Hub : Genes

Loxl2

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	Loxl2	0.03	0.03	6.6e-04	0.02	0.02	0.02	0.02	1.5e-03	1.9e-03	1.9e-03	2.4e-03
2	Brain	mRNA stability	Loxl2	0.04	0.04	6.6e-04	0.03	0.03	0.02	0.02	8.0e-04	1.1e-03	2.9e-03	2.3e-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	2
Bone: apparent density	1.6	2.7	2.8	1.7	-1.6
Area under the delay curve	0.1	0.1	0.1	-0.3	0.2
BMI with tail	0.3	1.1	1.2	-1.0	1.1
BMI without tail	0.8	1.6	1.7	1.3	-1.3
Body weight	0.3	1.4	1.5	-1.1	1.2
Weight adjusted by age	1.8	2.1	2.2	-1.4	1.5
Bone surface	0.7	1.2	1.2	1.1	-1.1
Bone volume	0.8	1.3	1.4	1.2	-1.1
Breakpoint value in progressive ratio session	0.1	0.1	0.1	-0.2	0.3
Number of licking bursts	0.0	0.0	0.0	0.0	0.0
Context. condit. distance diff. score	0.8	0.9	1.1	0.9	-1.0
Locomotion velocity, session 1	0.2	0.2	0.2	-0.5	0.4
Locomotion distance, session 1	0.0	0.0	0.0	-0.0	-0.0
Locomotion velocity, session 2	0.1	0.1	0.1	0.2	-0.3
Locomotion distance, session 2	0.0	0.0	0.1	0.3	-0.2
Locomotion velocity, session 3	0.5	0.6	0.6	-0.7	0.8
Locomotion distance, session 3	0.0	0.0	0.1	0.3	-0.1
Stereotopy head waving bouts, day 3	0.9	1.1	1.3	-1.1	1.0
Stereotopy head waving duration, day 3	3.1	3.7	4.1	-2.0	1.8
Locomotion velocity, session 7	4.4	4.8	4.9	2.2	-2.2
Locomotion distance, session 7	3.9	5.0	5.4	2.3	-2.1
Stereotopy head waving bouts, day 7	1.9	2.1	2.3	-1.5	1.4
Stereotopy head waving duration, day 7	2.6	3.2	3.4	-1.8	1.7
Locomotion velocity, session 8	0.0	0.0	0.0	0.1	-0.1
Locomotion distance, session 8	0.6	0.9	0.9	0.9	-1.0
Degree of sensitization distance	5.0	5.0	5.1	2.2	-2.3
Degree of sensitization stereotypy	1.1	1.3	1.4	-1.2	1.1
Conditioned locomotion	0.1	0.1	0.1	0.3	-0.2
Cocaine response after cond. corrected	0.2	0.2	0.2	-0.5	0.5
Cocaine response after cond. not corrected	0.1	0.1	0.2	-0.4	0.4
Cocaine response before conditioning	0.1	0.1	0.1	0.3	-0.4
Saline control response	0.2	0.2	0.2	0.4	-0.4
Bone: connectivity density	3.1	4.8	4.9	2.2	-2.2
Bone: cortical apparent density	0.0	0.0	0.0	0.2	-0.1
Bone: cortical area	0.0	0.0	0.0	0.2	-0.1
Bone: cortical porosity	1.4	1.5	1.7	-1.3	1.2
Bone: cortical porosity	0.6	0.6	0.6	-0.8	0.8
Bone: cortical thickness	0.0	0.0	0.1	0.3	-0.2
Bone: cortical thickness	0.0	0.0	0.1	0.2	-0.2
Bone: cortical tissue density	0.0	0.0	0.0	0.2	-0.1
Condit. Reinf. active minus inactive responses	0.7	0.8	0.9	-0.9	0.9
Condit. Reinf. active-inactive response ratio	2.7	2.9	2.9	-1.7	1.7
Condit. Reinf. active responses	0.0	0.0	0.1	-0.2	0.1
Condit. Reinf. inactive responses	2.8	3.4	3.6	1.8	-1.9
Incentive salience index mean	1.0	1.2	1.2	-1.1	1.1
Condit. Reinf. lever presses	0.3	0.4	0.4	-0.6	0.6
Condit. Reinf. active minus inactive responses	0.4	0.4	0.4	0.7	-0.7
Condit. Reinf. active-inactive response ratio	0.1	0.1	0.1	-0.4	0.4
Condit. Reinf. active responses	1.0	1.4	1.4	1.2	-1.2
Condit. Reinf. inactive responses	2.5	3.1	3.1	1.8	-1.7
Condit. Reinf. lever presses	0.1	0.1	0.1	0.3	-0.3
Condit. Reinf. lever reinforcers received	0.7	0.9	0.9	1.0	-1.0
Conditioned reinforcement - actives	2.7	2.7	2.7	1.6	-1.6
Conditioned reinforcement - inactives	2.8	3.1	3.2	1.7	-1.8
Conditioned locomotion	1.2	1.4	1.5	1.2	-1.2
Patch foraging indifference point 0 sec	2.1	3.4	3.6	1.8	-1.9
Patch foraging indifference point AUC	0.5	0.6	0.7	-0.7	0.8
Delay disc. indifference point, 0s delay	0.3	0.3	0.3	0.6	-0.5
Delay disc. indifference point, 16s delay	0.2	0.2	0.2	0.4	-0.4
Delay disc. indifference point, 2s delay	1.6	1.7	1.8	-1.3	1.3
Delay disc. indifference point, 24s delay	0.3	0.3	0.3	-0.5	0.5
Delay disc. indifference point, 4s delay	1.8	1.9	2.0	-1.4	1.3
Delay disc. indifference point, 8s delay	0.0	0.0	0.0	0.0	-0.1
Indifference point function ln k	0.0	0.0	0.0	0.1	-0.2
Indifference point function log k	0.0	0.0	0.0	0.1	-0.2
Patch foraging total patch changes 0 sec	1.8	2.9	3.0	1.7	-1.7
Patch foraging total patch changes 12 sec	0.7	1.0	1.0	1.0	-1.0
Patch foraging total patch changes 18 sec	1.9	2.5	2.6	1.6	-1.5
Patch foraging total patch changes 24 sec	0.0	0.0	0.0	0.1	-0.0
Patch foraging total patch changes 6 sec	0.3	0.4	0.4	0.6	-0.6
Patch foraging time to switch 0 sec	0.6	0.9	0.9	1.0	-0.9
Patch foraging water rate 0 sec	0.2	0.3	0.4	-0.6	0.5
Patch foraging water rate 12 sec	0.4	0.6	0.6	-0.8	0.8
Patch foraging water rate 18 sec	2.5	3.4	3.6	-1.9	1.8
Patch foraging water rate 24 sec	0.0	0.0	0.0	-0.1	0.0
Patch foraging water rate 6 sec	1.7	2.5	2.5	-1.6	1.6
Seeking ratio, delayed vs. immediate footshock	1.5	1.7	1.8	1.3	-1.3
Distance traveled before self-admin	1.2	1.2	1.3	-1.1	1.1
Distance traveled after self-admin	1.9	2.1	2.3	-1.5	1.4
Extensor digitorum longus weight	12.7	49.9	50.0	-7.1	7.1
Bone: elastic displacement	0.5	0.5	0.6	0.7	-0.7
Bone: elastic work	0.2	0.3	0.4	0.5	-0.6
Bone: endosteal estimation	0.1	0.2	0.2	-0.5	0.4
Bone: endosteal perimeter	0.0	0.1	0.1	-0.3	0.3
Epididymis fat weight	2.3	5.4	5.5	2.3	-2.3
Delta time in closed arm before/after self-admin	2.1	2.0	2.2	1.5	-1.4
Delta time in open arm before/after self-admin	0.1	0.1	0.2	0.1	-0.4
Diff in mean of infusions in LGA sessions	3.2	3.6	3.8	-1.8	2.0
Delay discount exponential model param	0.3	0.3	0.4	0.6	-0.5
Extinction: sum of active levers before priming	3.1	3.1	3.3	1.7	-1.8
Active lever presses in extinction session 6	0.3	0.3	0.4	0.7	-0.3
Bone: final force	0.1	0.2	0.2	-0.4	0.4
Bone: final moment	0.1	0.1	0.1	-0.3	0.4
Food consumed during 24 hour testing period	0.4	0.4	0.5	0.7	-0.6
Glucose	0.0	0.1	0.1	0.3	-0.1
Heart weight	0.0	0.1	0.1	0.3	-0.2
Delay discount hyperbolic model param	0.7	0.7	0.8	0.9	-0.8
Intermittent access intake day 1-15 change	2.6	2.6	2.6	1.6	-1.6
Intermittent access intake escalation	1.8	1.8	1.8	1.3	-1.3
Intermittent access intake escalation 2	0.6	0.6	0.7	0.7	-0.8
Intermitt. access day 1 inactive lever presses	0.1	0.1	0.1	0.3	-0.3
Intermitt. access day 15 inactive lever presses	0.0	0.0	0.0	-0.1	0.2
Intermitt. access escalation Index	0.7	0.6	0.6	-0.8	0.8
Intermittent access day 1 total infusions	0.0	0.0	0.0	0.1	-0.1
Intermittent access day 15 total infusions	1.0	1.2	1.2	1.1	-1.1
Intermittent access terminal intake (last 3 days)	0.3	0.3	0.3	0.5	-0.6
Intermittent access total infusions	0.4	0.5	0.5	0.7	-0.7
Intermittent access day 1 locomotion	0.3	0.3	0.3	0.5	-0.6
Intermittent access day 15 total locomotion	1.9	2.0	2.1	1.4	-1.5
Intermittent access total locomotion	0.6	0.6	0.7	0.8	-0.8
Intermittent access standard deviation	1.5	1.6	1.7	1.2	-1.3
Left kidney weight	0.1	0.4	0.4	-0.6	0.6
Right kidney weight	0.2	0.5	0.6	0.7	-0.8
Cocaine induced anxiety	0.2	0.2	0.2	-0.4	0.5
Post-drug Anxiety	0.5	0.5	0.5	0.7	-0.7
Baseline Anxiety	0.9	0.9	1.0	0.9	-1.0
Tail length	0.9	2.7	3.0	1.6	-1.7
Length with tail	0.1	0.2	0.2	-0.5	0.4
Length without tail	3.6	7.8	8.0	-2.8	2.8
Times rat made contact with spout	0.4	0.5	0.5	0.7	-0.7
Lifetime Intake	0.4	0.4	0.4	0.6	-0.6
Liver weight, left	2.0	3.2	3.4	-1.7	1.8
Liver weight, right	0.7	1.2	1.2	-1.1	1.1
Locomotor activity	1.4	2.2	2.3	-1.5	1.5
Locomotor testing distance	0.0	0.0	0.0	0.0	-0.1
Locomotor testing rearing	0.3	0.4	0.4	0.6	-0.6
Locomotion in novel chamber	0.2	0.2	0.2	0.5	-0.4
Locomotion in novel chamber post-restriction	0.6	0.7	0.7	-0.8	0.8
Fecal boli incidents, locomotor time 1	0.8	0.9	0.9	-0.9	0.9
Change in fecal boli incidents, locomotor task	0.2	0.2	0.2	-0.4	0.4
Time >=10cm from walls, locomotor time 1	0.5	0.5	0.5	0.7	-0.7
Bouts of movement, locomotor time 1	5.3	5.8	5.8	-2.4	2.4
Total resting periods, locomotor time 1	5.2	5.7	5.7	-2.4	2.4
Rest time, locomotor task time 1	3.5	3.8	3.8	-2.0	2.0
Distance moved, locomotor task time 1	3.4	3.7	3.7	1.9	-1.9
Vertical activity count, locomotor time 1	1.1	1.2	1.2	1.1	-1.1
Time >=10cm from walls, locomotor time 2	0.4	0.4	0.4	-0.6	0.6
Bouts of movement, locomotor time 2	3.7	4.0	4.0	-2.0	2.0
Total resting periods, locomotor time 2	4.3	4.6	4.6	-2.1	2.1
Rest time, locomotor task time 2	1.1	1.2	1.2	-1.1	1.1
Distance moved, locomotor task time 2	3.2	3.7	3.7	1.9	-1.9
Vertical activity count, locomotor time 2	0.4	0.4	0.4	0.6	-0.6
Light reinforcement 1	3.1	5.7	5.8	2.4	-2.4
Light reinforcement 2	0.9	1.2	1.4	1.2	-1.1
Bone: marrow area	0.0	0.1	0.1	-0.3	0.3
Bone: maximum diameter	0.2	0.4	0.5	-0.6	0.7
Bone: maximum force	0.2	0.4	0.4	-0.6	0.6
Bone: maximum moment	0.1	0.2	0.2	-0.4	0.5
Mean time between licks in bursts	2.0	2.9	2.9	1.7	-1.7
Mean num. licks in bursts	0.2	0.3	0.3	0.5	-0.6
Cd content in liver	0.1	0.1	0.2	0.1	-0.4
Co content in liver	4.2	4.9	5.1	-2.3	2.1
Cu content in liver	0.6	0.7	0.7	-0.8	0.9
Fe content in liver	2.1	2.5	2.6	1.6	-1.6
K content in liver	0.5	0.5	0.5	0.7	-0.7
Mg content in liver	1.1	1.1	1.1	1.0	-1.1
Mn content in liver	2.2	2.6	2.7	1.7	-1.5
Na content in liver	0.7	0.7	0.8	-0.8	0.9
Rb content in liver	0.3	0.3	0.4	0.5	-0.6
Se content in liver	0.8	1.0	1.1	0.9	-1.0
Sr content in liver	0.4	0.3	0.3	0.6	-0.6
Zn content in liver	1.2	1.3	1.4	-1.2	1.1
Bone: minimum diameter	0.1	0.2	0.2	-0.4	0.4
Time in familiar zone, hab. session 1	0.0	0.0	0.0	-0.1	0.1
Time in novel zone, hab. session 1	1.5	1.4	1.4	-1.2	1.2
Total zone transitions, hab. session 1	0.3	0.4	0.4	-0.6	0.6
Total locomotion distance, hab. session 1	0.0	0.0	0.0	-0.1	0.0
Locomotion velocity, hab. session 1	0.1	0.1	0.1	0.3	-0.3
Time in familiar zone, hab. session 2	2.1	2.2	2.4	-1.6	1.4
Time in novel zone, hab. session 2	0.8	0.8	0.9	1.0	-0.8
Total zone transitions, hab. session 2	1.5	2.0	2.0	-1.4	1.4
Total locomotion distance, hab. session 2	0.3	0.4	0.5	-0.7	0.6
Locomotion velocity, hab. session 2	0.6	0.9	0.9	-1.0	0.9
Novel to familiar place preference ratio	1.7	1.7	1.9	1.4	-1.2
Novelty place preference	1.3	1.4	1.5	1.2	-1.1
Time in novel zone, NPP test	0.6	0.7	0.8	0.9	-0.8
Total zone transitions, NPP test	0.1	0.1	0.1	0.3	-0.4
Total locomotion distance, NPP test	2.4	3.2	3.4	1.8	-1.8
Locomotion velocity, NPP test	2.3	3.3	3.4	1.8	-1.8
Intraocular pressure	0.5	0.7	0.7	0.9	-0.8
Delta distance traveled before/after self-admin	1.8	2.0	2.3	-1.5	1.3
Delta ambulatory time before/after self-admin	1.8	2.0	2.2	-1.5	1.3
Parametrial fat weight	3.7	7.3	7.4	2.7	-2.7
Pavlov. Cond. lever latency	0.0	0.0	0.0	-0.2	0.0
Pavlov. Cond. magazine entry latency	0.1	0.1	0.1	0.3	-0.2
Pavlov. Cond. change in total contacts	0.8	0.9	1.1	-0.8	1.0
Pavlov. Cond. index score	0.0	0.0	0.1	-0.1	0.3
Pavlov. Cond. latency score	0.0	0.0	0.0	0.0	0.1
Pavlov. Cond. lever contacts	0.0	0.0	0.1	0.3	-0.1
Pavlov. Cond. magazine entry number	0.4	0.5	0.6	0.6	-0.8
Pavlov. Cond. intertrial magazine entries	0.0	0.0	0.1	0.1	-0.3
Pavlov. Cond. lever-magazine prob. diff.	0.1	0.1	0.2	-0.3	0.4
Pavlov. Cond. response bias	0.1	0.1	0.2	-0.2	0.4
Pavlov. Cond. lever latency	0.3	0.5	0.5	0.7	-0.7
Pavlov. Cond. magazine entry latency	0.1	0.1	0.1	0.2	-0.3
Pavlov. Cond. change in total contacts	1.6	2.2	2.2	-1.5	1.5
Pavlov. Cond. index score	0.5	0.7	0.7	-0.8	0.8
Pavlov. Cond. latency score	0.3	0.4	0.4	-0.7	0.6
Pavlov. Cond. lever contacts	0.3	0.5	0.5	-0.7	0.7
Pavlov. Cond. magazine entry number	0.0	0.0	0.1	-0.2	0.2
Pavlov. Cond. intertrial magazine entries	6.5	8.4	8.5	2.9	-2.9
Pavlov. Cond. lever-magazine prob. diff.	0.6	0.8	0.8	-0.9	0.9
Pavlov. Cond. response bias	0.4	0.6	0.6	-0.8	0.8
Time in closed arm before self-admin	1.8	2.1	2.3	-1.5	1.4
Time in closed arm after self-admin	0.7	0.7	0.7	-0.8	0.8
Time in open arm before self-admin	0.2	0.2	0.4	-0.3	0.6
Time in open arm after self-admin	0.1	0.1	0.2	0.4	-0.4
Bone: periosteal estimation	0.0	0.0	0.0	-0.1	0.2
Bone: periosteal perimeter	0.0	0.0	0.0	0.0	0.0
Bone: post-yield work	0.2	0.2	0.2	0.5	-0.5
Progressive ratio test 1 active lever presses	0.3	0.3	0.3	-0.5	0.6
Progressive ratio test 1 breakpoint	0.1	0.1	0.2	-0.4	0.4
Progressive ratio test 1 inactive lever presses	1.1	1.2	1.2	1.1	-1.1
Progressive ratio test 2 active lever presses	0.2	0.2	0.2	0.5	-0.5
Progressive ratio test 2 breakpoint	0.3	0.3	0.3	0.5	-0.5
Progressive ratio test 2 inactive lever presses	0.3	0.3	0.3	0.6	-0.6
Incentive Sensitization - Responses	1.2	1.2	1.2	1.1	-1.1
Incentive Sensitization - Breakpoint	1.6	1.7	1.7	1.3	-1.3
Sum of active levers in priming session hrs 5-6	0.0	0.0	0.1	0.3	-0.1
Progressive ratio	0.1	0.1	0.1	0.3	-0.3
Food seeking constrained by brief footshock	1.3	1.6	1.7	-1.2	1.3
Seeking ratio, punishment vs. effort	0.8	1.0	1.0	-1.0	1.0
Retroperitoneal fat weight	0.3	1.0	1.1	0.9	-1.1
Reaction time number correct	0.4	0.5	0.6	-0.8	0.7
Reaction time mean minus median	0.2	0.3	0.3	-0.5	0.5
Reaction time mean minus median AUC	0.2	0.2	0.2	-0.4	0.5
Reaction time num false alarms	0.0	0.0	0.0	0.0	-0.0
Reaction time num false alarms AUC	0.0	0.0	0.0	0.2	-0.2
Reaction time trials correct on left	0.4	0.5	0.6	-0.8	0.7
Reaction time trials on left	0.3	0.4	0.4	-0.6	0.6
Reaction time mean	0.3	0.4	0.4	-0.6	0.7
Reaction time mean AUC	0.5	0.6	0.7	-0.7	0.8
Median of all reaction times	0.1	0.2	0.2	-0.3	0.4
Reaction time omissions	1.9	2.6	2.7	1.6	-1.6
Reaction time false alarm rate	0.2	0.3	0.3	0.5	-0.5
Reaction time premature initiation rate	1.8	2.4	2.4	-1.5	1.5
Reaction time premature initiations	2.3	3.2	3.3	-1.8	1.8
Std. dev. reaction times	0.2	0.3	0.3	-0.6	0.6
Reaction time trials completed	0.3	0.4	0.4	-0.6	0.6
Reaction time trials AUC	0.2	0.4	0.4	-0.6	0.6
Run reversals in cocaine runway, females	3.8	3.6	3.9	1.8	-2.0
Run reversals in cocaine runway, males	2.5	2.4	2.4	-1.5	1.5
Latency to leave start box in cocaine runway	0.5	0.5	0.6	-0.6	0.8
Latency to leave start box in cocaine runway, F	1.3	1.4	1.5	-1.1	1.2
Latency to leave start box in cocaine runway, M	1.3	1.2	1.2	1.1	-1.1
Std. dev. time between licks in bursts	1.3	1.6	1.6	1.3	-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	0.4	0.5	0.5	0.7	-0.7
Short access day 10 total inactive lever presses	0.2	0.3	0.3	0.5	-0.5
Short access day 1 total infusions	0.2	0.2	0.2	-0.4	0.4
Short access day 10 total infusions	0.0	0.0	0.0	0.0	-0.0
Short access total infusions	0.1	0.1	0.1	0.3	-0.3
Short access day 1 locomotion	0.2	0.2	0.2	-0.5	0.4
Short access day 10 total locomotion	0.5	0.6	0.6	0.8	-0.7
Short access total locomotion	0.6	0.6	0.6	0.8	-0.8
One hour access (0.3 mA shock)	0.4	0.4	0.5	0.7	-0.7
Compulsive drug intake	0.0	0.0	0.0	0.1	-0.1
One hour access (shock baseline)	0.0	0.0	0.0	-0.1	0.1
Social response proportion	0.0	0.0	0.1	-0.2	0.2
Social responses	1.1	1.4	1.4	1.2	-1.2
Social time	0.3	0.4	0.5	0.6	-0.7
Soleus weight	0.8	2.5	2.7	-1.7	1.5
Bone: stiffness	0.6	0.9	0.9	-0.9	0.9
Tibialis anterior weight	8.0	27.2	27.7	-5.3	5.2
Time to tail flick, vehicle, before self-admin	0.8	0.8	0.9	0.9	-0.8
Time to tail flick, vehicle, after self-admin	2.4	2.6	2.9	-1.5	1.7
Time to tail flick, test, before self-admin	0.8	0.8	0.9	1.0	-0.9
Time to tail flick, test, after self-admin	3.3	3.4	3.5	1.9	-1.8
Delta time to tail flick, vehicle, before/after SA	0.4	0.4	0.4	-0.6	0.7
Delta time to tail flick, test, before/after SA	0.3	0.3	0.3	0.5	-0.6
Tibia length	1.4	4.0	4.6	2.2	-1.8
Ambulatory time before self-admin	0.6	0.6	0.7	-0.8	0.8
Ambulatory time after self-admin	3.2	3.6	3.9	-2.0	1.8
Bone: tissue strength	0.1	0.1	0.2	0.4	-0.3
Total heroin consumption	0.4	0.4	0.5	-0.7	0.7
Bone: trabecular number	2.8	4.3	4.4	2.1	-2.1
Bone: trabecular spacing	2.3	2.9	3.0	-1.7	1.7
Bone: trabecular thickness	1.2	1.4	1.5	1.2	-1.2
Bone: trabecular tissue density	1.6	2.3	2.4	-1.6	1.5
Water consumed over 24 hours	1.2	1.5	1.5	-1.2	1.2
Number of responses in last shaping day	0.0	0.1	0.1	-0.1	0.3