Hub : Genes

Agr2

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	pVTA	alternative TSS	NM_001106725.1	0.04	0.03	6.9e-03	0.01	0.01	0	0.01	5.8e-02	2.3e-02	3.0e-01	7.9e-02
2	Adipose	gene expression	Agr2	0.08	0.04	1.9e-10	0.06	0.06	0.06	0.06	4.0e-07	3.4e-07	4.4e-07	4.5e-07

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	3.2	5.4	7.6	2.7	-1.8
Area under the delay curve	0.3	0.3	0.6	0.3	-0.8
BMI with tail	0.3	1.0	1.9	-0.4	1.4
BMI without tail	0.3	0.8	0.9	0.9	-0.9
Body weight	0.0	0.0	0.0	0.2	0.2
Weight adjusted by age	2.4	3.6	4.3	-2.1	1.7
Bone surface	2.0	3.6	4.9	2.2	-1.5
Bone volume	2.9	5.2	6.6	2.6	-2.0
Breakpoint value in progressive ratio session	0.3	0.3	0.5	0.7	-0.3
Number of licking bursts	1.9	3.1	3.7	-1.9	1.6
Context. condit. distance diff. score	0.1	0.1	0.2	0.4	-0.1
Locomotion velocity, session 1	0.1	0.1	0.1	0.2	-0.3
Locomotion distance, session 1	0.6	0.8	0.9	0.9	-0.8
Locomotion velocity, session 2	0.3	0.4	0.5	0.6	-0.7
Locomotion distance, session 2	2.3	3.2	3.4	1.8	-1.8
Locomotion velocity, session 3	0.0	0.0	0.0	-0.1	0.1
Locomotion distance, session 3	2.7	2.9	3.9	2.0	-1.4
Stereotopy head waving bouts, day 3	1.9	2.2	3.0	-1.7	1.1
Stereotopy head waving duration, day 3	3.4	4.0	5.5	-2.4	1.6
Locomotion velocity, session 7	1.7	1.9	2.3	1.5	-1.2
Locomotion distance, session 7	1.7	2.1	2.9	1.7	-1.2
Stereotopy head waving bouts, day 7	0.4	0.5	0.8	-0.9	0.3
Stereotopy head waving duration, day 7	0.9	1.1	1.7	-1.3	0.6
Locomotion velocity, session 8	0.0	0.0	0.0	-0.2	-0.2
Locomotion distance, session 8	2.1	3.0	3.4	1.9	-1.6
Degree of sensitization distance	0.0	0.0	0.1	-0.3	0.1
Degree of sensitization stereotypy	0.3	0.4	0.7	-0.8	0.2
Conditioned locomotion	1.2	1.4	2.4	-1.6	0.5
Cocaine response after cond. corrected	0.4	0.5	0.6	-0.8	0.7
Cocaine response after cond. not corrected	0.1	0.1	0.1	-0.2	0.4
Cocaine response before conditioning	1.4	1.6	2.1	1.4	-1.1
Saline control response	9.1	12.1	12.3	3.5	-3.4
Bone: connectivity density	1.9	3.0	4.9	2.2	-1.0
Bone: cortical apparent density	0.4	0.5	0.6	-0.6	0.8
Bone: cortical area	0.2	0.3	0.5	0.3	-0.7
Bone: cortical porosity	0.1	0.1	0.3	-0.5	0.0
Bone: cortical porosity	0.2	0.2	0.4	-0.6	0.0
Bone: cortical thickness	0.0	0.0	0.1	-0.3	0.1
Bone: cortical thickness	1.0	1.2	1.6	-1.3	0.9
Bone: cortical tissue density	0.4	0.5	0.6	-0.6	0.8
Condit. Reinf. active minus inactive responses	7.4	8.3	9.2	3.0	-2.7
Condit. Reinf. active-inactive response ratio	7.1	7.5	8.8	3.0	-2.5
Condit. Reinf. active responses	5.2	6.5	6.6	2.6	-2.5
Condit. Reinf. inactive responses	0.1	0.1	0.2	0.1	-0.4
Incentive salience index mean	8.0	9.9	9.9	3.2	-3.1
Condit. Reinf. lever presses	2.7	3.7	4.3	1.8	-2.1
Condit. Reinf. active minus inactive responses	0.7	0.9	0.9	0.9	-1.0
Condit. Reinf. active-inactive response ratio	0.3	0.3	0.5	-0.7	0.4
Condit. Reinf. active responses	2.5	3.5	3.7	1.8	-1.9
Condit. Reinf. inactive responses	3.2	4.1	4.3	2.0	-2.1
Condit. Reinf. lever presses	2.3	3.2	3.5	1.9	-1.7
Condit. Reinf. lever reinforcers received	3.6	5.0	5.0	2.2	-2.2
Conditioned reinforcement - actives	0.0	0.0	0.1	-0.2	0.1
Conditioned reinforcement - inactives	1.8	2.7	4.0	1.2	-2.0
Conditioned locomotion	0.1	0.1	0.2	-0.4	0.1
Patch foraging indifference point 0 sec	3.0	5.6	5.6	2.4	-2.4
Patch foraging indifference point AUC	0.8	1.2	1.3	1.2	-1.0
Delay disc. indifference point, 0s delay	0.2	0.2	0.4	-0.6	0.1
Delay disc. indifference point, 16s delay	2.0	2.2	2.3	1.5	-1.5
Delay disc. indifference point, 2s delay	0.3	0.3	0.5	-0.7	0.4
Delay disc. indifference point, 24s delay	0.6	0.7	1.1	0.5	-1.0
Delay disc. indifference point, 4s delay	0.0	0.0	0.0	0.1	0.0
Delay disc. indifference point, 8s delay	0.9	1.0	1.4	0.8	-1.2
Indifference point function ln k	0.0	0.0	0.0	-0.1	0.0
Indifference point function log k	0.0	0.0	0.0	-0.1	0.0
Patch foraging total patch changes 0 sec	2.7	5.1	5.3	2.2	-2.3
Patch foraging total patch changes 12 sec	2.1	2.7	3.8	2.0	-1.3
Patch foraging total patch changes 18 sec	1.0	1.5	1.7	1.1	-1.3
Patch foraging total patch changes 24 sec	0.2	0.4	0.5	0.5	-0.7
Patch foraging total patch changes 6 sec	3.8	5.8	6.1	2.5	-2.3
Patch foraging time to switch 0 sec	0.8	1.7	1.9	-1.2	1.4
Patch foraging water rate 0 sec	0.2	0.4	0.4	0.7	-0.6
Patch foraging water rate 12 sec	1.1	2.2	2.7	1.3	-1.6
Patch foraging water rate 18 sec	0.3	0.4	0.4	0.6	-0.6
Patch foraging water rate 24 sec	0.5	0.8	1.0	1.0	-0.7
Patch foraging water rate 6 sec	0.0	0.0	0.0	0.2	-0.2
Seeking ratio, delayed vs. immediate footshock	0.3	0.3	0.7	0.1	0.8
Distance traveled before self-admin	0.7	0.9	1.1	0.8	-1.1
Distance traveled after self-admin	3.3	4.1	4.1	2.0	-2.0
Extensor digitorum longus weight	3.5	13.9	18.4	3.1	-4.3
Bone: elastic displacement	0.3	0.4	0.6	-0.4	0.8
Bone: elastic work	0.0	0.0	0.0	0.1	-0.0
Bone: endosteal estimation	0.4	0.9	1.0	1.0	-0.8
Bone: endosteal perimeter	0.3	0.7	0.8	0.9	-0.8
Epididymis fat weight	1.8	6.1	8.9	-1.8	3.0
Delta time in closed arm before/after self-admin	1.5	1.4	1.6	-1.3	1.1
Delta time in open arm before/after self-admin	4.0	3.9	4.1	2.0	-2.0
Diff in mean of infusions in LGA sessions	0.4	0.5	0.8	0.9	-0.5
Delay discount exponential model param	0.3	0.3	0.5	-0.3	0.7
Extinction: sum of active levers before priming	0.0	0.0	0.0	-0.1	0.2
Active lever presses in extinction session 6	0.1	0.1	0.1	0.4	-0.1
Bone: final force	0.1	0.1	0.2	-0.5	0.2
Bone: final moment	0.0	0.0	0.0	-0.2	-0.1
Food consumed during 24 hour testing period	0.1	0.2	0.2	-0.4	0.3
Glucose	0.5	0.8	1.0	-0.7	1.0
Heart weight	0.1	0.2	0.3	0.2	-0.5
Delay discount hyperbolic model param	0.2	0.2	0.3	-0.2	0.6
Intermittent access intake day 1-15 change	0.4	0.8	0.9	0.9	-0.9
Intermittent access intake escalation	0.5	1.0	1.2	1.1	-0.9
Intermittent access intake escalation 2	0.0	0.0	0.1	0.1	-0.3
Intermitt. access day 1 inactive lever presses	0.4	1.5	2.3	-1.5	0.9
Intermitt. access day 15 inactive lever presses	0.2	0.3	0.4	-0.5	0.6
Intermitt. access escalation Index	0.3	0.4	0.6	-0.5	0.8
Intermittent access day 1 total infusions	1.5	2.4	2.6	-1.6	1.5
Intermittent access day 15 total infusions	0.1	0.1	0.2	-0.3	0.4
Intermittent access terminal intake (last 3 days)	1.1	1.5	1.9	-1.4	1.1
Intermittent access total infusions	0.8	0.9	1.0	-1.0	0.9
Intermittent access day 1 locomotion	0.4	0.6	0.8	-0.9	0.6
Intermittent access day 15 total locomotion	0.1	0.2	0.4	0.3	-0.6
Intermittent access total locomotion	0.0	0.0	0.0	-0.2	-0.1
Intermittent access standard deviation	0.0	0.0	0.0	-0.0	0.2
Left kidney weight	0.4	1.8	2.6	1.6	-1.0
Right kidney weight	0.0	0.1	0.1	0.3	-0.1
Cocaine induced anxiety	0.6	0.8	1.4	-1.2	0.4
Post-drug Anxiety	0.3	0.3	0.5	0.3	-0.7
Baseline Anxiety	1.9	2.2	3.4	1.8	-1.0
Tail length	1.4	5.5	7.4	1.9	-2.7
Length with tail	0.3	1.3	2.0	0.8	-1.4
Length without tail	1.1	3.4	3.7	-1.8	1.9
Times rat made contact with spout	1.4	1.6	2.1	-1.0	1.4
Lifetime Intake	0.3	0.4	0.4	-0.6	0.6
Liver weight, left	0.0	0.0	0.0	0.1	0.1
Liver weight, right	1.2	2.1	2.7	-1.2	1.6
Locomotor activity	8.1	12.6	14.0	3.7	-3.3
Locomotor testing distance	5.0	9.0	9.7	3.1	-2.9
Locomotor testing rearing	5.5	11.0	12.7	3.6	-3.1
Locomotion in novel chamber	0.1	0.2	0.3	0.5	-0.2
Locomotion in novel chamber post-restriction	0.4	0.7	0.9	-0.7	1.0
Fecal boli incidents, locomotor time 1	0.3	0.4	0.6	0.4	-0.8
Change in fecal boli incidents, locomotor task	0.1	0.1	0.1	-0.4	0.3
Time >=10cm from walls, locomotor time 1	0.0	0.0	0.1	-0.1	-0.3
Bouts of movement, locomotor time 1	1.0	1.2	1.9	-1.4	0.7
Total resting periods, locomotor time 1	1.2	1.4	2.1	-1.5	0.8
Rest time, locomotor task time 1	0.2	0.2	0.4	-0.6	-0.0
Distance moved, locomotor task time 1	0.1	0.2	0.3	-0.3	0.5
Vertical activity count, locomotor time 1	0.1	0.2	0.2	-0.5	0.4
Time >=10cm from walls, locomotor time 2	0.1	0.2	0.3	0.1	-0.6
Bouts of movement, locomotor time 2	0.0	0.0	0.1	-0.3	0.0
Total resting periods, locomotor time 2	0.0	0.1	0.1	-0.4	0.1
Rest time, locomotor task time 2	0.5	0.6	0.8	-0.9	0.7
Distance moved, locomotor task time 2	0.1	0.1	0.1	0.3	-0.2
Vertical activity count, locomotor time 2	0.1	0.1	0.2	0.3	-0.4
Light reinforcement 1	0.5	1.1	1.2	1.1	-1.0
Light reinforcement 2	0.3	0.4	0.5	0.6	-0.7
Bone: marrow area	0.5	1.0	1.2	1.1	-0.9
Bone: maximum diameter	0.2	0.4	0.6	0.3	-0.8
Bone: maximum force	0.2	0.3	0.5	0.4	-0.7
Bone: maximum moment	0.4	0.7	1.0	0.7	-1.0
Mean time between licks in bursts	0.0	0.1	0.2	-0.5	0.0
Mean num. licks in bursts	1.2	1.8	2.6	1.6	-1.0
Cd content in liver	0.2	0.3	0.5	0.7	-0.1
Co content in liver	1.1	1.3	1.3	1.2	-1.2
Cu content in liver	1.6	1.9	2.4	-1.2	1.5
Fe content in liver	3.1	3.8	4.8	-1.7	2.2
K content in liver	0.1	0.1	0.1	-0.3	0.2
Mg content in liver	0.0	0.0	0.0	0.2	-0.1
Mn content in liver	2.8	3.1	4.0	-1.5	2.0
Na content in liver	0.4	0.4	0.6	-0.8	0.5
Rb content in liver	0.3	0.4	0.4	-0.7	0.6
Se content in liver	4.6	5.4	5.6	-2.4	2.3
Sr content in liver	0.5	0.4	0.8	0.3	-0.9
Zn content in liver	0.9	1.0	1.1	-1.0	1.1
Bone: minimum diameter	2.3	4.2	4.7	2.2	-1.9
Time in familiar zone, hab. session 1	0.1	0.1	0.1	-0.2	-0.3
Time in novel zone, hab. session 1	0.5	0.5	1.0	-0.2	1.0
Total zone transitions, hab. session 1	0.2	0.2	0.3	-0.5	0.5
Total locomotion distance, hab. session 1	0.0	0.1	0.1	-0.1	-0.3
Locomotion velocity, hab. session 1	0.2	0.2	0.4	0.0	-0.7
Time in familiar zone, hab. session 2	0.3	0.3	0.4	0.5	-0.7
Time in novel zone, hab. session 2	1.4	1.4	1.6	-1.1	1.3
Total zone transitions, hab. session 2	0.5	0.6	0.9	0.6	-0.9
Total locomotion distance, hab. session 2	0.8	1.0	1.8	0.5	-1.3
Locomotion velocity, hab. session 2	1.2	1.6	2.6	0.8	-1.6
Novel to familiar place preference ratio	0.6	0.6	1.0	-1.0	0.5
Novelty place preference	0.8	0.8	1.3	-1.1	0.6
Time in novel zone, NPP test	1.1	1.2	1.7	-1.3	0.8
Total zone transitions, NPP test	0.6	0.8	0.9	0.9	-0.9
Total locomotion distance, NPP test	0.9	1.2	1.8	0.7	-1.4
Locomotion velocity, NPP test	1.8	2.6	3.6	1.3	-1.9
Intraocular pressure	0.0	0.0	0.1	0.3	0.0
Delta distance traveled before/after self-admin	1.2	1.2	1.5	1.2	-0.9
Delta ambulatory time before/after self-admin	1.4	1.7	2.2	1.5	-1.1
Parametrial fat weight	0.0	0.1	0.2	-0.0	-0.4
Pavlov. Cond. lever latency	2.8	3.5	3.8	-1.8	1.9
Pavlov. Cond. magazine entry latency	0.0	0.0	0.0	-0.0	-0.0
Pavlov. Cond. change in total contacts	0.6	0.6	0.8	0.7	-0.9
Pavlov. Cond. index score	1.0	1.3	1.5	1.0	-1.2
Pavlov. Cond. latency score	1.7	2.1	2.4	1.4	-1.6
Pavlov. Cond. lever contacts	3.1	3.7	4.1	1.8	-2.0
Pavlov. Cond. magazine entry number	0.6	0.8	0.8	-0.9	0.8
Pavlov. Cond. intertrial magazine entries	0.0	0.0	0.0	-0.1	-0.2
Pavlov. Cond. lever-magazine prob. diff.	0.6	0.7	0.9	0.7	-0.9
Pavlov. Cond. response bias	0.6	0.8	0.9	0.8	-1.0
Pavlov. Cond. lever latency	2.3	3.1	3.3	-1.8	1.7
Pavlov. Cond. magazine entry latency	0.1	0.2	0.2	0.4	0.4
Pavlov. Cond. change in total contacts	0.5	0.8	1.1	1.0	-0.7
Pavlov. Cond. index score	0.4	0.6	0.9	1.0	-0.5
Pavlov. Cond. latency score	0.4	0.5	0.9	0.9	-0.4
Pavlov. Cond. lever contacts	2.2	3.0	3.5	1.9	-1.6
Pavlov. Cond. magazine entry number	0.2	0.3	0.5	-0.7	-0.1
Pavlov. Cond. intertrial magazine entries	0.4	0.6	1.2	0.3	-1.1
Pavlov. Cond. lever-magazine prob. diff.	0.3	0.3	0.6	0.8	-0.2
Pavlov. Cond. response bias	1.1	1.5	2.0	1.4	-1.0
Time in closed arm before self-admin	4.0	5.1	5.5	2.4	-2.2
Time in closed arm after self-admin	1.5	1.6	1.7	1.3	-1.2
Time in open arm before self-admin	7.3	7.9	8.0	-2.8	2.8
Time in open arm after self-admin	0.3	0.4	0.4	0.6	-0.6
Bone: periosteal estimation	0.3	0.7	0.8	0.8	-0.9
Bone: periosteal perimeter	0.3	0.5	0.6	0.7	-0.8
Bone: post-yield work	2.6	3.8	4.9	1.7	-2.2
Progressive ratio test 1 active lever presses	0.1	0.1	0.2	-0.4	0.0
Progressive ratio test 1 breakpoint	0.1	0.1	0.2	-0.4	0.0
Progressive ratio test 1 inactive lever presses	0.1	0.1	0.2	0.0	-0.4
Progressive ratio test 2 active lever presses	0.4	0.5	0.6	-0.8	0.6
Progressive ratio test 2 breakpoint	0.4	0.5	0.6	-0.8	0.6
Progressive ratio test 2 inactive lever presses	0.2	0.3	0.5	-0.7	0.3
Incentive Sensitization - Responses	0.4	0.6	0.6	-0.8	0.8
Incentive Sensitization - Breakpoint	0.4	0.6	0.6	-0.8	0.7
Sum of active levers in priming session hrs 5-6	0.9	0.8	1.2	1.1	-0.6
Progressive ratio	0.3	0.4	0.7	-0.4	0.8
Food seeking constrained by brief footshock	1.3	1.6	1.7	-1.3	1.2
Seeking ratio, punishment vs. effort	0.1	0.2	0.4	-0.6	-0.0
Retroperitoneal fat weight	0.7	2.9	4.8	-1.0	2.2
Reaction time number correct	0.6	1.2	1.9	1.4	-0.7
Reaction time mean minus median	0.1	0.4	0.4	0.6	-0.6
Reaction time mean minus median AUC	0.6	1.4	1.5	1.2	-1.2
Reaction time num false alarms	0.1	0.1	0.2	-0.1	-0.5
Reaction time num false alarms AUC	0.1	0.1	0.2	0.0	-0.5
Reaction time trials correct on left	0.6	1.2	1.9	1.4	-0.7
Reaction time trials on left	0.6	1.2	1.9	1.4	-0.7
Reaction time mean	0.0	0.1	0.1	0.2	0.3
Reaction time mean AUC	0.0	0.1	0.1	0.3	0.2
Median of all reaction times	0.2	0.3	0.5	-0.2	0.7
Reaction time omissions	0.5	0.7	0.9	-0.7	1.0
Reaction time false alarm rate	0.2	0.3	0.5	-0.7	-0.1
Reaction time premature initiation rate	1.3	1.9	2.1	1.3	-1.5
Reaction time premature initiations	1.7	2.9	3.0	1.7	-1.7
Std. dev. reaction times	0.2	0.3	0.5	0.7	-0.3
Reaction time trials completed	0.6	1.2	1.9	1.4	-0.7
Reaction time trials AUC	0.4	0.8	1.3	1.2	-0.5
Run reversals in cocaine runway, females	1.0	1.0	1.1	-0.9	1.1
Run reversals in cocaine runway, males	0.1	0.1	0.2	-0.4	0.1
Latency to leave start box in cocaine runway	0.2	0.3	0.4	0.3	-0.7
Latency to leave start box in cocaine runway, F	0.3	0.3	0.4	0.6	-0.5
Latency to leave start box in cocaine runway, M	0.2	0.2	0.3	-0.5	-0.2
Std. dev. time between licks in bursts	0.9	1.3	1.4	-1.1	1.2
Total sessions with >9 infusions	0.0	0.0	0.0	0.1	-0.0
Short access day 1 total inactive lever presses	1.1	1.5	2.8	0.3	-1.7
Short access day 10 total inactive lever presses	0.7	1.8	2.1	1.2	-1.4
Short access day 1 total infusions	0.6	0.9	1.1	0.8	-1.1
Short access day 10 total infusions	0.5	0.7	1.0	-1.0	0.6
Short access total infusions	0.0	0.0	0.0	0.0	-0.2
Short access day 1 locomotion	0.9	1.1	1.6	0.8	-1.3
Short access day 10 total locomotion	0.1	0.1	0.2	-0.1	-0.4
Short access total locomotion	0.1	0.1	0.2	0.1	-0.4
One hour access (0.3 mA shock)	5.3	6.1	7.2	-2.7	2.2
Compulsive drug intake	1.8	2.1	2.4	-1.3	1.6
One hour access (shock baseline)	0.5	0.7	1.1	-1.1	0.6
Social response proportion	1.3	1.5	2.3	-0.8	1.5
Social responses	0.5	0.7	1.2	1.1	-0.4
Social time	0.0	0.0	0.0	0.0	-0.1
Soleus weight	1.8	5.3	9.4	1.1	-3.1
Bone: stiffness	0.1	0.2	0.5	-0.7	0.2
Tibialis anterior weight	6.8	23.1	28.4	4.2	-5.3
Time to tail flick, vehicle, before self-admin	0.9	0.9	1.3	1.1	-0.7
Time to tail flick, vehicle, after self-admin	1.5	1.9	2.0	1.4	-1.4
Time to tail flick, test, before self-admin	0.3	0.3	0.5	-0.7	-0.0
Time to tail flick, test, after self-admin	0.6	0.7	0.9	0.7	-0.9
Delta time to tail flick, vehicle, before/after SA	0.0	0.0	0.0	-0.2	0.0
Delta time to tail flick, test, before/after SA	0.4	0.4	0.7	0.8	-0.4
Tibia length	0.1	0.3	0.6	0.7	-0.3
Ambulatory time before self-admin	0.8	1.2	1.5	0.9	-1.2
Ambulatory time after self-admin	3.5	4.1	4.3	2.1	-2.0
Bone: tissue strength	1.0	1.0	1.3	0.8	-1.1
Total heroin consumption	0.6	0.7	0.7	0.9	-0.8
Bone: trabecular number	2.5	4.2	6.5	2.5	-1.4
Bone: trabecular spacing	0.2	0.2	0.5	-0.7	-0.0
Bone: trabecular thickness	2.3	2.9	3.4	1.9	-1.5
Bone: trabecular tissue density	0.2	0.2	0.5	-0.2	-0.7
Water consumed over 24 hours	0.2	0.2	0.4	-0.3	0.6
Number of responses in last shaping day	0.5	0.5	0.6	0.7	-0.7