Hub : Genes

Gc

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 Gc 0.05 0.03 7.1e-07 0.02 0.04 0.03 0.03 1.0e-03 4.7e-05 5.4e-04 5.3e-04
2 pVTA gene expression Gc 0.08 0.05 5.3e-03 0.01 0.02 -0.01 0 9.2e-02 3.0e-02 9.4e-01 2.0e-01
3 Liver mRNA stability Gc 0.52 0.1 0.0e+00 0.44 0.43 0.46 0.45 6.6e-54 2.8e-52 3.2e-56 2.1e-55

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 density1.93.24.42.1-2.01.2
Area under the delay curve1.41.54.1-0.5-0.42.0
BMI with tail2.58.213.13.3-3.60.9
BMI without tail0.10.20.30.5-0.4-0.2
Body weight0.10.41.0-0.10.21.0
Weight adjusted by age0.91.01.41.2-1.10.6
Bone surface0.61.02.21.5-0.9-0.1
Bone volume0.30.51.01.0-0.70.3
Breakpoint value in progressive ratio session0.10.10.10.20.1-0.4
Number of licking bursts0.10.10.20.5-0.30.1
Context. condit. distance diff. score1.01.21.6-1.10.8-1.3
Locomotion velocity, session 11.81.93.40.7-1.31.8
Locomotion distance, session 10.40.51.2-0.3-0.51.1
Locomotion velocity, session 20.81.02.8-0.3-0.31.7
Locomotion distance, session 20.60.92.2-0.6-0.31.5
Locomotion velocity, session 30.70.81.9-0.4-0.51.4
Locomotion distance, session 34.04.47.91.0-2.12.8
Stereotopy head waving bouts, day 30.10.10.3-0.50.2-0.2
Stereotopy head waving duration, day 30.50.60.9-0.70.6-0.9
Locomotion velocity, session 70.40.40.8-0.90.7-0.1
Locomotion distance, session 70.70.82.2-0.0-0.51.5
Stereotopy head waving bouts, day 70.30.40.50.6-0.5-0.7
Stereotopy head waving duration, day 70.20.20.40.5-0.6-0.1
Locomotion velocity, session 80.70.81.50.3-1.20.9
Locomotion distance, session 80.10.10.4-0.7-0.00.0
Degree of sensitization distance2.82.83.5-1.11.9-1.9
Degree of sensitization stereotypy0.10.20.20.4-0.5-0.2
Conditioned locomotion0.50.51.4-0.1-0.51.2
Cocaine response after cond. corrected0.60.60.9-1.00.9-0.4
Cocaine response after cond. not corrected0.60.61.2-0.40.7-1.1
Cocaine response before conditioning1.11.32.31.5-0.7-1.1
Saline control response0.10.20.3-0.50.60.1
Bone: connectivity density2.43.85.22.3-2.21.1
Bone: cortical apparent density1.01.42.60.6-1.11.6
Bone: cortical area0.71.13.00.40.4-1.7
Bone: cortical porosity0.91.01.71.1-1.30.3
Bone: cortical porosity1.11.21.81.3-1.3-0.2
Bone: cortical thickness1.42.33.51.9-1.1-1.5
Bone: cortical thickness1.21.43.2-0.11.0-1.8
Bone: cortical tissue density1.21.63.00.6-1.21.7
Condit. Reinf. active minus inactive responses0.00.00.10.3-0.2-0.1
Condit. Reinf. active-inactive response ratio1.01.12.40.8-0.4-1.6
Condit. Reinf. active responses0.20.20.60.0-0.10.8
Condit. Reinf. inactive responses0.70.82.4-0.30.11.5
Incentive salience index mean0.10.10.10.3-0.30.3
Condit. Reinf. lever presses0.40.60.70.7-0.70.8
Condit. Reinf. active minus inactive responses1.01.23.30.1-0.71.8
Condit. Reinf. active-inactive response ratio0.10.10.10.20.10.4
Condit. Reinf. active responses1.11.54.2-0.5-0.42.0
Condit. Reinf. inactive responses0.70.92.0-0.8-0.11.4
Condit. Reinf. lever presses1.41.93.2-1.81.50.5
Condit. Reinf. lever reinforcers received1.01.54.0-0.6-0.32.0
Conditioned reinforcement - actives0.50.51.0-0.6-0.01.0
Conditioned reinforcement - inactives1.11.21.9-1.21.4-0.7
Conditioned locomotion1.51.82.9-1.70.81.4
Patch foraging indifference point 0 sec0.40.61.0-0.0-0.91.0
Patch foraging indifference point AUC1.01.22.0-1.41.20.4
Delay disc. indifference point, 0s delay0.50.51.5-0.3-0.21.2
Delay disc. indifference point, 16s delay1.31.33.2-0.0-0.81.8
Delay disc. indifference point, 2s delay1.71.92.6-1.60.91.5
Delay disc. indifference point, 24s delay0.30.30.5-0.5-0.40.7
Delay disc. indifference point, 4s delay2.02.15.0-1.20.02.2
Delay disc. indifference point, 8s delay2.22.34.00.9-1.42.0
Indifference point function ln k0.60.81.80.7-0.2-1.3
Indifference point function log k0.60.81.80.7-0.2-1.3
Patch foraging total patch changes 0 sec0.20.30.5-0.1-0.70.6
Patch foraging total patch changes 12 sec0.70.92.0-0.8-0.21.4
Patch foraging total patch changes 18 sec0.00.10.10.2-0.30.2
Patch foraging total patch changes 24 sec0.60.71.2-1.1-0.20.9
Patch foraging total patch changes 6 sec0.40.61.0-0.9-0.11.0
Patch foraging time to switch 0 sec1.62.53.82.0-1.80.6
Patch foraging water rate 0 sec1.01.72.4-1.51.6-0.4
Patch foraging water rate 12 sec0.10.20.3-0.60.2-0.3
Patch foraging water rate 18 sec0.30.40.8-0.90.50.5
Patch foraging water rate 24 sec0.81.11.6-1.11.3-0.7
Patch foraging water rate 6 sec0.91.42.4-1.61.3-0.3
Seeking ratio, delayed vs. immediate footshock1.01.21.8-1.31.1-0.8
Distance traveled before self-admin0.80.81.7-1.30.8-0.1
Distance traveled after self-admin4.14.67.3-2.72.3-1.0
Extensor digitorum longus weight10.842.566.28.1-7.80.5
Bone: elastic displacement0.80.91.61.2-0.7-0.7
Bone: elastic work1.52.03.81.9-1.5-0.0
Bone: endosteal estimation2.04.36.9-2.32.6-0.8
Bone: endosteal perimeter0.61.32.4-1.11.5-0.4
Epididymis fat weight0.30.72.0-0.3-0.21.4
Delta time in closed arm before/after self-admin0.40.40.70.8-0.7-0.2
Delta time in open arm before/after self-admin1.21.21.9-1.10.61.4
Diff in mean of infusions in LGA sessions0.40.51.00.6-0.0-1.0
Delay discount exponential model param1.31.43.60.70.2-1.9
Extinction: sum of active levers before priming0.00.00.1-0.3-0.10.2
Active lever presses in extinction session 60.40.40.7-0.70.8-0.1
Bone: final force0.20.30.50.10.6-0.7
Bone: final moment0.20.30.5-0.10.7-0.6
Food consumed during 24 hour testing period0.20.30.80.1-0.30.9
Glucose1.52.23.5-1.91.7-0.5
Heart weight0.50.71.9-0.10.5-1.4
Delay discount hyperbolic model param1.81.94.70.90.1-2.2
Intermittent access intake day 1-15 change0.50.50.60.6-0.80.7
Intermittent access intake escalation0.30.30.60.2-0.50.8
Intermittent access intake escalation 21.61.62.6-1.61.30.7
Intermitt. access day 1 inactive lever presses0.50.51.10.5-1.00.4
Intermitt. access day 15 inactive lever presses1.31.42.5-0.21.3-1.6
Intermitt. access escalation Index2.32.02.91.7-0.6-1.7
Intermittent access day 1 total infusions1.01.12.0-1.41.1-0.4
Intermittent access day 15 total infusions1.21.32.6-1.61.2-0.0
Intermittent access terminal intake (last 3 days)3.03.35.5-2.32.1-0.4
Intermittent access total infusions1.31.42.5-1.61.3-0.3
Intermittent access day 1 locomotion0.40.40.8-0.90.6-0.3
Intermittent access day 15 total locomotion3.63.97.1-2.72.0-0.7
Intermittent access total locomotion1.41.53.0-1.71.3-0.2
Intermittent access standard deviation0.50.60.8-0.90.20.9
Left kidney weight1.02.74.6-1.92.1-0.4
Right kidney weight1.02.84.9-1.82.2-0.2
Cocaine induced anxiety0.50.61.40.30.6-1.2
Post-drug Anxiety0.50.50.7-0.80.80.5
Baseline Anxiety0.40.40.7-0.7-0.10.9
Tail length1.33.96.6-2.22.60.2
Length with tail3.111.417.9-4.04.20.3
Length without tail1.53.35.0-2.21.71.4
Times rat made contact with spout1.31.52.21.5-1.50.4
Lifetime Intake0.50.51.0-1.00.50.6
Liver weight, left1.72.77.0-1.0-0.22.6
Liver weight, right0.81.33.3-0.7-0.11.8
Locomotor activity0.60.91.3-1.10.61.0
Locomotor testing distance0.10.20.6-0.70.4-0.2
Locomotor testing rearing0.30.50.6-0.70.6-0.8
Locomotion in novel chamber0.20.30.6-0.2-0.50.8
Locomotion in novel chamber post-restriction1.31.62.0-1.41.01.3
Fecal boli incidents, locomotor time 10.10.10.10.40.20.3
Change in fecal boli incidents, locomotor task0.20.20.30.5-0.1-0.4
Time >=10cm from walls, locomotor time 10.20.20.30.5-0.30.4
Bouts of movement, locomotor time 11.01.02.5-0.40.7-1.6
Total resting periods, locomotor time 10.91.02.1-0.40.8-1.4
Rest time, locomotor task time 12.22.43.5-1.11.9-1.6
Distance moved, locomotor task time 11.61.72.90.7-1.41.7
Vertical activity count, locomotor time 11.01.02.6-0.2-0.71.6
Time >=10cm from walls, locomotor time 20.10.20.40.6-0.30.1
Bouts of movement, locomotor time 20.90.91.3-1.20.9-0.9
Total resting periods, locomotor time 20.90.91.1-1.10.9-0.9
Rest time, locomotor task time 22.63.04.5-1.31.6-2.1
Distance moved, locomotor task time 23.23.74.71.9-2.21.7
Vertical activity count, locomotor time 22.22.45.80.5-1.12.4
Light reinforcement 10.30.61.2-0.70.21.1
Light reinforcement 20.81.12.40.2-1.01.6
Bone: marrow area1.94.16.5-2.22.5-0.9
Bone: maximum diameter0.50.92.20.20.7-1.5
Bone: maximum force0.40.61.2-0.10.8-1.1
Bone: maximum moment0.40.61.0-0.30.9-1.0
Mean time between licks in bursts0.00.00.10.20.1-0.2
Mean num. licks in bursts0.10.10.10.1-0.20.3
Cd content in liver1.31.53.80.70.3-1.9
Co content in liver1.92.22.6-1.41.6-1.4
Cu content in liver0.91.12.0-1.41.1-0.1
Fe content in liver2.73.36.91.0-1.32.6
K content in liver1.91.94.8-0.8-0.42.2
Mg content in liver2.12.14.4-1.30.42.1
Mn content in liver0.40.40.70.3-0.70.8
Na content in liver1.31.43.5-0.6-0.51.9
Rb content in liver0.00.00.10.10.2-0.2
Se content in liver0.60.81.3-1.00.21.1
Sr content in liver3.63.38.60.21.1-2.9
Zn content in liver0.40.50.8-0.90.30.7
Bone: minimum diameter5.710.616.8-3.74.1-1.2
Time in familiar zone, hab. session 11.00.91.50.4-1.01.2
Time in novel zone, hab. session 10.90.81.4-0.81.2-0.7
Total zone transitions, hab. session 11.52.15.1-1.0-0.42.3
Total locomotion distance, hab. session 11.52.13.9-2.01.11.1
Locomotion velocity, hab. session 10.81.12.2-1.50.60.9
Time in familiar zone, hab. session 20.70.70.90.9-0.90.7
Time in novel zone, hab. session 21.31.31.6-0.91.2-1.2
Total zone transitions, hab. session 20.60.81.9-0.20.7-1.4
Total locomotion distance, hab. session 22.02.64.0-1.11.6-2.0
Locomotion velocity, hab. session 21.31.72.0-1.21.4-1.4
Novel to familiar place preference ratio0.10.10.2-0.40.10.3
Novelty place preference0.20.20.3-0.40.10.6
Time in novel zone, NPP test0.30.30.6-0.70.20.7
Total zone transitions, NPP test0.10.20.20.5-0.40.5
Total locomotion distance, NPP test0.00.00.1-0.30.2-0.1
Locomotion velocity, NPP test0.00.00.0-0.0-0.1-0.1
Intraocular pressure1.11.54.00.3-0.72.0
Delta distance traveled before/after self-admin0.40.40.6-0.60.8-0.6
Delta ambulatory time before/after self-admin0.30.30.7-0.10.4-0.9
Parametrial fat weight0.20.30.5-0.40.60.7
Pavlov. Cond. lever latency0.40.50.70.9-0.5-0.7
Pavlov. Cond. magazine entry latency0.20.20.5-0.0-0.50.7
Pavlov. Cond. change in total contacts0.10.10.2-0.40.20.4
Pavlov. Cond. index score0.40.61.5-0.3-0.41.2
Pavlov. Cond. latency score0.30.41.0-0.3-0.21.0
Pavlov. Cond. lever contacts0.40.50.7-0.80.60.7
Pavlov. Cond. magazine entry number0.10.10.2-0.10.4-0.5
Pavlov. Cond. intertrial magazine entries0.70.81.4-1.20.90.5
Pavlov. Cond. lever-magazine prob. diff.0.50.61.6-0.3-0.41.3
Pavlov. Cond. response bias0.50.61.3-0.60.11.2
Pavlov. Cond. lever latency0.20.20.60.20.0-0.8
Pavlov. Cond. magazine entry latency0.10.10.2-0.30.5-0.0
Pavlov. Cond. change in total contacts0.10.10.2-0.1-0.20.4
Pavlov. Cond. index score0.10.10.1-0.30.40.2
Pavlov. Cond. latency score0.00.00.00.00.20.0
Pavlov. Cond. lever contacts0.30.51.1-0.50.21.0
Pavlov. Cond. magazine entry number0.00.00.1-0.30.0-0.2
Pavlov. Cond. intertrial magazine entries0.20.30.8-0.30.30.9
Pavlov. Cond. lever-magazine prob. diff.0.10.10.2-0.30.40.3
Pavlov. Cond. response bias0.40.51.3-0.4-0.01.1
Time in closed arm before self-admin1.11.21.6-1.01.3-1.0
Time in closed arm after self-admin2.32.34.0-1.01.4-2.0
Time in open arm before self-admin1.31.42.31.5-1.30.2
Time in open arm after self-admin2.12.36.4-0.1-0.72.5
Bone: periosteal estimation1.12.23.2-1.11.8-1.5
Bone: periosteal perimeter0.40.71.4-0.30.8-1.2
Bone: post-yield work0.71.01.7-1.11.3-0.3
Progressive ratio test 1 active lever presses2.02.03.8-1.91.50.4
Progressive ratio test 1 breakpoint1.41.52.8-1.71.20.5
Progressive ratio test 1 inactive lever presses0.20.20.6-0.80.20.2
Progressive ratio test 2 active lever presses2.22.44.8-2.21.50.4
Progressive ratio test 2 breakpoint1.41.63.2-1.81.20.5
Progressive ratio test 2 inactive lever presses2.12.54.2-2.11.8-0.3
Incentive Sensitization - Responses0.80.81.2-1.11.1-0.2
Incentive Sensitization - Breakpoint0.91.01.4-1.21.2-0.3
Sum of active levers in priming session hrs 5-60.40.40.60.2-0.70.8
Progressive ratio0.70.81.21.1-1.1-0.2
Food seeking constrained by brief footshock0.10.10.30.4-0.5-0.2
Seeking ratio, punishment vs. effort0.20.30.5-0.70.60.1
Retroperitoneal fat weight0.72.22.7-1.61.21.6
Reaction time number correct0.10.20.3-0.30.5-0.4
Reaction time mean minus median0.30.41.10.3-0.31.0
Reaction time mean minus median AUC0.20.31.0-0.10.01.0
Reaction time num false alarms0.10.20.5-0.70.2-0.0
Reaction time num false alarms AUC0.10.10.3-0.5-0.20.2
Reaction time trials correct on left0.10.20.3-0.30.5-0.4
Reaction time trials on left0.10.20.3-0.30.5-0.3
Reaction time mean0.10.10.30.10.5-0.3
Reaction time mean AUC0.20.20.5-0.20.7-0.4
Median of all reaction times0.20.30.60.10.6-0.8
Reaction time omissions0.30.30.50.5-0.50.7
Reaction time false alarm rate0.10.20.2-0.4-0.30.5
Reaction time premature initiation rate0.40.50.9-1.00.7-0.3
Reaction time premature initiations0.71.01.6-1.31.1-0.4
Std. dev. reaction times0.10.10.2-0.30.50.2
Reaction time trials completed0.10.20.3-0.30.5-0.3
Reaction time trials AUC0.10.20.3-0.30.6-0.4
Run reversals in cocaine runway, females0.10.10.2-0.30.4-0.0
Run reversals in cocaine runway, males0.50.50.80.9-0.70.4
Latency to leave start box in cocaine runway3.63.95.0-1.52.1-2.2
Latency to leave start box in cocaine runway, F4.24.66.0-2.22.4-1.7
Latency to leave start box in cocaine runway, M1.11.12.21.00.1-1.5
Std. dev. time between licks in bursts0.81.02.40.2-0.81.5
Total sessions with >9 infusions1.82.02.91.2-1.71.2
Short access day 1 total inactive lever presses0.20.20.5-0.70.4-0.1
Short access day 10 total inactive lever presses0.70.82.10.10.4-1.5
Short access day 1 total infusions0.30.30.9-0.1-0.30.9
Short access day 10 total infusions0.30.40.6-0.70.00.7
Short access total infusions1.01.12.30.4-0.91.5
Short access day 1 locomotion0.40.51.1-0.4-0.11.1
Short access day 10 total locomotion0.20.20.4-0.50.2-0.7
Short access total locomotion0.10.10.20.2-0.50.3
One hour access (0.3 mA shock)2.83.35.7-2.41.80.9
Compulsive drug intake1.61.62.81.7-1.40.3
One hour access (shock baseline)2.83.36.0-2.51.71.0
Social response proportion0.20.20.5-0.30.20.7
Social responses0.40.51.2-0.5-0.01.1
Social time0.50.71.1-1.00.90.1
Soleus weight1.75.09.02.5-3.00.1
Bone: stiffness0.61.01.8-1.31.10.3
Tibialis anterior weight3.913.221.24.2-4.60.9
Time to tail flick, vehicle, before self-admin1.11.12.2-1.11.5-0.0
Time to tail flick, vehicle, after self-admin1.01.12.4-1.60.90.0
Time to tail flick, test, before self-admin0.10.10.20.3-0.3-0.4
Time to tail flick, test, after self-admin3.03.15.0-2.22.1-0.0
Delta time to tail flick, vehicle, before/after SA0.30.30.7-0.3-0.50.8
Delta time to tail flick, test, before/after SA2.32.13.2-1.81.41.0
Tibia length1.95.310.1-1.93.2-1.4
Ambulatory time before self-admin1.21.32.9-1.71.00.0
Ambulatory time after self-admin4.34.78.0-2.82.3-0.9
Bone: tissue strength0.50.50.8-0.90.60.5
Total heroin consumption2.32.73.4-1.61.8-1.5
Bone: trabecular number1.72.73.31.6-1.81.5
Bone: trabecular spacing0.40.50.8-0.90.8-0.5
Bone: trabecular thickness0.30.40.50.6-0.60.7
Bone: trabecular tissue density0.10.10.20.20.1-0.5
Water consumed over 24 hours0.00.00.10.1-0.10.4
Number of responses in last shaping day3.03.14.31.2-1.92.1