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 5.6e-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 1.4e-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 density0.00.00.10.4-0.1-0.10.1
Area under the delay curve0.61.02.31.5-0.80.7-0.7
BMI with tail0.51.64.2-2.10.2-1.11.1
BMI without tail0.20.91.4-0.50.5-1.21.2
Body weight0.62.59.3-3.0-0.6-0.40.4
Weight adjusted by age0.10.20.50.30.7-0.40.4
Bone surface0.20.40.40.6-0.60.6-0.6
Bone volume0.00.00.10.1-0.30.0-0.0
Breakpoint value in progressive ratio session0.10.30.3-0.3-0.60.6-0.6
Number of licking bursts0.20.72.31.50.2-0.40.4
Context. condit. distance diff. score2.83.39.9-3.11.0-1.11.1
Locomotion velocity, session 11.21.41.90.5-1.41.3-1.3
Locomotion distance, session 11.41.86.42.5-0.50.4-0.4
Locomotion velocity, session 20.20.30.4-0.5-0.70.4-0.4
Locomotion distance, session 22.53.56.42.5-1.51.6-1.6
Locomotion velocity, session 31.51.82.2-0.91.4-1.51.5
Locomotion distance, session 32.63.03.61.21.8-1.91.9
Stereotopy head waving bouts, day 31.21.42.3-1.0-1.51.1-1.1
Stereotopy head waving duration, day 32.32.85.2-2.3-1.81.2-1.2
Locomotion velocity, session 70.20.31.0-1.00.2-0.10.1
Locomotion distance, session 70.70.81.30.0-0.91.1-1.1
Stereotopy head waving bouts, day 72.12.44.5-2.10.8-1.51.5
Stereotopy head waving duration, day 72.53.05.0-2.21.1-1.71.7
Locomotion velocity, session 81.11.32.6-1.6-1.20.8-0.8
Locomotion distance, session 80.30.40.9-0.90.7-0.40.4
Degree of sensitization distance4.54.85.9-1.8-2.02.4-2.4
Degree of sensitization stereotypy2.02.23.3-1.81.0-1.51.5
Conditioned locomotion0.10.10.5-0.7-0.00.2-0.2
Cocaine response after cond. corrected0.71.01.6-0.3-0.91.3-1.3
Cocaine response after cond. not corrected0.30.50.9-0.2-0.40.9-0.9
Cocaine response before conditioning0.91.01.40.31.1-1.21.2
Saline control response0.40.61.6-0.11.3-0.60.6
Bone: connectivity density0.10.20.30.1-0.50.5-0.5
Bone: cortical apparent density1.72.63.30.91.8-1.81.8
Bone: cortical area1.22.02.7-1.3-1.61.3-1.3
Bone: cortical porosity0.91.01.6-1.3-0.51.1-1.1
Bone: cortical porosity2.52.83.6-1.9-1.31.7-1.7
Bone: cortical thickness0.30.40.8-0.3-0.90.7-0.7
Bone: cortical thickness1.01.22.30.3-1.51.1-1.1
Bone: cortical tissue density1.52.32.90.81.7-1.71.7
Condit. Reinf. active minus inactive responses0.10.10.30.5-0.10.2-0.2
Condit. Reinf. active-inactive response ratio0.10.10.2-0.40.4-0.20.2
Condit. Reinf. active responses0.50.61.71.30.6-0.50.5
Condit. Reinf. inactive responses1.31.62.71.61.1-1.21.2
Incentive salience index mean0.10.20.70.80.00.1-0.1
Condit. Reinf. lever presses0.20.20.70.80.2-0.30.3
Condit. Reinf. active minus inactive responses1.52.32.90.6-1.71.7-1.7
Condit. Reinf. active-inactive response ratio1.42.23.0-0.1-1.71.7-1.7
Condit. Reinf. active responses1.41.92.7-0.1-1.61.6-1.6
Condit. Reinf. inactive responses0.20.30.5-0.4-0.70.5-0.5
Condit. Reinf. lever presses0.20.20.70.8-0.30.4-0.4
Condit. Reinf. lever reinforcers received1.52.12.9-0.0-1.61.7-1.7
Conditioned reinforcement - actives0.21.01.40.6-1.21.0-1.0
Conditioned reinforcement - inactives1.02.83.71.6-1.91.6-1.6
Conditioned locomotion1.92.84.4-0.3-2.11.8-1.8
Patch foraging indifference point 0 sec0.10.40.50.6-0.30.7-0.7
Patch foraging indifference point AUC0.51.23.71.9-0.80.4-0.4
Delay disc. indifference point, 0s delay0.80.91.0-0.9-0.81.0-1.0
Delay disc. indifference point, 16s delay0.81.23.92.0-0.50.5-0.5
Delay disc. indifference point, 2s delay0.40.50.60.8-0.70.6-0.6
Delay disc. indifference point, 24s delay0.50.81.51.2-1.10.5-0.5
Delay disc. indifference point, 4s delay0.70.70.80.9-0.90.8-0.8
Delay disc. indifference point, 8s delay0.50.93.11.8-0.50.3-0.3
Indifference point function ln k0.51.64.7-2.21.0-0.70.7
Indifference point function log k0.51.64.7-2.21.0-0.70.7
Patch foraging total patch changes 0 sec0.10.30.70.8-0.10.4-0.4
Patch foraging total patch changes 12 sec0.91.21.90.4-0.91.4-1.4
Patch foraging total patch changes 18 sec1.22.93.61.0-1.91.9-1.9
Patch foraging total patch changes 24 sec0.20.51.21.1-0.40.6-0.6
Patch foraging total patch changes 6 sec1.22.02.51.6-1.51.3-1.3
Patch foraging time to switch 0 sec0.10.40.7-0.8-0.30.7-0.7
Patch foraging water rate 0 sec0.00.10.40.6-0.30.1-0.1
Patch foraging water rate 12 sec0.10.61.00.51.0-0.70.7
Patch foraging water rate 18 sec0.10.31.31.10.00.1-0.1
Patch foraging water rate 24 sec0.10.20.6-0.80.3-0.20.2
Patch foraging water rate 6 sec1.11.62.71.11.6-1.21.2
Seeking ratio, delayed vs. immediate footshock0.60.91.20.80.7-1.11.1
Distance traveled before self-admin0.20.40.50.6-0.50.7-0.7
Distance traveled after self-admin1.32.43.10.7-1.61.8-1.8
Extensor digitorum longus weight0.31.41.61.31.1-1.21.2
Bone: elastic displacement0.00.00.1-0.20.10.1-0.1
Bone: elastic work2.22.93.0-1.7-1.71.7-1.7
Bone: endosteal estimation1.12.63.0-1.3-1.71.7-1.7
Bone: endosteal perimeter0.92.14.2-2.0-1.21.2-1.2
Epididymis fat weight0.94.517.4-4.2-0.60.2-0.2
Delta time in closed arm before/after self-admin0.30.30.5-0.1-0.70.5-0.5
Delta time in open arm before/after self-admin0.10.10.40.60.20.0-0.0
Diff in mean of infusions in LGA sessions0.30.61.2-0.3-1.10.7-0.7
Delay discount exponential model param0.70.92.5-1.60.7-0.60.6
Extinction: sum of active levers before priming0.91.32.2-0.8-1.51.1-1.1
Active lever presses in extinction session 60.30.30.4-0.6-0.60.5-0.5
Bone: final force1.93.24.8-1.3-2.21.8-1.8
Bone: final moment2.33.75.5-1.3-2.31.9-1.9
Food consumed during 24 hour testing period1.02.12.8-1.3-1.71.4-1.4
Glucose0.20.40.5-0.6-0.20.7-0.7
Heart weight1.82.95.6-2.4-1.81.2-1.2
Delay discount hyperbolic model param0.60.82.3-1.50.6-0.50.5
Intermittent access intake day 1-15 change0.10.50.60.50.7-0.80.8
Intermittent access intake escalation0.10.80.90.70.9-1.01.0
Intermittent access intake escalation 20.30.50.60.60.7-0.80.8
Intermitt. access day 1 inactive lever presses0.22.64.1-0.6-1.42.0-2.0
Intermitt. access day 15 inactive lever presses0.20.91.10.9-1.01.0-1.0
Intermitt. access escalation Index0.30.91.20.70.9-1.11.1
Intermittent access day 1 total infusions1.23.64.90.1-2.22.2-2.2
Intermittent access day 15 total infusions0.30.61.21.1-0.70.7-0.7
Intermittent access terminal intake (last 3 days)0.40.60.80.9-0.80.7-0.7
Intermittent access total infusions2.73.24.60.6-2.12.0-2.0
Intermittent access day 1 locomotion1.01.83.00.4-1.71.4-1.4
Intermittent access day 15 total locomotion0.41.52.8-0.3-1.71.3-1.3
Intermittent access total locomotion2.22.64.9-0.2-2.21.7-1.7
Intermittent access standard deviation0.73.65.5-0.5-1.72.3-2.3
Left kidney weight2.218.048.1-6.9-3.12.6-2.6
Right kidney weight3.222.259.1-7.7-3.52.9-2.9
Cocaine induced anxiety0.30.92.6-1.6-0.90.0-0.0
Post-drug Anxiety0.50.60.8-0.70.3-0.90.9
Baseline Anxiety0.71.22.71.61.1-0.60.6
Tail length0.10.60.70.60.8-0.80.8
Length with tail0.20.72.8-1.7-0.1-0.10.1
Length without tail0.84.19.3-3.0-1.81.4-1.4
Times rat made contact with spout0.10.10.40.3-0.6-0.10.1
Lifetime Intake3.94.87.20.1-2.72.5-2.5
Liver weight, left0.61.11.6-1.31.0-0.90.9
Liver weight, right3.05.37.3-2.72.1-2.22.2
Locomotor activity0.50.82.7-1.6-0.50.3-0.3
Locomotor testing distance0.10.20.30.30.4-0.50.5
Locomotor testing rearing0.20.72.4-1.5-0.40.4-0.4
Locomotion in novel chamber3.34.55.61.52.4-2.22.2
Locomotion in novel chamber post-restriction0.30.81.00.81.0-0.90.9
Fecal boli incidents, locomotor time 10.92.32.90.9-1.71.6-1.6
Change in fecal boli incidents, locomotor task0.60.70.9-0.60.6-1.01.0
Time >=10cm from walls, locomotor time 11.11.41.6-0.9-1.21.3-1.3
Bouts of movement, locomotor time 10.30.41.3-1.1-0.50.2-0.2
Total resting periods, locomotor time 10.50.60.8-0.9-0.80.7-0.7
Rest time, locomotor task time 11.01.61.8-1.0-1.31.3-1.3
Distance moved, locomotor task time 10.41.11.3-0.51.1-1.11.1
Vertical activity count, locomotor time 10.00.20.4-0.00.3-0.60.6
Time >=10cm from walls, locomotor time 20.00.10.20.0-0.40.3-0.3
Bouts of movement, locomotor time 20.10.40.5-0.70.4-0.70.7
Total resting periods, locomotor time 20.00.10.3-0.5-0.0-0.30.3
Rest time, locomotor task time 20.40.60.80.4-0.80.9-0.9
Distance moved, locomotor task time 20.40.50.8-0.90.8-0.50.5
Vertical activity count, locomotor time 20.00.10.3-0.6-0.1-0.10.1
Light reinforcement 10.00.10.10.4-0.30.3-0.3
Light reinforcement 20.61.32.1-1.41.0-1.01.0
Bone: marrow area1.22.83.3-1.3-1.81.8-1.8
Bone: maximum diameter2.65.26.7-2.6-2.42.1-2.1
Bone: maximum force2.85.69.0-1.5-3.02.3-2.3
Bone: maximum moment3.36.29.7-1.6-3.12.5-2.5
Mean time between licks in bursts0.10.50.91.00.9-0.40.4
Mean num. licks in bursts0.20.62.2-1.5-0.50.1-0.1
Cd content in liver0.10.10.1-0.4-0.2-0.20.2
Co content in liver0.50.60.80.9-0.90.7-0.7
Cu content in liver2.32.78.32.90.7-1.01.0
Fe content in liver1.31.72.0-1.4-1.31.2-1.2
K content in liver0.40.40.90.90.6-0.40.4
Mg content in liver0.10.10.50.7-0.1-0.10.1
Mn content in liver0.50.50.70.00.8-0.80.8
Na content in liver0.30.41.11.00.3-0.40.4
Rb content in liver0.70.81.70.3-1.30.8-0.8
Se content in liver2.22.73.80.51.7-1.91.9
Sr content in liver3.32.83.41.81.6-1.61.6
Zn content in liver0.20.30.40.40.2-0.60.6
Bone: minimum diameter1.12.12.6-1.0-1.51.6-1.6
Time in familiar zone, hab. session 10.50.60.90.3-0.90.9-0.9
Time in novel zone, hab. session 10.40.51.0-1.00.5-0.60.6
Total zone transitions, hab. session 12.73.86.52.51.8-1.71.7
Total locomotion distance, hab. session 11.62.32.91.71.7-1.31.3
Locomotion velocity, hab. session 11.41.93.71.91.3-1.11.1
Time in familiar zone, hab. session 21.41.62.20.11.5-1.41.4
Time in novel zone, hab. session 21.41.62.1-0.1-1.41.5-1.5
Total zone transitions, hab. session 21.11.53.21.8-1.00.9-0.9
Total locomotion distance, hab. session 21.21.62.51.6-0.81.3-1.3
Locomotion velocity, hab. session 21.41.93.71.9-0.81.3-1.3
Novel to familiar place preference ratio0.50.61.6-1.30.2-0.60.6
Novelty place preference0.81.12.4-1.60.4-0.90.9
Time in novel zone, NPP test1.11.33.0-1.70.3-1.01.0
Total zone transitions, NPP test1.72.58.42.90.8-0.70.7
Total locomotion distance, NPP test0.71.03.71.90.10.4-0.4
Locomotion velocity, NPP test0.91.24.82.20.40.2-0.2
Intraocular pressure0.30.51.1-1.0-0.30.6-0.6
Delta distance traveled before/after self-admin0.70.71.2-0.5-1.10.8-0.8
Delta ambulatory time before/after self-admin0.71.22.0-0.4-1.41.1-1.1
Parametrial fat weight0.82.02.7-0.41.5-1.71.7
Pavlov. Cond. lever latency0.10.10.2-0.4-0.3-0.10.1
Pavlov. Cond. magazine entry latency0.30.40.90.9-0.30.6-0.6
Pavlov. Cond. change in total contacts1.01.11.91.4-0.91.0-1.0
Pavlov. Cond. index score0.40.50.70.6-0.50.8-0.8
Pavlov. Cond. latency score0.20.30.30.5-0.30.6-0.6
Pavlov. Cond. lever contacts0.30.31.01.00.20.3-0.3
Pavlov. Cond. magazine entry number0.30.41.2-1.10.3-0.50.5
Pavlov. Cond. intertrial magazine entries0.50.61.91.4-0.40.3-0.3
Pavlov. Cond. lever-magazine prob. diff.0.20.30.40.7-0.30.6-0.6
Pavlov. Cond. response bias0.30.40.80.9-0.30.6-0.6
Pavlov. Cond. lever latency0.10.10.4-0.60.1-0.30.3
Pavlov. Cond. magazine entry latency1.01.43.01.7-0.91.0-1.0
Pavlov. Cond. change in total contacts1.64.05.70.1-2.22.4-2.4
Pavlov. Cond. index score0.60.91.51.2-0.70.9-0.9
Pavlov. Cond. latency score0.71.12.11.5-0.70.9-0.9
Pavlov. Cond. lever contacts0.10.20.50.7-0.00.2-0.2
Pavlov. Cond. magazine entry number0.40.51.2-1.10.5-0.50.5
Pavlov. Cond. intertrial magazine entries0.41.01.1-1.0-1.10.9-0.9
Pavlov. Cond. lever-magazine prob. diff.0.50.71.41.2-0.60.7-0.7
Pavlov. Cond. response bias0.50.60.70.9-0.70.8-0.8
Time in closed arm before self-admin0.40.72.81.70.2-0.10.1
Time in closed arm after self-admin0.30.30.5-0.2-0.70.5-0.5
Time in open arm before self-admin0.40.50.8-0.00.9-0.80.8
Time in open arm after self-admin1.21.41.70.61.3-1.31.3
Bone: periosteal estimation1.53.64.3-1.7-2.11.9-1.9
Bone: periosteal perimeter2.14.17.1-2.7-1.71.7-1.7
Bone: post-yield work1.22.15.40.2-2.31.3-1.3
Progressive ratio test 1 active lever presses1.52.74.30.4-2.11.8-1.8
Progressive ratio test 1 breakpoint1.32.33.60.5-1.91.6-1.6
Progressive ratio test 1 inactive lever presses1.95.07.20.5-2.32.7-2.7
Progressive ratio test 2 active lever presses1.72.43.70.5-1.91.7-1.7
Progressive ratio test 2 breakpoint1.82.33.40.6-1.81.6-1.6
Progressive ratio test 2 inactive lever presses0.31.02.11.5-0.80.7-0.7
Incentive Sensitization - Responses0.10.20.40.7-0.10.3-0.3
Incentive Sensitization - Breakpoint0.10.20.20.5-0.30.4-0.4
Sum of active levers in priming session hrs 5-60.00.00.0-0.10.00.2-0.2
Progressive ratio0.10.20.40.2-0.70.4-0.4
Food seeking constrained by brief footshock0.30.40.9-0.7-0.90.2-0.2
Seeking ratio, punishment vs. effort0.10.20.4-0.6-0.40.4-0.4
Retroperitoneal fat weight1.56.826.4-5.1-0.80.2-0.2
Reaction time number correct0.72.63.60.71.9-1.81.8
Reaction time mean minus median0.00.00.0-0.10.10.2-0.2
Reaction time mean minus median AUC0.00.30.9-1.00.30.1-0.1
Reaction time num false alarms0.10.20.3-0.00.6-0.50.5
Reaction time num false alarms AUC0.20.40.60.20.8-0.70.7
Reaction time trials correct on left0.72.63.60.71.9-1.81.8
Reaction time trials on left0.82.73.70.81.9-1.81.8
Reaction time mean0.00.00.0-0.10.2-0.00.0
Reaction time mean AUC0.00.00.0-0.10.2-0.10.1
Median of all reaction times0.00.00.1-0.00.2-0.10.1
Reaction time omissions0.20.20.70.90.5-0.10.1
Reaction time false alarm rate0.00.00.1-0.20.00.0-0.0
Reaction time premature initiation rate2.43.86.00.0-1.82.4-2.4
Reaction time premature initiations0.41.32.30.1-0.81.5-1.5
Std. dev. reaction times0.00.10.3-0.60.10.1-0.1
Reaction time trials completed0.82.73.70.81.9-1.81.8
Reaction time trials AUC0.62.12.90.51.7-1.61.6
Run reversals in cocaine runway, females0.20.20.60.30.8-0.40.4
Run reversals in cocaine runway, males0.10.20.3-0.4-0.50.3-0.3
Latency to leave start box in cocaine runway0.30.51.3-1.20.6-0.30.3
Latency to leave start box in cocaine runway, F0.00.00.1-0.20.3-0.00.0
Latency to leave start box in cocaine runway, M0.90.92.4-1.60.7-0.60.6
Std. dev. time between licks in bursts0.30.51.61.3-0.40.4-0.4
Total sessions with >9 infusions4.65.78.1-1.6-2.82.5-2.5
Short access day 1 total inactive lever presses3.87.611.40.3-3.43.1-3.1
Short access day 10 total inactive lever presses0.10.60.7-0.6-0.80.8-0.8
Short access day 1 total infusions1.52.94.2-0.4-2.11.9-1.9
Short access day 10 total infusions2.43.95.0-1.1-2.22.2-2.2
Short access total infusions4.36.19.5-1.0-3.12.7-2.7
Short access day 1 locomotion0.71.21.6-0.2-1.21.3-1.3
Short access day 10 total locomotion0.51.93.20.5-1.01.8-1.8
Short access total locomotion1.72.53.5-0.6-1.61.9-1.9
One hour access (0.3 mA shock)0.70.81.81.4-0.80.6-0.6
Compulsive drug intake0.40.61.91.40.1-0.40.4
One hour access (shock baseline)0.10.30.40.1-0.50.6-0.6
Social response proportion0.20.20.3-0.6-0.10.5-0.5
Social responses0.50.70.90.8-0.50.9-0.9
Social time0.91.33.61.9-0.10.9-0.9
Soleus weight0.31.01.51.2-0.91.0-1.0
Bone: stiffness1.83.35.2-1.4-2.31.7-1.7
Tibialis anterior weight0.51.76.22.50.3-0.40.4
Time to tail flick, vehicle, before self-admin0.30.30.50.1-0.70.7-0.7
Time to tail flick, vehicle, after self-admin0.10.20.80.90.3-0.10.1
Time to tail flick, test, before self-admin0.10.10.2-0.40.3-0.30.3
Time to tail flick, test, after self-admin0.80.81.20.60.7-1.11.1
Delta time to tail flick, vehicle, before/after SA0.20.20.30.2-0.40.5-0.5
Delta time to tail flick, test, before/after SA1.62.02.51.61.1-1.41.4
Tibia length0.82.12.7-1.2-1.71.5-1.5
Ambulatory time before self-admin0.10.20.91.00.10.1-0.1
Ambulatory time after self-admin0.60.92.11.5-0.70.7-0.7
Bone: tissue strength0.10.10.4-0.6-0.1-0.10.1
Total heroin consumption0.50.51.30.0-1.10.7-0.7
Bone: trabecular number0.20.30.4-0.20.6-0.60.6
Bone: trabecular spacing2.23.25.0-0.8-2.21.9-1.9
Bone: trabecular thickness0.81.11.6-0.01.2-1.21.2
Bone: trabecular tissue density0.61.11.61.30.9-1.01.0
Water consumed over 24 hours0.20.41.00.3-1.00.4-0.4
Number of responses in last shaping day2.22.93.90.6-1.82.0-2.0