Chka

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 IL isoform ratio XM_039103104.2 0.2 0.14 4.7e-03 0.03 0.08 0.1 0.07 7.0e-02 6.2e-03 1.8e-03 8.3e-03
2 PL mRNA stability Chka 0.04 0.03 1.5e-03 0.03 0.03 0.02 0.03 5.7e-04 4.1e-04 1.4e-03 8.6e-04
3 Liver isoform ratio NM_017127.3 0.02 0.02 2.8e-03 0 0.01 0.01 0.01 1.7e-01 8.3e-03 1.2e-02 7.0e-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
Bone: apparent density1.73.26.3-0.8-1.62.5
Area under the delay curve0.30.51.4-0.2-0.41.2
BMI with tail2.17.58.9-2.5-3.02.7
BMI without tail0.84.16.1-2.2-2.51.2
Body weight2.410.415.5-3.9-3.90.8
Weight adjusted by age0.30.91.7-1.3-1.0-0.3
Bone surface3.26.28.1-2.2-2.82.4
Bone volume1.52.94.8-1.1-1.72.2
Breakpoint value in progressive ratio session1.12.03.1-1.8-1.70.1
Number of licking bursts0.00.10.10.1-0.20.4
Context. condit. distance diff. score0.80.91.71.31.00.4
Locomotion velocity, session 10.00.00.00.00.00.1
Locomotion distance, session 11.11.42.5-0.8-1.11.6
Locomotion velocity, session 21.72.03.3-1.8-1.6-0.1
Locomotion distance, session 21.01.31.7-1.3-1.30.8
Locomotion velocity, session 30.91.02.7-0.2-0.61.6
Locomotion distance, session 30.10.10.20.1-0.10.5
Stereotopy head waving bouts, day 30.60.82.20.3-0.11.5
Stereotopy head waving duration, day 30.60.71.10.90.61.1
Locomotion velocity, session 70.50.61.5-0.1-0.51.2
Locomotion distance, session 70.30.30.6-0.5-0.80.4
Stereotopy head waving bouts, day 70.70.82.40.3-0.21.5
Stereotopy head waving duration, day 71.11.42.3-0.8-1.21.5
Locomotion velocity, session 81.01.22.0-1.3-1.40.0
Locomotion distance, session 80.30.40.60.70.30.7
Degree of sensitization distance0.40.40.6-0.6-0.80.6
Degree of sensitization stereotypy0.50.50.9-0.4-0.71.0
Conditioned locomotion1.72.03.0-1.5-1.0-1.7
Cocaine response after cond. corrected0.10.10.10.40.20.3
Cocaine response after cond. not corrected0.10.20.50.30.10.7
Cocaine response before conditioning0.10.10.2-0.2-0.30.4
Saline control response2.33.24.9-2.2-2.10.1
Bone: connectivity density3.65.87.3-2.0-2.72.4
Bone: cortical apparent density0.20.40.6-0.6-0.3-0.8
Bone: cortical area0.30.60.8-0.8-0.5-0.9
Bone: cortical porosity0.00.00.0-0.2-0.20.2
Bone: cortical porosity0.20.20.4-0.6-0.60.0
Bone: cortical thickness3.05.06.8-2.6-1.8-2.2
Bone: cortical thickness1.31.52.5-1.6-1.2-0.9
Bone: cortical tissue density0.30.50.7-0.8-0.5-0.8
Condit. Reinf. active minus inactive responses0.30.30.6-0.3-0.50.8
Condit. Reinf. active-inactive response ratio0.10.10.40.1-0.10.6
Condit. Reinf. active responses0.00.00.10.0-0.10.3
Condit. Reinf. inactive responses0.10.10.20.40.4-0.2
Incentive salience index mean0.20.20.4-0.3-0.50.6
Condit. Reinf. lever presses0.00.00.00.0-0.0-0.1
Condit. Reinf. active minus inactive responses0.60.92.10.70.31.5
Condit. Reinf. active-inactive response ratio1.01.62.21.51.21.0
Condit. Reinf. active responses0.71.13.00.0-0.51.7
Condit. Reinf. inactive responses1.11.62.2-1.2-1.51.0
Condit. Reinf. lever presses0.91.31.6-0.9-1.31.3
Condit. Reinf. lever reinforcers received0.91.33.1-0.3-0.81.8
Conditioned reinforcement - actives0.20.81.10.60.9-1.1
Conditioned reinforcement - inactives1.02.84.42.11.90.4
Conditioned locomotion6.49.614.23.83.8-0.6
Patch foraging indifference point 0 sec0.10.30.60.80.50.2
Patch foraging indifference point AUC0.30.81.0-1.0-0.7-1.0
Delay disc. indifference point, 0s delay1.01.13.1-0.2-0.51.8
Delay disc. indifference point, 16s delay0.60.81.21.11.00.4
Delay disc. indifference point, 2s delay0.40.50.90.60.31.0
Delay disc. indifference point, 24s delay0.10.20.4-0.3-0.1-0.6
Delay disc. indifference point, 4s delay0.30.30.7-0.3-0.40.9
Delay disc. indifference point, 8s delay0.20.30.5-0.4-0.50.7
Indifference point function ln k1.54.57.22.72.5-0.0
Indifference point function log k1.54.57.22.72.5-0.0
Patch foraging total patch changes 0 sec0.00.10.20.50.3-0.3
Patch foraging total patch changes 12 sec1.62.23.5-1.9-1.8-0.2
Patch foraging total patch changes 18 sec0.10.30.5-0.6-0.70.2
Patch foraging total patch changes 24 sec0.20.70.9-0.9-0.8-0.7
Patch foraging total patch changes 6 sec0.81.32.0-1.2-1.40.7
Patch foraging time to switch 0 sec1.03.74.2-1.7-2.02.1
Patch foraging water rate 0 sec2.18.110.52.93.2-2.3
Patch foraging water rate 12 sec2.711.115.33.63.9-2.3
Patch foraging water rate 18 sec0.92.13.01.71.7-0.7
Patch foraging water rate 24 sec3.14.45.62.02.4-2.0
Patch foraging water rate 6 sec2.43.53.91.72.0-1.9
Seeking ratio, delayed vs. immediate footshock0.40.51.2-0.4-0.41.1
Distance traveled before self-admin0.10.30.6-0.2-0.40.8
Distance traveled after self-admin0.00.00.0-0.1-0.20.2
Extensor digitorum longus weight5.020.033.5-5.8-5.0-1.4
Bone: elastic displacement1.41.84.60.30.8-2.1
Bone: elastic work1.41.82.4-1.5-1.1-1.4
Bone: endosteal estimation0.92.33.01.71.11.6
Bone: endosteal perimeter2.04.86.42.51.62.3
Epididymis fat weight2.210.916.74.04.10.0
Delta time in closed arm before/after self-admin0.90.81.2-1.1-1.0-0.6
Delta time in open arm before/after self-admin0.10.20.50.1-0.10.7
Diff in mean of infusions in LGA sessions0.30.50.9-0.9-0.8-0.3
Delay discount exponential model param0.30.41.00.30.4-1.0
Extinction: sum of active levers before priming1.52.23.2-1.6-1.80.8
Active lever presses in extinction session 60.80.81.3-1.2-0.9-0.6
Bone: final force1.11.72.6-1.6-1.60.4
Bone: final moment1.01.62.5-1.6-1.50.3
Food consumed during 24 hour testing period0.30.50.70.80.8-0.5
Glucose1.72.64.71.51.02.2
Heart weight0.71.13.40.2-0.11.8
Delay discount hyperbolic model param0.30.41.10.20.3-1.1
Intermittent access intake day 1-15 change0.63.55.52.22.3-0.3
Intermittent access intake escalation0.63.14.92.12.2-0.4
Intermittent access intake escalation 21.32.23.61.81.9-0.2
Intermitt. access day 1 inactive lever presses0.00.00.00.10.1-0.1
Intermitt. access day 15 inactive lever presses0.21.21.31.21.11.0
Intermitt. access escalation Index1.03.34.62.12.1-0.8
Intermittent access day 1 total infusions0.72.15.01.00.72.2
Intermittent access day 15 total infusions2.15.27.52.72.61.0
Intermittent access terminal intake (last 3 days)2.23.84.92.22.11.4
Intermittent access total infusions1.82.22.41.51.41.5
Intermittent access day 1 locomotion0.51.02.00.90.61.4
Intermittent access day 15 total locomotion1.24.76.62.62.51.1
Intermittent access total locomotion4.95.98.12.92.71.5
Intermittent access standard deviation0.10.71.11.01.00.4
Left kidney weight0.43.35.12.32.20.3
Right kidney weight0.42.84.42.02.1-0.5
Cocaine induced anxiety0.00.10.20.2-0.00.4
Post-drug Anxiety0.30.40.6-0.7-0.80.3
Baseline Anxiety0.30.50.9-0.9-0.7-0.4
Tail length0.42.22.7-1.6-1.3-1.6
Length with tail1.66.910.5-3.2-2.8-1.5
Length without tail0.95.08.1-2.8-2.4-1.0
Times rat made contact with spout0.70.81.1-0.8-1.00.9
Lifetime Intake0.91.21.31.11.01.1
Liver weight, left0.50.91.10.91.0-0.9
Liver weight, right1.11.92.81.51.7-0.7
Locomotor activity0.91.42.01.31.4-0.7
Locomotor testing distance0.71.72.51.41.6-0.8
Locomotor testing rearing0.30.91.41.21.00.6
Locomotion in novel chamber4.05.48.02.82.70.8
Locomotion in novel chamber post-restriction1.33.86.12.52.30.3
Fecal boli incidents, locomotor time 10.00.10.10.40.3-0.1
Change in fecal boli incidents, locomotor task0.10.10.2-0.3-0.40.2
Time >=10cm from walls, locomotor time 11.31.62.91.20.71.7
Bouts of movement, locomotor time 10.50.71.2-0.7-0.6-1.1
Total resting periods, locomotor time 10.30.41.0-0.3-0.2-1.0
Rest time, locomotor task time 11.42.23.51.61.9-0.9
Distance moved, locomotor task time 10.30.81.7-0.5-0.71.3
Vertical activity count, locomotor time 10.10.60.80.80.60.9
Time >=10cm from walls, locomotor time 20.10.30.40.50.6-0.5
Bouts of movement, locomotor time 20.10.30.5-0.6-0.7-0.2
Total resting periods, locomotor time 20.00.10.2-0.3-0.50.0
Rest time, locomotor task time 20.91.62.11.51.31.0
Distance moved, locomotor task time 20.60.81.0-1.0-0.6-1.0
Vertical activity count, locomotor time 20.51.23.5-0.00.3-1.9
Light reinforcement 10.21.01.61.01.3-0.5
Light reinforcement 21.22.64.21.82.1-0.5
Bone: marrow area1.02.43.21.81.11.7
Bone: maximum diameter0.10.20.30.60.6-0.2
Bone: maximum force1.83.54.4-1.7-2.11.7
Bone: maximum moment1.73.14.1-1.7-2.01.6
Mean time between licks in bursts0.10.60.9-0.9-0.9-0.2
Mean num. licks in bursts0.00.10.1-0.3-0.20.3
Cd content in liver1.51.72.81.71.50.2
Co content in liver1.41.62.90.61.2-1.7
Cu content in liver0.00.00.10.10.2-0.2
Fe content in liver0.10.10.3-0.5-0.3-0.2
K content in liver0.60.60.7-0.8-0.80.6
Mg content in liver0.30.30.50.50.40.7
Mn content in liver1.61.82.9-1.7-1.6-0.0
Na content in liver0.40.41.00.20.4-1.0
Rb content in liver0.91.01.41.00.81.2
Se content in liver0.20.30.60.30.20.8
Sr content in liver1.51.31.8-1.3-1.0-1.1
Zn content in liver0.30.40.5-0.6-0.4-0.7
Bone: minimum diameter1.02.04.01.30.52.0
Time in familiar zone, hab. session 10.40.50.70.80.50.6
Time in novel zone, hab. session 10.10.10.1-0.3-0.1-0.3
Total zone transitions, hab. session 10.40.50.8-0.9-0.80.3
Total locomotion distance, hab. session 10.30.40.60.80.70.4
Locomotion velocity, hab. session 10.10.10.10.30.40.2
Time in familiar zone, hab. session 20.30.40.8-0.4-0.4-0.9
Time in novel zone, hab. session 20.50.51.5-0.1-0.21.2
Total zone transitions, hab. session 23.03.95.7-1.4-2.02.4
Total locomotion distance, hab. session 20.70.92.5-0.2-0.51.6
Locomotion velocity, hab. session 20.60.82.30.2-0.11.5
Novel to familiar place preference ratio0.30.40.6-0.5-0.60.8
Novelty place preference0.20.30.7-0.2-0.30.8
Time in novel zone, NPP test0.30.30.7-0.2-0.40.9
Total zone transitions, NPP test1.11.62.2-1.1-1.51.2
Total locomotion distance, NPP test0.20.20.70.1-0.10.8
Locomotion velocity, NPP test0.10.10.40.20.00.6
Intraocular pressure0.91.41.71.01.3-1.3
Delta distance traveled before/after self-admin0.10.10.3-0.00.1-0.5
Delta ambulatory time before/after self-admin0.10.10.4-0.2-0.0-0.6
Parametrial fat weight2.04.87.52.72.41.1
Pavlov. Cond. lever latency0.20.30.50.50.7-0.3
Pavlov. Cond. magazine entry latency0.40.61.50.4-0.21.2
Pavlov. Cond. change in total contacts0.40.40.60.70.40.8
Pavlov. Cond. index score0.10.10.20.40.10.2
Pavlov. Cond. latency score0.10.10.20.2-0.10.4
Pavlov. Cond. lever contacts0.10.10.1-0.1-0.30.3
Pavlov. Cond. magazine entry number0.10.10.3-0.5-0.3-0.0
Pavlov. Cond. intertrial magazine entries0.40.50.90.40.7-1.0
Pavlov. Cond. lever-magazine prob. diff.0.10.10.10.40.10.3
Pavlov. Cond. response bias0.10.10.20.40.2-0.1
Pavlov. Cond. lever latency0.00.00.00.00.00.0
Pavlov. Cond. magazine entry latency2.94.16.0-2.1-2.41.4
Pavlov. Cond. change in total contacts0.30.71.3-0.4-0.81.1
Pavlov. Cond. index score0.71.11.6-0.9-1.30.9
Pavlov. Cond. latency score0.50.81.1-0.8-1.10.8
Pavlov. Cond. lever contacts0.00.00.0-0.1-0.20.1
Pavlov. Cond. magazine entry number3.84.97.32.32.7-1.4
Pavlov. Cond. intertrial magazine entries0.71.62.41.41.5-0.5
Pavlov. Cond. lever-magazine prob. diff.1.01.52.2-1.2-1.50.9
Pavlov. Cond. response bias0.81.21.6-1.0-1.30.9
Time in closed arm before self-admin0.40.70.90.90.70.9
Time in closed arm after self-admin0.10.10.10.20.3-0.2
Time in open arm before self-admin0.50.70.9-0.7-0.7-1.0
Time in open arm after self-admin0.50.60.9-0.8-1.00.2
Bone: periosteal estimation0.10.20.30.60.40.4
Bone: periosteal perimeter0.20.41.10.50.01.1
Bone: post-yield work3.35.716.00.2-1.04.0
Progressive ratio test 1 active lever presses0.00.10.10.20.2-0.3
Progressive ratio test 1 breakpoint0.00.10.10.20.2-0.3
Progressive ratio test 1 inactive lever presses0.00.00.00.10.1-0.1
Progressive ratio test 2 active lever presses0.91.31.91.41.40.5
Progressive ratio test 2 breakpoint1.01.31.91.41.30.4
Progressive ratio test 2 inactive lever presses1.96.29.03.03.00.8
Incentive Sensitization - Responses0.10.41.0-0.2-0.31.0
Incentive Sensitization - Breakpoint0.10.30.90.0-0.11.0
Sum of active levers in priming session hrs 5-62.01.95.00.30.8-2.2
Progressive ratio1.33.96.5-1.3-1.92.5
Food seeking constrained by brief footshock0.20.20.3-0.4-0.60.4
Seeking ratio, punishment vs. effort1.12.53.31.21.6-1.8
Retroperitoneal fat weight5.625.239.16.36.00.6
Reaction time number correct0.10.40.9-0.4-0.3-1.0
Reaction time mean minus median0.32.23.7-1.6-1.90.6
Reaction time mean minus median AUC0.21.52.3-1.5-1.5-0.1
Reaction time num false alarms0.30.51.60.00.2-1.3
Reaction time num false alarms AUC0.30.71.1-0.7-0.6-1.1
Reaction time trials correct on left0.10.40.9-0.4-0.3-1.0
Reaction time trials on left0.10.51.1-0.5-0.4-1.0
Reaction time mean0.10.20.6-0.1-0.30.8
Reaction time mean AUC0.10.30.80.0-0.20.9
Median of all reaction times0.20.41.00.30.11.0
Reaction time omissions1.42.33.5-1.8-1.9-0.0
Reaction time false alarm rate0.10.20.5-0.3-0.1-0.7
Reaction time premature initiation rate1.92.94.3-2.1-2.1-0.1
Reaction time premature initiations1.33.85.6-2.4-2.3-0.9
Std. dev. reaction times0.20.71.2-0.8-1.10.6
Reaction time trials completed0.10.51.1-0.5-0.4-1.0
Reaction time trials AUC0.10.40.8-0.4-0.4-0.9
Run reversals in cocaine runway, females1.11.31.5-1.1-1.21.0
Run reversals in cocaine runway, males0.30.41.1-0.30.1-1.0
Latency to leave start box in cocaine runway0.50.61.90.2-0.11.4
Latency to leave start box in cocaine runway, F0.40.51.6-0.0-0.21.3
Latency to leave start box in cocaine runway, M0.00.00.1-0.0-0.10.2
Std. dev. time between licks in bursts0.40.82.1-0.6-0.3-1.4
Total sessions with >9 infusions0.20.20.2-0.5-0.40.4
Short access day 1 total inactive lever presses0.81.52.31.51.50.2
Short access day 10 total inactive lever presses0.00.00.0-0.0-0.00.2
Short access day 1 total infusions0.30.60.90.81.00.5
Short access day 10 total infusions0.61.03.0-0.1-0.31.7
Short access total infusions0.20.30.9-0.2-0.21.0
Short access day 1 locomotion0.40.71.11.10.90.5
Short access day 10 total locomotion0.10.61.10.70.51.0
Short access total locomotion0.50.71.01.00.70.8
One hour access (0.3 mA shock)3.03.55.22.32.20.7
Compulsive drug intake1.62.32.9-1.7-1.5-1.3
One hour access (shock baseline)2.36.09.03.02.90.8
Social response proportion0.50.71.0-0.7-1.00.7
Social responses0.20.30.4-0.5-0.6-0.5
Social time0.40.61.0-1.0-0.9-0.0
Soleus weight3.811.216.63.94.1-1.3
Bone: stiffness1.42.63.4-1.2-1.71.8
Tibialis anterior weight5.820.132.3-5.7-4.2-3.2
Time to tail flick, vehicle, before self-admin1.01.22.4-0.7-0.91.5
Time to tail flick, vehicle, after self-admin1.22.53.3-1.5-1.81.4
Time to tail flick, test, before self-admin1.01.12.90.60.21.7
Time to tail flick, test, after self-admin0.00.00.10.20.0-0.3
Delta time to tail flick, vehicle, before/after SA0.60.71.1-0.9-1.10.3
Delta time to tail flick, test, before/after SA1.72.15.8-0.6-0.0-2.4
Tibia length0.30.92.7-0.30.2-1.6
Ambulatory time before self-admin0.10.41.1-0.1-0.41.1
Ambulatory time after self-admin0.40.61.10.80.51.0
Bone: tissue strength0.20.20.30.30.20.6
Total heroin consumption3.03.65.6-2.4-2.3-0.2
Bone: trabecular number1.63.15.6-0.9-1.72.4
Bone: trabecular spacing0.60.91.30.61.0-1.1
Bone: trabecular thickness0.71.02.90.4-0.11.7
Bone: trabecular tissue density4.88.412.53.33.5-1.3
Water consumed over 24 hours0.61.21.7-1.2-1.30.6
Number of responses in last shaping day0.10.10.1-0.2-0.2-0.4