Atf4

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 gene expression Atf4 0.02 0.01 9.1e-04 0.02 0.02 0.01 0.01 1.6e-03 4.4e-04 2.9e-03 5.7e-03
2 Adipose mRNA stability Atf4 0.04 0.02 4.5e-04 0.02 0.03 0.03 0.03 1.6e-03 2.1e-04 4.6e-04 5.6e-04
3 LHb alternative TSS NM_024403.2 0.36 0.16 1.9e-03 0.13 0.09 0.04 0.1 4.5e-04 3.2e-03 4.7e-02 2.7e-03
4 LHb alternative TSS XM_039079942.2 0.35 0.16 1.6e-03 0.14 0.1 0.08 0.11 3.5e-04 2.7e-03 5.5e-03 1.3e-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 4
Bone: apparent density0.00.00.10.4-0.10.1-0.1
Area under the delay curve0.81.02.31.5-0.8-0.70.7
BMI with tail0.51.64.2-2.10.21.1-1.1
BMI without tail0.30.91.4-0.50.51.2-1.2
Body weight0.62.59.3-3.0-0.60.4-0.4
Weight adjusted by age0.20.20.50.30.70.4-0.4
Bone surface0.20.40.40.6-0.6-0.60.6
Bone volume0.00.00.10.1-0.3-0.00.0
Breakpoint value in progressive ratio session0.20.30.3-0.3-0.6-0.60.6
Number of licking bursts0.40.72.31.50.20.4-0.4
Context. condit. distance diff. score2.83.39.9-3.11.01.1-1.1
Locomotion velocity, session 11.31.41.90.5-1.4-1.31.3
Locomotion distance, session 11.41.86.42.5-0.5-0.40.4
Locomotion velocity, session 20.20.30.4-0.5-0.7-0.40.4
Locomotion distance, session 22.53.56.42.5-1.5-1.61.6
Locomotion velocity, session 31.51.82.2-0.91.41.5-1.5
Locomotion distance, session 32.73.03.61.21.81.9-1.9
Stereotopy head waving bouts, day 31.21.42.3-1.0-1.5-1.11.1
Stereotopy head waving duration, day 32.42.85.2-2.3-1.8-1.21.2
Locomotion velocity, session 70.20.31.0-1.00.20.1-0.1
Locomotion distance, session 70.70.81.30.0-0.9-1.11.1
Stereotopy head waving bouts, day 72.22.44.5-2.10.81.5-1.5
Stereotopy head waving duration, day 72.53.05.0-2.21.11.7-1.7
Locomotion velocity, session 81.11.32.6-1.6-1.2-0.80.8
Locomotion distance, session 80.30.40.9-0.90.70.4-0.4
Degree of sensitization distance4.74.85.9-1.8-2.0-2.42.4
Degree of sensitization stereotypy2.12.23.3-1.81.01.5-1.5
Conditioned locomotion0.10.10.5-0.7-0.0-0.20.2
Cocaine response after cond. corrected0.91.01.6-0.3-0.9-1.31.3
Cocaine response after cond. not corrected0.40.50.9-0.2-0.4-0.90.9
Cocaine response before conditioning0.91.01.40.31.11.2-1.2
Saline control response0.40.61.6-0.11.30.6-0.6
Bone: connectivity density0.10.20.30.1-0.5-0.50.5
Bone: cortical apparent density1.92.63.30.91.81.8-1.8
Bone: cortical area1.32.02.7-1.3-1.6-1.31.3
Bone: cortical porosity0.91.01.6-1.3-0.5-1.11.1
Bone: cortical porosity2.62.83.6-1.9-1.3-1.71.7
Bone: cortical thickness0.30.40.8-0.3-0.9-0.70.7
Bone: cortical thickness1.01.22.30.3-1.5-1.11.1
Bone: cortical tissue density1.72.32.90.81.71.7-1.7
Condit. Reinf. active minus inactive responses0.10.10.30.5-0.1-0.20.2
Condit. Reinf. active-inactive response ratio0.10.10.2-0.40.40.2-0.2
Condit. Reinf. active responses0.50.61.71.30.60.5-0.5
Condit. Reinf. inactive responses1.31.62.71.61.11.2-1.2
Incentive salience index mean0.10.20.70.80.0-0.10.1
Condit. Reinf. lever presses0.20.20.70.80.20.3-0.3
Condit. Reinf. active minus inactive responses1.72.32.90.6-1.7-1.71.7
Condit. Reinf. active-inactive response ratio1.92.23.0-0.1-1.7-1.71.7
Condit. Reinf. active responses1.41.92.7-0.1-1.6-1.61.6
Condit. Reinf. inactive responses0.20.30.5-0.4-0.7-0.50.5
Condit. Reinf. lever presses0.20.20.70.8-0.3-0.40.4
Condit. Reinf. lever reinforcers received1.52.12.9-0.0-1.6-1.71.7
Conditioned reinforcement - actives0.61.01.40.6-1.2-1.01.0
Conditioned reinforcement - inactives1.92.83.71.6-1.9-1.61.6
Conditioned locomotion2.12.84.4-0.3-2.1-1.81.8
Patch foraging indifference point 0 sec0.20.40.50.6-0.3-0.70.7
Patch foraging indifference point AUC0.81.23.71.9-0.8-0.40.4
Delay disc. indifference point, 0s delay0.80.91.0-0.9-0.8-1.01.0
Delay disc. indifference point, 16s delay1.11.23.92.0-0.5-0.50.5
Delay disc. indifference point, 2s delay0.40.50.60.8-0.7-0.60.6
Delay disc. indifference point, 24s delay0.70.81.51.2-1.1-0.50.5
Delay disc. indifference point, 4s delay0.70.70.80.9-0.9-0.80.8
Delay disc. indifference point, 8s delay0.80.93.11.8-0.5-0.30.3
Indifference point function ln k0.91.64.7-2.21.00.7-0.7
Indifference point function log k0.91.64.7-2.21.00.7-0.7
Patch foraging total patch changes 0 sec0.10.30.70.8-0.1-0.40.4
Patch foraging total patch changes 12 sec0.91.21.90.4-0.9-1.41.4
Patch foraging total patch changes 18 sec1.92.93.61.0-1.9-1.91.9
Patch foraging total patch changes 24 sec0.30.51.21.1-0.4-0.60.6
Patch foraging total patch changes 6 sec1.32.02.51.6-1.5-1.31.3
Patch foraging time to switch 0 sec0.20.40.7-0.8-0.3-0.70.7
Patch foraging water rate 0 sec0.10.10.40.6-0.3-0.10.1
Patch foraging water rate 12 sec0.30.61.00.51.00.7-0.7
Patch foraging water rate 18 sec0.20.31.31.10.0-0.10.1
Patch foraging water rate 24 sec0.10.20.6-0.80.30.2-0.2
Patch foraging water rate 6 sec1.11.62.71.11.61.2-1.2
Seeking ratio, delayed vs. immediate footshock0.70.91.20.80.71.1-1.1
Distance traveled before self-admin0.30.40.50.6-0.5-0.70.7
Distance traveled after self-admin1.92.43.10.7-1.6-1.81.8
Extensor digitorum longus weight0.41.41.61.31.11.2-1.2
Bone: elastic displacement0.00.00.1-0.20.1-0.10.1
Bone: elastic work2.22.93.0-1.7-1.7-1.71.7
Bone: endosteal estimation1.22.63.0-1.3-1.7-1.71.7
Bone: endosteal perimeter1.02.14.2-2.0-1.2-1.21.2
Epididymis fat weight1.34.517.4-4.2-0.6-0.20.2
Delta time in closed arm before/after self-admin0.30.30.5-0.1-0.7-0.50.5
Delta time in open arm before/after self-admin0.10.10.40.60.2-0.00.0
Diff in mean of infusions in LGA sessions0.50.61.2-0.3-1.1-0.70.7
Delay discount exponential model param0.80.92.5-1.60.70.6-0.6
Extinction: sum of active levers before priming1.21.32.2-0.8-1.5-1.11.1
Active lever presses in extinction session 60.30.30.4-0.6-0.6-0.50.5
Bone: final force2.03.24.8-1.3-2.2-1.81.8
Bone: final moment2.33.75.5-1.3-2.3-1.91.9
Food consumed during 24 hour testing period1.52.12.8-1.3-1.7-1.41.4
Glucose0.20.40.5-0.6-0.2-0.70.7
Heart weight1.92.95.6-2.4-1.8-1.21.2
Delay discount hyperbolic model param0.70.82.3-1.50.60.5-0.5
Intermittent access intake day 1-15 change0.20.50.60.50.70.8-0.8
Intermittent access intake escalation0.40.80.90.70.91.0-1.0
Intermittent access intake escalation 20.50.50.60.60.70.8-0.8
Intermitt. access day 1 inactive lever presses0.72.64.1-0.6-1.4-2.02.0
Intermitt. access day 15 inactive lever presses0.50.91.10.9-1.0-1.01.0
Intermitt. access escalation Index0.70.91.20.70.91.1-1.1
Intermittent access day 1 total infusions2.23.64.90.1-2.2-2.22.2
Intermittent access day 15 total infusions0.40.61.21.1-0.7-0.70.7
Intermittent access terminal intake (last 3 days)0.50.60.80.9-0.8-0.70.7
Intermittent access total infusions2.73.24.60.6-2.1-2.02.0
Intermittent access day 1 locomotion1.41.83.00.4-1.7-1.41.4
Intermittent access day 15 total locomotion0.81.52.8-0.3-1.7-1.31.3
Intermittent access total locomotion2.22.64.9-0.2-2.2-1.71.7
Intermittent access standard deviation1.73.65.5-0.5-1.7-2.32.3
Left kidney weight3.918.048.1-6.9-3.1-2.62.6
Right kidney weight4.922.259.1-7.7-3.5-2.92.9
Cocaine induced anxiety0.60.92.6-1.6-0.9-0.00.0
Post-drug Anxiety0.50.60.8-0.70.30.9-0.9
Baseline Anxiety1.01.22.71.61.10.6-0.6
Tail length0.20.60.70.60.80.8-0.8
Length with tail0.20.72.8-1.7-0.10.1-0.1
Length without tail1.34.19.3-3.0-1.8-1.41.4
Times rat made contact with spout0.10.10.40.3-0.60.1-0.1
Lifetime Intake4.04.87.20.1-2.7-2.52.5
Liver weight, left0.71.11.6-1.31.00.9-0.9
Liver weight, right3.05.37.3-2.72.12.2-2.2
Locomotor activity0.50.82.7-1.6-0.5-0.30.3
Locomotor testing distance0.10.20.30.30.40.5-0.5
Locomotor testing rearing0.40.72.4-1.5-0.4-0.40.4
Locomotion in novel chamber3.54.55.61.52.42.2-2.2
Locomotion in novel chamber post-restriction0.50.81.00.81.00.9-0.9
Fecal boli incidents, locomotor time 11.62.32.90.9-1.7-1.61.6
Change in fecal boli incidents, locomotor task0.70.70.9-0.60.61.0-1.0
Time >=10cm from walls, locomotor time 11.31.41.6-0.9-1.2-1.31.3
Bouts of movement, locomotor time 10.40.41.3-1.1-0.5-0.20.2
Total resting periods, locomotor time 10.50.60.8-0.9-0.8-0.70.7
Rest time, locomotor task time 11.31.61.8-1.0-1.3-1.31.3
Distance moved, locomotor task time 10.71.11.3-0.51.11.1-1.1
Vertical activity count, locomotor time 10.10.20.4-0.00.30.6-0.6
Time >=10cm from walls, locomotor time 20.10.10.20.0-0.4-0.30.3
Bouts of movement, locomotor time 20.30.40.5-0.70.40.7-0.7
Total resting periods, locomotor time 20.10.10.3-0.5-0.00.3-0.3
Rest time, locomotor task time 20.50.60.80.4-0.8-0.90.9
Distance moved, locomotor task time 20.40.50.8-0.90.80.5-0.5
Vertical activity count, locomotor time 20.10.10.3-0.6-0.10.1-0.1
Light reinforcement 10.00.10.10.4-0.3-0.30.3
Light reinforcement 20.81.32.1-1.41.01.0-1.0
Bone: marrow area1.32.83.3-1.3-1.8-1.81.8
Bone: maximum diameter2.85.26.7-2.6-2.4-2.12.1
Bone: maximum force3.15.69.0-1.5-3.0-2.32.3
Bone: maximum moment3.56.29.7-1.6-3.1-2.52.5
Mean time between licks in bursts0.20.50.91.00.90.4-0.4
Mean num. licks in bursts0.40.62.2-1.5-0.5-0.10.1
Cd content in liver0.10.10.1-0.4-0.20.2-0.2
Co content in liver0.60.60.80.9-0.9-0.70.7
Cu content in liver2.32.78.32.90.71.0-1.0
Fe content in liver1.41.72.0-1.4-1.3-1.21.2
K content in liver0.40.40.90.90.60.4-0.4
Mg content in liver0.10.10.50.7-0.10.1-0.1
Mn content in liver0.50.50.70.00.80.8-0.8
Na content in liver0.40.41.11.00.30.4-0.4
Rb content in liver0.70.81.70.3-1.3-0.80.8
Se content in liver2.22.73.80.51.71.9-1.9
Sr content in liver3.32.83.41.81.61.6-1.6
Zn content in liver0.20.30.40.40.20.6-0.6
Bone: minimum diameter1.22.12.6-1.0-1.5-1.61.6
Time in familiar zone, hab. session 10.60.60.90.3-0.9-0.90.9
Time in novel zone, hab. session 10.50.51.0-1.00.50.6-0.6
Total zone transitions, hab. session 12.73.86.52.51.81.7-1.7
Total locomotion distance, hab. session 11.62.32.91.71.71.3-1.3
Locomotion velocity, hab. session 11.41.93.71.91.31.1-1.1
Time in familiar zone, hab. session 21.51.62.20.11.51.4-1.4
Time in novel zone, hab. session 21.51.62.1-0.1-1.4-1.51.5
Total zone transitions, hab. session 21.11.53.21.8-1.0-0.90.9
Total locomotion distance, hab. session 21.21.62.51.6-0.8-1.31.3
Locomotion velocity, hab. session 21.41.93.71.9-0.8-1.31.3
Novel to familiar place preference ratio0.60.61.6-1.30.20.6-0.6
Novelty place preference1.01.12.4-1.60.40.9-0.9
Time in novel zone, NPP test1.21.33.0-1.70.31.0-1.0
Total zone transitions, NPP test1.72.58.42.90.80.7-0.7
Total locomotion distance, NPP test0.71.03.71.90.1-0.40.4
Locomotion velocity, NPP test0.91.24.82.20.4-0.20.2
Intraocular pressure0.30.51.1-1.0-0.3-0.60.6
Delta distance traveled before/after self-admin0.70.71.2-0.5-1.1-0.80.8
Delta ambulatory time before/after self-admin0.91.22.0-0.4-1.4-1.11.1
Parametrial fat weight0.82.02.7-0.41.51.7-1.7
Pavlov. Cond. lever latency0.10.10.2-0.4-0.30.1-0.1
Pavlov. Cond. magazine entry latency0.30.40.90.9-0.3-0.60.6
Pavlov. Cond. change in total contacts1.11.11.91.4-0.9-1.01.0
Pavlov. Cond. index score0.40.50.70.6-0.5-0.80.8
Pavlov. Cond. latency score0.20.30.30.5-0.3-0.60.6
Pavlov. Cond. lever contacts0.30.31.01.00.2-0.30.3
Pavlov. Cond. magazine entry number0.30.41.2-1.10.30.5-0.5
Pavlov. Cond. intertrial magazine entries0.50.61.91.4-0.4-0.30.3
Pavlov. Cond. lever-magazine prob. diff.0.30.30.40.7-0.3-0.60.6
Pavlov. Cond. response bias0.30.40.80.9-0.3-0.60.6
Pavlov. Cond. lever latency0.10.10.4-0.60.10.3-0.3
Pavlov. Cond. magazine entry latency1.21.43.01.7-0.9-1.01.0
Pavlov. Cond. change in total contacts2.54.05.70.1-2.2-2.42.4
Pavlov. Cond. index score0.60.91.51.2-0.7-0.90.9
Pavlov. Cond. latency score0.81.12.11.5-0.7-0.90.9
Pavlov. Cond. lever contacts0.10.20.50.7-0.0-0.20.2
Pavlov. Cond. magazine entry number0.40.51.2-1.10.50.5-0.5
Pavlov. Cond. intertrial magazine entries0.61.01.1-1.0-1.1-0.90.9
Pavlov. Cond. lever-magazine prob. diff.0.50.71.41.2-0.6-0.70.7
Pavlov. Cond. response bias0.50.60.70.9-0.7-0.80.8
Time in closed arm before self-admin0.60.72.81.70.20.1-0.1
Time in closed arm after self-admin0.30.30.5-0.2-0.7-0.50.5
Time in open arm before self-admin0.50.50.8-0.00.90.8-0.8
Time in open arm after self-admin1.21.41.70.61.31.3-1.3
Bone: periosteal estimation1.73.64.3-1.7-2.1-1.91.9
Bone: periosteal perimeter2.44.17.1-2.7-1.7-1.71.7
Bone: post-yield work1.52.15.40.2-2.3-1.31.3
Progressive ratio test 1 active lever presses2.22.74.30.4-2.1-1.81.8
Progressive ratio test 1 breakpoint1.92.33.60.5-1.9-1.61.6
Progressive ratio test 1 inactive lever presses3.55.07.20.5-2.3-2.72.7
Progressive ratio test 2 active lever presses2.12.43.70.5-1.9-1.71.7
Progressive ratio test 2 breakpoint2.02.33.40.6-1.8-1.61.6
Progressive ratio test 2 inactive lever presses0.61.02.11.5-0.8-0.70.7
Incentive Sensitization - Responses0.10.20.40.7-0.1-0.30.3
Incentive Sensitization - Breakpoint0.10.20.20.5-0.3-0.40.4
Sum of active levers in priming session hrs 5-60.00.00.0-0.10.0-0.20.2
Progressive ratio0.10.20.40.2-0.7-0.40.4
Food seeking constrained by brief footshock0.30.40.9-0.7-0.9-0.20.2
Seeking ratio, punishment vs. effort0.10.20.4-0.6-0.4-0.40.4
Retroperitoneal fat weight1.66.826.4-5.1-0.8-0.20.2
Reaction time number correct1.32.63.60.71.91.8-1.8
Reaction time mean minus median0.00.00.0-0.10.1-0.20.2
Reaction time mean minus median AUC0.10.30.9-1.00.3-0.10.1
Reaction time num false alarms0.10.20.3-0.00.60.5-0.5
Reaction time num false alarms AUC0.20.40.60.20.80.7-0.7
Reaction time trials correct on left1.32.63.60.71.91.8-1.8
Reaction time trials on left1.42.73.70.81.91.8-1.8
Reaction time mean0.00.00.0-0.10.20.0-0.0
Reaction time mean AUC0.00.00.0-0.10.20.1-0.1
Median of all reaction times0.00.00.1-0.00.20.1-0.1
Reaction time omissions0.20.20.70.90.50.1-0.1
Reaction time false alarm rate0.00.00.1-0.20.0-0.00.0
Reaction time premature initiation rate2.73.86.00.0-1.8-2.42.4
Reaction time premature initiations0.71.32.30.1-0.8-1.51.5
Std. dev. reaction times0.00.10.3-0.60.1-0.10.1
Reaction time trials completed1.42.73.70.81.91.8-1.8
Reaction time trials AUC1.12.12.90.51.71.6-1.6
Run reversals in cocaine runway, females0.20.20.60.30.80.4-0.4
Run reversals in cocaine runway, males0.20.20.3-0.4-0.5-0.30.3
Latency to leave start box in cocaine runway0.40.51.3-1.20.60.3-0.3
Latency to leave start box in cocaine runway, F0.00.00.1-0.20.30.0-0.0
Latency to leave start box in cocaine runway, M1.00.92.4-1.60.70.6-0.6
Std. dev. time between licks in bursts0.40.51.61.3-0.4-0.40.4
Total sessions with >9 infusions4.75.78.1-1.6-2.8-2.52.5
Short access day 1 total inactive lever presses5.87.611.40.3-3.4-3.13.1
Short access day 10 total inactive lever presses0.30.60.7-0.6-0.8-0.80.8
Short access day 1 total infusions2.22.94.2-0.4-2.1-1.91.9
Short access day 10 total infusions3.13.95.0-1.1-2.2-2.22.2
Short access total infusions4.86.19.5-1.0-3.1-2.72.7
Short access day 1 locomotion0.91.21.6-0.2-1.2-1.31.3
Short access day 10 total locomotion1.01.93.20.5-1.0-1.81.8
Short access total locomotion2.12.53.5-0.6-1.6-1.91.9
One hour access (0.3 mA shock)0.70.81.81.4-0.8-0.60.6
Compulsive drug intake0.50.61.91.40.10.4-0.4
One hour access (shock baseline)0.20.30.40.1-0.5-0.60.6
Social response proportion0.20.20.3-0.6-0.1-0.50.5
Social responses0.50.70.90.8-0.5-0.90.9
Social time1.01.33.61.9-0.1-0.90.9
Soleus weight0.31.01.51.2-0.9-1.01.0
Bone: stiffness2.03.35.2-1.4-2.3-1.71.7
Tibialis anterior weight0.51.76.22.50.30.4-0.4
Time to tail flick, vehicle, before self-admin0.30.30.50.1-0.7-0.70.7
Time to tail flick, vehicle, after self-admin0.20.20.80.90.30.1-0.1
Time to tail flick, test, before self-admin0.10.10.2-0.40.30.3-0.3
Time to tail flick, test, after self-admin0.80.81.20.60.71.1-1.1
Delta time to tail flick, vehicle, before/after SA0.20.20.30.2-0.4-0.50.5
Delta time to tail flick, test, before/after SA1.92.02.51.61.11.4-1.4
Tibia length0.82.12.7-1.2-1.7-1.51.5
Ambulatory time before self-admin0.20.20.91.00.1-0.10.1
Ambulatory time after self-admin0.80.92.11.5-0.7-0.70.7
Bone: tissue strength0.10.10.4-0.6-0.10.1-0.1
Total heroin consumption0.50.51.30.0-1.1-0.70.7
Bone: trabecular number0.20.30.4-0.20.60.6-0.6
Bone: trabecular spacing2.43.25.0-0.8-2.2-1.91.9
Bone: trabecular thickness0.91.11.6-0.01.21.2-1.2
Bone: trabecular tissue density0.71.11.61.30.91.0-1.0
Water consumed over 24 hours0.30.41.00.3-1.0-0.40.4
Number of responses in last shaping day2.62.93.90.6-1.8-2.02.0