Ythdf3

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 alternative polyA XM_063282042.1 0.05 0.04 1.3e-03 0.01 0.01 0.01 0.01 2.7e-02 1.8e-02 2.2e-02 4.0e-02
2 Adipose alternative polyA XM_006232168.3 0.06 0.05 5.0e-04 0.01 0.01 0.01 0.01 2.0e-02 2.6e-02 1.9e-02 3.8e-02
3 Adipose alternative polyA XM_063282040.1 0.06 0.05 2.9e-04 0.01 0.01 0.01 0.01 1.1e-02 8.7e-03 6.9e-03 1.7e-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 density0.40.71.11.10.7-0.7
Area under the delay curve0.40.61.2-1.1-0.60.5
BMI with tail2.89.711.5-3.4-3.02.9
BMI without tail1.26.48.2-2.9-2.42.3
Body weight2.29.512.9-3.6-2.92.7
Weight adjusted by age0.30.81.1-1.0-0.90.8
Bone surface0.10.30.4-0.4-0.60.6
Bone volume0.00.00.00.0-0.20.2
Breakpoint value in progressive ratio session0.00.00.1-0.30.0-0.0
Number of licking bursts0.72.13.5-1.9-1.21.1
Context. condit. distance diff. score0.10.10.3-0.50.0-0.0
Locomotion velocity, session 10.40.50.5-0.7-0.70.7
Locomotion distance, session 10.30.30.4-0.6-0.50.6
Locomotion velocity, session 23.03.64.7-2.2-1.71.7
Locomotion distance, session 20.40.50.5-0.7-0.70.7
Locomotion velocity, session 30.91.01.9-1.4-0.80.7
Locomotion distance, session 30.80.91.5-1.2-0.80.7
Stereotopy head waving bouts, day 30.30.40.80.90.5-0.4
Stereotopy head waving duration, day 30.30.40.80.90.4-0.3
Locomotion velocity, session 71.81.92.91.71.2-1.2
Locomotion distance, session 71.21.52.41.51.1-1.0
Stereotopy head waving bouts, day 70.20.20.6-0.8-0.10.0
Stereotopy head waving duration, day 70.10.10.4-0.6-0.10.1
Locomotion velocity, session 80.60.71.4-1.2-0.60.5
Locomotion distance, session 80.71.12.0-1.4-0.80.7
Degree of sensitization distance2.42.65.02.21.3-1.2
Degree of sensitization stereotypy0.91.02.5-1.6-0.60.5
Conditioned locomotion2.12.52.71.71.5-1.5
Cocaine response after cond. corrected0.10.10.10.2-0.30.4
Cocaine response after cond. not corrected0.10.10.10.3-0.30.3
Cocaine response before conditioning0.10.10.20.50.3-0.3
Saline control response0.30.50.7-0.9-0.60.6
Bone: connectivity density0.40.71.51.20.6-0.5
Bone: cortical apparent density0.40.60.7-0.9-0.70.7
Bone: cortical area0.10.10.2-0.50.1-0.2
Bone: cortical porosity0.30.30.60.80.4-0.4
Bone: cortical porosity0.20.20.40.60.4-0.4
Bone: cortical thickness0.71.21.70.71.2-1.3
Bone: cortical thickness1.31.61.9-1.4-1.31.2
Bone: cortical tissue density0.40.70.9-0.9-0.80.8
Condit. Reinf. active minus inactive responses0.10.10.1-0.00.3-0.4
Condit. Reinf. active-inactive response ratio0.00.00.0-0.1-0.00.0
Condit. Reinf. active responses0.00.00.0-0.20.1-0.1
Condit. Reinf. inactive responses0.10.10.1-0.3-0.30.3
Incentive salience index mean0.00.10.1-0.30.2-0.2
Condit. Reinf. lever presses0.30.40.6-0.8-0.50.5
Condit. Reinf. active minus inactive responses0.30.40.6-0.8-0.50.5
Condit. Reinf. active-inactive response ratio0.40.71.0-1.0-0.80.7
Condit. Reinf. active responses0.10.10.2-0.4-0.30.3
Condit. Reinf. inactive responses0.00.00.00.20.1-0.1
Condit. Reinf. lever presses0.60.80.80.90.9-0.9
Condit. Reinf. lever reinforcers received0.10.10.1-0.3-0.20.2
Conditioned reinforcement - actives0.00.00.00.10.1-0.1
Conditioned reinforcement - inactives0.00.00.0-0.2-0.20.2
Conditioned locomotion0.40.60.7-0.8-0.70.7
Patch foraging indifference point 0 sec0.10.40.7-0.10.8-0.8
Patch foraging indifference point AUC0.20.51.41.20.3-0.2
Delay disc. indifference point, 0s delay0.10.10.1-0.40.2-0.2
Delay disc. indifference point, 16s delay0.10.10.10.10.3-0.4
Delay disc. indifference point, 2s delay0.20.20.6-0.8-0.30.2
Delay disc. indifference point, 24s delay0.20.40.50.70.6-0.5
Delay disc. indifference point, 4s delay1.71.82.9-1.7-1.11.1
Delay disc. indifference point, 8s delay0.40.61.0-1.0-0.70.6
Indifference point function ln k0.82.43.4-1.8-1.41.3
Indifference point function log k0.82.43.4-1.8-1.41.3
Patch foraging total patch changes 0 sec0.10.20.2-0.40.4-0.5
Patch foraging total patch changes 12 sec0.20.30.30.60.5-0.5
Patch foraging total patch changes 18 sec0.20.40.60.80.6-0.5
Patch foraging total patch changes 24 sec0.20.60.70.80.8-0.7
Patch foraging total patch changes 6 sec0.00.00.00.10.1-0.1
Patch foraging time to switch 0 sec0.20.61.0-1.0-0.60.6
Patch foraging water rate 0 sec0.10.20.30.60.4-0.4
Patch foraging water rate 12 sec0.20.61.61.30.4-0.3
Patch foraging water rate 18 sec0.20.51.11.10.4-0.4
Patch foraging water rate 24 sec0.10.20.20.3-0.40.5
Patch foraging water rate 6 sec0.10.10.10.3-0.20.3
Seeking ratio, delayed vs. immediate footshock1.11.62.41.61.1-1.0
Distance traveled before self-admin1.63.55.6-2.4-1.61.5
Distance traveled after self-admin2.64.57.3-2.7-1.81.7
Extensor digitorum longus weight5.923.628.1-5.3-4.74.5
Bone: elastic displacement1.51.93.01.71.2-1.1
Bone: elastic work0.60.80.91.00.8-0.8
Bone: endosteal estimation2.05.05.7-2.4-2.22.2
Bone: endosteal perimeter0.61.52.7-1.6-1.00.9
Epididymis fat weight1.78.410.7-3.3-2.72.7
Delta time in closed arm before/after self-admin0.20.20.30.50.4-0.4
Delta time in open arm before/after self-admin0.81.01.0-1.0-1.01.0
Diff in mean of infusions in LGA sessions0.81.41.41.21.2-1.2
Delay discount exponential model param0.40.61.11.10.6-0.5
Extinction: sum of active levers before priming0.81.21.4-1.2-1.01.0
Active lever presses in extinction session 60.20.20.4-0.6-0.40.3
Bone: final force1.52.43.4-1.9-1.41.4
Bone: final moment1.11.82.7-1.6-1.21.2
Food consumed during 24 hour testing period1.63.25.2-2.3-1.61.4
Glucose0.10.20.4-0.7-0.40.3
Heart weight0.91.41.7-1.3-1.11.1
Delay discount hyperbolic model param0.60.71.41.20.7-0.6
Intermittent access intake day 1-15 change0.00.00.0-0.2-0.20.2
Intermittent access intake escalation0.00.00.0-0.2-0.20.2
Intermittent access intake escalation 20.00.00.00.20.0-0.0
Intermitt. access day 1 inactive lever presses0.10.70.9-1.0-0.80.8
Intermitt. access day 15 inactive lever presses0.00.00.0-0.0-0.10.1
Intermitt. access escalation Index0.00.10.20.40.4-0.3
Intermittent access day 1 total infusions0.00.00.10.20.1-0.1
Intermittent access day 15 total infusions0.20.50.80.90.6-0.6
Intermittent access terminal intake (last 3 days)0.10.10.20.40.2-0.2
Intermittent access total infusions0.20.30.40.60.4-0.4
Intermittent access day 1 locomotion0.40.70.8-0.9-0.80.8
Intermittent access day 15 total locomotion0.00.20.2-0.4-0.40.4
Intermittent access total locomotion0.40.40.4-0.7-0.70.7
Intermittent access standard deviation0.00.00.0-0.1-0.20.2
Left kidney weight0.54.25.0-2.2-2.01.9
Right kidney weight0.53.25.3-2.3-1.51.4
Cocaine induced anxiety0.10.30.30.60.5-0.5
Post-drug Anxiety0.40.40.40.70.6-0.6
Baseline Anxiety0.00.10.1-0.3-0.20.2
Tail length0.00.10.4-0.6-0.0-0.0
Length with tail0.52.23.8-2.0-1.21.1
Length without tail0.84.05.2-2.3-1.91.8
Times rat made contact with spout2.12.44.5-2.1-1.21.1
Lifetime Intake0.10.20.20.50.4-0.4
Liver weight, left0.71.32.1-1.5-0.90.9
Liver weight, right5.39.310.4-3.2-3.02.9
Locomotor activity1.93.03.6-1.9-1.71.6
Locomotor testing distance1.33.13.7-1.9-1.71.6
Locomotor testing rearing0.00.00.10.20.0-0.0
Locomotion in novel chamber0.00.00.1-0.00.3-0.3
Locomotion in novel chamber post-restriction0.00.10.10.40.3-0.3
Fecal boli incidents, locomotor time 10.61.61.8-1.1-1.31.3
Change in fecal boli incidents, locomotor task0.70.80.80.80.9-0.9
Time >=10cm from walls, locomotor time 10.00.00.10.0-0.20.2
Bouts of movement, locomotor time 10.10.20.2-0.2-0.40.4
Total resting periods, locomotor time 10.20.20.3-0.2-0.50.6
Rest time, locomotor task time 11.52.43.3-0.7-1.81.8
Distance moved, locomotor task time 10.51.42.20.21.4-1.5
Vertical activity count, locomotor time 10.42.84.30.42.0-2.1
Time >=10cm from walls, locomotor time 20.00.00.00.10.1-0.1
Bouts of movement, locomotor time 20.72.43.20.91.7-1.8
Total resting periods, locomotor time 20.41.42.00.61.4-1.4
Rest time, locomotor task time 20.50.81.1-0.5-1.01.0
Distance moved, locomotor task time 20.81.11.30.71.2-1.1
Vertical activity count, locomotor time 20.00.10.20.00.4-0.4
Light reinforcement 10.52.03.0-1.7-1.31.2
Light reinforcement 20.51.12.8-1.7-0.60.5
Bone: marrow area2.25.35.9-2.4-2.22.2
Bone: maximum diameter0.50.91.9-1.4-0.70.6
Bone: maximum force1.42.93.6-1.9-1.61.5
Bone: maximum moment1.22.22.8-1.7-1.41.4
Mean time between licks in bursts0.21.01.4-0.2-1.21.2
Mean num. licks in bursts0.30.70.80.90.8-0.8
Cd content in liver2.02.22.5-1.3-1.61.6
Co content in liver1.11.31.4-1.0-1.21.2
Cu content in liver0.10.20.40.60.2-0.2
Fe content in liver1.41.72.50.51.5-1.6
K content in liver0.90.91.00.91.0-1.0
Mg content in liver0.20.20.60.80.3-0.3
Mn content in liver0.20.20.3-0.5-0.40.4
Na content in liver0.10.10.2-0.20.4-0.4
Rb content in liver1.51.82.11.51.3-1.3
Se content in liver0.20.20.3-0.10.5-0.6
Sr content in liver0.20.20.20.5-0.30.4
Zn content in liver0.00.10.10.2-0.20.3
Bone: minimum diameter0.10.10.3-0.5-0.30.2
Time in familiar zone, hab. session 10.20.20.20.50.4-0.4
Time in novel zone, hab. session 10.10.10.2-0.1-0.40.4
Total zone transitions, hab. session 10.40.50.7-0.8-0.70.7
Total locomotion distance, hab. session 10.10.10.3-0.5-0.20.2
Locomotion velocity, hab. session 10.30.40.6-0.8-0.50.5
Time in familiar zone, hab. session 20.10.10.20.4-0.20.2
Time in novel zone, hab. session 20.20.20.30.50.4-0.4
Total zone transitions, hab. session 20.50.71.1-1.0-0.70.7
Total locomotion distance, hab. session 20.10.10.2-0.5-0.20.1
Locomotion velocity, hab. session 20.10.10.3-0.6-0.20.2
Novel to familiar place preference ratio2.22.93.01.71.7-1.7
Novelty place preference1.62.12.21.41.5-1.5
Time in novel zone, NPP test2.02.42.61.51.6-1.6
Total zone transitions, NPP test0.20.30.7-0.8-0.30.3
Total locomotion distance, NPP test0.10.20.4-0.6-0.30.3
Locomotion velocity, NPP test0.10.10.3-0.5-0.20.2
Intraocular pressure3.15.16.6-2.6-2.12.1
Delta distance traveled before/after self-admin0.10.10.10.30.3-0.3
Delta ambulatory time before/after self-admin0.30.50.70.90.7-0.6
Parametrial fat weight1.12.64.0-2.0-1.41.3
Pavlov. Cond. lever latency0.00.00.10.3-0.10.1
Pavlov. Cond. magazine entry latency1.01.31.3-1.1-1.11.1
Pavlov. Cond. change in total contacts0.80.91.4-1.2-0.80.8
Pavlov. Cond. index score1.11.52.0-1.4-1.11.1
Pavlov. Cond. latency score0.60.81.3-1.1-0.80.7
Pavlov. Cond. lever contacts0.20.20.4-0.7-0.40.4
Pavlov. Cond. magazine entry number2.02.52.81.71.5-1.5
Pavlov. Cond. intertrial magazine entries0.81.01.21.10.9-0.9
Pavlov. Cond. lever-magazine prob. diff.1.31.62.2-1.5-1.11.1
Pavlov. Cond. response bias1.51.92.4-1.6-1.31.3
Pavlov. Cond. lever latency1.52.12.2-1.4-1.51.5
Pavlov. Cond. magazine entry latency0.30.40.6-0.3-0.70.7
Pavlov. Cond. change in total contacts0.30.70.80.70.9-0.9
Pavlov. Cond. index score0.10.10.10.40.3-0.3
Pavlov. Cond. latency score0.00.10.10.30.2-0.2
Pavlov. Cond. lever contacts1.62.32.51.41.6-1.6
Pavlov. Cond. magazine entry number0.00.00.10.10.2-0.2
Pavlov. Cond. intertrial magazine entries0.00.00.1-0.1-0.20.2
Pavlov. Cond. lever-magazine prob. diff.0.00.00.10.20.1-0.2
Pavlov. Cond. response bias0.60.90.90.90.9-0.9
Time in closed arm before self-admin0.40.70.80.90.8-0.7
Time in closed arm after self-admin0.60.70.80.90.8-0.8
Time in open arm before self-admin0.00.00.10.10.2-0.3
Time in open arm after self-admin3.53.94.7-2.2-1.91.8
Bone: periosteal estimation1.02.43.4-1.9-1.41.3
Bone: periosteal perimeter0.20.51.3-1.1-0.40.3
Bone: post-yield work2.23.94.3-1.8-2.02.1
Progressive ratio test 1 active lever presses0.20.40.5-0.7-0.60.6
Progressive ratio test 1 breakpoint0.30.40.5-0.7-0.60.6
Progressive ratio test 1 inactive lever presses0.00.10.20.50.3-0.3
Progressive ratio test 2 active lever presses0.00.10.10.30.2-0.2
Progressive ratio test 2 breakpoint0.10.10.10.30.2-0.2
Progressive ratio test 2 inactive lever presses0.00.10.1-0.3-0.30.3
Incentive Sensitization - Responses0.20.50.60.80.6-0.6
Incentive Sensitization - Breakpoint0.20.40.60.70.6-0.6
Sum of active levers in priming session hrs 5-61.21.21.4-1.2-1.01.0
Progressive ratio0.10.20.50.70.4-0.3
Food seeking constrained by brief footshock0.20.30.80.9-0.10.2
Seeking ratio, punishment vs. effort0.10.20.2-0.2-0.50.5
Retroperitoneal fat weight1.15.15.1-2.3-2.32.2
Reaction time number correct0.20.91.31.10.8-0.8
Reaction time mean minus median1.38.69.4-2.6-3.13.1
Reaction time mean minus median AUC1.49.310.5-2.6-3.23.2
Reaction time num false alarms0.50.80.80.80.9-0.9
Reaction time num false alarms AUC0.20.40.40.60.6-0.6
Reaction time trials correct on left0.20.91.31.10.8-0.8
Reaction time trials on left0.20.71.21.10.7-0.7
Reaction time mean2.65.76.5-2.0-2.52.5
Reaction time mean AUC2.45.76.7-2.0-2.62.6
Median of all reaction times2.03.23.8-1.4-1.92.0
Reaction time omissions2.44.04.2-1.9-2.12.0
Reaction time false alarm rate0.00.10.1-0.00.3-0.3
Reaction time premature initiation rate0.00.00.10.30.1-0.0
Reaction time premature initiations0.00.10.20.50.1-0.1
Std. dev. reaction times2.37.68.2-2.5-2.92.9
Reaction time trials completed0.20.71.21.10.7-0.7
Reaction time trials AUC0.20.71.01.00.7-0.7
Run reversals in cocaine runway, females0.20.20.4-0.6-0.30.3
Run reversals in cocaine runway, males0.40.40.50.30.7-0.7
Latency to leave start box in cocaine runway0.00.00.0-0.10.0-0.0
Latency to leave start box in cocaine runway, F0.00.00.00.1-0.10.1
Latency to leave start box in cocaine runway, M0.00.00.1-0.30.1-0.1
Std. dev. time between licks in bursts0.00.10.20.50.0-0.0
Total sessions with >9 infusions0.20.20.4-0.6-0.40.4
Short access day 1 total inactive lever presses0.10.20.4-0.6-0.30.3
Short access day 10 total inactive lever presses0.21.52.01.41.1-1.1
Short access day 1 total infusions0.51.01.7-1.3-0.80.8
Short access day 10 total infusions0.30.40.50.60.7-0.7
Short access total infusions0.00.00.0-0.00.2-0.2
Short access day 1 locomotion0.61.01.6-1.3-0.80.8
Short access day 10 total locomotion0.10.40.6-0.8-0.60.6
Short access total locomotion1.01.52.1-1.5-1.11.0
One hour access (0.3 mA shock)0.00.00.10.30.2-0.2
Compulsive drug intake0.00.10.10.10.3-0.3
One hour access (shock baseline)0.30.81.31.10.8-0.7
Social response proportion0.60.80.8-0.9-0.90.9
Social responses1.11.41.6-1.2-1.21.1
Social time0.10.10.30.5-0.20.2
Soleus weight0.30.81.7-1.3-0.70.6
Bone: stiffness1.73.14.2-2.0-1.61.6
Tibialis anterior weight5.518.824.0-4.9-4.13.9
Time to tail flick, vehicle, before self-admin0.10.10.10.00.4-0.4
Time to tail flick, vehicle, after self-admin1.42.83.41.81.6-1.6
Time to tail flick, test, before self-admin0.10.10.1-0.3-0.20.2
Time to tail flick, test, after self-admin4.64.95.92.42.1-2.1
Delta time to tail flick, vehicle, before/after SA3.03.34.52.11.6-1.6
Delta time to tail flick, test, before/after SA0.91.11.51.21.0-0.9
Tibia length0.10.20.3-0.6-0.40.4
Ambulatory time before self-admin1.64.87.4-2.7-1.91.8
Ambulatory time after self-admin0.91.42.5-1.6-1.00.9
Bone: tissue strength0.10.10.10.30.4-0.4
Total heroin consumption0.00.00.00.10.1-0.1
Bone: trabecular number0.40.71.01.00.8-0.8
Bone: trabecular spacing0.00.00.00.10.1-0.1
Bone: trabecular thickness0.10.10.20.40.2-0.2
Bone: trabecular tissue density0.50.82.2-1.5-0.40.3
Water consumed over 24 hours0.30.51.0-1.0-0.50.5
Number of responses in last shaping day1.21.51.9-1.4-1.21.1