Lrfn3

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 BLA gene expression ENSRNOG00000020839 0.08 0.07 4.2e-03 0.04 0.03 0 0.03 2.9e-03 7.9e-03 1.9e-01 7.6e-03
2 Brain gene expression ENSRNOG00000020839 0.07 0.06 5.8e-05 0.04 0.04 0.04 0.04 9.2e-05 7.0e-05 1.5e-04 1.0e-04
3 OFC gene expression ENSRNOG00000020839 0.27 0.21 2.3e-03 0.01 0.03 0.01 -0.01 1.5e-01 6.0e-02 2.2e-01 4.7e-01
4 PL gene expression ENSRNOG00000020839 0.08 0.05 5.2e-05 0.03 0.05 0.05 0.04 1.8e-03 6.8e-05 2.0e-04 3.6e-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 tail0.20.60.8-0.9-0.8-0.8-0.6
BMI without tail0.00.00.0-0.10.20.10.2
Body weight2.711.313.83.53.73.52.6
Epididymis fat weight0.10.30.40.70.60.60.4
Glucose0.20.31.0-0.2-0.1-0.4-1.0
Heart weight0.30.40.80.50.30.60.9
Left kidney weight2.88.011.53.23.42.91.5
Right kidney weight4.813.718.04.04.23.82.5
Tail length4.413.216.13.74.03.73.0
Length with tail8.129.633.15.65.85.64.7
Length without tail6.013.014.43.83.73.73.1
Liver weight, left0.60.92.0-0.8-0.5-0.9-1.4
Liver weight, right0.30.40.6-0.7-0.4-0.7-0.8
Parametrial fat weight0.51.03.3-0.40.3-0.6-1.8
Retroperitoneal fat weight1.44.79.1-1.8-1.4-2.1-3.0
Intraocular pressure0.00.00.1-0.0-0.2-0.00.3
Extensor digitorum longus weight0.20.72.4-0.4-0.1-0.6-1.6
Soleus weight0.10.30.6-0.5-0.4-0.6-0.8
Tibialis anterior weight0.10.51.80.20.4-0.1-1.3
Tibia length3.08.49.43.13.13.12.4
Number of licking bursts2.53.04.0-1.7-2.0-1.7-1.4
Food consumed during 24 hour testing period0.91.12.30.80.61.01.5
Times rat made contact with spout0.60.72.3-0.2-0.1-0.5-1.5
Mean time between licks in bursts0.10.10.2-0.4-0.3-0.10.4
Mean num. licks in bursts1.21.52.71.31.61.20.3
Std. dev. time between licks in bursts0.60.82.7-0.3-0.50.21.7
Water consumed over 24 hours0.50.60.70.80.80.80.6
Indifference point 0 sec0.10.10.4-0.10.00.20.6
Indifference point AUC0.50.60.7-0.8-0.6-0.8-0.9
Indifference point function ln k0.40.60.60.80.70.70.8
Indifference point function log k0.40.60.60.80.70.70.8
Delay discounting total patch changes 0 sec0.10.20.70.10.20.40.8
Delay discounting total patch changes 12 sec0.10.20.4-0.7-0.4-0.40.0
Delay discounting total patch changes 18 sec0.00.00.00.0-0.10.10.2
Delay discounting total patch changes 24 sec1.01.31.61.10.91.21.3
Delay discounting total patch changes 6 sec0.00.00.0-0.2-0.0-0.00.2
Delay discounting time to switch 0 sec0.71.11.3-1.1-1.0-1.1-1.0
Delay discounting water rate 0 sec0.60.91.0-1.0-1.0-1.0-0.7
Delay discounting water rate 12 sec0.81.31.61.31.11.21.0
Delay discounting water rate 18 sec0.10.20.2-0.5-0.4-0.5-0.4
Delay discounting water rate 24 sec0.20.30.90.4-0.20.30.9
Delay discounting water rate 6 sec1.52.13.01.41.21.51.7
Locomotor activity0.71.12.1-0.9-0.5-1.0-1.5
Locomotor testing distance0.40.71.6-0.6-0.4-0.8-1.2
Locomotor testing rearing1.52.44.2-1.2-1.2-1.5-2.1
Light reinforcement 10.10.10.2-0.3-0.5-0.3-0.0
Light reinforcement 22.83.74.1-2.0-2.0-2.0-1.6
Reaction time number correct0.00.00.10.10.2-0.0-0.4
Reaction time mean minus median0.50.70.80.90.90.90.6
Reaction time mean minus median AUC1.21.52.01.41.41.30.7
Reaction time num false alarms0.70.91.0-0.9-1.0-1.0-1.0
Reaction time num false alarms AUC0.91.31.3-1.1-1.1-1.1-1.1
Reaction time trials correct on left0.00.00.10.10.2-0.0-0.4
Reaction time trials on left0.00.10.20.10.3-0.0-0.4
Reaction time mean0.30.50.70.90.70.70.3
Reaction time mean AUC0.20.30.40.60.60.50.1
Median of all reaction times0.10.20.30.50.40.40.1
Reaction time omissions0.00.10.2-0.00.2-0.1-0.5
Reaction time false alarm rate0.60.81.1-0.9-1.0-0.9-0.7
Reaction time premature initiation rate0.20.20.9-0.2-0.30.00.9
Reaction time premature initiations0.10.10.5-0.1-0.10.00.7
Std. dev. reaction times1.01.31.81.31.21.20.8
Reaction time trials completed0.00.10.20.10.3-0.0-0.4
Reaction time trials AUC0.10.10.40.00.2-0.1-0.6
Social response proportion1.71.93.51.11.01.31.9
Social responses0.40.51.70.30.30.51.3
Social time3.24.15.42.01.72.12.3
Conditioned locomotion0.70.91.2-1.1-1.1-1.0-0.5
Cocaine response after cond. corrected0.30.30.7-0.5-0.1-0.5-0.8
Cocaine response after cond. not corrected0.20.30.8-0.20.1-0.4-0.9
Cocaine response before conditioning1.51.82.21.51.41.31.1
Saline control response0.00.00.10.00.1-0.1-0.2
Condit. Reinf. active minus inactive responses1.11.42.11.01.11.21.5
Condit. Reinf. active-inactive response ratio0.00.00.1-0.1-0.2-0.2-0.3
Condit. Reinf. active responses3.34.56.12.01.92.12.5
Condit. Reinf. inactive responses4.45.48.82.01.92.33.0
Condit. Reinf. lever presses6.59.09.32.93.03.13.0
Condit. Reinf. lever reinforcers received3.65.17.02.12.02.32.6
Pavlov. Cond. lever latency4.86.67.2-2.5-2.4-2.6-2.7
Pavlov. Cond. magazine entry latency2.42.74.01.41.51.62.0
Pavlov. Cond. change in total contacts8.411.713.63.33.13.53.7
Pavlov. Cond. index score4.96.47.22.52.42.62.7
Pavlov. Cond. latency score4.55.76.92.32.22.42.6
Pavlov. Cond. lever contacts4.56.36.72.52.42.62.6
Pavlov. Cond. magazine entry number4.04.95.3-2.3-2.2-2.3-2.1
Pavlov. Cond. intertrial magazine entries0.81.01.3-0.9-0.9-1.0-1.1
Pavlov. Cond. lever-magazine prob. diff.4.86.26.52.52.42.52.6
Pavlov. Cond. response bias5.37.47.82.72.52.82.8
Conditioned reinforcement - actives0.10.10.1-0.3-0.4-0.3-0.3
Conditioned reinforcement - inactives0.91.03.40.40.00.71.9
Conditioned locomotion2.02.53.7-1.6-1.9-1.6-0.9
Intermittent access intake day 1-15 change2.92.93.51.91.81.81.3
Intermittent access intake escalation2.92.93.41.81.71.81.4
Intermittent access intake escalation 21.71.71.91.41.41.31.1
Intermitt. access day 1 inactive lever presses2.73.05.11.41.51.72.3
Intermitt. access day 15 inactive lever presses0.50.51.80.20.10.51.4
Intermitt. access escalation Index0.00.00.1-0.1-0.3-0.10.1
Intermittent access day 1 total infusions1.71.93.5-1.4-1.9-1.4-0.7
Intermittent access day 15 total infusions0.20.20.60.1-0.40.20.8
Intermittent access terminal intake (last 3 days)0.30.30.7-0.4-0.8-0.30.5
Intermittent access total infusions0.40.41.1-0.5-1.0-0.50.2
Intermittent access day 1 locomotion1.01.12.3-1.1-1.5-0.90.2
Intermittent access day 15 total locomotion0.20.20.80.1-0.30.20.9
Intermittent access total locomotion1.01.22.2-1.2-1.5-1.0-0.2
Intermittent access standard deviation5.76.17.92.42.12.52.8
Cocaine induced anxiety0.30.40.40.50.70.60.6
Post-drug Anxiety0.20.30.5-0.7-0.5-0.5-0.2
Baseline Anxiety1.51.62.1-1.4-1.5-1.3-0.8
Lifetime Intake0.40.41.0-0.6-1.0-0.6-0.2
Incentive Sensitization - Responses0.00.00.10.0-0.2-0.00.0
Incentive Sensitization - Breakpoint0.00.00.00.1-0.2-0.0-0.0
Progressive ratio test 1 active lever presses0.80.81.80.80.40.81.3
Progressive ratio test 1 breakpoint1.21.22.21.00.61.11.5
Progressive ratio test 1 inactive lever presses0.70.82.70.40.00.61.6
Progressive ratio test 2 active lever presses0.20.20.50.3-0.10.30.7
Progressive ratio test 2 breakpoint0.10.10.30.2-0.20.20.5
Progressive ratio test 2 inactive lever presses1.31.55.50.3-0.20.82.3
Total sessions with >9 infusions0.91.01.3-0.9-1.0-1.0-1.1
Short access day 1 total inactive lever presses0.60.72.40.0-0.40.31.6
Short access day 10 total inactive lever presses1.41.53.40.90.81.11.8
Short access day 1 total infusions0.10.10.1-0.1-0.4-0.2-0.2
Short access day 10 total infusions0.30.30.4-0.4-0.7-0.5-0.5
Short access total infusions0.70.81.1-0.7-0.9-0.9-1.0
Short access day 1 locomotion0.20.20.3-0.4-0.5-0.5-0.5
Short access day 10 total locomotion0.80.82.50.50.30.71.6
Short access total locomotion0.91.01.4-1.1-1.2-1.0-0.6
Compulsive drug intake0.00.00.00.20.20.20.1
One hour access (0.3 mA shock)1.41.63.51.00.61.21.9
One hour access (shock baseline)0.20.20.70.1-0.20.30.9
Number of responses in last shaping day0.20.20.4-0.2-0.5-0.10.6
Context. condit. distance diff. score0.00.00.10.1-0.20.10.4
Locomotion velocity, session 10.60.61.5-0.5-0.4-0.8-1.2
Locomotion distance, session 10.70.91.01.00.80.91.0
Locomotion velocity, session 20.70.91.0-1.0-1.0-1.0-0.7
Locomotion distance, session 21.01.42.1-1.2-1.4-1.2-0.7
Locomotion velocity, session 30.20.20.3-0.4-0.5-0.5-0.5
Locomotion distance, session 33.13.46.61.51.21.82.6
Stereotopy head waving bouts, day 31.11.32.3-1.0-0.7-1.1-1.5
Stereotopy head waving duration, day 32.12.53.9-1.5-1.2-1.6-2.0
Locomotion velocity, session 70.50.50.90.70.50.71.0
Locomotion distance, session 70.30.30.50.70.60.60.3
Stereotopy head waving bouts, day 70.91.11.6-1.1-1.3-1.1-0.6
Stereotopy head waving duration, day 72.42.93.2-1.8-1.8-1.8-1.5
Locomotion velocity, session 83.33.95.2-2.1-2.3-2.0-1.5
Locomotion distance, session 80.40.61.3-0.7-1.1-0.7-0.1
Degree of sensitization distance0.50.61.7-0.3-0.2-0.6-1.3
Degree of sensitization stereotypy1.11.22.0-1.2-1.4-1.1-0.5
Condit. Reinf. active minus inactive responses0.30.30.4-0.6-0.6-0.6-0.4
Condit. Reinf. active-inactive response ratio0.50.60.8-0.9-0.5-0.7-0.8
Condit. Reinf. active responses2.12.63.3-1.7-1.8-1.7-1.2
Condit. Reinf. inactive responses1.82.13.3-1.4-1.8-1.5-0.8
Incentive salience index mean0.30.40.5-0.7-0.7-0.6-0.2
Condit. Reinf. lever presses0.10.20.3-0.3-0.4-0.10.6
Time in familiar zone, hab. session 10.60.61.10.91.00.6-0.3
Time in novel zone, hab. session 11.71.72.7-1.5-1.6-1.2-0.3
Total zone transitions, hab. session 10.00.00.10.0-0.20.00.3
Total locomotion distance, hab. session 10.81.12.30.80.81.01.5
Locomotion velocity, hab. session 10.40.61.20.60.60.71.1
Time in familiar zone, hab. session 21.21.31.60.91.31.11.2
Time in novel zone, hab. session 21.01.01.3-0.8-1.0-1.0-1.1
Total zone transitions, hab. session 23.14.14.8-2.1-2.2-2.1-1.6
Total locomotion distance, hab. session 20.30.40.6-0.7-0.8-0.50.3
Locomotion velocity, hab. session 20.30.40.7-0.7-0.8-0.60.0
Novel to familiar place preference ratio0.10.10.30.30.20.40.5
Novelty place preference0.10.10.20.30.20.30.5
Time in novel zone, NPP test0.00.00.10.1-0.00.10.3
Total zone transitions, NPP test0.00.00.1-0.1-0.1-0.2-0.3
Total locomotion distance, NPP test2.12.93.01.71.71.71.6
Locomotion velocity, NPP test2.13.03.11.71.81.71.7
Pavlov. Cond. lever latency0.30.40.60.70.80.60.1
Pavlov. Cond. magazine entry latency0.50.60.7-0.8-0.8-0.9-0.7
Pavlov. Cond. change in total contacts0.50.50.9-0.8-1.0-0.60.1
Pavlov. Cond. index score0.70.91.1-1.1-1.1-1.0-0.6
Pavlov. Cond. latency score0.40.50.8-0.8-0.9-0.8-0.3
Pavlov. Cond. lever contacts0.10.10.2-0.4-0.4-0.20.5
Pavlov. Cond. magazine entry number0.70.81.00.91.01.00.8
Pavlov. Cond. intertrial magazine entries0.70.80.9-0.9-0.8-0.9-1.0
Pavlov. Cond. lever-magazine prob. diff.0.91.21.4-1.2-1.2-1.1-0.7
Pavlov. Cond. response bias0.30.40.4-0.7-0.6-0.7-0.5
Bone: apparent density0.71.11.81.21.31.10.3
Bone surface1.83.23.61.91.81.81.6
Bone volume1.83.13.92.01.91.81.3
Bone: connectivity density0.20.40.50.70.70.60.5
Bone: cortical apparent density1.51.92.2-1.3-1.5-1.4-1.4
Bone: cortical area1.21.82.21.41.51.41.1
Bone: cortical porosity1.71.83.0-1.5-1.7-1.3-0.4
Bone: cortical porosity2.12.23.6-1.6-1.9-1.5-0.5
Bone: cortical thickness0.20.30.60.60.80.60.2
Bone: cortical thickness0.81.01.6-0.9-0.7-1.0-1.3
Bone: cortical tissue density1.82.32.6-1.4-1.6-1.6-1.5
Bone: elastic displacement0.00.00.1-0.10.1-0.1-0.4
Bone: elastic work1.52.02.41.41.51.51.2
Bone: endosteal estimation1.63.43.61.81.81.91.9
Bone: endosteal perimeter1.53.14.01.61.61.82.0
Bone: final force1.52.42.61.51.51.61.6
Bone: final moment1.93.23.51.81.81.91.7
Bone: marrow area1.63.53.71.81.81.91.9
Bone: maximum diameter1.32.32.51.51.61.61.5
Bone: maximum force2.54.44.72.12.02.22.1
Bone: maximum moment3.05.25.62.32.32.42.2
Bone: minimum diameter3.15.88.12.22.12.42.9
Bone: periosteal estimation2.04.04.32.02.12.11.9
Bone: periosteal perimeter1.11.82.01.31.41.41.3
Bone: post-yield work2.02.74.51.41.21.62.1
Bone: stiffness1.32.12.31.51.31.51.5
Bone: tissue strength3.63.44.81.71.51.92.2
Bone: trabecular number1.62.52.81.71.61.61.3
Bone: trabecular spacing0.00.00.10.00.30.20.2
Bone: trabecular thickness0.10.10.20.30.20.1-0.5
Bone: trabecular tissue density2.63.67.8-1.4-1.1-1.8-2.8
Breakpoint value in progressive ratio session1.31.54.00.60.71.12.0
Distance traveled before self-admin0.00.00.00.1-0.00.00.1
Distance traveled after self-admin4.04.55.32.11.92.12.3
Delta time in closed arm before/after self-admin2.72.73.21.71.81.71.3
Delta time in open arm before/after self-admin0.80.71.0-0.8-0.7-0.9-1.0
Diff in mean of infusions in LGA sessions0.60.71.2-1.0-1.1-0.70.2
Extinction: sum of active levers before priming3.33.44.21.92.01.91.5
Active lever presses in extinction session 62.12.03.41.41.81.40.8
Delta distance traveled before/after self-admin4.95.35.52.22.22.42.3
Delta ambulatory time before/after self-admin5.76.26.52.42.42.62.5
Time in closed arm before self-admin2.32.63.7-1.6-1.9-1.6-1.2
Time in closed arm after self-admin0.10.10.3-0.0-0.20.10.6
Time in open arm before self-admin4.14.35.42.12.32.11.8
Time in open arm after self-admin1.11.22.01.11.41.10.6
Sum of active levers in priming session hrs 5-60.10.10.20.40.40.40.3
Time to tail flick, vehicle, before self-admin0.90.91.2-1.0-1.1-1.0-0.8
Time to tail flick, vehicle, after self-admin0.10.10.2-0.5-0.3-0.30.2
Time to tail flick, test, before self-admin0.10.10.2-0.0-0.5-0.10.1
Time to tail flick, test, after self-admin0.00.00.00.00.10.00.0
Delta time to tail flick, vehicle, before/after SA0.50.50.80.50.70.70.9
Delta time to tail flick, test, before/after SA0.40.40.8-0.6-0.1-0.6-0.9
Ambulatory time before self-admin0.00.00.1-0.1-0.2-0.20.1
Ambulatory time after self-admin7.78.510.62.82.62.93.3
Total heroin consumption0.40.51.30.30.20.61.1
Area under the delay curve0.30.41.30.1-0.00.41.2
Delay disc. indifference point, 0s delay0.30.41.20.3-0.20.41.1
Delay disc. indifference point, 16s delay0.80.82.90.10.10.61.7
Delay disc. indifference point, 2s delay1.11.32.11.00.81.21.4
Delay disc. indifference point, 24s delay2.22.24.01.21.11.42.0
Delay disc. indifference point, 4s delay0.20.20.4-0.6-0.7-0.30.4
Delay disc. indifference point, 8s delay0.20.20.40.20.20.40.6
Delay discount exponential model param0.40.41.4-0.2-0.1-0.5-1.2
Delay discount hyperbolic model param0.30.31.2-0.1-0.1-0.4-1.1
Fecal boli incidents, locomotor time 12.83.03.8-2.0-1.8-1.9-1.3
Change in fecal boli incidents, locomotor task0.00.00.1-0.00.30.0-0.3
Time >=10cm from walls, locomotor time 10.10.10.1-0.2-0.2-0.2-0.3
Bouts of movement, locomotor time 10.70.82.10.70.40.81.5
Total resting periods, locomotor time 10.60.61.80.50.20.71.4
Rest time, locomotor task time 11.51.72.3-1.5-1.3-1.4-0.8
Distance moved, locomotor task time 10.20.20.40.60.50.50.0
Vertical activity count, locomotor time 12.42.52.71.61.61.61.5
Time >=10cm from walls, locomotor time 22.22.32.9-1.7-1.7-1.6-1.1
Bouts of movement, locomotor time 20.00.00.00.2-0.00.10.1
Total resting periods, locomotor time 20.00.00.0-0.1-0.2-0.2-0.1
Rest time, locomotor task time 20.70.81.2-1.1-0.9-1.0-0.5
Distance moved, locomotor task time 20.00.00.10.2-0.00.1-0.2
Vertical activity count, locomotor time 21.01.11.31.11.01.11.0
Weight adjusted by age0.10.10.30.30.50.4-0.2
Seeking ratio, delayed vs. immediate footshock1.51.82.71.30.91.41.6
Locomotion in novel chamber0.40.50.9-0.9-0.7-0.8-0.3
Locomotion in novel chamber post-restriction0.10.10.1-0.2-0.4-0.20.4
Progressive ratio0.10.10.1-0.3-0.2-0.10.3
Food seeking constrained by brief footshock2.93.54.61.71.71.92.1
Seeking ratio, punishment vs. effort0.60.80.91.00.70.91.0
Run reversals in cocaine runway, females0.90.91.21.11.01.00.7
Run reversals in cocaine runway, males0.50.51.7-0.30.1-0.5-1.3
Latency to leave start box in cocaine runway0.30.40.60.80.50.60.5
Latency to leave start box in cocaine runway, F0.00.00.10.20.00.20.3
Latency to leave start box in cocaine runway, M0.20.20.30.60.40.4-0.0
Cd content in liver0.20.20.30.50.50.4-0.1
Co content in liver0.40.50.7-0.8-0.7-0.7-0.6
Cu content in liver0.50.60.70.80.80.80.7
Fe content in liver0.00.00.1-0.2-0.3-0.20.0
K content in liver0.10.10.1-0.3-0.2-0.10.3
Mg content in liver1.01.01.5-1.2-1.0-1.0-0.7
Mn content in liver1.51.71.9-1.4-1.1-1.4-1.3
Na content in liver1.61.72.51.31.01.31.6
Rb content in liver0.20.20.4-0.5-0.6-0.30.4
Se content in liver8.310.110.7-3.2-3.1-3.3-3.2
Sr content in liver1.00.91.1-1.0-0.8-1.0-1.0
Zn content in liver0.10.20.2-0.5-0.4-0.4-0.2