Hub : Genes

Best1

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	Best1	0.02	0.02	6.6e-03	-0	-0	-0	-0	7.0e-01	4.5e-01	8.1e-01	8.1e-01
2	pVTA	gene expression	Best1	0.06	0.04	3.0e-05	0.07	0.05	0.04	0.06	4.0e-06	6.0e-05	1.6e-04	1.3e-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 density	0.1	0.2	0.3	-0.1	0.6
Area under the delay curve	0.0	0.0	0.0	0.1	0.2
BMI with tail	1.4	5.0	7.9	-1.4	2.8
BMI without tail	0.2	1.1	1.4	-0.9	1.2
Body weight	2.4	10.7	14.3	-2.7	3.8
Weight adjusted by age	0.4	1.1	1.5	-1.2	0.8
Bone surface	1.1	2.2	3.6	-0.9	1.9
Bone volume	0.3	0.7	1.3	-0.3	1.1
Breakpoint value in progressive ratio session	2.3	4.1	4.9	-2.2	1.8
Number of licking bursts	0.0	0.0	0.0	0.1	-0.0
Context. condit. distance diff. score	0.1	0.1	0.2	0.3	-0.4
Locomotion velocity, session 1	0.0	0.0	0.0	-0.2	0.1
Locomotion distance, session 1	0.6	0.8	0.8	-0.9	0.9
Locomotion velocity, session 2	2.7	3.2	3.8	-1.6	2.0
Locomotion distance, session 2	0.4	0.6	0.8	-0.9	0.6
Locomotion velocity, session 3	0.1	0.1	0.3	0.2	0.5
Locomotion distance, session 3	0.0	0.0	0.0	0.2	0.1
Stereotopy head waving bouts, day 3	0.2	0.2	0.3	0.6	-0.2
Stereotopy head waving duration, day 3	0.0	0.0	0.0	0.2	-0.1
Locomotion velocity, session 7	0.0	0.0	0.0	0.2	0.1
Locomotion distance, session 7	0.0	0.1	0.1	0.3	-0.2
Stereotopy head waving bouts, day 7	0.2	0.2	0.3	-0.3	0.6
Stereotopy head waving duration, day 7	1.4	1.8	2.2	-1.2	1.5
Locomotion velocity, session 8	0.1	0.1	0.2	-0.4	0.0
Locomotion distance, session 8	0.1	0.2	0.2	0.4	-0.5
Degree of sensitization distance	0.0	0.0	0.1	0.3	-0.1
Degree of sensitization stereotypy	1.1	1.2	1.5	-0.9	1.2
Conditioned locomotion	0.5	0.6	0.6	-0.8	0.8
Cocaine response after cond. corrected	0.3	0.4	0.5	0.5	-0.7
Cocaine response after cond. not corrected	0.2	0.3	0.4	0.6	-0.6
Cocaine response before conditioning	0.3	0.3	0.6	-0.3	0.7
Saline control response	3.1	4.3	4.4	-2.0	2.1
Bone: connectivity density	1.1	1.7	2.6	-1.0	1.6
Bone: cortical apparent density	0.4	0.7	0.9	-1.0	0.7
Bone: cortical area	0.6	0.9	1.5	-0.6	1.2
Bone: cortical porosity	0.2	0.3	0.5	-0.7	0.1
Bone: cortical porosity	0.4	0.4	0.8	-0.9	0.3
Bone: cortical thickness	3.9	6.5	7.1	-2.7	2.4
Bone: cortical thickness	0.4	0.5	0.7	-0.8	0.7
Bone: cortical tissue density	0.6	1.0	1.3	-1.2	0.8
Condit. Reinf. active minus inactive responses	1.1	1.3	1.4	-1.1	1.2
Condit. Reinf. active-inactive response ratio	0.8	0.8	1.1	-1.1	0.7
Condit. Reinf. active responses	0.8	1.0	1.4	-0.7	1.2
Condit. Reinf. inactive responses	0.1	0.2	0.4	0.6	-0.0
Incentive salience index mean	0.9	1.1	1.7	-0.8	1.3
Condit. Reinf. lever presses	0.4	0.6	1.2	-0.2	1.1
Condit. Reinf. active minus inactive responses	0.0	0.1	0.1	0.3	-0.2
Condit. Reinf. active-inactive response ratio	0.3	0.4	0.6	0.8	-0.5
Condit. Reinf. active responses	0.1	0.1	0.2	-0.2	0.5
Condit. Reinf. inactive responses	0.1	0.2	0.3	-0.4	0.5
Condit. Reinf. lever presses	0.6	0.8	1.3	-0.5	1.2
Condit. Reinf. lever reinforcers received	0.3	0.4	0.5	-0.5	0.7
Conditioned reinforcement - actives	0.0	0.1	0.1	0.2	-0.3
Conditioned reinforcement - inactives	0.1	0.2	0.3	0.6	-0.1
Conditioned locomotion	2.1	3.1	3.7	1.9	-1.6
Patch foraging indifference point 0 sec	0.3	0.9	1.0	-0.8	1.0
Patch foraging indifference point AUC	0.8	1.9	1.9	-1.4	1.4
Delay disc. indifference point, 0s delay	0.5	0.6	0.8	0.9	-0.6
Delay disc. indifference point, 16s delay	0.0	0.0	0.1	-0.0	0.3
Delay disc. indifference point, 2s delay	0.7	0.7	1.3	1.1	-0.4
Delay disc. indifference point, 24s delay	0.0	0.0	0.1	-0.0	0.3
Delay disc. indifference point, 4s delay	0.1	0.1	0.3	-0.1	0.5
Delay disc. indifference point, 8s delay	0.2	0.3	0.4	0.5	-0.7
Indifference point function ln k	1.9	5.7	6.1	2.5	-2.3
Indifference point function log k	1.9	5.7	6.1	2.5	-2.3
Patch foraging total patch changes 0 sec	0.3	1.0	1.0	-1.0	1.0
Patch foraging total patch changes 12 sec	7.3	9.7	10.4	-3.2	3.0
Patch foraging total patch changes 18 sec	0.4	1.1	1.2	-1.1	1.0
Patch foraging total patch changes 24 sec	2.2	7.4	8.2	-2.6	2.9
Patch foraging total patch changes 6 sec	0.9	1.5	1.9	-1.1	1.4
Patch foraging time to switch 0 sec	0.1	0.4	0.7	-0.2	0.8
Patch foraging water rate 0 sec	0.2	0.6	0.8	0.6	-0.9
Patch foraging water rate 12 sec	0.7	2.8	3.4	1.5	-1.8
Patch foraging water rate 18 sec	0.4	0.8	0.9	0.9	-0.9
Patch foraging water rate 24 sec	1.0	1.4	1.6	1.1	-1.3
Patch foraging water rate 6 sec	1.2	1.8	2.5	1.0	-1.6
Seeking ratio, delayed vs. immediate footshock	0.0	0.0	0.0	0.2	0.1
Distance traveled before self-admin	0.9	2.1	3.0	-1.1	1.7
Distance traveled after self-admin	0.3	0.6	0.7	-0.8	0.7
Extensor digitorum longus weight	5.5	22.0	24.8	-4.4	5.0
Bone: elastic displacement	0.2	0.2	0.4	-0.1	-0.6
Bone: elastic work	1.2	1.6	2.1	-1.4	1.1
Bone: endosteal estimation	1.8	4.3	6.2	2.5	-1.5
Bone: endosteal perimeter	2.6	6.4	9.3	3.0	-1.9
Epididymis fat weight	0.9	4.6	6.7	2.6	-1.6
Delta time in closed arm before/after self-admin	1.8	1.7	2.4	-1.6	1.0
Delta time in open arm before/after self-admin	1.8	2.1	2.5	-1.3	1.6
Diff in mean of infusions in LGA sessions	2.0	3.7	4.2	-2.0	1.8
Delay discount exponential model param	0.0	0.0	0.0	-0.1	-0.2
Extinction: sum of active levers before priming	2.5	3.8	4.4	-1.8	2.1
Active lever presses in extinction session 6	3.1	3.2	3.7	-1.6	1.9
Bone: final force	1.1	1.8	2.6	-1.0	1.6
Bone: final moment	1.2	1.9	2.6	-1.0	1.6
Food consumed during 24 hour testing period	0.1	0.2	0.2	0.4	-0.4
Glucose	3.7	5.8	6.8	2.6	-2.2
Heart weight	0.6	1.0	1.6	1.3	-0.6
Delay discount hyperbolic model param	0.0	0.1	0.1	-0.3	-0.1
Intermittent access intake day 1-15 change	0.4	2.0	2.0	1.4	-1.4
Intermittent access intake escalation	0.5	2.5	2.7	1.5	-1.6
Intermittent access intake escalation 2	0.4	0.7	0.7	0.8	-0.9
Intermitt. access day 1 inactive lever presses	0.1	1.0	1.3	0.8	-1.2
Intermitt. access day 15 inactive lever presses	0.1	0.4	0.8	0.1	0.9
Intermitt. access escalation Index	0.3	1.1	1.3	0.9	-1.1
Intermittent access day 1 total infusions	0.5	1.4	2.7	1.6	-0.4
Intermittent access day 15 total infusions	2.4	5.8	7.8	2.8	-2.0
Intermittent access terminal intake (last 3 days)	1.3	2.2	3.7	1.9	-0.9
Intermittent access total infusions	1.9	2.3	3.8	2.0	-0.8
Intermittent access day 1 locomotion	0.2	0.4	0.7	0.9	0.0
Intermittent access day 15 total locomotion	0.2	0.6	1.2	1.1	-0.2
Intermittent access total locomotion	1.3	1.5	3.0	1.7	-0.2
Intermittent access standard deviation	0.1	0.6	0.8	0.7	-0.9
Left kidney weight	0.2	1.6	2.8	1.7	-0.6
Right kidney weight	0.1	0.9	1.5	1.2	-0.5
Cocaine induced anxiety	0.0	0.1	0.2	-0.4	0.3
Post-drug Anxiety	0.2	0.2	0.3	-0.4	0.6
Baseline Anxiety	0.1	0.1	0.2	-0.2	0.5
Tail length	0.3	1.5	2.3	-1.5	0.9
Length with tail	1.2	5.2	5.2	-2.3	2.3
Length without tail	1.5	7.8	8.8	-2.6	3.0
Times rat made contact with spout	0.4	0.4	0.7	-0.9	0.4
Lifetime Intake	1.3	1.6	2.6	1.6	-0.8
Liver weight, left	1.0	1.8	2.4	1.1	-1.5
Liver weight, right	1.9	3.3	3.5	1.9	-1.8
Locomotor activity	0.6	0.9	1.5	0.6	-1.2
Locomotor testing distance	0.5	1.1	1.5	0.8	-1.2
Locomotor testing rearing	0.3	1.2	1.6	0.9	-1.3
Locomotion in novel chamber	2.0	2.6	3.2	1.8	-1.4
Locomotion in novel chamber post-restriction	0.6	1.8	2.3	1.1	-1.5
Fecal boli incidents, locomotor time 1	0.1	0.2	0.2	0.4	-0.4
Change in fecal boli incidents, locomotor task	1.5	1.6	1.9	1.4	-1.2
Time >=10cm from walls, locomotor time 1	2.0	2.5	3.1	1.8	-1.4
Bouts of movement, locomotor time 1	1.2	1.5	2.7	-1.6	0.7
Total resting periods, locomotor time 1	0.9	1.1	1.8	-1.3	0.6
Rest time, locomotor task time 1	1.1	1.8	2.1	1.2	-1.4
Distance moved, locomotor task time 1	0.1	0.2	0.3	-0.3	0.5
Vertical activity count, locomotor time 1	0.1	0.6	0.7	0.7	-0.9
Time >=10cm from walls, locomotor time 2	0.0	0.0	0.1	0.3	-0.1
Bouts of movement, locomotor time 2	0.7	2.2	2.6	-1.6	1.3
Total resting periods, locomotor time 2	0.3	1.2	1.6	-1.3	0.9
Rest time, locomotor task time 2	2.0	3.3	4.2	1.5	-2.1
Distance moved, locomotor task time 2	0.6	0.8	0.9	-0.9	0.9
Vertical activity count, locomotor time 2	0.0	0.1	0.1	-0.3	-0.1
Light reinforcement 1	0.0	0.1	0.1	0.4	-0.1
Light reinforcement 2	0.3	0.7	1.4	1.2	-0.2
Bone: marrow area	2.0	4.9	7.0	2.6	-1.7
Bone: maximum diameter	0.1	0.2	0.3	0.3	0.5
Bone: maximum force	1.3	2.5	4.1	-1.0	2.0
Bone: maximum moment	1.4	2.6	4.0	-1.0	2.0
Mean time between licks in bursts	0.1	0.3	0.5	-0.7	0.4
Mean num. licks in bursts	0.0	0.1	0.2	-0.4	-0.1
Cd content in liver	0.7	0.8	0.9	0.9	-0.8
Co content in liver	0.4	0.4	0.8	0.2	-0.9
Cu content in liver	0.0	0.0	0.0	-0.2	-0.1
Fe content in liver	0.0	0.0	0.0	0.1	-0.1
K content in liver	0.2	0.2	0.3	-0.1	0.6
Mg content in liver	0.1	0.1	0.1	0.3	0.1
Mn content in liver	2.7	3.0	3.5	-1.6	1.9
Na content in liver	0.3	0.3	0.5	-0.2	0.7
Rb content in liver	2.6	3.0	3.3	1.7	-1.8
Se content in liver	0.0	0.0	0.1	-0.1	0.2
Sr content in liver	5.5	4.7	5.0	-2.2	2.1
Zn content in liver	3.0	3.5	3.7	-1.8	1.9
Bone: minimum diameter	1.3	2.5	4.0	2.0	-1.0
Time in familiar zone, hab. session 1	0.0	0.0	0.1	0.0	0.2
Time in novel zone, hab. session 1	1.2	1.4	1.7	1.0	-1.3
Total zone transitions, hab. session 1	0.4	0.5	0.7	-0.8	0.6
Total locomotion distance, hab. session 1	0.0	0.0	0.1	0.3	-0.1
Locomotion velocity, hab. session 1	0.2	0.2	0.3	-0.4	0.5
Time in familiar zone, hab. session 2	0.3	0.4	0.5	0.5	-0.7
Time in novel zone, hab. session 2	0.4	0.5	0.6	-0.5	0.8
Total zone transitions, hab. session 2	1.0	1.3	1.7	-1.0	1.3
Total locomotion distance, hab. session 2	0.1	0.1	0.2	-0.1	0.4
Locomotion velocity, hab. session 2	0.0	0.0	0.1	0.1	0.3
Novel to familiar place preference ratio	1.4	1.9	2.1	-1.3	1.4
Novelty place preference	0.8	1.0	1.1	-1.0	1.1
Time in novel zone, NPP test	1.0	1.2	1.2	-1.0	1.1
Total zone transitions, NPP test	1.5	2.2	2.4	-1.5	1.4
Total locomotion distance, NPP test	0.1	0.2	0.2	-0.4	0.4
Locomotion velocity, NPP test	0.1	0.1	0.1	-0.4	0.3
Intraocular pressure	0.1	0.1	0.2	-0.1	-0.4
Delta distance traveled before/after self-admin	0.3	0.4	0.7	0.1	-0.8
Delta ambulatory time before/after self-admin	0.4	0.6	1.2	0.2	-1.1
Parametrial fat weight	2.7	6.3	9.2	3.0	-1.8
Pavlov. Cond. lever latency	0.6	0.8	1.2	0.6	-1.1
Pavlov. Cond. magazine entry latency	0.7	0.9	1.5	-0.5	1.2
Pavlov. Cond. change in total contacts	0.3	0.3	0.6	-0.3	0.8
Pavlov. Cond. index score	0.5	0.7	1.0	-0.6	1.0
Pavlov. Cond. latency score	0.4	0.5	0.8	-0.4	0.9
Pavlov. Cond. lever contacts	0.2	0.3	0.5	-0.2	0.7
Pavlov. Cond. magazine entry number	0.8	1.0	1.4	0.9	-1.2
Pavlov. Cond. intertrial magazine entries	0.1	0.2	0.2	-0.5	0.3
Pavlov. Cond. lever-magazine prob. diff.	0.6	0.7	1.1	-0.6	1.0
Pavlov. Cond. response bias	0.8	1.0	1.4	-0.7	1.2
Pavlov. Cond. lever latency	0.3	0.4	0.7	0.4	-0.9
Pavlov. Cond. magazine entry latency	4.8	6.8	7.8	-2.4	2.8
Pavlov. Cond. change in total contacts	0.6	1.6	2.3	-0.9	1.5
Pavlov. Cond. index score	2.1	3.3	4.4	-1.5	2.1
Pavlov. Cond. latency score	1.8	3.0	4.1	-1.4	2.0
Pavlov. Cond. lever contacts	0.3	0.4	0.6	-0.4	0.8
Pavlov. Cond. magazine entry number	8.0	10.3	11.7	3.0	-3.4
Pavlov. Cond. intertrial magazine entries	0.9	2.0	2.3	1.3	-1.5
Pavlov. Cond. lever-magazine prob. diff.	2.5	3.8	4.9	-1.6	2.2
Pavlov. Cond. response bias	1.7	2.3	3.1	-1.2	1.7
Time in closed arm before self-admin	0.2	0.3	0.5	0.7	-0.2
Time in closed arm after self-admin	0.8	0.9	1.1	0.8	-1.0
Time in open arm before self-admin	0.6	0.8	1.3	0.5	-1.2
Time in open arm after self-admin	0.7	0.8	1.0	-1.0	0.7
Bone: periosteal estimation	0.3	0.7	1.3	1.1	-0.1
Bone: periosteal perimeter	0.2	0.3	0.7	0.8	-0.0
Bone: post-yield work	0.8	1.3	2.6	1.6	-0.3
Progressive ratio test 1 active lever presses	0.2	0.3	0.4	0.7	-0.4
Progressive ratio test 1 breakpoint	0.2	0.3	0.4	0.7	-0.4
Progressive ratio test 1 inactive lever presses	0.3	0.7	1.0	-0.6	1.0
Progressive ratio test 2 active lever presses	0.9	1.3	2.1	1.5	-0.7
Progressive ratio test 2 breakpoint	1.0	1.3	2.1	1.5	-0.6
Progressive ratio test 2 inactive lever presses	0.3	0.9	1.7	1.3	-0.4
Incentive Sensitization - Responses	0.1	0.4	0.8	0.0	0.9
Incentive Sensitization - Breakpoint	0.1	0.3	0.6	0.2	0.8
Sum of active levers in priming session hrs 5-6	1.3	1.3	1.3	-1.1	1.1
Progressive ratio	0.1	0.2	0.4	0.6	-0.0
Food seeking constrained by brief footshock	0.0	0.0	0.0	0.2	-0.1
Seeking ratio, punishment vs. effort	0.0	0.1	0.1	-0.3	-0.1
Retroperitoneal fat weight	4.5	19.9	22.2	4.7	-4.2
Reaction time number correct	0.1	0.4	0.5	-0.7	0.6
Reaction time mean minus median	0.2	1.0	1.2	-1.1	0.9
Reaction time mean minus median AUC	0.1	0.6	1.0	-1.0	0.5
Reaction time num false alarms	0.1	0.2	0.4	0.0	-0.6
Reaction time num false alarms AUC	0.1	0.2	0.4	-0.6	-0.1
Reaction time trials correct on left	0.1	0.4	0.5	-0.7	0.6
Reaction time trials on left	0.1	0.5	0.6	-0.8	0.6
Reaction time mean	0.0	0.0	0.1	-0.3	-0.0
Reaction time mean AUC	0.0	0.0	0.0	0.0	-0.2
Median of all reaction times	0.0	0.0	0.0	-0.1	-0.0
Reaction time omissions	0.5	0.9	1.1	-1.0	0.8
Reaction time false alarm rate	0.1	0.1	0.2	0.1	-0.5
Reaction time premature initiation rate	2.7	4.2	5.9	-1.6	2.4
Reaction time premature initiations	2.0	6.0	7.1	-2.2	2.7
Std. dev. reaction times	0.0	0.1	0.3	-0.5	-0.0
Reaction time trials completed	0.1	0.5	0.6	-0.8	0.6
Reaction time trials AUC	0.1	0.3	0.4	-0.6	0.5
Run reversals in cocaine runway, females	0.1	0.2	0.3	0.1	0.6
Run reversals in cocaine runway, males	0.4	0.5	0.5	0.6	-0.7
Latency to leave start box in cocaine runway	0.9	1.2	1.9	1.4	-0.7
Latency to leave start box in cocaine runway, F	0.1	0.1	0.1	0.3	0.2
Latency to leave start box in cocaine runway, M	3.1	2.9	3.3	1.8	-1.6
Std. dev. time between licks in bursts	0.1	0.2	0.2	0.4	-0.4
Total sessions with >9 infusions	0.6	0.8	0.9	0.8	-0.9
Short access day 1 total inactive lever presses	0.0	0.1	0.2	0.4	-0.2
Short access day 10 total inactive lever presses	0.1	0.5	0.9	0.3	-0.9
Short access day 1 total infusions	0.8	1.5	1.6	1.3	-1.2
Short access day 10 total infusions	0.5	0.8	1.5	1.2	-0.3
Short access total infusions	0.7	1.0	1.4	1.2	-0.7
Short access day 1 locomotion	0.1	0.2	0.3	0.4	-0.5
Short access day 10 total locomotion	0.1	0.2	0.4	0.7	0.2
Short access total locomotion	0.2	0.3	0.5	0.7	-0.2
One hour access (0.3 mA shock)	1.6	1.9	2.9	1.7	-1.0
Compulsive drug intake	0.9	1.3	2.1	-1.5	0.7
One hour access (shock baseline)	1.9	5.0	7.1	2.7	-1.7
Social response proportion	0.0	0.0	0.1	0.0	0.3
Social responses	0.1	0.1	0.2	-0.5	0.2
Social time	0.2	0.3	0.5	-0.7	-0.0
Soleus weight	2.8	8.3	8.8	2.8	-3.0
Bone: stiffness	0.2	0.4	0.8	-0.3	0.9
Tibialis anterior weight	9.5	32.8	33.2	-5.7	5.8
Time to tail flick, vehicle, before self-admin	0.1	0.1	0.2	0.2	0.4
Time to tail flick, vehicle, after self-admin	0.1	0.2	0.3	-0.4	0.5
Time to tail flick, test, before self-admin	0.0	0.1	0.1	0.3	0.2
Time to tail flick, test, after self-admin	0.0	0.0	0.0	-0.1	0.1
Delta time to tail flick, vehicle, before/after SA	0.3	0.3	0.5	-0.7	0.4
Delta time to tail flick, test, before/after SA	0.3	0.3	0.6	-0.8	0.2
Tibia length	1.2	3.4	4.6	-1.5	2.1
Ambulatory time before self-admin	0.6	1.8	2.7	-0.9	1.6
Ambulatory time after self-admin	0.1	0.1	0.2	-0.2	0.4
Bone: tissue strength	0.6	0.7	0.7	0.8	-0.9
Total heroin consumption	7.9	9.3	10.9	-3.3	2.8
Bone: trabecular number	0.4	0.8	1.3	-0.6	1.1
Bone: trabecular spacing	0.2	0.3	0.6	0.1	-0.8
Bone: trabecular thickness	0.3	0.4	0.6	0.8	-0.5
Bone: trabecular tissue density	3.3	5.8	7.2	2.1	-2.7
Water consumed over 24 hours	0.4	0.7	0.8	-0.9	0.8
Number of responses in last shaping day	0.6	0.7	1.2	-1.1	0.5