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 0.11 0.07 7.0e-02 6.2e-03 1.4e-03 8.0e-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 9.4e-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 6.8e-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 density1.93.26.30.8-1.62.5
Area under the delay curve0.50.51.40.2-0.41.2
BMI with tail2.27.58.92.5-3.02.7
BMI without tail1.44.16.12.2-2.51.2
Body weight2.410.415.53.9-3.90.8
Weight adjusted by age0.60.91.71.3-1.0-0.3
Bone surface3.46.28.12.2-2.82.4
Bone volume1.62.94.81.1-1.72.2
Breakpoint value in progressive ratio session1.72.03.11.8-1.70.1
Number of licking bursts0.00.10.1-0.1-0.20.4
Context. condit. distance diff. score0.80.91.7-1.31.00.4
Locomotion velocity, session 10.00.00.0-0.00.00.1
Locomotion distance, session 11.11.42.50.8-1.11.6
Locomotion velocity, session 21.72.03.31.8-1.6-0.1
Locomotion distance, session 21.01.31.71.3-1.30.8
Locomotion velocity, session 30.91.02.70.2-0.61.6
Locomotion distance, session 30.10.10.2-0.1-0.10.5
Stereotopy head waving bouts, day 30.70.82.2-0.3-0.11.5
Stereotopy head waving duration, day 30.60.71.1-0.90.61.1
Locomotion velocity, session 70.50.61.50.1-0.51.2
Locomotion distance, session 70.30.30.60.5-0.80.4
Stereotopy head waving bouts, day 70.70.82.4-0.3-0.21.5
Stereotopy head waving duration, day 71.21.42.30.8-1.21.5
Locomotion velocity, session 81.01.22.01.3-1.40.0
Locomotion distance, session 80.30.40.6-0.70.30.7
Degree of sensitization distance0.40.40.60.6-0.80.6
Degree of sensitization stereotypy0.50.50.90.4-0.71.0
Conditioned locomotion1.82.03.01.5-1.0-1.7
Cocaine response after cond. corrected0.10.10.1-0.40.20.3
Cocaine response after cond. not corrected0.20.20.5-0.30.10.7
Cocaine response before conditioning0.10.10.20.2-0.30.4
Saline control response2.43.24.92.2-2.10.1
Bone: connectivity density3.75.87.32.0-2.72.4
Bone: cortical apparent density0.30.40.60.6-0.3-0.8
Bone: cortical area0.40.60.80.8-0.5-0.9
Bone: cortical porosity0.00.00.00.2-0.20.2
Bone: cortical porosity0.20.20.40.6-0.60.0
Bone: cortical thickness3.05.06.82.6-1.8-2.2
Bone: cortical thickness1.31.52.51.6-1.2-0.9
Bone: cortical tissue density0.40.50.70.8-0.5-0.8
Condit. Reinf. active minus inactive responses0.30.30.60.3-0.50.8
Condit. Reinf. active-inactive response ratio0.10.10.4-0.1-0.10.6
Condit. Reinf. active responses0.00.00.1-0.0-0.10.3
Condit. Reinf. inactive responses0.10.10.2-0.40.4-0.2
Incentive salience index mean0.20.20.40.3-0.50.6
Condit. Reinf. lever presses0.00.00.0-0.0-0.0-0.1
Condit. Reinf. active minus inactive responses0.70.92.1-0.70.31.5
Condit. Reinf. active-inactive response ratio1.41.62.2-1.51.21.0
Condit. Reinf. active responses0.81.13.0-0.0-0.51.7
Condit. Reinf. inactive responses1.21.62.21.2-1.51.0
Condit. Reinf. lever presses1.01.31.60.9-1.31.3
Condit. Reinf. lever reinforcers received0.91.33.10.3-0.81.8
Conditioned reinforcement - actives0.40.81.1-0.60.9-1.1
Conditioned reinforcement - inactives1.92.84.4-2.11.90.4
Conditioned locomotion7.49.614.2-3.83.8-0.6
Patch foraging indifference point 0 sec0.20.30.6-0.80.50.2
Patch foraging indifference point AUC0.50.81.01.0-0.7-1.0
Delay disc. indifference point, 0s delay1.01.13.10.2-0.51.8
Delay disc. indifference point, 16s delay0.70.81.2-1.11.00.4
Delay disc. indifference point, 2s delay0.40.50.9-0.60.31.0
Delay disc. indifference point, 24s delay0.10.20.40.3-0.1-0.6
Delay disc. indifference point, 4s delay0.30.30.70.3-0.40.9
Delay disc. indifference point, 8s delay0.20.30.50.4-0.50.7
Indifference point function ln k2.64.57.2-2.72.5-0.0
Indifference point function log k2.64.57.2-2.72.5-0.0
Patch foraging total patch changes 0 sec0.10.10.2-0.50.3-0.3
Patch foraging total patch changes 12 sec1.72.23.41.9-1.8-0.2
Patch foraging total patch changes 18 sec0.20.30.50.6-0.70.2
Patch foraging total patch changes 24 sec0.40.70.90.9-0.8-0.7
Patch foraging total patch changes 6 sec0.91.32.01.2-1.40.7
Patch foraging time to switch 0 sec1.83.74.21.7-2.02.1
Patch foraging water rate 0 sec3.98.110.5-2.93.2-2.3
Patch foraging water rate 12 sec5.311.115.3-3.63.9-2.3
Patch foraging water rate 18 sec1.32.13.0-1.71.7-0.7
Patch foraging water rate 24 sec3.24.45.6-2.02.4-2.0
Patch foraging water rate 6 sec2.43.53.9-1.72.0-1.9
Seeking ratio, delayed vs. immediate footshock0.40.51.20.4-0.41.1
Distance traveled before self-admin0.20.30.60.2-0.40.8
Distance traveled after self-admin0.00.00.00.1-0.20.2
Extensor digitorum longus weight5.120.033.55.8-5.0-1.4
Bone: elastic displacement1.61.84.6-0.30.8-2.1
Bone: elastic work1.41.82.41.5-1.1-1.4
Bone: endosteal estimation1.12.33.0-1.71.11.6
Bone: endosteal perimeter2.34.86.4-2.51.62.3
Epididymis fat weight3.210.916.7-4.04.10.0
Delta time in closed arm before/after self-admin0.90.81.21.1-1.0-0.6
Delta time in open arm before/after self-admin0.20.20.5-0.1-0.10.7
Diff in mean of infusions in LGA sessions0.40.50.90.9-0.8-0.3
Delay discount exponential model param0.40.41.0-0.30.4-1.0
Extinction: sum of active levers before priming2.02.23.21.6-1.80.8
Active lever presses in extinction session 60.80.81.31.2-0.9-0.6
Bone: final force1.11.72.61.6-1.60.4
Bone: final moment1.01.62.51.6-1.50.3
Food consumed during 24 hour testing period0.40.50.7-0.80.8-0.5
Glucose1.72.64.7-1.51.02.2
Heart weight0.71.13.4-0.2-0.11.8
Delay discount hyperbolic model param0.40.41.1-0.20.3-1.1
Intermittent access intake day 1-15 change1.73.55.5-2.22.3-0.3
Intermittent access intake escalation1.53.14.9-2.12.2-0.4
Intermittent access intake escalation 22.02.23.6-1.81.9-0.2
Intermitt. access day 1 inactive lever presses0.00.00.0-0.10.1-0.1
Intermitt. access day 15 inactive lever presses0.61.21.3-1.21.11.0
Intermitt. access escalation Index2.33.34.6-2.12.1-0.8
Intermittent access day 1 total infusions1.32.15.0-1.00.72.2
Intermittent access day 15 total infusions3.55.27.5-2.72.61.0
Intermittent access terminal intake (last 3 days)2.93.84.9-2.22.11.4
Intermittent access total infusions1.92.22.4-1.51.41.5
Intermittent access day 1 locomotion0.81.02.0-0.90.61.4
Intermittent access day 15 total locomotion2.64.76.6-2.62.51.1
Intermittent access total locomotion4.95.98.1-2.92.71.5
Intermittent access standard deviation0.30.71.1-1.01.00.4
Left kidney weight0.73.35.1-2.32.20.3
Right kidney weight0.62.84.4-2.02.1-0.5
Cocaine induced anxiety0.10.10.2-0.2-0.00.4
Post-drug Anxiety0.40.40.60.7-0.80.3
Baseline Anxiety0.40.50.90.9-0.7-0.4
Tail length0.62.22.71.6-1.3-1.6
Length with tail1.66.910.53.2-2.8-1.5
Length without tail1.55.08.12.8-2.4-1.0
Times rat made contact with spout0.70.81.10.8-1.00.9
Lifetime Intake1.01.21.3-1.11.01.1
Liver weight, left0.50.91.1-0.91.0-0.9
Liver weight, right1.11.92.8-1.51.7-0.7
Locomotor activity0.91.42.0-1.31.4-0.7
Locomotor testing distance0.91.72.5-1.41.6-0.8
Locomotor testing rearing0.50.91.4-1.21.00.6
Locomotion in novel chamber4.25.48.0-2.82.70.8
Locomotion in novel chamber post-restriction2.33.86.1-2.52.30.3
Fecal boli incidents, locomotor time 10.10.10.1-0.40.3-0.1
Change in fecal boli incidents, locomotor task0.10.10.20.3-0.40.2
Time >=10cm from walls, locomotor time 11.51.62.9-1.20.71.7
Bouts of movement, locomotor time 10.60.71.20.7-0.6-1.1
Total resting periods, locomotor time 10.30.41.00.3-0.2-1.0
Rest time, locomotor task time 11.82.23.5-1.61.9-0.9
Distance moved, locomotor task time 10.60.81.70.5-0.71.3
Vertical activity count, locomotor time 10.30.60.8-0.80.60.9
Time >=10cm from walls, locomotor time 20.20.30.4-0.50.6-0.5
Bouts of movement, locomotor time 20.20.30.50.6-0.7-0.2
Total resting periods, locomotor time 20.10.10.20.3-0.50.0
Rest time, locomotor task time 21.21.62.1-1.51.31.0
Distance moved, locomotor task time 20.70.81.01.0-0.6-1.0
Vertical activity count, locomotor time 20.91.23.50.00.3-1.9
Light reinforcement 10.41.01.6-1.01.3-0.5
Light reinforcement 21.72.64.2-1.82.1-0.5
Bone: marrow area1.12.43.2-1.81.11.7
Bone: maximum diameter0.10.20.3-0.60.6-0.2
Bone: maximum force2.03.54.41.7-2.11.7
Bone: maximum moment1.83.14.11.7-2.01.6
Mean time between licks in bursts0.20.60.90.9-0.9-0.2
Mean num. licks in bursts0.10.10.10.3-0.20.3
Cd content in liver1.51.72.8-1.71.50.2
Co content in liver1.41.62.9-0.61.2-1.7
Cu content in liver0.00.00.1-0.10.2-0.2
Fe content in liver0.10.10.30.5-0.3-0.2
K content in liver0.60.60.70.8-0.80.6
Mg content in liver0.30.30.5-0.50.40.7
Mn content in liver1.71.82.91.7-1.6-0.0
Na content in liver0.40.41.0-0.20.4-1.0
Rb content in liver0.91.01.4-1.00.81.2
Se content in liver0.20.30.6-0.30.20.8
Sr content in liver1.51.31.81.3-1.0-1.1
Zn content in liver0.30.40.50.6-0.4-0.7
Bone: minimum diameter1.12.04.0-1.30.52.0
Time in familiar zone, hab. session 10.50.50.7-0.80.50.6
Time in novel zone, hab. session 10.10.10.10.3-0.1-0.3
Total zone transitions, hab. session 10.40.50.80.9-0.80.3
Total locomotion distance, hab. session 10.30.40.6-0.80.70.4
Locomotion velocity, hab. session 10.10.10.1-0.30.40.2
Time in familiar zone, hab. session 20.30.40.80.4-0.4-0.9
Time in novel zone, hab. session 20.50.51.50.1-0.21.2
Total zone transitions, hab. session 23.03.95.71.4-2.02.4
Total locomotion distance, hab. session 20.70.92.50.2-0.51.6
Locomotion velocity, hab. session 20.60.82.3-0.2-0.11.5
Novel to familiar place preference ratio0.40.40.60.5-0.60.8
Novelty place preference0.30.30.70.2-0.30.8
Time in novel zone, NPP test0.30.30.70.2-0.40.9
Total zone transitions, NPP test1.11.62.21.1-1.51.2
Total locomotion distance, NPP test0.20.20.7-0.1-0.10.8
Locomotion velocity, NPP test0.10.10.4-0.20.00.6
Intraocular pressure1.01.41.7-1.01.3-1.3
Delta distance traveled before/after self-admin0.10.10.30.00.1-0.5
Delta ambulatory time before/after self-admin0.10.10.40.2-0.0-0.6
Parametrial fat weight2.04.87.5-2.72.41.1
Pavlov. Cond. lever latency0.20.30.5-0.50.7-0.3
Pavlov. Cond. magazine entry latency0.40.61.5-0.4-0.21.2
Pavlov. Cond. change in total contacts0.40.40.6-0.70.40.8
Pavlov. Cond. index score0.10.10.2-0.40.10.2
Pavlov. Cond. latency score0.10.10.2-0.2-0.10.4
Pavlov. Cond. lever contacts0.10.10.10.1-0.30.3
Pavlov. Cond. magazine entry number0.10.10.30.5-0.3-0.0
Pavlov. Cond. intertrial magazine entries0.40.50.9-0.40.7-1.0
Pavlov. Cond. lever-magazine prob. diff.0.10.10.1-0.40.10.3
Pavlov. Cond. response bias0.10.10.2-0.40.2-0.1
Pavlov. Cond. lever latency0.00.00.0-0.00.00.0
Pavlov. Cond. magazine entry latency3.44.16.02.1-2.41.4
Pavlov. Cond. change in total contacts0.40.71.30.4-0.81.1
Pavlov. Cond. index score0.81.11.60.9-1.30.9
Pavlov. Cond. latency score0.60.81.10.8-1.10.8
Pavlov. Cond. lever contacts0.00.00.00.1-0.20.1
Pavlov. Cond. magazine entry number4.04.97.3-2.32.7-1.4
Pavlov. Cond. intertrial magazine entries1.01.62.4-1.41.5-0.5
Pavlov. Cond. lever-magazine prob. diff.1.11.52.21.2-1.50.9
Pavlov. Cond. response bias0.91.21.61.0-1.30.9
Time in closed arm before self-admin0.60.70.9-0.90.70.9
Time in closed arm after self-admin0.10.10.1-0.20.3-0.2
Time in open arm before self-admin0.60.70.90.7-0.7-1.0
Time in open arm after self-admin0.50.60.90.8-1.00.2
Bone: periosteal estimation0.10.20.3-0.60.40.4
Bone: periosteal perimeter0.30.41.1-0.50.01.1
Bone: post-yield work3.95.716.0-0.2-1.04.0
Progressive ratio test 1 active lever presses0.00.10.1-0.20.2-0.3
Progressive ratio test 1 breakpoint0.00.10.1-0.20.2-0.3
Progressive ratio test 1 inactive lever presses0.00.00.0-0.10.1-0.1
Progressive ratio test 2 active lever presses1.11.31.9-1.41.40.5
Progressive ratio test 2 breakpoint1.11.31.9-1.41.30.4
Progressive ratio test 2 inactive lever presses3.86.29.0-3.03.00.8
Incentive Sensitization - Responses0.30.41.00.2-0.31.0
Incentive Sensitization - Breakpoint0.20.30.9-0.0-0.11.0
Sum of active levers in priming session hrs 5-62.11.95.0-0.30.8-2.2
Progressive ratio2.53.96.51.3-1.92.5
Food seeking constrained by brief footshock0.20.20.30.4-0.60.4
Seeking ratio, punishment vs. effort1.72.53.3-1.21.6-1.8
Retroperitoneal fat weight5.925.239.1-6.36.00.6
Reaction time number correct0.20.40.90.4-0.3-1.0
Reaction time mean minus median0.92.23.71.6-1.90.6
Reaction time mean minus median AUC0.61.52.31.5-1.5-0.1
Reaction time num false alarms0.40.51.6-0.00.2-1.3
Reaction time num false alarms AUC0.40.71.10.7-0.6-1.1
Reaction time trials correct on left0.20.40.90.4-0.3-1.0
Reaction time trials on left0.30.51.10.5-0.4-1.0
Reaction time mean0.10.20.60.1-0.30.8
Reaction time mean AUC0.20.30.8-0.0-0.20.9
Median of all reaction times0.30.41.0-0.30.11.0
Reaction time omissions1.62.33.51.8-1.9-0.0
Reaction time false alarm rate0.10.20.50.3-0.1-0.7
Reaction time premature initiation rate2.12.94.32.1-2.1-0.1
Reaction time premature initiations2.23.85.62.4-2.3-0.9
Std. dev. reaction times0.40.71.20.8-1.10.6
Reaction time trials completed0.30.51.10.5-0.4-1.0
Reaction time trials AUC0.20.40.80.4-0.4-0.9
Run reversals in cocaine runway, females1.31.31.51.1-1.21.0
Run reversals in cocaine runway, males0.40.41.10.30.1-1.0
Latency to leave start box in cocaine runway0.60.61.9-0.2-0.11.4
Latency to leave start box in cocaine runway, F0.50.51.60.0-0.21.3
Latency to leave start box in cocaine runway, M0.00.00.10.0-0.10.2
Std. dev. time between licks in bursts0.60.82.10.6-0.3-1.4
Total sessions with >9 infusions0.20.20.20.5-0.40.4
Short access day 1 total inactive lever presses1.21.52.3-1.51.50.2
Short access day 10 total inactive lever presses0.00.00.00.0-0.00.2
Short access day 1 total infusions0.50.60.9-0.81.00.5
Short access day 10 total infusions0.81.03.00.1-0.31.7
Short access total infusions0.30.30.90.2-0.21.0
Short access day 1 locomotion0.60.71.1-1.10.90.5
Short access day 10 total locomotion0.30.61.1-0.70.51.0
Short access total locomotion0.60.71.0-1.00.70.8
One hour access (0.3 mA shock)3.03.55.2-2.32.20.7
Compulsive drug intake1.92.32.91.7-1.5-1.3
One hour access (shock baseline)4.06.09.0-3.02.90.8
Social response proportion0.60.71.00.7-1.00.7
Social responses0.20.30.40.6-0.6-0.5
Social time0.50.61.01.0-0.9-0.0
Soleus weight3.811.216.6-3.94.1-1.3
Bone: stiffness1.62.63.41.2-1.71.8
Tibialis anterior weight5.920.132.35.7-4.2-3.2
Time to tail flick, vehicle, before self-admin1.21.22.40.7-0.91.5
Time to tail flick, vehicle, after self-admin1.92.53.31.5-1.81.4
Time to tail flick, test, before self-admin1.11.12.9-0.60.21.7
Time to tail flick, test, after self-admin0.00.00.1-0.20.0-0.3
Delta time to tail flick, vehicle, before/after SA0.70.71.10.9-1.10.3
Delta time to tail flick, test, before/after SA2.02.15.80.6-0.0-2.4
Tibia length0.30.92.70.30.2-1.6
Ambulatory time before self-admin0.30.41.10.1-0.41.1
Ambulatory time after self-admin0.50.61.1-0.80.51.0
Bone: tissue strength0.20.20.3-0.30.20.6
Total heroin consumption3.03.65.62.4-2.3-0.2
Bone: trabecular number1.93.15.60.9-1.72.4
Bone: trabecular spacing0.60.91.3-0.61.0-1.1
Bone: trabecular thickness0.81.02.9-0.4-0.11.7
Bone: trabecular tissue density5.78.412.5-3.33.5-1.3
Water consumed over 24 hours0.91.21.71.2-1.30.6
Number of responses in last shaping day0.10.10.10.2-0.2-0.4