Hub : Genes

Gnmt

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 gene expression Gnmt 0.36 0.13 0.0e+00 0.32 0.32 0.32 0.32 1.3e-35 1.5e-36 2.4e-36 8.3e-36
2 Liver mRNA stability Gnmt 0.14 0.08 1.8e-07 0.04 0.04 0.04 0.04 3.1e-05 1.5e-05 3.0e-05 8.1e-05

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
Bone: apparent density0.20.40.5-0.70.6
Area under the delay curve8.59.09.1-3.03.0
BMI with tail4.113.414.73.8-3.5
BMI without tail12.525.928.45.3-4.8
Body weight3.012.414.53.8-3.2
Weight adjusted by age0.20.20.20.5-0.5
Bone surface1.32.32.3-1.51.5
Bone volume0.50.80.8-0.90.9
Breakpoint value in progressive ratio session0.00.00.0-0.10.1
Number of licking bursts4.14.85.32.1-2.3
Context. condit. distance diff. score0.10.10.30.5-0.2
Locomotion velocity, session 10.40.40.60.8-0.5
Locomotion distance, session 12.22.83.41.8-1.5
Locomotion velocity, session 25.26.07.52.7-2.1
Locomotion distance, session 21.31.92.21.5-1.2
Locomotion velocity, session 30.30.40.60.8-0.4
Locomotion distance, session 30.91.01.3-0.91.1
Stereotopy head waving bouts, day 31.51.71.91.2-1.4
Stereotopy head waving duration, day 32.22.72.91.6-1.7
Locomotion velocity, session 70.10.10.30.5-0.1
Locomotion distance, session 70.00.00.10.3-0.1
Stereotopy head waving bouts, day 70.20.20.30.5-0.4
Stereotopy head waving duration, day 70.00.00.0-0.20.1
Locomotion velocity, session 80.50.60.80.9-0.6
Locomotion distance, session 81.01.41.91.4-1.0
Degree of sensitization distance1.91.92.01.4-1.3
Degree of sensitization stereotypy0.50.50.6-0.60.8
Conditioned locomotion1.92.32.6-1.41.6
Cocaine response after cond. corrected0.20.20.3-0.60.4
Cocaine response after cond. not corrected0.40.40.6-0.80.5
Cocaine response before conditioning0.00.00.00.2-0.1
Saline control response0.00.00.00.00.2
Bone: connectivity density0.60.91.2-1.10.7
Bone: cortical apparent density0.91.21.5-1.01.2
Bone: cortical area0.50.71.31.2-0.2
Bone: cortical porosity0.10.10.20.3-0.4
Bone: cortical porosity0.10.10.10.2-0.3
Bone: cortical thickness0.71.11.91.4-0.5
Bone: cortical thickness0.00.00.0-0.00.2
Bone: cortical tissue density0.81.01.2-0.91.1
Condit. Reinf. active minus inactive responses1.82.02.11.4-1.4
Condit. Reinf. active-inactive response ratio0.40.40.60.5-0.7
Condit. Reinf. active responses2.93.53.92.0-1.8
Condit. Reinf. inactive responses2.22.63.21.8-1.4
Incentive salience index mean2.12.63.11.8-1.4
Condit. Reinf. lever presses3.85.16.42.5-2.0
Condit. Reinf. active minus inactive responses0.00.10.1-0.0-0.3
Condit. Reinf. active-inactive response ratio1.11.11.60.8-1.3
Condit. Reinf. active responses0.00.00.0-0.1-0.1
Condit. Reinf. inactive responses0.10.10.2-0.10.4
Condit. Reinf. lever presses0.50.70.70.8-0.8
Condit. Reinf. lever reinforcers received0.00.00.0-0.1-0.0
Conditioned reinforcement - actives0.90.91.2-0.91.1
Conditioned reinforcement - inactives0.70.71.01.0-0.7
Conditioned locomotion0.00.00.00.1-0.0
Patch foraging indifference point 0 sec0.91.41.61.1-1.3
Patch foraging indifference point AUC0.70.80.91.0-0.8
Delay disc. indifference point, 0s delay1.11.22.2-1.50.6
Delay disc. indifference point, 16s delay12.512.613.0-3.53.6
Delay disc. indifference point, 2s delay2.83.24.0-2.01.5
Delay disc. indifference point, 24s delay1.41.31.3-1.21.1
Delay disc. indifference point, 4s delay3.03.23.6-1.61.9
Delay disc. indifference point, 8s delay5.25.45.6-2.32.4
Indifference point function ln k0.40.50.7-0.90.6
Indifference point function log k0.40.50.7-0.90.6
Patch foraging total patch changes 0 sec1.21.92.01.3-1.4
Patch foraging total patch changes 12 sec0.81.11.61.3-0.7
Patch foraging total patch changes 18 sec1.41.72.11.4-1.2
Patch foraging total patch changes 24 sec0.81.01.21.1-0.9
Patch foraging total patch changes 6 sec2.13.13.71.9-1.6
Patch foraging time to switch 0 sec4.77.37.4-2.72.7
Patch foraging water rate 0 sec2.33.64.52.1-1.7
Patch foraging water rate 12 sec5.38.19.33.0-2.6
Patch foraging water rate 18 sec1.21.61.91.4-1.2
Patch foraging water rate 24 sec2.12.92.91.7-1.7
Patch foraging water rate 6 sec0.20.20.40.6-0.3
Seeking ratio, delayed vs. immediate footshock2.12.42.7-1.71.5
Distance traveled before self-admin0.10.10.20.5-0.2
Distance traveled after self-admin4.24.75.22.1-2.3
Extensor digitorum longus weight0.10.30.40.6-0.4
Bone: elastic displacement0.40.40.5-0.60.7
Bone: elastic work0.00.00.10.20.1
Bone: endosteal estimation0.40.81.0-1.00.8
Bone: endosteal perimeter0.00.00.00.10.1
Epididymis fat weight2.04.75.42.3-2.0
Delta time in closed arm before/after self-admin0.10.10.10.4-0.4
Delta time in open arm before/after self-admin0.30.30.5-0.70.3
Diff in mean of infusions in LGA sessions0.30.40.40.7-0.6
Delay discount exponential model param8.48.99.22.9-3.0
Extinction: sum of active levers before priming0.00.00.00.0-0.2
Active lever presses in extinction session 60.00.00.00.2-0.2
Bone: final force0.30.51.01.0-0.3
Bone: final moment0.30.50.90.9-0.2
Food consumed during 24 hour testing period0.50.60.60.8-0.7
Glucose5.48.18.32.8-2.9
Heart weight1.42.02.1-1.41.5
Delay discount hyperbolic model param7.47.87.92.8-2.8
Intermittent access intake day 1-15 change0.10.10.10.30.2
Intermittent access intake escalation0.00.00.10.10.3
Intermittent access intake escalation 20.10.10.10.30.1
Intermitt. access day 1 inactive lever presses1.51.61.71.3-1.2
Intermitt. access day 15 inactive lever presses1.92.12.31.5-1.3
Intermitt. access escalation Index0.00.00.0-0.2-0.1
Intermittent access day 1 total infusions0.70.81.10.8-1.0
Intermittent access day 15 total infusions0.30.40.40.6-0.6
Intermittent access terminal intake (last 3 days)0.20.20.20.4-0.4
Intermittent access total infusions0.10.20.20.3-0.5
Intermittent access day 1 locomotion0.40.40.60.4-0.8
Intermittent access day 15 total locomotion0.30.40.40.6-0.6
Intermittent access total locomotion0.10.10.10.1-0.3
Intermittent access standard deviation3.43.63.7-1.91.9
Left kidney weight0.10.30.70.8-0.0
Right kidney weight0.00.10.10.20.3
Cocaine induced anxiety0.10.10.20.3-0.4
Post-drug Anxiety0.00.00.0-0.00.1
Baseline Anxiety0.30.30.4-0.50.6
Tail length1.85.46.72.6-2.0
Length with tail0.10.20.50.70.0
Length without tail3.06.67.4-2.42.7
Times rat made contact with spout5.76.67.32.4-2.7
Lifetime Intake0.00.00.1-0.20.1
Liver weight, left0.30.50.70.8-0.5
Liver weight, right0.50.81.21.1-0.6
Locomotor activity2.23.53.92.0-1.8
Locomotor testing distance1.83.03.51.9-1.6
Locomotor testing rearing3.35.05.32.3-2.2
Locomotion in novel chamber0.91.11.3-0.91.1
Locomotion in novel chamber post-restriction1.41.72.1-1.11.5
Fecal boli incidents, locomotor time 10.50.50.8-0.50.9
Change in fecal boli incidents, locomotor task0.10.00.1-0.20.2
Time >=10cm from walls, locomotor time 10.30.30.30.6-0.6
Bouts of movement, locomotor time 10.10.10.1-0.4-0.3
Total resting periods, locomotor time 10.30.30.60.2-0.8
Rest time, locomotor task time 10.60.60.9-1.00.6
Distance moved, locomotor task time 10.00.00.00.2-0.1
Vertical activity count, locomotor time 10.70.80.9-0.81.0
Time >=10cm from walls, locomotor time 20.50.50.60.8-0.7
Bouts of movement, locomotor time 20.30.40.40.6-0.6
Total resting periods, locomotor time 20.10.10.10.2-0.3
Rest time, locomotor task time 20.50.60.9-0.90.6
Distance moved, locomotor task time 21.11.31.41.1-1.2
Vertical activity count, locomotor time 20.10.10.2-0.30.4
Light reinforcement 12.03.64.02.0-1.8
Light reinforcement 22.73.63.81.9-1.8
Bone: marrow area0.51.01.1-1.00.9
Bone: maximum diameter0.10.20.40.6-0.2
Bone: maximum force0.00.00.10.30.1
Bone: maximum moment0.00.00.00.20.2
Mean time between licks in bursts1.21.72.4-1.51.0
Mean num. licks in bursts0.50.50.6-0.80.7
Cd content in liver1.01.01.3-1.20.9
Co content in liver0.10.10.20.0-0.5
Cu content in liver0.60.70.8-0.80.9
Fe content in liver0.70.81.2-0.61.1
K content in liver0.40.40.5-0.70.5
Mg content in liver2.32.42.9-1.41.7
Mn content in liver1.41.62.50.8-1.6
Na content in liver0.10.10.10.40.2
Rb content in liver7.59.310.6-2.83.3
Se content in liver0.10.20.30.3-0.5
Sr content in liver0.90.80.90.8-1.0
Zn content in liver5.05.66.0-2.32.4
Bone: minimum diameter0.20.40.60.8-0.3
Time in familiar zone, hab. session 10.40.40.70.9-0.3
Time in novel zone, hab. session 10.70.61.2-1.10.3
Total zone transitions, hab. session 14.25.86.72.6-2.2
Total locomotion distance, hab. session 14.46.27.22.7-2.3
Locomotion velocity, hab. session 13.85.46.62.6-2.0
Time in familiar zone, hab. session 22.22.32.6-1.41.6
Time in novel zone, hab. session 20.50.50.70.5-0.8
Total zone transitions, hab. session 23.03.94.21.9-2.1
Total locomotion distance, hab. session 23.54.64.82.1-2.2
Locomotion velocity, hab. session 22.73.73.91.9-2.0
Novel to familiar place preference ratio0.10.10.10.3-0.3
Novelty place preference0.00.00.00.10.0
Time in novel zone, NPP test0.00.00.00.1-0.0
Total zone transitions, NPP test6.89.711.03.3-2.9
Total locomotion distance, NPP test6.28.59.33.0-2.8
Locomotion velocity, NPP test6.59.210.63.3-2.8
Intraocular pressure0.71.01.8-1.30.6
Delta distance traveled before/after self-admin5.76.17.52.2-2.7
Delta ambulatory time before/after self-admin4.85.26.52.0-2.5
Parametrial fat weight6.212.113.53.7-3.3
Pavlov. Cond. lever latency2.12.73.9-2.01.2
Pavlov. Cond. magazine entry latency0.50.71.01.0-0.5
Pavlov. Cond. change in total contacts1.92.12.41.6-1.3
Pavlov. Cond. index score2.22.74.02.0-1.2
Pavlov. Cond. latency score1.41.82.81.7-0.8
Pavlov. Cond. lever contacts3.13.65.12.3-1.5
Pavlov. Cond. magazine entry number1.51.92.7-1.61.1
Pavlov. Cond. intertrial magazine entries0.81.01.2-1.10.9
Pavlov. Cond. lever-magazine prob. diff.2.02.53.61.9-1.2
Pavlov. Cond. response bias3.84.76.02.5-1.8
Pavlov. Cond. lever latency2.43.23.7-1.91.6
Pavlov. Cond. magazine entry latency1.61.82.51.6-1.1
Pavlov. Cond. change in total contacts2.23.13.71.9-1.6
Pavlov. Cond. index score4.25.46.72.6-2.1
Pavlov. Cond. latency score4.75.87.02.6-2.1
Pavlov. Cond. lever contacts2.53.44.32.1-1.6
Pavlov. Cond. magazine entry number0.60.81.3-1.10.5
Pavlov. Cond. intertrial magazine entries0.00.00.1-0.1-0.2
Pavlov. Cond. lever-magazine prob. diff.4.25.36.52.6-2.0
Pavlov. Cond. response bias0.71.01.61.3-0.7
Time in closed arm before self-admin0.10.20.2-0.50.3
Time in closed arm after self-admin0.00.00.0-0.1-0.2
Time in open arm before self-admin2.42.73.51.9-1.3
Time in open arm after self-admin0.50.50.50.7-0.7
Bone: periosteal estimation0.00.10.10.30.1
Bone: periosteal perimeter0.50.81.41.2-0.5
Bone: post-yield work0.00.00.00.0-0.1
Progressive ratio test 1 active lever presses1.31.31.61.0-1.2
Progressive ratio test 1 breakpoint1.01.11.21.0-1.1
Progressive ratio test 1 inactive lever presses1.01.11.11.1-1.0
Progressive ratio test 2 active lever presses1.21.31.41.2-1.1
Progressive ratio test 2 breakpoint1.82.02.21.5-1.4
Progressive ratio test 2 inactive lever presses0.50.60.70.8-0.7
Incentive Sensitization - Responses1.11.21.41.2-1.0
Incentive Sensitization - Breakpoint1.21.21.41.2-1.0
Sum of active levers in priming session hrs 5-60.90.80.9-0.91.0
Progressive ratio0.80.91.3-0.71.2
Food seeking constrained by brief footshock0.00.00.00.2-0.1
Seeking ratio, punishment vs. effort0.70.81.00.8-1.0
Retroperitoneal fat weight1.55.06.22.5-1.9
Reaction time number correct0.10.10.2-0.20.4
Reaction time mean minus median0.20.20.3-0.30.6
Reaction time mean minus median AUC0.40.50.5-0.70.7
Reaction time num false alarms0.71.01.0-1.01.0
Reaction time num false alarms AUC0.50.70.8-0.90.9
Reaction time trials correct on left0.10.10.2-0.20.4
Reaction time trials on left0.10.10.1-0.20.4
Reaction time mean0.10.10.2-0.40.3
Reaction time mean AUC0.10.10.1-0.30.1
Median of all reaction times0.00.00.0-0.20.0
Reaction time omissions0.50.60.60.8-0.8
Reaction time false alarm rate0.60.91.0-1.00.9
Reaction time premature initiation rate1.01.41.51.2-1.1
Reaction time premature initiations0.81.21.41.2-1.0
Std. dev. reaction times0.10.20.3-0.40.5
Reaction time trials completed0.10.10.1-0.20.4
Reaction time trials AUC0.00.00.0-0.00.2
Run reversals in cocaine runway, females0.60.50.80.9-0.5
Run reversals in cocaine runway, males0.10.10.10.2-0.3
Latency to leave start box in cocaine runway1.92.02.31.5-1.3
Latency to leave start box in cocaine runway, F0.20.20.20.5-0.5
Latency to leave start box in cocaine runway, M4.74.65.22.3-2.0
Std. dev. time between licks in bursts1.82.22.2-1.51.5
Total sessions with >9 infusions0.00.00.0-0.10.0
Short access day 1 total inactive lever presses0.00.10.10.3-0.1
Short access day 10 total inactive lever presses0.80.91.11.0-0.9
Short access day 1 total infusions0.30.40.4-0.60.6
Short access day 10 total infusions0.00.00.0-0.0-0.2
Short access total infusions0.30.40.4-0.70.5
Short access day 1 locomotion0.60.60.7-0.80.7
Short access day 10 total locomotion2.02.22.6-1.61.3
Short access total locomotion2.22.22.5-1.61.4
One hour access (0.3 mA shock)0.30.30.4-0.50.7
Compulsive drug intake0.00.00.0-0.10.2
One hour access (shock baseline)0.20.20.20.5-0.4
Social response proportion1.21.31.8-0.91.3
Social responses2.83.64.9-1.52.2
Social time1.82.33.3-1.21.8
Soleus weight0.31.01.51.2-0.7
Bone: stiffness0.00.00.0-0.00.2
Tibialis anterior weight0.20.70.70.8-0.8
Time to tail flick, vehicle, before self-admin0.40.40.7-0.40.8
Time to tail flick, vehicle, after self-admin2.62.82.9-1.61.7
Time to tail flick, test, before self-admin5.55.45.9-2.22.4
Time to tail flick, test, after self-admin0.60.60.8-0.70.9
Delta time to tail flick, vehicle, before/after SA0.50.50.6-0.80.7
Delta time to tail flick, test, before/after SA1.31.11.11.1-1.1
Tibia length2.36.57.12.7-2.4
Ambulatory time before self-admin0.10.10.2-0.00.4
Ambulatory time after self-admin4.04.44.62.0-2.1
Bone: tissue strength0.10.10.2-0.30.4
Total heroin consumption0.10.10.10.3-0.3
Bone: trabecular number0.50.80.9-0.81.0
Bone: trabecular spacing0.40.60.60.8-0.7
Bone: trabecular thickness0.70.81.0-1.00.8
Bone: trabecular tissue density0.00.10.1-0.30.2
Water consumed over 24 hours1.92.33.01.7-1.3
Number of responses in last shaping day0.10.10.10.4-0.2