Atf3

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 Liver alternative polyA NM_012912.2 0.03 0.02 1.5e-03 0.02 0.02 0.02 0.02 2.6e-03 9.7e-04 5.2e-03 3.2e-03
2 Liver alternative polyA XM_039090385.2 0.03 0.02 2.4e-03 0.02 0.02 0.01 0.02 5.0e-03 1.4e-03 8.3e-03 6.5e-03
3 Liver gene expression Atf3 0.09 0.06 7.0e-08 0.05 0.06 0.06 0.06 1.4e-06 3.1e-07 3.8e-07 2.3e-07

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 density0.30.50.8-0.90.90.0
Area under the delay curve1.11.31.4-1.21.2-1.0
BMI with tail0.00.10.20.3-0.30.5
BMI without tail1.13.34.1-2.02.0-1.4
Body weight3.314.214.9-3.83.9-3.6
Weight adjusted by age0.81.11.2-1.11.1-1.0
Bone surface0.20.30.5-0.70.7-0.3
Bone volume0.61.11.6-1.31.2-0.5
Breakpoint value in progressive ratio session1.21.51.9-1.41.3-0.9
Number of licking bursts0.10.20.2-0.50.50.3
Context. condit. distance diff. score0.40.40.6-0.80.7-0.4
Locomotion velocity, session 10.10.10.20.2-0.30.4
Locomotion distance, session 10.00.00.1-0.1-0.00.3
Locomotion velocity, session 20.60.70.9-1.00.9-0.6
Locomotion distance, session 20.00.00.0-0.20.2-0.2
Locomotion velocity, session 32.02.32.5-1.61.6-1.4
Locomotion distance, session 30.80.90.9-0.91.0-0.9
Stereotopy head waving bouts, day 30.80.91.20.9-0.91.1
Stereotopy head waving duration, day 30.30.41.00.1-0.31.0
Locomotion velocity, session 70.40.40.60.6-0.5-0.8
Locomotion distance, session 70.20.30.40.6-0.5-0.4
Stereotopy head waving bouts, day 71.11.21.7-1.31.2-0.6
Stereotopy head waving duration, day 71.11.32.0-1.41.3-0.3
Locomotion velocity, session 80.10.10.2-0.30.20.4
Locomotion distance, session 80.20.20.3-0.50.5-0.4
Degree of sensitization distance1.11.21.41.2-1.20.8
Degree of sensitization stereotypy1.21.31.9-1.41.3-0.6
Conditioned locomotion1.21.42.11.0-1.01.4
Cocaine response after cond. corrected0.10.20.20.4-0.40.4
Cocaine response after cond. not corrected0.20.20.50.3-0.30.7
Cocaine response before conditioning0.20.30.4-0.70.6-0.0
Saline control response1.62.13.2-1.81.7-0.4
Bone: connectivity density0.30.50.7-0.90.80.4
Bone: cortical apparent density0.10.20.20.4-0.4-0.4
Bone: cortical area2.64.04.5-2.12.1-1.8
Bone: cortical porosity0.20.20.7-0.10.00.8
Bone: cortical porosity0.20.30.80.1-0.10.9
Bone: cortical thickness0.81.31.7-1.31.2-0.8
Bone: cortical thickness1.92.33.3-1.81.7-0.7
Bone: cortical tissue density0.10.20.20.5-0.4-0.4
Condit. Reinf. active minus inactive responses0.00.00.00.00.0-0.2
Condit. Reinf. active-inactive response ratio0.60.60.80.7-0.70.9
Condit. Reinf. active responses0.91.11.7-0.90.9-1.3
Condit. Reinf. inactive responses1.92.32.9-1.41.4-1.7
Incentive salience index mean0.50.60.7-0.70.8-0.8
Condit. Reinf. lever presses1.92.63.0-1.71.7-1.5
Condit. Reinf. active minus inactive responses0.20.30.5-0.70.60.1
Condit. Reinf. active-inactive response ratio0.30.40.40.6-0.60.6
Condit. Reinf. active responses0.71.01.4-1.21.2-0.5
Condit. Reinf. inactive responses2.53.23.6-1.91.9-1.6
Condit. Reinf. lever presses1.72.42.9-1.71.7-1.2
Condit. Reinf. lever reinforcers received0.70.91.2-1.11.1-0.7
Conditioned reinforcement - actives0.61.01.4-1.21.1-0.7
Conditioned reinforcement - inactives1.21.82.2-1.51.5-1.0
Conditioned locomotion1.01.31.9-1.41.3-0.5
Patch foraging indifference point 0 sec1.83.35.0-2.22.1-0.5
Patch foraging indifference point AUC0.40.60.90.9-0.90.3
Delay disc. indifference point, 0s delay0.30.30.4-0.60.6-0.5
Delay disc. indifference point, 16s delay2.52.83.6-1.91.9-1.2
Delay disc. indifference point, 2s delay0.10.10.2-0.50.40.0
Delay disc. indifference point, 24s delay2.83.13.5-1.91.9-1.5
Delay disc. indifference point, 4s delay0.60.71.3-0.60.6-1.1
Delay disc. indifference point, 8s delay0.00.10.1-0.30.30.0
Indifference point function ln k0.10.10.1-0.30.20.4
Indifference point function log k0.10.10.1-0.30.20.4
Patch foraging total patch changes 0 sec1.73.24.9-2.22.1-0.6
Patch foraging total patch changes 12 sec2.02.53.2-1.81.8-1.1
Patch foraging total patch changes 18 sec0.50.80.8-0.90.9-0.9
Patch foraging total patch changes 24 sec1.32.22.5-1.61.6-1.3
Patch foraging total patch changes 6 sec2.03.03.8-2.02.0-1.2
Patch foraging time to switch 0 sec0.20.30.50.5-0.5-0.7
Patch foraging water rate 0 sec0.40.91.2-1.11.00.7
Patch foraging water rate 12 sec0.20.30.5-0.70.70.1
Patch foraging water rate 18 sec0.40.60.9-1.00.9-0.1
Patch foraging water rate 24 sec0.00.10.1-0.20.10.4
Patch foraging water rate 6 sec0.50.71.1-1.01.00.1
Seeking ratio, delayed vs. immediate footshock0.30.40.5-0.70.7-0.6
Distance traveled before self-admin0.40.50.6-0.80.70.6
Distance traveled after self-admin0.10.20.3-0.40.30.5
Extensor digitorum longus weight0.10.41.0-0.20.3-1.0
Bone: elastic displacement1.21.42.01.0-1.11.4
Bone: elastic work0.50.71.10.7-0.71.0
Bone: endosteal estimation0.10.10.2-0.20.2-0.5
Bone: endosteal perimeter0.81.72.4-1.11.2-1.6
Epididymis fat weight0.31.01.6-1.31.2-0.3
Delta time in closed arm before/after self-admin0.60.50.80.9-0.90.2
Delta time in open arm before/after self-admin5.04.95.5-2.32.3-2.0
Diff in mean of infusions in LGA sessions0.60.81.2-1.11.0-0.2
Delay discount exponential model param1.31.51.61.3-1.31.1
Extinction: sum of active levers before priming4.24.65.3-2.32.3-1.8
Active lever presses in extinction session 62.32.32.6-1.61.6-1.3
Bone: final force0.40.60.6-0.80.8-0.8
Bone: final moment0.71.11.2-1.01.0-1.1
Food consumed during 24 hour testing period0.10.10.2-0.50.4-0.1
Glucose1.11.81.81.3-1.31.3
Heart weight2.43.74.0-2.02.0-1.8
Delay discount hyperbolic model param1.51.71.91.4-1.41.2
Intermittent access intake day 1-15 change1.63.24.22.0-2.01.2
Intermittent access intake escalation1.73.44.12.0-2.01.4
Intermittent access intake escalation 20.70.81.00.9-1.00.8
Intermitt. access day 1 inactive lever presses0.00.10.2-0.10.1-0.4
Intermitt. access day 15 inactive lever presses1.12.32.7-1.41.5-1.6
Intermitt. access escalation Index0.20.31.0-0.10.1-1.0
Intermittent access day 1 total infusions1.93.13.8-1.91.9-1.3
Intermittent access day 15 total infusions0.20.30.40.5-0.50.6
Intermittent access terminal intake (last 3 days)0.10.10.20.4-0.40.2
Intermittent access total infusions0.10.10.1-0.40.30.1
Intermittent access day 1 locomotion1.51.92.2-1.51.4-1.2
Intermittent access day 15 total locomotion0.10.10.2-0.40.3-0.2
Intermittent access total locomotion0.50.60.9-0.90.9-0.5
Intermittent access standard deviation0.00.00.00.1-0.1-0.1
Left kidney weight2.19.810.6-3.23.2-2.9
Right kidney weight1.67.37.8-2.82.8-2.5
Cocaine induced anxiety1.72.54.8-1.11.2-2.2
Post-drug Anxiety0.30.40.9-0.30.3-1.0
Baseline Anxiety5.15.98.92.0-2.23.0
Tail length5.521.622.8-4.74.8-4.4
Length with tail6.327.527.7-5.25.3-5.3
Length without tail1.54.76.1-2.02.0-2.5
Times rat made contact with spout0.10.10.1-0.40.30.3
Lifetime Intake0.30.30.6-0.70.7-0.1
Liver weight, left0.61.01.1-1.01.0-0.9
Liver weight, right0.20.31.00.1-0.21.0
Locomotor activity0.71.11.11.0-1.11.0
Locomotor testing distance0.40.70.70.8-0.90.8
Locomotor testing rearing0.10.10.1-0.40.30.3
Locomotion in novel chamber0.00.00.00.1-0.10.1
Locomotion in novel chamber post-restriction0.10.10.2-0.30.20.4
Fecal boli incidents, locomotor time 10.81.11.41.2-1.20.7
Change in fecal boli incidents, locomotor task0.10.10.3-0.50.4-0.1
Time >=10cm from walls, locomotor time 10.80.91.20.8-0.91.1
Bouts of movement, locomotor time 10.70.81.00.8-0.91.0
Total resting periods, locomotor time 10.60.70.70.8-0.80.8
Rest time, locomotor task time 11.11.41.61.2-1.31.1
Distance moved, locomotor task time 10.30.50.8-0.60.6-0.9
Vertical activity count, locomotor time 10.00.00.1-0.10.10.3
Time >=10cm from walls, locomotor time 20.10.10.10.3-0.3-0.4
Bouts of movement, locomotor time 20.40.70.80.9-0.90.7
Total resting periods, locomotor time 20.30.50.70.8-0.80.5
Rest time, locomotor task time 23.74.75.92.4-2.41.5
Distance moved, locomotor task time 21.31.61.9-1.31.4-1.0
Vertical activity count, locomotor time 20.30.40.7-0.80.80.0
Light reinforcement 10.30.71.60.5-0.61.2
Light reinforcement 20.50.81.30.7-0.81.1
Bone: marrow area0.00.00.1-0.10.1-0.3
Bone: maximum diameter1.42.73.1-1.81.7-1.4
Bone: maximum force0.30.40.6-0.80.7-0.5
Bone: maximum moment0.50.91.0-1.01.0-0.8
Mean time between licks in bursts0.61.62.51.6-1.5-0.1
Mean num. licks in bursts0.10.10.10.3-0.3-0.3
Cd content in liver15.517.219.5-4.44.4-3.6
Co content in liver0.40.51.20.3-0.41.1
Cu content in liver5.46.47.82.8-2.81.9
Fe content in liver1.72.13.11.7-1.70.6
K content in liver0.60.60.80.9-0.90.3
Mg content in liver0.30.30.4-0.60.6-0.4
Mn content in liver1.01.11.3-1.11.1-0.9
Na content in liver2.02.13.01.7-1.70.7
Rb content in liver0.91.01.61.2-1.20.3
Se content in liver0.30.30.5-0.70.60.3
Sr content in liver1.51.32.0-0.91.0-1.4
Zn content in liver3.94.36.5-2.62.4-0.8
Bone: minimum diameter2.54.65.4-2.02.1-2.3
Time in familiar zone, hab. session 10.10.10.20.4-0.3-0.5
Time in novel zone, hab. session 11.41.41.6-1.31.2-1.0
Total zone transitions, hab. session 11.62.32.7-1.61.6-1.3
Total locomotion distance, hab. session 10.10.10.2-0.20.2-0.4
Locomotion velocity, hab. session 10.00.00.0-0.0-0.0-0.0
Time in familiar zone, hab. session 20.50.50.80.9-0.90.2
Time in novel zone, hab. session 22.52.52.9-1.71.7-1.3
Total zone transitions, hab. session 20.91.21.3-1.21.1-0.9
Total locomotion distance, hab. session 20.10.20.4-0.30.3-0.6
Locomotion velocity, hab. session 20.10.10.1-0.30.3-0.4
Novel to familiar place preference ratio0.50.60.9-1.00.90.0
Novelty place preference0.91.01.5-1.21.2-0.2
Time in novel zone, NPP test1.01.11.7-1.31.2-0.3
Total zone transitions, NPP test1.82.63.5-1.91.8-1.0
Total locomotion distance, NPP test0.50.70.9-0.90.9-0.7
Locomotion velocity, NPP test0.30.50.6-0.80.7-0.5
Intraocular pressure1.21.72.21.2-1.21.5
Delta distance traveled before/after self-admin0.10.10.3-0.20.2-0.5
Delta ambulatory time before/after self-admin0.00.10.10.3-0.3-0.1
Parametrial fat weight0.00.00.10.00.0-0.3
Pavlov. Cond. lever latency4.65.86.92.6-2.61.9
Pavlov. Cond. magazine entry latency3.95.07.2-1.92.0-2.7
Pavlov. Cond. change in total contacts6.16.57.3-2.72.7-2.2
Pavlov. Cond. index score4.15.25.4-2.32.3-2.2
Pavlov. Cond. latency score4.55.76.1-2.42.5-2.3
Pavlov. Cond. lever contacts2.73.23.8-1.91.9-1.5
Pavlov. Cond. magazine entry number3.95.07.11.9-2.02.7
Pavlov. Cond. intertrial magazine entries0.50.60.80.7-0.70.9
Pavlov. Cond. lever-magazine prob. diff.4.35.35.5-2.32.4-2.3
Pavlov. Cond. response bias4.25.26.1-2.22.2-2.5
Pavlov. Cond. lever latency2.73.74.62.1-2.11.4
Pavlov. Cond. magazine entry latency0.50.60.7-0.80.9-0.7
Pavlov. Cond. change in total contacts0.30.50.7-0.80.8-0.3
Pavlov. Cond. index score1.92.53.0-1.71.7-1.3
Pavlov. Cond. latency score2.02.73.1-1.81.8-1.4
Pavlov. Cond. lever contacts2.12.83.6-1.91.9-1.2
Pavlov. Cond. magazine entry number0.60.70.91.0-1.00.6
Pavlov. Cond. intertrial magazine entries0.00.00.1-0.10.1-0.2
Pavlov. Cond. lever-magazine prob. diff.1.41.92.3-1.51.5-1.0
Pavlov. Cond. response bias1.31.82.2-1.51.5-1.0
Time in closed arm before self-admin0.10.10.30.1-0.10.6
Time in closed arm after self-admin2.62.83.21.8-1.81.5
Time in open arm before self-admin0.10.10.2-0.30.3-0.5
Time in open arm after self-admin5.05.56.1-2.52.5-2.1
Bone: periosteal estimation1.12.42.5-1.61.6-1.5
Bone: periosteal perimeter1.52.62.7-1.61.6-1.6
Bone: post-yield work0.00.00.0-0.00.00.1
Progressive ratio test 1 active lever presses1.41.82.2-1.21.3-1.5
Progressive ratio test 1 breakpoint1.41.71.9-1.21.2-1.4
Progressive ratio test 1 inactive lever presses2.43.44.2-1.71.8-2.1
Progressive ratio test 2 active lever presses0.70.80.9-0.90.9-0.9
Progressive ratio test 2 breakpoint0.60.60.7-0.80.8-0.8
Progressive ratio test 2 inactive lever presses1.72.83.2-1.81.7-1.5
Incentive Sensitization - Responses0.20.20.4-0.40.4-0.7
Incentive Sensitization - Breakpoint0.20.30.5-0.40.3-0.7
Sum of active levers in priming session hrs 5-63.12.83.4-1.81.8-1.4
Progressive ratio1.62.53.7-1.91.70.9
Food seeking constrained by brief footshock0.30.30.60.7-0.70.1
Seeking ratio, punishment vs. effort1.72.53.92.0-1.8-0.6
Retroperitoneal fat weight1.04.34.8-2.22.2-1.8
Reaction time number correct2.34.56.5-2.52.5-0.9
Reaction time mean minus median2.56.37.12.6-2.72.2
Reaction time mean minus median AUC2.15.36.02.4-2.42.0
Reaction time num false alarms2.23.13.71.9-1.91.4
Reaction time num false alarms AUC2.33.74.12.0-2.01.7
Reaction time trials correct on left2.34.56.5-2.52.5-0.9
Reaction time trials on left2.24.16.0-2.52.4-0.8
Reaction time mean6.410.113.03.6-3.62.1
Reaction time mean AUC5.99.511.73.4-3.42.2
Median of all reaction times5.47.610.33.2-3.21.6
Reaction time omissions2.23.34.11.7-1.72.0
Reaction time false alarm rate4.56.17.82.8-2.81.7
Reaction time premature initiation rate0.30.40.50.7-0.6-0.5
Reaction time premature initiations0.20.30.3-0.50.5-0.5
Std. dev. reaction times4.88.910.03.1-3.22.7
Reaction time trials completed2.24.16.0-2.52.4-0.8
Reaction time trials AUC2.44.66.7-2.62.5-0.9
Run reversals in cocaine runway, females0.10.10.2-0.10.2-0.4
Run reversals in cocaine runway, males1.01.01.41.2-1.20.5
Latency to leave start box in cocaine runway1.51.72.01.4-1.41.1
Latency to leave start box in cocaine runway, F3.43.94.62.1-2.11.6
Latency to leave start box in cocaine runway, M0.00.00.1-0.10.1-0.3
Std. dev. time between licks in bursts0.20.20.60.3-0.2-0.8
Total sessions with >9 infusions1.92.32.8-1.71.7-1.2
Short access day 1 total inactive lever presses0.00.10.2-0.10.1-0.4
Short access day 10 total inactive lever presses0.30.81.2-0.80.8-1.1
Short access day 1 total infusions0.71.01.3-1.11.1-0.7
Short access day 10 total infusions1.01.31.7-1.31.3-0.6
Short access total infusions1.11.42.1-1.41.4-0.5
Short access day 1 locomotion3.64.56.0-2.52.4-1.3
Short access day 10 total locomotion0.20.40.50.7-0.70.4
Short access total locomotion0.40.50.8-0.90.9-0.3
One hour access (0.3 mA shock)1.11.21.7-1.01.0-1.3
Compulsive drug intake1.01.22.6-0.70.8-1.6
One hour access (shock baseline)0.10.20.30.3-0.40.6
Social response proportion0.10.10.20.3-0.30.5
Social responses0.40.60.8-0.90.9-0.3
Social time0.10.10.2-0.40.40.1
Soleus weight1.64.69.71.3-1.53.1
Bone: stiffness0.71.21.2-1.11.1-1.0
Tibialis anterior weight0.51.62.7-1.01.1-1.6
Time to tail flick, vehicle, before self-admin2.42.53.41.8-1.80.9
Time to tail flick, vehicle, after self-admin0.40.50.7-0.80.8-0.5
Time to tail flick, test, before self-admin0.20.20.20.4-0.40.4
Time to tail flick, test, after self-admin0.30.30.40.6-0.70.2
Delta time to tail flick, vehicle, before/after SA1.51.51.9-1.41.3-0.8
Delta time to tail flick, test, before/after SA0.00.00.00.1-0.10.1
Tibia length1.95.25.9-2.22.3-2.4
Ambulatory time before self-admin0.40.61.7-0.10.01.3
Ambulatory time after self-admin0.70.92.00.5-0.61.4
Bone: tissue strength0.70.71.11.0-1.0-0.1
Total heroin consumption3.44.05.0-2.22.2-1.5
Bone: trabecular number0.20.30.4-0.40.40.7
Bone: trabecular spacing0.81.12.5-0.60.6-1.6
Bone: trabecular thickness0.20.30.4-0.50.50.7
Bone: trabecular tissue density1.21.82.81.7-1.5-0.5
Water consumed over 24 hours0.60.71.1-1.11.0-0.3
Number of responses in last shaping day0.20.30.6-0.40.30.7