/after self-admin0.30.20.8-0.20.3-0.1-0.9
Delta time in open arm before/after self-admin1.21.12.0-1.00.9-0.91.4
Diff in mean of infusions in LGA sessions1.11.31.81.1-1.01.3-1.2
Delay discount exponential model param1.01.11.7-0.90.9-1.01.3
Extinction: sum of active levers before priming1.11.21.81.3-1.31.10.0
Active lever presses in extinction session 61.01.01.21.1-1.01.1-0.8
Bone: final force9.715.417.94.2-4.14.2-3.0
Bone: final moment10.116.218.94.4-4.24.3-3.1
Food consumed during 24 hour testing period1.72.33.71.4-1.31.4-1.9
Glucose0.30.40.50.6-0.70.70.6
Heart weight0.10.10.20.3-0.30.3-0.4
Delay discount hyperbolic model param1.01.11.8-0.90.8-1.01.4
Intermittent access intake day 1-15 change0.10.20.7-0.20.30.0-0.8
Intermittent access intake escalation0.10.31.00.00.00.2-1.0
Intermittent access intake escalation 20.20.20.8-0.30.3-0.0-0.9
Intermitt. access day 1 inactive lever presses0.93.69.6-1.21.0-1.53.1
Intermitt. access day 15 inactive lever presses0.81.61.9-1.21.2-1.41.2
Intermitt. access escalation Index0.40.50.70.8-0.90.8-0.2
Intermittent access day 1 total infusions0.60.91.3-1.11.1-1.00.5
Intermittent access day 15 total infusions0.40.50.8-0.90.9-0.70.3
Intermittent access terminal intake (last 3 days)0.70.91.4-1.21.1-0.90.4
Intermittent access total infusions1.01.21.7-1.31.2-1.00.7
Intermittent access day 1 locomotion0.40.51.8-0.30.2-0.31.3
Intermittent access day 15 total locomotion0.30.51.8-0.40.2-0.11.4
Intermittent access total locomotion1.51.84.1-1.10.9-1.02.0
Intermittent access standard deviation0.10.20.4-0.60.6-0.3-0.2
Left kidney weight1.56.814.12.1-1.92.2-3.8
Right kidney weight4.218.921.44.5-4.54.6-3.7
Cocaine induced anxiety2.53.54.62.0-2.12.2-0.9
Post-drug Anxiety2.93.13.61.9-1.91.9-1.3
Baseline Anxiety0.10.10.20.2-0.10.0-0.5
Tail length0.00.00.10.2-0.30.20.1
Length with tail1.66.98.32.8-2.82.9-1.9
Length without tail6.019.220.34.4-4.24.5-4.4
Times rat made contact with spout0.10.10.4-0.10.2-0.0-0.6
Lifetime Intake1.21.52.1-1.51.4-1.10.8
Liver weight, left9.014.918.14.2-4.14.3-2.6
Liver weight, right2.03.54.62.1-2.12.0-1.0
Locomotor activity1.01.61.9-1.31.2-1.21.4
Locomotor testing distance2.44.34.7-2.12.0-2.02.2
Locomotor testing rearing2.14.26.4-1.91.8-1.92.5
Locomotion in novel chamber1.01.31.91.3-1.41.2-0.1
Locomotion in novel chamber post-restriction0.00.00.0-0.10.10.10.1
Fecal boli incidents, locomotor time 11.21.82.3-1.41.5-1.0-1.4
Change in fecal boli incidents, locomotor task0.50.50.70.8-0.80.80.2
Time >=10cm from walls, locomotor time 10.40.41.30.3-0.30.4-1.2
Bouts of movement, locomotor time 10.30.31.10.1-0.10.4-1.1
Total resting periods, locomotor time 10.20.30.7-0.40.5-0.1-0.8
Rest time, locomotor task time 10.30.30.9-0.40.5-0.1-0.9
Distance moved, locomotor task time 10.10.20.6-0.0-0.0-0.20.8
Vertical activity count, locomotor time 10.71.72.31.2-1.21.3-1.5
Time >=10cm from walls, locomotor time 20.30.40.7-0.80.8-0.50.3
Bouts of movement, locomotor time 21.82.94.21.9-2.02.1-0.4
Total resting periods, locomotor time 21.83.24.42.0-2.12.1-0.4
Rest time, locomotor task time 20.20.30.70.2-0.20.5-0.8
Distance moved, locomotor task time 20.30.30.6-0.40.4-0.60.8
Vertical activity count, locomotor time 20.00.10.10.3-0.30.20.1
Light reinforcement 12.35.67.5-2.32.1-2.22.7
Light reinforcement 20.50.81.1-1.01.0-0.80.5
Bone: marrow area5.912.916.74.1-4.13.9-1.8
Bone: maximum diameter4.07.49.43.0-3.03.1-1.4
Bone: maximum force12.622.427.65.3-5.25.1-3.0
Bone: maximum moment13.122.928.35.3-5.25.1-3.2
Mean time between licks in bursts0.10.30.4-0.60.6-0.60.3
Mean num. licks in bursts0.71.14.1-0.10.3-0.1-2.0
Cd content in liver0.60.71.0-0.91.0-0.9-0.3
Co content in liver0.10.10.2-0.10.10.2-0.5
Cu content in liver1.82.22.71.4-1.31.6-1.6
Fe content in liver1.21.52.0-1.41.4-1.30.7
K content in liver0.20.20.30.3-0.40.5-0.3
Mg content in liver0.10.10.1-0.20.2-0.1-0.4
Mn content in liver0.20.20.9-0.10.1-0.20.9
Na content in liver0.20.20.9-0.1-0.10.10.9
Rb content in liver0.10.10.20.1-0.20.4-0.4
Se content in liver0.91.11.5-1.21.2-1.10.4
Sr content in liver1.61.41.81.3-1.41.3-0.5
Zn content in liver0.70.81.1-0.90.8-0.81.1
Bone: minimum diameter8.014.618.44.3-4.34.2-2.0
Time in familiar zone, hab. session 10.30.30.4-0.50.6-0.6-0.5
Time in novel zone, hab. session 10.50.50.90.5-0.70.50.9
Total zone transitions, hab. session 10.30.40.5-0.70.6-0.70.4
Total locomotion distance, hab. session 10.00.00.2-0.00.1-0.1-0.4
Locomotion velocity, hab. session 10.00.00.10.1-0.0-0.0-0.3
Time in familiar zone, hab. session 20.40.51.30.5-0.40.4-1.2
Time in novel zone, hab. session 21.01.03.5-0.40.3-0.41.9
Total zone transitions, hab. session 20.20.30.4-0.60.6-0.5-0.5
Total locomotion distance, hab. session 20.10.20.3-0.40.5-0.4-0.5
Locomotion velocity, hab. session 20.10.20.6-0.20.3-0.2-0.8
Novel to familiar place preference ratio1.51.72.31.4-1.51.40.6
Novelty place preference1.21.31.71.2-1.31.20.8
Time in novel zone, NPP test1.21.21.51.1-1.21.11.1
Total zone transitions, NPP test0.91.31.9-1.31.4-1.2-0.5
Total locomotion distance, NPP test1.41.92.7-1.61.6-1.60.1
Locomotion velocity, NPP test0.71.01.5-1.11.2-1.1-0.4
Intraocular pressure6.49.210.8-3.23.2-3.32.4
Delta distance traveled before/after self-admin0.20.20.90.00.10.0-1.0
Delta ambulatory time before/after self-admin0.00.10.2-0.10.2-0.1-0.4
Parametrial fat weight0.61.31.9-1.41.3-1.10.6
Pavlov. Cond. lever latency0.10.20.60.1-0.0-0.20.8
Pavlov. Cond. magazine entry latency0.20.30.9-0.20.3-0.2-0.9
Pavlov. Cond. change in total contacts0.10.10.20.3-0.30.3-0.4
Pavlov. Cond. index score0.30.30.70.3-0.40.6-0.9
Pavlov. Cond. latency score0.30.30.80.3-0.30.5-0.9
Pavlov. Cond. lever contacts0.10.10.2-0.50.4-0.3-0.2
Pavlov. Cond. magazine entry number0.10.20.7-0.0-0.0-0.10.8
Pavlov. Cond. intertrial magazine entries0.30.40.5-0.70.7-0.70.0
Pavlov. Cond. lever-magazine prob. diff.0.50.61.10.6-0.60.8-1.1
Pavlov. Cond. response bias0.20.20.6-0.30.3-0.2-0.8
Pavlov. Cond. lever latency0.00.00.10.3-0.30.10.1
Pavlov. Cond. magazine entry latency0.70.91.21.1-1.11.0-0.4
Pavlov. Cond. change in total contacts1.72.73.21.7-1.61.8-1.5
Pavlov. Cond. index score0.60.81.11.0-1.01.0-0.6
Pavlov. Cond. latency score0.60.70.90.9-0.91.0-0.6
Pavlov. Cond. lever contacts0.00.00.1-0.10.10.1-0.3
Pavlov. Cond. magazine entry number2.12.53.3-1.81.8-1.80.6
Pavlov. Cond. intertrial magazine entries4.56.88.8-2.93.0-2.91.2
Pavlov. Cond. lever-magazine prob. diff.0.81.11.41.1-1.11.2-0.6
Pavlov. Cond. response bias0.10.10.20.3-0.30.4-0.3
Time in closed arm before self-admin1.82.33.21.7-1.81.6-0.7
Time in closed arm after self-admin0.10.10.20.3-0.30.2-0.5
Time in open arm before self-admin0.00.00.1-0.20.1-0.10.3
Time in open arm after self-admin0.20.31.0-0.10.1-0.11.0
Bone: periosteal estimation11.123.529.05.4-5.45.3-2.8
Bone: periosteal perimeter10.417.920.34.5-4.44.5-3.4
Bone: post-yield work6.49.412.63.5-3.63.3-1.4
Progressive ratio test 1 active lever presses4.45.56.6-2.42.2-2.12.6
Progressive ratio test 1 breakpoint4.15.06.2-2.32.1-2.02.5
Progressive ratio test 1 inactive lever presses1.82.63.4-1.61.4-1.51.8
Progressive ratio test 2 active lever presses1.72.04.0-1.31.1-1.02.0
Progressive ratio test 2 breakpoint1.72.04.1-1.31.1-1.02.0
Progressive ratio test 2 inactive lever presses1.11.83.1-1.31.1-1.11.8
Incentive Sensitization - Responses0.20.30.50.5-0.60.7-0.0
Incentive Sensitization - Breakpoint0.20.20.40.4-0.50.70.1
Sum of active levers in priming session hrs 5-60.00.00.0-0.00.0-0.10.1
Progressive ratio0.20.30.4-0.50.6-0.7-0.2
Food seeking constrained by brief footshock0.40.50.7-0.80.8-0.8-0.3
Seeking ratio, punishment vs. effort0.00.00.0-0.10.00.1-0.1
Retroperitoneal fat weight0.20.71.1-1.11.1-0.80.0
Reaction time number correct0.51.01.51.2-1.21.0-0.5
Reaction time mean minus median3.58.812.3-3.43.5-3.30.8
Reaction time mean minus median AUC2.56.48.9-2.93.0-2.80.8
Reaction time num false alarms1.52.22.9-1.51.6-1.70.9
Reaction time num false alarms AUC2.03.14.2-1.92.0-2.10.7
Reaction time trials correct on left0.51.01.51.2-1.21.0-0.5
Reaction time trials on left0.40.71.11.1-1.00.8-0.4
Reaction time mean0.30.50.8-0.90.9-0.50.0
Reaction time mean AUC0.20.20.5-0.60.7-0.3-0.2
Median of all reaction times0.10.10.30.2-0.20.6-0.4
Reaction time omissions7.611.115.2-3.83.9-3.61.2
Reaction time false alarm rate2.12.93.8-1.91.9-1.90.8
Reaction time premature initiation rate4.76.46.9-2.62.5-2.52.5
Reaction time premature initiations2.13.74.8-1.91.8-1.92.2
Std. dev. reaction times3.66.79.5-3.03.1-2.70.8
Reaction time trials completed0.40.71.11.1-1.00.8-0.4
Reaction time trials AUC0.71.32.01.4-1.31.1-0.6
Run reversals in cocaine runway, females0.10.10.4-0.00.0-0.20.7
Run reversals in cocaine runway, males1.01.01.2-1.11.1-1.00.7
Latency to leave start box in cocaine runway0.10.10.2-0.20.1-0.10.5
Latency to leave start box in cocaine runway, F1.21.42.2-1.11.0-1.11.5
Latency to leave start box in cocaine runway, M1.51.41.71.3-1.21.3-0.9
Std. dev. time between licks in bursts0.81.11.5-1.00.9-1.01.2
Total sessions with >9 infusions0.91.11.7-1.31.2-0.90.3
Short access day 1 total inactive lever presses1.21.51.9-1.41.3-1.30.8
Short access day 10 total inactive lever presses0.20.40.8-0.50.5-0.50.9
Short access day 1 total infusions0.20.30.5-0.70.7-0.4-0.3
Short access day 10 total infusions0.60.81.3-1.21.1-0.70.3
Short access total infusions1.21.62.2-1.51.4-1.20.9
Short access day 1 locomotion0.10.10.4-0.20.1-0.10.6
Short access day 10 total locomotion0.71.34.5-0.60.4-0.52.1
Short access total locomotion1.11.33.4-0.90.7-0.71.8
One hour access (0.3 mA shock)0.00.00.1-0.20.20.1-0.2
Compulsive drug intake0.10.10.3-0.10.2-0.4-0.5
One hour access (shock baseline)0.10.10.30.2-0.20.6-0.4
Social response proportion0.10.10.2-0.30.4-0.4-0.2
Social responses6.78.610.9-3.13.0-3.32.1
Social time0.40.62.2-0.00.2-0.0-1.5
Soleus weight0.51.41.81.3-1.31.3-0.7
Bone: stiffness15.324.830.15.5-5.45.4-3.3
Tibialis anterior weight1.13.85.82.0-2.32.4-0.3
Time to tail flick, vehicle, before self-admin1.91.92.5-1.51.5-1.60.9
Time to tail flick, vehicle, after self-admin0.10.10.30.3-0.30.20.5
Time to tail flick, test, before self-admin0.30.30.4-0.60.7-0.6-0.2
Time to tail flick, test, after self-admin0.70.71.20.8-0.70.7-1.1
Delta time to tail flick, vehicle, before/after SA0.60.60.70.8-0.80.8-0.7
Delta time to tail flick, test, before/after SA0.20.20.30.6-0.60.4-0.3
Tibia length6.618.222.54.7-4.74.7-2.5
Ambulatory time before self-admin1.82.73.3-1.61.5-1.61.8
Ambulatory time after self-admin1.11.31.7-1.11.1-1.11.3
Bone: tissue strength0.50.50.80.9-0.90.7-0.2
Total heroin consumption1.01.21.41.0-1.21.11.0
Bone: trabecular number5.89.511.33.1-2.92.9-3.4
Bone: trabecular spacing2.63.56.6-1.71.5-1.52.6
Bone: trabecular thickness0.10.10.2-0.20.3-0.2-0.4
Bone: trabecular tissue density0.40.52.1-0.10.0-0.21.4
Water consumed over 24 hours0.10.10.10.3-0.20.2-0.3
Number of responses in last shaping day0.40.51.8-0.1-0.1-0.11.4