Hub : Genes

Cgref1

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 PL gene expression Cgref1 0.02 0.02 4.2e-03 0.02 0.02 0.02 0.02 4.2e-03 5.9e-03 5.0e-03 6.7e-03

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
Bone: apparent density3.25.95.9-2.4
Area under the delay curve0.00.00.0-0.1
BMI with tail0.20.70.70.8
BMI without tail0.31.41.41.2
Body weight2.410.510.53.2
Weight adjusted by age0.10.40.4-0.6
Bone surface0.61.21.2-1.1
Bone volume0.81.61.6-1.3
Breakpoint value in progressive ratio session0.40.70.7-0.8
Number of licking bursts0.00.10.10.3
Context. condit. distance diff. score0.00.00.0-0.2
Locomotion velocity, session 10.50.60.60.8
Locomotion distance, session 10.20.20.2-0.5
Locomotion velocity, session 20.20.20.20.5
Locomotion distance, session 20.00.10.10.3
Locomotion velocity, session 31.51.81.8-1.3
Locomotion distance, session 30.40.50.5-0.7
Stereotopy head waving bouts, day 32.83.43.4-1.8
Stereotopy head waving duration, day 30.40.50.5-0.7
Locomotion velocity, session 70.91.01.0-1.0
Locomotion distance, session 70.00.00.00.1
Stereotopy head waving bouts, day 70.10.10.1-0.4
Stereotopy head waving duration, day 71.11.31.3-1.1
Locomotion velocity, session 80.30.30.3-0.6
Locomotion distance, session 80.10.20.2-0.5
Degree of sensitization distance1.31.41.41.2
Degree of sensitization stereotypy0.00.00.00.0
Conditioned locomotion3.64.34.3-2.1
Cocaine response after cond. corrected0.00.00.0-0.0
Cocaine response after cond. not corrected0.30.40.4-0.7
Cocaine response before conditioning3.84.54.5-2.1
Saline control response1.52.12.1-1.5
Bone: connectivity density3.14.94.9-2.2
Bone: cortical apparent density0.20.40.4-0.6
Bone: cortical area0.00.00.0-0.1
Bone: cortical porosity2.62.82.8-1.7
Bone: cortical porosity1.71.91.9-1.4
Bone: cortical thickness0.20.30.30.5
Bone: cortical thickness0.40.50.5-0.7
Bone: cortical tissue density0.10.20.2-0.5
Condit. Reinf. active minus inactive responses1.61.81.81.3
Condit. Reinf. active-inactive response ratio1.71.81.81.3
Condit. Reinf. active responses0.00.00.00.1
Condit. Reinf. inactive responses1.51.91.9-1.4
Incentive salience index mean0.30.40.40.6
Condit. Reinf. lever presses0.00.10.1-0.3
Condit. Reinf. active minus inactive responses5.17.87.8-2.8
Condit. Reinf. active-inactive response ratio2.03.13.1-1.8
Condit. Reinf. active responses4.36.26.2-2.5
Condit. Reinf. inactive responses0.91.31.3-1.1
Condit. Reinf. lever presses2.84.04.0-2.0
Condit. Reinf. lever reinforcers received4.05.75.7-2.4
Conditioned reinforcement - actives0.83.33.3-1.8
Conditioned reinforcement - inactives1.33.63.6-1.9
Conditioned locomotion0.71.01.0-1.0
Patch foraging indifference point 0 sec0.30.80.80.9
Patch foraging indifference point AUC0.10.30.3-0.6
Delay disc. indifference point, 0s delay4.34.84.82.2
Delay disc. indifference point, 16s delay0.10.10.1-0.3
Delay disc. indifference point, 2s delay0.40.50.50.7
Delay disc. indifference point, 24s delay0.20.40.4-0.6
Delay disc. indifference point, 4s delay0.00.00.00.1
Delay disc. indifference point, 8s delay0.00.00.0-0.1
Indifference point function ln k0.10.30.3-0.5
Indifference point function log k0.10.30.3-0.5
Patch foraging total patch changes 0 sec0.20.70.70.8
Patch foraging total patch changes 12 sec1.11.51.51.2
Patch foraging total patch changes 18 sec0.10.30.30.6
Patch foraging total patch changes 24 sec0.20.80.80.9
Patch foraging total patch changes 6 sec0.20.30.30.6
Patch foraging time to switch 0 sec0.00.00.00.1
Patch foraging water rate 0 sec0.00.00.0-0.2
Patch foraging water rate 12 sec0.20.90.91.0
Patch foraging water rate 18 sec0.00.10.10.3
Patch foraging water rate 24 sec0.71.01.01.0
Patch foraging water rate 6 sec0.60.90.91.0
Seeking ratio, delayed vs. immediate footshock0.00.00.0-0.1
Distance traveled before self-admin0.10.20.20.4
Distance traveled after self-admin2.34.04.02.0
Extensor digitorum longus weight4.417.517.5-4.2
Bone: elastic displacement0.60.70.7-0.9
Bone: elastic work0.40.50.5-0.7
Bone: endosteal estimation0.00.10.1-0.3
Bone: endosteal perimeter0.00.00.0-0.2
Epididymis fat weight9.949.849.87.1
Delta time in closed arm before/after self-admin0.00.00.00.2
Delta time in open arm before/after self-admin0.50.60.6-0.8
Diff in mean of infusions in LGA sessions0.00.00.0-0.2
Delay discount exponential model param0.10.20.20.4
Extinction: sum of active levers before priming0.30.40.4-0.6
Active lever presses in extinction session 60.80.80.8-0.9
Bone: final force0.00.00.00.1
Bone: final moment0.00.00.00.1
Food consumed during 24 hour testing period0.10.10.1-0.3
Glucose0.40.60.60.8
Heart weight3.76.06.02.4
Delay discount hyperbolic model param0.00.00.00.2
Intermittent access intake day 1-15 change0.00.00.0-0.1
Intermittent access intake escalation0.00.00.00.2
Intermittent access intake escalation 20.00.10.10.3
Intermitt. access day 1 inactive lever presses0.22.12.1-1.4
Intermitt. access day 15 inactive lever presses1.26.66.6-2.6
Intermitt. access escalation Index0.20.50.50.7
Intermittent access day 1 total infusions2.05.85.8-2.4
Intermittent access day 15 total infusions0.82.02.0-1.4
Intermittent access terminal intake (last 3 days)1.62.82.8-1.7
Intermittent access total infusions2.73.23.2-1.8
Intermittent access day 1 locomotion1.73.13.1-1.8
Intermittent access day 15 total locomotion0.10.40.4-0.6
Intermittent access total locomotion0.70.90.9-0.9
Intermittent access standard deviation0.31.71.7-1.3
Left kidney weight0.00.00.00.2
Right kidney weight0.42.82.81.7
Cocaine induced anxiety0.10.20.2-0.5
Post-drug Anxiety1.41.61.61.3
Baseline Anxiety2.23.83.81.9
Tail length0.42.32.31.5
Length with tail1.98.38.32.9
Length without tail0.52.62.61.6
Times rat made contact with spout1.51.71.7-1.3
Lifetime Intake3.03.73.7-1.9
Liver weight, left4.27.37.32.7
Liver weight, right6.912.112.13.5
Locomotor activity0.10.20.20.5
Locomotor testing distance0.10.20.2-0.5
Locomotor testing rearing0.72.62.6-1.6
Locomotion in novel chamber0.00.00.0-0.2
Locomotion in novel chamber post-restriction1.23.63.61.9
Fecal boli incidents, locomotor time 10.10.10.1-0.4
Change in fecal boli incidents, locomotor task3.84.04.02.0
Time >=10cm from walls, locomotor time 10.00.00.00.2
Bouts of movement, locomotor time 11.11.41.4-1.2
Total resting periods, locomotor time 11.51.71.7-1.3
Rest time, locomotor task time 10.00.10.10.3
Distance moved, locomotor task time 10.30.90.90.9
Vertical activity count, locomotor time 10.10.60.60.7
Time >=10cm from walls, locomotor time 20.10.20.2-0.4
Bouts of movement, locomotor time 20.00.10.10.4
Total resting periods, locomotor time 20.00.00.00.1
Rest time, locomotor task time 20.50.80.8-0.9
Distance moved, locomotor task time 20.40.60.60.8
Vertical activity count, locomotor time 20.10.30.30.5
Light reinforcement 11.14.94.9-2.2
Light reinforcement 21.02.32.3-1.5
Bone: marrow area0.00.10.1-0.3
Bone: maximum diameter0.10.10.1-0.3
Bone: maximum force0.00.10.1-0.3
Bone: maximum moment0.00.10.1-0.3
Mean time between licks in bursts0.63.63.61.9
Mean num. licks in bursts0.20.50.5-0.7
Cd content in liver0.00.10.10.2
Co content in liver4.25.05.0-2.2
Cu content in liver0.20.30.3-0.5
Fe content in liver2.22.72.7-1.6
K content in liver0.20.20.20.4
Mg content in liver0.20.20.20.5
Mn content in liver0.10.10.10.4
Na content in liver0.60.70.7-0.8
Rb content in liver0.30.40.40.6
Se content in liver0.00.00.00.2
Sr content in liver0.10.10.10.3
Zn content in liver1.31.51.51.2
Bone: minimum diameter0.30.50.50.7
Time in familiar zone, hab. session 11.01.11.11.0
Time in novel zone, hab. session 10.00.00.0-0.1
Total zone transitions, hab. session 10.20.30.3-0.6
Total locomotion distance, hab. session 10.10.10.1-0.3
Locomotion velocity, hab. session 10.50.70.7-0.8
Time in familiar zone, hab. session 20.00.00.0-0.2
Time in novel zone, hab. session 20.60.70.70.8
Total zone transitions, hab. session 20.00.00.00.2
Total locomotion distance, hab. session 20.00.00.0-0.0
Locomotion velocity, hab. session 20.00.00.0-0.2
Novel to familiar place preference ratio1.01.21.21.1
Novelty place preference1.31.71.71.3
Time in novel zone, NPP test1.21.51.51.2
Total zone transitions, NPP test0.81.11.1-1.1
Total locomotion distance, NPP test1.42.02.0-1.4
Locomotion velocity, NPP test2.02.82.8-1.7
Intraocular pressure5.59.09.03.0
Delta distance traveled before/after self-admin1.71.91.91.4
Delta ambulatory time before/after self-admin0.20.40.40.6
Parametrial fat weight12.830.230.25.5
Pavlov. Cond. lever latency0.70.90.91.0
Pavlov. Cond. magazine entry latency0.00.00.00.0
Pavlov. Cond. change in total contacts0.00.00.0-0.1
Pavlov. Cond. index score0.10.10.1-0.3
Pavlov. Cond. latency score0.10.10.1-0.3
Pavlov. Cond. lever contacts0.30.30.3-0.6
Pavlov. Cond. magazine entry number0.10.10.10.3
Pavlov. Cond. intertrial magazine entries2.22.62.6-1.6
Pavlov. Cond. lever-magazine prob. diff.0.50.60.6-0.8
Pavlov. Cond. response bias0.50.70.7-0.8
Pavlov. Cond. lever latency2.02.82.81.7
Pavlov. Cond. magazine entry latency0.40.50.5-0.7
Pavlov. Cond. change in total contacts0.71.61.6-1.3
Pavlov. Cond. index score1.32.12.1-1.4
Pavlov. Cond. latency score1.32.12.1-1.4
Pavlov. Cond. lever contacts1.42.12.1-1.5
Pavlov. Cond. magazine entry number0.30.30.30.6
Pavlov. Cond. intertrial magazine entries2.96.46.42.5
Pavlov. Cond. lever-magazine prob. diff.0.81.31.3-1.1
Pavlov. Cond. response bias2.43.33.3-1.8
Time in closed arm before self-admin0.61.01.01.0
Time in closed arm after self-admin1.21.31.31.1
Time in open arm before self-admin0.00.00.0-0.0
Time in open arm after self-admin1.51.71.7-1.3
Bone: periosteal estimation0.10.20.2-0.4
Bone: periosteal perimeter0.00.00.0-0.2
Bone: post-yield work1.42.32.3-1.5
Progressive ratio test 1 active lever presses1.42.52.5-1.6
Progressive ratio test 1 breakpoint1.52.52.5-1.6
Progressive ratio test 1 inactive lever presses2.05.45.4-2.3
Progressive ratio test 2 active lever presses0.30.40.4-0.6
Progressive ratio test 2 breakpoint0.20.30.3-0.5
Progressive ratio test 2 inactive lever presses0.72.32.3-1.5
Incentive Sensitization - Responses0.00.00.0-0.2
Incentive Sensitization - Breakpoint0.00.00.0-0.0
Sum of active levers in priming session hrs 5-60.10.10.1-0.3
Progressive ratio0.00.00.0-0.0
Food seeking constrained by brief footshock5.77.17.1-2.7
Seeking ratio, punishment vs. effort0.30.60.6-0.8
Retroperitoneal fat weight20.390.890.89.5
Reaction time number correct0.10.40.4-0.6
Reaction time mean minus median0.10.40.4-0.6
Reaction time mean minus median AUC0.00.10.1-0.3
Reaction time num false alarms0.20.30.30.6
Reaction time num false alarms AUC0.10.30.30.6
Reaction time trials correct on left0.10.40.4-0.6
Reaction time trials on left0.10.40.4-0.7
Reaction time mean0.51.11.11.1
Reaction time mean AUC0.30.80.80.9
Median of all reaction times1.11.71.71.3
Reaction time omissions0.10.10.1-0.4
Reaction time false alarm rate0.50.80.80.9
Reaction time premature initiation rate0.00.00.00.1
Reaction time premature initiations0.00.00.0-0.2
Std. dev. reaction times0.00.10.10.3
Reaction time trials completed0.10.40.4-0.7
Reaction time trials AUC0.20.70.7-0.8
Run reversals in cocaine runway, females0.00.10.10.2
Run reversals in cocaine runway, males0.20.20.2-0.4
Latency to leave start box in cocaine runway0.71.01.0-1.0
Latency to leave start box in cocaine runway, F0.30.30.3-0.6
Latency to leave start box in cocaine runway, M0.30.30.3-0.5
Std. dev. time between licks in bursts0.30.50.50.7
Total sessions with >9 infusions1.31.61.6-1.3
Short access day 1 total inactive lever presses3.87.67.6-2.8
Short access day 10 total inactive lever presses0.64.24.2-2.1
Short access day 1 total infusions3.26.46.4-2.5
Short access day 10 total infusions1.62.62.6-1.6
Short access total infusions1.42.02.0-1.4
Short access day 1 locomotion2.84.74.7-2.2
Short access day 10 total locomotion0.62.52.5-1.6
Short access total locomotion0.30.50.5-0.7
One hour access (0.3 mA shock)1.01.21.2-1.1
Compulsive drug intake1.21.81.81.3
One hour access (shock baseline)1.02.52.5-1.6
Social response proportion0.60.70.70.8
Social responses0.40.60.60.8
Social time0.10.20.20.5
Soleus weight3.710.910.9-3.3
Bone: stiffness0.00.10.1-0.3
Tibialis anterior weight3.211.011.0-3.3
Time to tail flick, vehicle, before self-admin0.40.40.40.7
Time to tail flick, vehicle, after self-admin1.83.73.71.9
Time to tail flick, test, before self-admin0.10.10.1-0.3
Time to tail flick, test, after self-admin0.10.10.1-0.3
Delta time to tail flick, vehicle, before/after SA0.10.10.10.3
Delta time to tail flick, test, before/after SA0.91.11.1-1.0
Tibia length3.49.69.63.1
Ambulatory time before self-admin0.00.10.10.3
Ambulatory time after self-admin1.72.62.61.6
Bone: tissue strength1.01.01.01.0
Total heroin consumption2.12.52.5-1.6
Bone: trabecular number1.63.13.1-1.8
Bone: trabecular spacing1.21.81.81.3
Bone: trabecular thickness0.10.20.2-0.4
Bone: trabecular tissue density0.40.70.7-0.8
Water consumed over 24 hours0.00.10.1-0.3
Number of responses in last shaping day0.20.20.2-0.5