Hub : Genes

Larp4

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	Brain	alternative TSS	ENSRNOT00000112803	0.04	0.05	7.3e-03	0.02	0.02	0.01	0.01	8.6e-03	6.3e-03	4.7e-02	2.5e-02
2	Liver	isoform ratio	ENSRNOT00000096188	0.02	0.02	8.1e-03	0.01	0.01	0.01	0.01	8.6e-03	1.1e-02	2.7e-02	1.5e-02

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 strong Z-scores (below -2 or above 2): lower negative Z-scores are darker blue, higher positive Z-scores are darker red.

Trait	Avg chi2 ratio	Avg chi2	Max chi2	1	2
BMI with tail	3.9	12.5	12.9	3.5	-3.6
BMI without tail	0.4	0.7	1.1	1.0	-0.6
Body weight	4.2	17.9	18.8	4.1	-4.3
Epididymis fat weight	0.0	0.0	0.1	0.2	-0.1
Glucose	0.3	0.4	0.5	-0.7	0.6
Heart weight	0.1	0.1	0.2	0.4	-0.3
Left kidney weight	1.0	2.8	3.3	1.8	-1.5
Right kidney weight	1.8	5.2	5.3	2.3	-2.3
Tail length	0.0	0.0	0.0	0.2	0.1
Length with tail	1.5	5.6	5.9	2.3	-2.4
Length without tail	3.9	8.4	9.6	2.7	-3.1
Liver weight, left	1.6	2.6	2.7	1.6	-1.6
Liver weight, right	1.6	2.6	2.6	1.6	-1.6
Parametrial fat weight	0.8	1.6	1.9	-1.1	1.4
Retroperitoneal fat weight	1.0	3.1	3.4	-1.7	1.9
Intraocular pressure	4.0	5.7	6.6	-2.2	2.6
Extensor digitorum longus weight	4.0	16.1	17.1	3.9	-4.1
Soleus weight	1.0	3.0	3.1	1.8	-1.7
Tibialis anterior weight	2.9	10.0	10.0	3.2	-3.1
Tibia length	4.0	11.1	11.7	3.3	-3.4
Number of licking bursts	1.0	1.2	1.4	-1.2	1.0
Food consumed during 24 hour testing period	1.7	2.1	2.1	1.5	-1.4
Times rat made contact with spout	0.0	0.0	0.0	0.1	0.1
Mean time between licks in bursts	0.1	0.1	0.1	-0.3	0.2
Mean num. licks in bursts	0.5	0.6	0.9	0.9	-0.6
Std. dev. time between licks in bursts	1.2	1.4	1.6	-1.1	1.3
Water consumed over 24 hours	0.0	0.1	0.1	-0.2	0.3
Indifference point 0 sec	5.6	9.1	9.3	-3.0	3.1
Indifference point AUC	0.2	0.2	0.3	-0.4	0.5
Indifference point function ln k	4.7	6.7	7.0	2.5	-2.7
Indifference point function log k	4.7	6.7	7.0	2.5	-2.7
Delay discounting total patch changes 0 sec	5.1	8.3	8.4	-2.8	2.9
Delay discounting total patch changes 12 sec	5.8	7.7	7.8	-2.8	2.8
Delay discounting total patch changes 18 sec	6.6	8.7	9.0	-2.9	3.0
Delay discounting total patch changes 24 sec	3.9	4.9	5.1	-2.2	2.3
Delay discounting total patch changes 6 sec	6.9	10.5	11.0	-3.2	3.3
Delay discounting time to switch 0 sec	2.3	3.5	3.6	-1.8	1.9
Delay discounting water rate 0 sec	3.3	5.3	5.5	2.3	-2.3
Delay discounting water rate 12 sec	2.6	3.9	4.6	1.8	-2.2
Delay discounting water rate 18 sec	0.5	0.6	0.8	0.7	-0.9
Delay discounting water rate 24 sec	4.5	6.2	6.8	2.4	-2.6
Delay discounting water rate 6 sec	5.9	8.6	8.9	2.9	-3.0
Locomotor activity	1.1	1.7	2.1	-1.2	1.5
Locomotor testing distance	3.0	4.9	5.7	-2.0	2.4
Locomotor testing rearing	2.0	3.2	4.1	-1.5	2.0
Light reinforcement 1	0.5	0.8	1.0	-0.8	1.0
Light reinforcement 2	0.1	0.1	0.1	0.4	-0.2
Reaction time number correct	1.3	1.9	2.3	1.2	-1.5
Reaction time mean minus median	4.6	6.0	7.0	-2.2	2.6
Reaction time mean minus median AUC	3.4	4.3	4.9	-1.9	2.2
Reaction time num false alarms	1.3	1.7	1.8	-1.3	1.3
Reaction time num false alarms AUC	1.4	2.0	2.0	-1.4	1.4
Reaction time trials correct on left	1.3	1.9	2.3	1.2	-1.5
Reaction time trials on left	1.1	1.5	1.8	1.1	-1.4
Reaction time mean	0.5	0.7	0.8	-0.8	0.9
Reaction time mean AUC	0.3	0.4	0.5	-0.5	0.7
Median of all reaction times	0.0	0.0	0.0	-0.0	0.1
Reaction time omissions	6.9	9.3	10.4	-2.9	3.2
Reaction time false alarm rate	1.8	2.6	2.8	-1.5	1.7
Reaction time premature initiation rate	3.9	5.2	6.1	-2.1	2.5
Reaction time premature initiations	1.3	1.9	2.2	-1.3	1.5
Std. dev. reaction times	4.3	5.9	6.7	-2.3	2.6
Reaction time trials completed	1.1	1.5	1.8	1.1	-1.4
Reaction time trials AUC	1.7	2.4	2.9	1.4	-1.7
Social response proportion	0.0	0.0	0.1	-0.0	0.2
Social responses	3.9	5.1	5.8	-2.1	2.4
Social time	0.3	0.4	0.6	0.8	-0.6
Conditioned locomotion	0.0	0.0	0.0	-0.1	0.1
Cocaine response after cond. corrected	0.0	0.0	0.0	-0.1	0.0
Cocaine response after cond. not corrected	0.2	0.2	0.2	-0.4	0.5
Cocaine response before conditioning	1.4	1.8	2.3	-1.1	1.5
Saline control response	0.0	0.0	0.0	-0.0	0.1
Condit. Reinf. active minus inactive responses	1.2	1.5	1.7	1.3	-1.2
Condit. Reinf. active-inactive response ratio	1.2	1.3	1.6	1.3	-1.0
Condit. Reinf. active responses	0.2	0.2	0.3	0.5	-0.4
Condit. Reinf. inactive responses	0.8	1.0	1.1	-1.0	1.0
Condit. Reinf. lever presses	0.0	0.0	0.0	0.1	0.0
Condit. Reinf. lever reinforcers received	0.0	0.0	0.0	0.2	0.0
Pavlov. Cond. lever latency	1.1	1.5	1.5	1.2	-1.2
Pavlov. Cond. magazine entry latency	0.2	0.3	0.4	-0.6	0.4
Pavlov. Cond. change in total contacts	0.3	0.5	0.6	0.6	-0.8
Pavlov. Cond. index score	0.6	0.8	1.0	-1.0	0.8
Pavlov. Cond. latency score	0.6	0.8	0.9	-0.9	0.8
Pavlov. Cond. lever contacts	0.8	1.2	1.3	-1.0	1.1
Pavlov. Cond. magazine entry number	0.1	0.1	0.2	0.4	-0.2
Pavlov. Cond. intertrial magazine entries	1.3	1.6	2.3	-1.0	1.5
Pavlov. Cond. lever-magazine prob. diff.	0.3	0.4	0.5	-0.7	0.5
Pavlov. Cond. response bias	0.5	0.6	0.7	-0.8	0.8
Conditioned reinforcement - actives	0.9	0.8	0.9	-1.0	0.9
Conditioned reinforcement - inactives	1.6	1.8	1.9	-1.3	1.4
Conditioned locomotion	0.0	0.0	0.1	-0.3	0.1
Intermittent access intake day 1-15 change	0.0	0.0	0.1	-0.1	0.3
Intermittent access intake escalation	0.0	0.0	0.1	0.3	-0.1
Intermittent access intake escalation 2	0.0	0.0	0.0	0.2	0.2
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	-0.0	0.0
Intermitt. access escalation Index	0.9	0.8	1.1	-1.0	0.7
Intermittent access day 1 total infusions	1.0	1.1	1.3	-1.1	1.0
Intermittent access day 15 total infusions	1.1	1.2	1.3	-1.1	1.1
Intermittent access terminal intake (last 3 days)	1.1	1.2	1.2	-1.1	1.1
Intermittent access total infusions	1.1	1.2	1.2	-1.1	1.1
Intermittent access day 1 locomotion	1.2	1.2	1.4	-1.2	1.0
Intermittent access day 15 total locomotion	0.5	0.6	0.6	-0.8	0.7
Intermittent access total locomotion	2.9	3.2	3.6	-1.9	1.7
Intermittent access standard deviation	0.1	0.1	0.1	0.3	-0.1
Cocaine induced anxiety	0.8	1.0	1.0	1.0	-1.0
Post-drug Anxiety	4.9	5.4	5.6	2.3	-2.4
Baseline Anxiety	0.7	0.7	0.7	0.8	-0.9
Lifetime Intake	1.9	2.1	2.2	-1.4	1.5
Incentive Sensitization - Responses	0.5	0.5	0.6	0.8	-0.7
Incentive Sensitization - Breakpoint	0.4	0.4	0.5	0.7	-0.6
Progressive ratio test 1 active lever presses	7.6	7.9	8.3	-2.9	2.7
Progressive ratio test 1 breakpoint	6.3	6.5	6.9	-2.6	2.5
Progressive ratio test 1 inactive lever presses	1.7	1.8	1.8	-1.3	1.3
Progressive ratio test 2 active lever presses	1.4	1.4	1.5	-1.2	1.2
Progressive ratio test 2 breakpoint	1.4	1.6	1.7	-1.2	1.3
Progressive ratio test 2 inactive lever presses	0.6	0.7	0.8	-0.8	0.9
Total sessions with >9 infusions	1.2	1.4	1.4	-1.1	1.2
Short access day 1 total inactive lever presses	0.9	1.0	1.0	-1.0	1.0
Short access day 10 total inactive lever presses	0.1	0.1	0.2	0.4	-0.2
Short access day 1 total infusions	0.6	0.6	0.6	-0.8	0.8
Short access day 10 total infusions	2.7	3.0	3.1	-1.8	1.7
Short access total infusions	1.6	1.8	1.8	-1.3	1.3
Short access day 1 locomotion	0.2	0.2	0.2	-0.5	0.4
Short access day 10 total locomotion	0.1	0.1	0.1	-0.4	0.4
Short access total locomotion	0.4	0.4	0.5	-0.7	0.6
Compulsive drug intake	1.9	1.8	1.9	1.3	-1.4
One hour access (0.3 mA shock)	0.1	0.1	0.2	0.5	-0.3
One hour access (shock baseline)	0.0	0.0	0.1	0.2	-0.1
Number of responses in last shaping day	0.4	0.4	0.4	0.7	-0.6
Context. condit. distance diff. score	0.3	0.4	0.4	0.6	-0.6
Locomotion velocity, session 1	4.7	5.1	5.2	-2.3	2.2
Locomotion distance, session 1	2.8	3.7	3.7	-1.9	1.9
Locomotion velocity, session 2	0.3	0.4	0.4	-0.6	0.6
Locomotion distance, session 2	3.1	4.4	4.6	-2.1	2.1
Locomotion velocity, session 3	4.3	5.0	5.3	-2.2	2.3
Locomotion distance, session 3	2.2	2.4	3.0	-1.3	1.7
Stereotopy head waving bouts, day 3	0.1	0.1	0.2	-0.4	0.0
Stereotopy head waving duration, day 3	0.2	0.2	0.4	-0.6	0.3
Locomotion velocity, session 7	3.2	3.6	3.6	-1.9	1.9
Locomotion distance, session 7	4.0	5.1	5.3	-2.2	2.3
Stereotopy head waving bouts, day 7	0.3	0.4	0.5	0.5	-0.7
Stereotopy head waving duration, day 7	0.8	0.9	1.1	0.9	-1.0
Locomotion velocity, session 8	0.7	0.8	0.8	-0.9	0.9
Locomotion distance, session 8	0.9	1.4	1.4	-1.2	1.2
Degree of sensitization distance	0.0	0.0	0.1	-0.2	0.0
Degree of sensitization stereotypy	0.6	0.7	0.7	0.8	-0.8
Condit. Reinf. active minus inactive responses	0.0	0.1	0.1	-0.3	0.2
Condit. Reinf. active-inactive response ratio	0.2	0.2	0.3	0.4	-0.5
Condit. Reinf. active responses	0.7	0.9	0.9	-0.9	0.9
Condit. Reinf. inactive responses	3.0	3.5	3.6	-1.8	1.9
Incentive salience index mean	0.0	0.0	0.0	0.1	-0.1
Condit. Reinf. lever presses	0.5	0.7	0.7	0.8	-0.8
Time in familiar zone, hab. session 1	0.0	0.0	0.0	0.2	-0.1
Time in novel zone, hab. session 1	0.0	0.0	0.0	-0.0	-0.2
Total zone transitions, hab. session 1	0.1	0.1	0.1	-0.4	0.2
Total locomotion distance, hab. session 1	0.5	0.7	0.9	-0.9	0.6
Locomotion velocity, hab. session 1	0.3	0.4	0.6	-0.8	0.5
Time in familiar zone, hab. session 2	1.7	1.7	1.9	1.4	-1.3
Time in novel zone, hab. session 2	1.9	1.9	2.2	-1.5	1.3
Total zone transitions, hab. session 2	0.2	0.3	0.3	-0.5	0.5
Total locomotion distance, hab. session 2	0.4	0.6	0.7	-0.9	0.7
Locomotion velocity, hab. session 2	0.2	0.3	0.4	-0.6	0.5
Novel to familiar place preference ratio	1.2	1.3	1.5	1.0	-1.2
Novelty place preference	0.7	0.7	0.9	0.7	-1.0
Time in novel zone, NPP test	0.4	0.5	0.6	0.5	-0.8
Total zone transitions, NPP test	2.8	4.1	4.3	-2.1	1.9
Total locomotion distance, NPP test	3.7	5.1	5.5	-2.3	2.2
Locomotion velocity, NPP test	2.4	3.5	3.8	-1.9	1.8
Pavlov. Cond. lever latency	0.3	0.3	0.4	-0.7	0.5
Pavlov. Cond. magazine entry latency	1.3	1.6	1.7	1.3	-1.3
Pavlov. Cond. change in total contacts	1.6	1.7	1.9	1.4	-1.2
Pavlov. Cond. index score	1.0	1.2	1.4	1.2	-1.0
Pavlov. Cond. latency score	0.8	1.0	1.1	1.1	-0.9
Pavlov. Cond. lever contacts	0.2	0.2	0.4	0.6	-0.3
Pavlov. Cond. magazine entry number	0.5	0.7	0.8	-0.9	0.8
Pavlov. Cond. intertrial magazine entries	5.9	7.1	7.7	-2.8	2.6
Pavlov. Cond. lever-magazine prob. diff.	1.3	1.6	1.7	1.3	-1.2
Pavlov. Cond. response bias	0.4	0.5	0.6	0.8	-0.7
Bone: apparent density	6.3	10.4	11.2	3.1	-3.3
Bone surface	8.9	15.6	16.6	3.8	-4.1
Bone volume	8.4	14.2	14.7	3.7	-3.8
Bone: connectivity density	3.1	4.8	5.4	2.0	-2.3
Bone: cortical apparent density	0.4	0.5	0.5	-0.7	0.6
Bone: cortical area	5.1	7.7	8.2	2.7	-2.9
Bone: cortical porosity	0.2	0.3	0.3	0.6	-0.4
Bone: cortical porosity	0.1	0.1	0.1	0.3	-0.1
Bone: cortical thickness	1.2	2.1	2.2	1.4	-1.5
Bone: cortical thickness	0.3	0.3	0.3	-0.5	0.6
Bone: cortical tissue density	0.5	0.6	0.7	-0.8	0.8
Bone: elastic displacement	7.1	8.0	8.3	-2.8	2.9
Bone: elastic work	0.0	0.0	0.0	-0.2	0.2
Bone: endosteal estimation	7.1	15.3	16.2	3.8	-4.0
Bone: endosteal perimeter	6.6	13.6	14.0	3.6	-3.7
Bone: final force	10.1	16.5	17.0	4.0	-4.1
Bone: final moment	11.6	19.1	19.6	4.3	-4.4
Bone: marrow area	6.6	14.2	15.1	3.6	-3.9
Bone: maximum diameter	1.4	2.5	2.7	1.5	-1.6
Bone: maximum force	12.8	22.2	23.7	4.5	-4.9
Bone: maximum moment	14.5	25.3	26.8	4.9	-5.2
Bone: minimum diameter	7.8	14.3	15.2	3.7	-3.9
Bone: periosteal estimation	8.8	18.0	19.1	4.1	-4.4
Bone: periosteal perimeter	8.7	14.5	15.3	3.7	-3.9
Bone: post-yield work	7.7	10.5	11.5	3.1	-3.4
Bone: stiffness	17.3	27.3	28.9	5.1	-5.4
Bone: tissue strength	1.8	1.8	2.0	1.2	-1.4
Bone: trabecular number	3.3	5.2	5.6	2.2	-2.4
Bone: trabecular spacing	0.8	1.0	1.1	-1.0	1.1
Bone: trabecular thickness	0.6	0.8	0.9	1.0	-0.8
Bone: trabecular tissue density	0.8	1.2	1.3	1.1	-1.1
Breakpoint value in progressive ratio session	0.0	0.0	0.1	0.1	0.3
Distance traveled before self-admin	2.8	3.0	3.3	-1.7	1.8
Distance traveled after self-admin	0.9	1.0	1.3	-0.8	1.1
Delta time in closed arm before/after self-admin	0.1	0.1	0.1	0.3	-0.4
Delta time in open arm before/after self-admin	3.4	3.2	4.0	-1.6	2.0
Diff in mean of infusions in LGA sessions	1.5	1.7	2.2	1.1	-1.5
Extinction: sum of active levers before priming	1.0	1.0	1.3	0.8	-1.1
Active lever presses in extinction session 6	0.0	0.0	0.0	0.1	0.1
Delta distance traveled before/after self-admin	0.3	0.3	0.4	0.6	-0.5
Delta ambulatory time before/after self-admin	0.1	0.2	0.3	0.5	-0.2
Time in closed arm before self-admin	0.5	0.6	0.7	0.9	-0.6
Time in closed arm after self-admin	0.2	0.2	0.3	0.5	-0.4
Time in open arm before self-admin	0.4	0.4	0.7	-0.1	-0.9
Time in open arm after self-admin	0.2	0.2	0.3	-0.6	0.3
Sum of active levers in priming session hrs 5-6	0.6	0.6	0.7	-0.8	0.7
Time to tail flick, vehicle, before self-admin	1.0	1.0	1.4	-0.8	1.2
Time to tail flick, vehicle, after self-admin	0.3	0.3	0.6	0.8	-0.2
Time to tail flick, test, before self-admin	0.2	0.2	0.2	-0.4	0.5
Time to tail flick, test, after self-admin	0.6	0.7	1.0	1.0	-0.6
Delta time to tail flick, vehicle, before/after SA	0.8	0.7	0.9	0.9	-0.8
Delta time to tail flick, test, before/after SA	0.8	0.7	1.1	1.0	-0.6
Ambulatory time before self-admin	4.2	4.4	4.6	-2.0	2.2
Ambulatory time after self-admin	1.8	2.0	2.6	-1.2	1.6
Total heroin consumption	1.0	1.2	1.3	1.1	-1.1
Area under the delay curve	1.1	1.2	1.3	1.0	-1.2
Delay disc. indifference point, 0s delay	2.0	2.1	2.3	1.4	-1.5
Delay disc. indifference point, 16s delay	0.9	0.9	1.0	0.9	-1.0
Delay disc. indifference point, 2s delay	1.8	2.0	2.4	1.2	-1.6
Delay disc. indifference point, 24s delay	0.5	0.5	0.6	0.6	-0.7
Delay disc. indifference point, 4s delay	1.1	1.1	1.3	1.1	-1.0
Delay disc. indifference point, 8s delay	1.4	1.4	1.6	1.1	-1.3
Delay discount exponential model param	1.1	1.1	1.3	-1.0	1.1
Delay discount hyperbolic model param	1.2	1.2	1.4	-1.0	1.2
Fecal boli incidents, locomotor time 1	0.6	0.7	0.7	-0.8	0.9
Change in fecal boli incidents, locomotor task	0.1	0.1	0.2	0.2	-0.5
Time >=10cm from walls, locomotor time 1	0.4	0.4	0.6	-0.7	0.5
Bouts of movement, locomotor time 1	0.0	0.0	0.0	-0.0	-0.0
Total resting periods, locomotor time 1	0.4	0.5	0.5	-0.7	0.6
Rest time, locomotor task time 1	0.5	0.6	0.7	-0.8	0.7
Distance moved, locomotor task time 1	0.0	0.0	0.0	-0.2	0.1
Vertical activity count, locomotor time 1	0.7	0.8	0.9	0.8	-0.9
Time >=10cm from walls, locomotor time 2	0.2	0.3	0.3	-0.5	0.5
Bouts of movement, locomotor time 2	3.2	3.4	3.6	1.8	-1.9
Total resting periods, locomotor time 2	3.6	3.8	4.0	1.9	-2.0
Rest time, locomotor task time 2	0.1	0.1	0.1	-0.3	0.4
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	0.1	0.3	-0.4
Weight adjusted by age	0.0	0.0	0.1	0.1	-0.3
Seeking ratio, delayed vs. immediate footshock	0.8	0.9	0.9	0.9	-1.0
Locomotion in novel chamber	2.9	3.6	4.0	2.0	-1.8
Locomotion in novel chamber post-restriction	0.6	0.7	0.8	0.9	-0.8
Progressive ratio	1.2	1.3	1.5	-1.2	1.1
Food seeking constrained by brief footshock	2.0	2.4	2.7	-1.6	1.5
Seeking ratio, punishment vs. effort	0.1	0.1	0.2	0.4	-0.4
Run reversals in cocaine runway, females	0.6	0.6	0.7	0.8	-0.6
Run reversals in cocaine runway, males	0.9	0.9	1.2	-0.8	1.1
Latency to leave start box in cocaine runway	0.0	0.0	0.0	-0.2	-0.2
Latency to leave start box in cocaine runway, F	1.6	1.8	2.0	-1.4	1.2
Latency to leave start box in cocaine runway, M	2.4	2.3	2.5	1.5	-1.6
Cd content in liver	0.4	0.4	0.5	-0.6	0.7
Co content in liver	0.4	0.4	0.6	-0.5	0.8
Cu content in liver	0.2	0.2	0.3	0.4	-0.5
Fe content in liver	1.1	1.3	1.3	-1.1	1.2
K content in liver	0.1	0.1	0.2	-0.4	0.3
Mg content in liver	0.2	0.2	0.2	-0.5	0.4
Mn content in liver	0.1	0.1	0.2	0.3	-0.4
Na content in liver	0.3	0.3	0.4	-0.5	0.6
Rb content in liver	2.1	2.7	2.7	-1.6	1.6
Se content in liver	2.2	2.7	2.8	-1.6	1.7
Sr content in liver	0.0	0.0	0.0	0.1	-0.1
Zn content in liver	2.4	2.7	2.7	-1.6	1.6