Rpa1

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 gene expression ENSRNOG00000003123 0.1 0.08 1.1e-06 0.05 0.03 0.03 0.03 5.6e-06 1.2e-04 1.1e-04 1.3e-04
2 Liver gene expression ENSRNOG00000003123 0.13 0.08 5.4e-13 0.1 0.1 0.09 0.09 1.2e-10 1.1e-10 2.1e-10 1.4e-10
3 Liver isoform ratio ENSRNOT00000116502 0.03 0.03 1.1e-03 0.03 0.02 0.02 0.03 6.4e-04 1.2e-03 1.5e-03 7.7e-04
4 PL gene expression ENSRNOG00000003123 0.07 0.05 1.3e-04 0.04 0.04 0.04 0.04 2.3e-04 2.3e-04 2.9e-04 3.3e-04

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 strong Z-scores (below -2 or above 2): lower negative Z-scores are darker blue, higher positive Z-scores are darker red.

Trait Avg chi2 ratio Avg chi2 Max chi2 1 2 3 4
BMI with tail0.92.94.6-1.22.11.02.1
BMI without tail0.20.30.80.20.40.90.6
Body weight0.94.09.61.31.53.11.6
Epididymis fat weight2.35.37.7-0.22.62.82.6
Glucose2.43.75.31.0-2.3-1.8-2.3
Heart weight0.10.10.30.40.10.50.1
Left kidney weight3.510.014.13.8-3.6-0.3-3.6
Right kidney weight3.18.713.33.7-3.3-0.0-3.3
Tail length2.47.216.54.1-1.33.1-1.1
Length with tail1.14.18.52.9-0.52.8-0.4
Length without tail0.71.63.70.61.11.91.0
Liver weight, left1.52.55.82.4-0.91.7-0.7
Liver weight, right0.71.12.41.4-0.31.6-0.1
Parametrial fat weight5.09.818.60.63.14.33.3
Retroperitoneal fat weight0.00.10.60.7-0.1-0.0-0.1
Intraocular pressure1.21.73.4-1.80.9-1.40.8
Extensor digitorum longus weight4.819.330.5-3.75.51.75.5
Soleus weight2.36.812.51.12.63.52.6
Tibialis anterior weight7.224.839.4-3.36.23.16.3
Tibia length1.23.25.82.4-1.71.4-1.6
Number of licking bursts0.30.30.40.5-0.7-0.6-0.6
Food consumed during 24 hour testing period0.20.20.3-0.40.50.50.5
Times rat made contact with spout1.71.92.91.7-1.60.1-1.5
Mean time between licks in bursts0.50.71.81.3-0.30.9-0.2
Mean num. licks in bursts0.30.40.50.7-0.50.7-0.5
Std. dev. time between licks in bursts0.40.40.8-0.50.80.20.9
Water consumed over 24 hours1.01.12.21.5-0.90.8-0.9
Indifference point 0 sec0.20.20.4-0.50.60.20.5
Indifference point AUC0.30.41.2-0.60.0-1.1-0.0
Indifference point function ln k0.60.81.0-0.71.00.91.0
Indifference point function log k0.60.81.0-0.71.00.91.0
Delay discounting total patch changes 0 sec0.20.30.5-0.70.70.10.6
Delay discounting total patch changes 12 sec0.50.60.80.9-0.9-0.5-0.9
Delay discounting total patch changes 18 sec0.81.11.51.2-1.1-0.3-1.2
Delay discounting total patch changes 24 sec0.60.70.90.4-0.9-0.9-0.9
Delay discounting total patch changes 6 sec0.20.41.0-0.70.1-1.0-0.0
Delay discounting time to switch 0 sec2.03.05.72.4-1.80.4-1.7
Delay discounting water rate 0 sec0.91.42.8-1.71.1-0.61.0
Delay discounting water rate 12 sec0.00.00.1-0.20.10.20.1
Delay discounting water rate 18 sec2.73.65.2-1.72.31.02.2
Delay discounting water rate 24 sec0.30.50.8-0.90.8-0.10.7
Delay discounting water rate 6 sec0.20.30.6-0.8-0.1-0.8-0.2
Locomotor activity0.10.10.10.30.20.30.3
Locomotor testing distance0.00.00.10.20.20.10.3
Locomotor testing rearing0.40.60.9-0.91.0-0.11.0
Light reinforcement 10.00.00.10.10.20.10.2
Light reinforcement 22.43.14.41.9-2.1-0.7-2.1
Reaction time number correct0.00.10.20.20.20.40.2
Reaction time mean minus median0.20.30.6-0.70.2-0.80.2
Reaction time mean minus median AUC1.31.72.6-1.61.5-0.41.4
Reaction time num false alarms1.42.04.5-2.11.0-1.20.9
Reaction time num false alarms AUC1.31.84.1-2.00.9-1.30.9
Reaction time trials correct on left0.00.10.20.20.20.40.2
Reaction time trials on left0.00.10.10.20.20.40.2
Reaction time mean0.10.10.1-0.4-0.3-0.4-0.3
Reaction time mean AUC0.30.30.7-0.6-0.4-0.8-0.4
Median of all reaction times0.20.20.4-0.1-0.6-0.3-0.6
Reaction time omissions0.00.00.0-0.2-0.1-0.0-0.1
Reaction time false alarm rate1.11.53.4-1.80.9-1.20.8
Reaction time premature initiation rate0.50.71.0-0.91.00.31.0
Reaction time premature initiations0.60.91.2-0.91.10.41.1
Std. dev. reaction times0.30.40.8-0.90.3-0.80.3
Reaction time trials completed0.00.10.10.20.20.40.2
Reaction time trials AUC0.00.10.10.10.20.30.2
Social response proportion1.61.75.31.00.52.30.6
Social responses1.11.43.00.51.01.71.1
Social time1.92.53.9-0.21.72.01.8
Conditioned locomotion0.40.51.1-0.7-0.5-1.1-0.5
Cocaine response after cond. corrected0.10.10.40.3-0.10.7-0.1
Cocaine response after cond. not corrected0.20.31.00.20.21.00.2
Cocaine response before conditioning0.80.91.5-0.21.20.91.1
Saline control response0.60.81.2-0.81.10.21.0
Condit. Reinf. active minus inactive responses0.30.40.6-0.70.80.40.7
Condit. Reinf. active-inactive response ratio0.10.10.2-0.2-0.40.2-0.5
Condit. Reinf. active responses1.11.52.3-1.21.50.11.5
Condit. Reinf. inactive responses2.73.45.5-1.62.3-0.32.3
Condit. Reinf. lever presses0.40.51.4-0.80.2-1.20.1
Condit. Reinf. lever reinforcers received1.01.42.2-1.21.5-0.01.4
Pavlov. Cond. lever latency0.81.11.7-0.51.11.31.1
Pavlov. Cond. magazine entry latency1.41.62.41.6-1.4-0.3-1.4
Pavlov. Cond. change in total contacts0.81.11.41.0-1.1-0.7-1.2
Pavlov. Cond. index score1.21.61.90.9-1.3-1.3-1.4
Pavlov. Cond. latency score1.41.72.30.8-1.4-1.5-1.4
Pavlov. Cond. lever contacts0.70.91.20.9-1.1-0.8-1.1
Pavlov. Cond. magazine entry number1.51.92.8-1.71.50.61.5
Pavlov. Cond. intertrial magazine entries2.22.94.0-1.72.00.81.9
Pavlov. Cond. lever-magazine prob. diff.1.11.41.70.8-1.3-1.3-1.3
Pavlov. Cond. response bias1.11.52.01.3-1.4-0.8-1.4
Conditioned reinforcement - actives2.32.33.5-1.51.90.41.8
Conditioned reinforcement - inactives0.70.81.2-0.81.1-0.01.1
Conditioned locomotion0.10.10.2-0.1-0.1-0.4-0.1
Intermittent access intake day 1-15 change1.51.53.3-1.80.7-1.40.5
Intermittent access intake escalation1.11.12.9-1.2-0.1-1.7-0.2
Intermittent access intake escalation 21.31.33.6-1.0-0.5-1.9-0.7
Intermitt. access day 1 inactive lever presses2.02.22.90.7-1.7-1.6-1.7
Intermitt. access day 15 inactive lever presses0.40.41.0-0.2-0.6-1.0-0.6
Intermitt. access escalation Index3.22.86.02.3-0.42.4-0.3
Intermittent access day 1 total infusions0.60.61.0-0.71.00.51.0
Intermittent access day 15 total infusions1.61.83.6-1.91.3-0.81.2
Intermittent access terminal intake (last 3 days)1.71.92.8-1.51.70.31.6
Intermittent access total infusions0.91.01.9-1.41.0-0.30.9
Intermittent access day 1 locomotion0.30.30.40.6-0.6-0.1-0.6
Intermittent access day 15 total locomotion0.30.30.9-0.5-0.1-0.9-0.2
Intermittent access total locomotion0.00.00.1-0.2-0.1-0.4-0.1
Intermittent access standard deviation2.83.06.3-2.50.7-2.20.4
Cocaine induced anxiety0.60.71.5-1.20.4-1.00.4
Post-drug Anxiety0.30.30.7-0.80.6-0.20.6
Baseline Anxiety0.20.20.40.6-0.20.5-0.2
Lifetime Intake1.01.12.1-1.51.0-0.40.9
Incentive Sensitization - Responses0.30.30.4-0.70.5-0.50.5
Incentive Sensitization - Breakpoint0.20.20.3-0.60.4-0.50.3
Progressive ratio test 1 active lever presses0.30.30.5-0.50.70.30.6
Progressive ratio test 1 breakpoint0.70.71.1-0.61.10.61.0
Progressive ratio test 1 inactive lever presses0.30.30.80.0-0.5-0.9-0.5
Progressive ratio test 2 active lever presses0.60.71.3-1.10.9-0.30.8
Progressive ratio test 2 breakpoint0.70.81.6-1.30.9-0.40.7
Progressive ratio test 2 inactive lever presses0.50.61.1-1.10.5-0.80.4
Total sessions with >9 infusions0.10.10.2-0.30.40.20.4
Short access day 1 total inactive lever presses0.10.10.20.00.40.50.4
Short access day 10 total inactive lever presses0.50.51.01.0-0.80.2-0.7
Short access day 1 total infusions0.80.91.8-1.30.4-1.20.3
Short access day 10 total infusions1.11.21.9-1.41.3-0.11.2
Short access total infusions1.11.22.6-1.60.9-0.80.8
Short access day 1 locomotion0.20.20.5-0.6-0.0-0.7-0.1
Short access day 10 total locomotion0.30.40.50.1-0.7-0.7-0.7
Short access total locomotion0.20.20.6-0.5-0.1-0.8-0.2
Compulsive drug intake0.50.51.01.0-0.50.9-0.4
One hour access (0.3 mA shock)2.02.33.9-2.01.7-0.21.6
One hour access (shock baseline)1.51.83.2-1.81.4-0.51.3
Number of responses in last shaping day0.60.61.3-0.2-0.7-1.1-0.8
Context. condit. distance diff. score0.91.11.6-0.41.21.11.2
Locomotion velocity, session 12.12.24.20.11.52.11.6
Locomotion distance, session 10.60.81.4-0.61.20.41.2
Locomotion velocity, session 20.60.71.0-0.21.00.81.0
Locomotion distance, session 21.52.13.2-1.21.80.81.8
Locomotion velocity, session 33.84.46.81.6-2.6-1.3-2.6
Locomotion distance, session 30.10.20.3-0.60.2-0.40.2
Stereotopy head waving bouts, day 30.80.93.01.7-0.40.5-0.5
Stereotopy head waving duration, day 30.40.51.01.0-0.4-0.6-0.6
Locomotion velocity, session 71.11.21.7-1.21.30.31.3
Locomotion distance, session 71.72.13.0-1.51.70.61.7
Stereotopy head waving bouts, day 70.60.71.00.61.00.81.0
Stereotopy head waving duration, day 70.81.01.60.41.30.91.2
Locomotion velocity, session 80.50.60.9-0.61.00.31.0
Locomotion distance, session 81.62.43.5-0.21.71.71.9
Degree of sensitization distance0.80.81.3-0.20.91.11.0
Degree of sensitization stereotypy0.91.01.40.41.11.21.1
Condit. Reinf. active minus inactive responses0.20.30.40.6-0.60.1-0.6
Condit. Reinf. active-inactive response ratio3.03.24.62.1-2.10.2-2.0
Condit. Reinf. active responses0.30.30.5-0.70.60.20.6
Condit. Reinf. inactive responses4.85.79.3-3.12.6-0.22.5
Incentive salience index mean0.20.30.30.6-0.50.5-0.5
Condit. Reinf. lever presses0.40.62.00.60.21.40.2
Time in familiar zone, hab. session 12.12.03.6-1.91.5-0.51.4
Time in novel zone, hab. session 12.01.93.71.9-1.40.4-1.3
Total zone transitions, hab. session 12.33.34.7-1.92.2-0.12.1
Total locomotion distance, hab. session 10.60.91.7-0.61.20.21.3
Locomotion velocity, hab. session 10.81.22.1-1.01.30.11.4
Time in familiar zone, hab. session 21.81.83.2-1.01.80.31.8
Time in novel zone, hab. session 24.34.37.11.7-2.6-0.6-2.7
Total zone transitions, hab. session 20.91.11.9-0.51.40.71.4
Total locomotion distance, hab. session 20.10.10.20.30.30.40.4
Locomotion velocity, hab. session 20.10.10.10.20.20.30.3
Novel to familiar place preference ratio0.50.51.5-1.2-0.0-0.80.0
Novelty place preference0.20.20.7-0.8-0.1-0.40.0
Time in novel zone, NPP test0.20.20.6-0.80.2-0.10.2
Total zone transitions, NPP test1.11.52.7-0.81.70.21.6
Total locomotion distance, NPP test0.40.50.8-0.50.9-0.50.9
Locomotion velocity, NPP test0.30.50.9-0.60.5-0.90.5
Pavlov. Cond. lever latency0.40.60.8-0.90.7-0.50.8
Pavlov. Cond. magazine entry latency0.30.31.30.20.11.10.2
Pavlov. Cond. change in total contacts0.50.61.10.5-1.0-0.3-1.0
Pavlov. Cond. index score0.40.51.40.8-0.21.2-0.1
Pavlov. Cond. latency score0.70.81.71.2-0.41.3-0.4
Pavlov. Cond. lever contacts0.30.40.60.8-0.60.6-0.6
Pavlov. Cond. magazine entry number0.10.10.3-0.0-0.1-0.6-0.1
Pavlov. Cond. intertrial magazine entries0.70.91.1-1.11.0-0.80.8
Pavlov. Cond. lever-magazine prob. diff.0.30.31.00.5-0.01.00.0
Pavlov. Cond. response bias0.10.20.70.10.00.80.1
Bone: apparent density3.15.28.1-1.32.81.82.9
Bone surface3.05.38.2-1.82.81.42.9
Bone volume3.25.48.6-1.72.91.42.9
Bone: connectivity density4.87.511.7-1.93.31.93.4
Bone: cortical apparent density0.30.41.1-0.7-0.1-1.1-0.3
Bone: cortical area1.31.93.40.3-1.7-1.2-1.8
Bone: cortical porosity0.10.10.20.30.30.40.4
Bone: cortical porosity0.00.00.10.3-0.10.20.0
Bone: cortical thickness4.57.412.51.9-3.4-1.6-3.5
Bone: cortical thickness1.41.62.41.3-1.50.0-1.5
Bone: cortical tissue density0.30.30.8-0.70.0-0.9-0.1
Bone: elastic displacement0.30.31.0-0.3-0.4-1.0-0.3
Bone: elastic work3.44.56.81.6-2.6-1.4-2.6
Bone: endosteal estimation0.10.30.5-0.70.6-0.10.6
Bone: endosteal perimeter1.22.64.8-2.21.7-0.21.6
Bone: final force1.11.82.61.6-1.40.4-1.5
Bone: final moment0.81.31.91.3-1.30.2-1.4
Bone: marrow area0.10.30.5-0.70.6-0.10.5
Bone: maximum diameter0.61.03.2-1.80.5-0.90.3
Bone: maximum force1.01.72.51.5-1.50.1-1.6
Bone: maximum moment0.71.32.01.2-1.3-0.1-1.4
Bone: minimum diameter0.71.42.31.0-1.5-0.2-1.5
Bone: periosteal estimation0.20.40.8-0.0-0.8-0.6-0.9
Bone: periosteal perimeter0.30.41.1-1.00.0-0.7-0.1
Bone: post-yield work0.20.30.70.30.30.80.3
Bone: stiffness0.61.02.61.00.51.60.5
Bone: tissue strength2.32.23.11.5-1.7-0.7-1.8
Bone: trabecular number3.45.48.7-1.42.91.62.9
Bone: trabecular spacing0.50.71.10.5-1.0-0.7-1.0
Bone: trabecular thickness0.30.30.5-0.50.70.40.7
Bone: trabecular tissue density1.82.54.00.9-1.9-1.4-2.0
Breakpoint value in progressive ratio session0.80.91.91.10.51.40.6
Distance traveled before self-admin1.41.52.00.4-1.4-1.3-1.4
Distance traveled after self-admin0.20.20.40.6-0.40.2-0.4
Delta time in closed arm before/after self-admin0.20.20.5-0.2-0.2-0.7-0.2
Delta time in open arm before/after self-admin0.60.61.30.20.71.10.7
Diff in mean of infusions in LGA sessions0.60.71.71.1-0.01.30.0
Extinction: sum of active levers before priming1.51.62.3-0.41.51.21.5
Active lever presses in extinction session 61.00.91.4-0.21.20.91.2
Delta distance traveled before/after self-admin1.21.33.10.40.91.81.0
Delta ambulatory time before/after self-admin0.91.02.40.30.81.60.9
Time in closed arm before self-admin1.21.42.70.41.11.61.2
Time in closed arm after self-admin0.00.10.10.1-0.3-0.2-0.3
Time in open arm before self-admin3.94.16.10.8-2.4-2.0-2.5
Time in open arm after self-admin0.60.71.10.3-1.0-0.8-1.1
Sum of active levers in priming session hrs 5-61.31.32.70.60.91.71.1
Time to tail flick, vehicle, before self-admin4.64.76.7-0.92.52.22.6
Time to tail flick, vehicle, after self-admin1.61.73.2-1.81.4-0.01.3
Time to tail flick, test, before self-admin0.50.50.6-0.50.80.60.8
Time to tail flick, test, after self-admin0.20.20.60.30.10.80.1
Delta time to tail flick, vehicle, before/after SA0.80.82.0-1.0-0.4-1.4-0.5
Delta time to tail flick, test, before/after SA0.10.00.1-0.30.2-0.20.2
Ambulatory time before self-admin2.02.13.21.1-1.8-1.1-1.7
Ambulatory time after self-admin1.11.22.51.6-0.71.2-0.6
Total heroin consumption2.42.85.60.11.72.41.7
Area under the delay curve1.51.62.31.2-1.5-0.8-1.4
Delay disc. indifference point, 0s delay0.10.10.20.40.20.20.3
Delay disc. indifference point, 16s delay0.70.70.90.7-0.9-0.7-0.9
Delay disc. indifference point, 2s delay1.11.21.61.0-1.3-0.8-1.2
Delay disc. indifference point, 24s delay0.20.20.30.4-0.6-0.3-0.5
Delay disc. indifference point, 4s delay1.21.21.91.4-1.3-0.2-1.2
Delay disc. indifference point, 8s delay0.80.81.20.8-1.1-0.5-1.0
Delay discount exponential model param1.61.72.4-1.31.60.71.5
Delay discount hyperbolic model param1.51.62.2-1.31.50.81.4
Fecal boli incidents, locomotor time 10.00.00.10.20.20.20.0
Change in fecal boli incidents, locomotor task0.60.60.90.7-0.90.1-0.9
Time >=10cm from walls, locomotor time 10.20.20.3-0.50.5-0.20.5
Bouts of movement, locomotor time 10.10.10.2-0.50.40.20.3
Total resting periods, locomotor time 10.20.20.5-0.70.4-0.00.3
Rest time, locomotor task time 10.40.51.2-1.10.3-0.80.2
Distance moved, locomotor task time 10.10.10.2-0.00.30.10.4
Vertical activity count, locomotor time 10.70.71.2-0.61.00.41.1
Time >=10cm from walls, locomotor time 20.70.81.10.8-1.1-0.7-1.0
Bouts of movement, locomotor time 20.20.20.30.4-0.50.0-0.5
Total resting periods, locomotor time 20.00.00.10.1-0.10.2-0.1
Rest time, locomotor task time 20.30.30.6-0.80.5-0.20.6
Distance moved, locomotor task time 20.20.20.7-0.30.0-0.80.0
Vertical activity count, locomotor time 20.30.30.40.5-0.7-0.4-0.7
Weight adjusted by age0.60.71.1-0.61.00.61.1
Seeking ratio, delayed vs. immediate footshock1.01.12.8-0.0-0.9-1.7-0.9
Locomotion in novel chamber2.22.77.8-1.7-0.3-2.8-0.5
Locomotion in novel chamber post-restriction0.20.20.3-0.50.6-0.20.5
Progressive ratio0.81.02.0-1.40.9-0.50.9
Food seeking constrained by brief footshock0.10.10.2-0.1-0.3-0.4-0.3
Seeking ratio, punishment vs. effort1.01.31.91.4-1.30.0-1.2
Run reversals in cocaine runway, females0.50.51.0-0.90.2-1.00.1
Run reversals in cocaine runway, males0.80.81.7-1.30.8-0.60.6
Latency to leave start box in cocaine runway0.20.20.40.6-0.50.0-0.5
Latency to leave start box in cocaine runway, F0.30.40.70.9-0.60.4-0.5
Latency to leave start box in cocaine runway, M0.00.00.10.2-0.10.1-0.2
Cd content in liver1.11.21.6-1.31.20.51.2
Co content in liver0.20.20.30.5-0.5-0.2-0.5
Cu content in liver1.01.21.81.1-1.3-0.1-1.3
Fe content in liver0.50.61.01.0-0.41.0-0.4
K content in liver2.32.35.82.4-1.11.0-1.1
Mg content in liver0.00.00.1-0.0-0.0-0.3-0.1
Mn content in liver0.30.30.5-0.40.70.20.7
Na content in liver3.33.54.82.0-2.1-0.7-2.2
Rb content in liver1.41.82.5-1.41.60.11.6
Se content in liver0.91.11.80.9-1.3-0.5-1.3
Sr content in liver0.80.71.0-0.81.00.51.0
Zn content in liver1.01.12.3-1.51.0-0.11.0