Hub : Genes

Limd2

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	Eye	intron excision ratio	chr10:91091672:91092281	0.28	0.16	7.5e-03	0.05	0.13	0.08	0.09	5.6e-02	4.5e-03	2.2e-02	1.6e-02
2	Eye	intron excision ratio	chr10:91091672:91092602	0.37	0.17	2.5e-03	0.15	0.17	0.11	0.14	2.7e-03	1.2e-03	8.8e-03	3.7e-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 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	0.5	1.6	2.0	-1.1	1.4
BMI without tail	2.2	4.6	5.0	-2.0	2.2
Body weight	2.7	11.4	11.5	-3.4	3.4
Epididymis fat weight	1.0	2.3	2.5	-1.5	1.6
Glucose	0.2	0.3	0.4	0.6	-0.5
Heart weight	0.1	0.2	0.2	-0.4	0.4
Left kidney weight	0.5	1.4	1.5	1.2	-1.2
Right kidney weight	0.4	1.1	1.3	1.0	-1.2
Tail length	1.6	5.0	5.4	-2.3	2.1
Length with tail	1.4	5.2	6.0	-2.4	2.1
Length without tail	0.1	0.2	0.3	-0.5	0.3
Liver weight, left	0.1	0.2	0.4	-0.6	0.3
Liver weight, right	1.7	2.9	3.3	1.6	-1.8
Parametrial fat weight	0.1	0.2	0.3	-0.5	0.3
Retroperitoneal fat weight	1.1	3.5	3.7	-1.9	1.9
Intraocular pressure	1.6	2.2	2.5	-1.4	1.6
Extensor digitorum longus weight	0.0	0.1	0.2	0.4	0.3
Soleus weight	0.3	0.8	0.8	-0.9	0.9
Tibialis anterior weight	0.8	2.9	3.5	-1.5	1.9
Tibia length	0.2	0.6	0.9	0.6	-0.9
Number of licking bursts	0.0	0.0	0.0	-0.1	0.0
Food consumed during 24 hour testing period	4.3	5.2	5.3	-2.3	2.3
Times rat made contact with spout	0.8	0.9	0.9	-1.0	0.9
Mean time between licks in bursts	0.3	0.5	0.5	-0.7	0.7
Mean num. licks in bursts	0.3	0.3	0.4	-0.5	0.6
Std. dev. time between licks in bursts	0.0	0.0	0.1	-0.1	0.3
Water consumed over 24 hours	0.0	0.0	0.0	0.1	-0.1
Indifference point 0 sec	2.8	4.5	4.9	-2.2	2.0
Indifference point AUC	1.3	1.5	1.6	-1.3	1.2
Indifference point function ln k	0.7	0.9	1.0	0.9	-1.0
Indifference point function log k	0.7	0.9	1.0	0.9	-1.0
Delay discounting total patch changes 0 sec	3.1	5.1	5.5	-2.3	2.1
Delay discounting total patch changes 12 sec	4.2	5.6	6.1	-2.5	2.3
Delay discounting total patch changes 18 sec	3.5	4.7	4.7	-2.2	2.1
Delay discounting total patch changes 24 sec	2.0	2.5	2.9	-1.7	1.5
Delay discounting total patch changes 6 sec	1.8	2.7	3.0	-1.7	1.6
Delay discounting time to switch 0 sec	0.1	0.1	0.1	0.4	-0.3
Delay discounting water rate 0 sec	1.0	1.6	1.7	-1.3	1.3
Delay discounting water rate 12 sec	1.3	1.9	2.0	1.3	-1.4
Delay discounting water rate 18 sec	0.7	0.9	1.2	0.8	-1.1
Delay discounting water rate 24 sec	0.1	0.1	0.1	0.2	-0.4
Delay discounting water rate 6 sec	0.5	0.7	0.8	0.8	-0.9
Locomotor activity	0.5	0.9	0.9	-1.0	0.9
Locomotor testing distance	2.2	3.7	3.8	-1.9	2.0
Locomotor testing rearing	2.7	4.2	4.6	-1.9	2.2
Light reinforcement 1	0.0	0.0	0.0	-0.1	0.0
Light reinforcement 2	0.0	0.0	0.0	0.0	-0.1
Reaction time number correct	0.8	1.2	1.4	1.0	-1.2
Reaction time mean minus median	0.1	0.2	0.3	0.5	-0.4
Reaction time mean minus median AUC	1.5	1.9	1.9	1.4	-1.4
Reaction time num false alarms	3.3	4.6	5.0	-2.2	2.0
Reaction time num false alarms AUC	3.1	4.3	4.8	-2.2	2.0
Reaction time trials correct on left	0.8	1.2	1.4	1.0	-1.2
Reaction time trials on left	0.9	1.2	1.4	1.0	-1.2
Reaction time mean	1.4	1.9	1.9	1.4	-1.4
Reaction time mean AUC	1.6	2.1	2.2	1.5	-1.4
Median of all reaction times	1.5	2.1	2.1	1.4	-1.5
Reaction time omissions	0.3	0.4	0.4	0.6	-0.6
Reaction time false alarm rate	3.8	5.3	5.6	-2.4	2.3
Reaction time premature initiation rate	0.8	1.1	1.1	-1.0	1.1
Reaction time premature initiations	0.1	0.2	0.2	-0.5	0.4
Std. dev. reaction times	0.6	0.8	0.9	0.9	-0.9
Reaction time trials completed	0.9	1.2	1.4	1.0	-1.2
Reaction time trials AUC	0.9	1.3	1.4	1.0	-1.2
Social response proportion	0.0	0.0	0.0	-0.1	0.2
Social responses	0.2	0.3	0.3	-0.5	0.6
Social time	0.7	0.9	1.0	-0.9	1.0
Conditioned locomotion	0.6	0.7	0.7	-0.8	0.8
Cocaine response after cond. corrected	0.1	0.2	0.2	0.3	-0.4
Cocaine response after cond. not corrected	0.5	0.6	0.7	0.7	-0.8
Cocaine response before conditioning	0.4	0.5	0.6	0.6	-0.8
Saline control response	2.6	3.5	3.8	-1.8	2.0
Condit. Reinf. active minus inactive responses	3.0	3.7	4.6	-2.1	1.7
Condit. Reinf. active-inactive response ratio	1.8	1.9	2.3	-1.5	1.2
Condit. Reinf. active responses	4.4	6.1	6.8	-2.6	2.3
Condit. Reinf. inactive responses	1.6	2.0	2.0	-1.4	1.4
Condit. Reinf. lever presses	1.3	1.7	1.8	-1.4	1.3
Condit. Reinf. lever reinforcers received	3.5	5.0	5.6	-2.4	2.1
Pavlov. Cond. lever latency	0.2	0.3	0.3	0.6	-0.5
Pavlov. Cond. magazine entry latency	1.6	1.8	1.8	1.3	-1.3
Pavlov. Cond. change in total contacts	0.4	0.6	0.7	-0.8	0.7
Pavlov. Cond. index score	0.0	0.0	0.0	-0.1	0.0
Pavlov. Cond. latency score	0.0	0.0	0.0	0.0	-0.1
Pavlov. Cond. lever contacts	0.1	0.1	0.2	-0.4	0.3
Pavlov. Cond. magazine entry number	2.4	2.9	3.0	-1.7	1.7
Pavlov. Cond. intertrial magazine entries	12.6	16.3	16.5	-4.1	4.0
Pavlov. Cond. lever-magazine prob. diff.	0.0	0.0	0.0	0.0	-0.1
Pavlov. Cond. response bias	0.0	0.0	0.0	0.0	-0.1
Conditioned reinforcement - actives	1.3	1.3	1.3	-1.1	1.1
Conditioned reinforcement - inactives	1.2	1.3	1.4	-1.2	1.1
Conditioned locomotion	2.6	3.2	3.3	-1.8	1.8
Intermittent access intake day 1-15 change	1.3	1.3	1.4	-1.0	1.2
Intermittent access intake escalation	0.4	0.4	0.5	-0.5	0.7
Intermittent access intake escalation 2	1.2	1.2	1.3	-1.0	1.1
Intermitt. access day 1 inactive lever presses	3.2	3.5	3.9	-2.0	1.7
Intermitt. access day 15 inactive lever presses	1.7	1.9	2.0	-1.3	1.4
Intermitt. access escalation Index	2.1	1.8	1.9	1.3	-1.4
Intermittent access day 1 total infusions	0.7	0.8	0.9	-1.0	0.9
Intermittent access day 15 total infusions	1.4	1.5	1.6	-1.2	1.3
Intermittent access terminal intake (last 3 days)	3.4	3.8	3.8	-1.9	1.9
Intermittent access total infusions	3.2	3.6	3.7	-1.9	1.8
Intermittent access day 1 locomotion	4.0	4.1	4.3	-2.1	2.0
Intermittent access day 15 total locomotion	5.8	6.1	6.4	-2.5	2.4
Intermittent access total locomotion	7.4	8.4	8.7	-3.0	2.8
Intermittent access standard deviation	1.6	1.7	1.8	-1.2	1.3
Cocaine induced anxiety	0.4	0.4	0.4	0.6	-0.6
Post-drug Anxiety	0.4	0.4	0.5	0.7	-0.6
Baseline Anxiety	0.8	0.9	0.9	1.0	-0.9
Lifetime Intake	3.3	3.7	3.8	-2.0	1.9
Incentive Sensitization - Responses	3.8	3.7	4.0	-2.0	1.9
Incentive Sensitization - Breakpoint	3.5	3.5	3.8	-1.9	1.8
Progressive ratio test 1 active lever presses	4.1	4.2	4.6	-2.1	1.9
Progressive ratio test 1 breakpoint	6.0	6.2	6.6	-2.6	2.4
Progressive ratio test 1 inactive lever presses	4.5	4.8	5.2	-2.3	2.1
Progressive ratio test 2 active lever presses	4.7	5.0	5.3	-2.3	2.1
Progressive ratio test 2 breakpoint	6.2	6.8	7.3	-2.7	2.5
Progressive ratio test 2 inactive lever presses	3.9	4.5	4.8	-2.2	2.1
Total sessions with >9 infusions	0.0	0.1	0.1	-0.3	0.2
Short access day 1 total inactive lever presses	0.6	0.7	0.8	-0.9	0.8
Short access day 10 total inactive lever presses	0.8	0.8	0.9	-0.9	0.9
Short access day 1 total infusions	0.9	1.0	1.1	-1.0	1.0
Short access day 10 total infusions	6.5	7.2	7.3	-2.7	2.7
Short access total infusions	3.5	3.9	4.0	-2.0	1.9
Short access day 1 locomotion	3.9	4.1	4.1	-2.0	2.0
Short access day 10 total locomotion	12.3	13.4	13.5	-3.7	3.7
Short access total locomotion	6.9	7.0	7.1	-2.6	2.7
Compulsive drug intake	1.5	1.5	1.6	1.2	-1.3
One hour access (0.3 mA shock)	1.9	2.2	2.3	-1.5	1.5
One hour access (shock baseline)	2.5	2.9	2.9	-1.7	1.7
Number of responses in last shaping day	1.4	1.4	1.4	-1.2	1.2
Context. condit. distance diff. score	0.1	0.1	0.1	-0.2	0.4
Locomotion velocity, session 1	0.1	0.1	0.2	-0.4	0.2
Locomotion distance, session 1	0.2	0.2	0.3	0.4	-0.5
Locomotion velocity, session 2	0.1	0.1	0.2	-0.4	0.3
Locomotion distance, session 2	0.1	0.1	0.1	0.2	-0.4
Locomotion velocity, session 3	0.4	0.5	0.5	0.7	-0.7
Locomotion distance, session 3	0.0	0.0	0.0	0.1	-0.2
Stereotopy head waving bouts, day 3	1.0	1.2	1.3	1.1	-1.1
Stereotopy head waving duration, day 3	0.5	0.6	0.6	0.8	-0.8
Locomotion velocity, session 7	0.6	0.7	0.7	0.8	-0.8
Locomotion distance, session 7	0.0	0.0	0.0	0.0	-0.0
Stereotopy head waving bouts, day 7	1.0	1.1	1.2	1.0	-1.1
Stereotopy head waving duration, day 7	2.7	3.3	3.4	1.8	-1.9
Locomotion velocity, session 8	1.5	1.8	1.8	-1.3	1.3
Locomotion distance, session 8	0.0	0.1	0.1	-0.3	0.3
Degree of sensitization distance	0.3	0.3	0.4	-0.5	0.6
Degree of sensitization stereotypy	1.2	1.3	1.4	1.1	-1.2
Condit. Reinf. active minus inactive responses	2.9	3.2	3.3	-1.8	1.8
Condit. Reinf. active-inactive response ratio	1.2	1.3	1.4	-1.2	1.1
Condit. Reinf. active responses	3.3	4.0	4.2	-2.0	1.9
Condit. Reinf. inactive responses	0.5	0.6	0.7	-0.9	0.7
Incentive salience index mean	1.7	2.1	2.3	-1.5	1.4
Condit. Reinf. lever presses	0.1	0.1	0.1	-0.3	0.2
Time in familiar zone, hab. session 1	1.9	1.8	1.9	-1.3	1.4
Time in novel zone, hab. session 1	2.1	2.0	2.1	1.4	-1.4
Total zone transitions, hab. session 1	0.1	0.2	0.2	-0.4	0.4
Total locomotion distance, hab. session 1	0.0	0.0	0.1	-0.2	0.1
Locomotion velocity, hab. session 1	0.1	0.2	0.3	-0.5	0.4
Time in familiar zone, hab. session 2	3.2	3.3	3.4	-1.8	1.8
Time in novel zone, hab. session 2	4.0	4.0	4.2	2.0	-2.0
Total zone transitions, hab. session 2	0.1	0.1	0.1	-0.3	0.3
Total locomotion distance, hab. session 2	0.0	0.0	0.0	-0.1	0.1
Locomotion velocity, hab. session 2	0.0	0.0	0.0	-0.1	-0.0
Novel to familiar place preference ratio	0.2	0.2	0.3	-0.5	0.5
Novelty place preference	0.1	0.1	0.1	-0.3	0.3
Time in novel zone, NPP test	0.0	0.0	0.0	-0.1	0.1
Total zone transitions, NPP test	0.1	0.2	0.3	0.3	-0.5
Total locomotion distance, NPP test	0.0	0.0	0.1	0.0	-0.2
Locomotion velocity, NPP test	0.0	0.0	0.0	-0.1	-0.1
Pavlov. Cond. lever latency	0.9	1.2	1.4	1.2	-1.0
Pavlov. Cond. magazine entry latency	2.1	2.8	3.1	-1.8	1.6
Pavlov. Cond. change in total contacts	1.9	2.0	2.2	-1.5	1.4
Pavlov. Cond. index score	1.9	2.4	2.7	-1.7	1.5
Pavlov. Cond. latency score	1.7	2.2	2.4	-1.6	1.4
Pavlov. Cond. lever contacts	1.3	1.6	1.7	-1.3	1.2
Pavlov. Cond. magazine entry number	1.1	1.4	1.7	1.3	-1.1
Pavlov. Cond. intertrial magazine entries	1.6	1.9	1.9	-1.4	1.4
Pavlov. Cond. lever-magazine prob. diff.	1.8	2.2	2.5	-1.6	1.4
Pavlov. Cond. response bias	1.3	1.6	1.8	-1.4	1.1
Bone: apparent density	0.0	0.0	0.1	-0.1	-0.3
Bone surface	1.9	3.4	4.4	-2.1	1.6
Bone volume	1.3	2.2	2.8	-1.7	1.2
Bone: connectivity density	0.1	0.1	0.2	-0.5	0.1
Bone: cortical apparent density	6.8	8.9	9.1	3.0	-2.9
Bone: cortical area	0.5	0.8	1.0	-1.0	0.8
Bone: cortical porosity	9.1	9.8	10.1	-3.2	3.1
Bone: cortical porosity	5.3	5.8	6.1	-2.5	2.3
Bone: cortical thickness	5.8	9.5	9.6	3.1	-3.1
Bone: cortical thickness	5.5	6.4	6.5	2.6	-2.5
Bone: cortical tissue density	6.5	8.4	8.7	2.9	-2.9
Bone: elastic displacement	2.1	2.3	2.4	1.5	-1.5
Bone: elastic work	0.1	0.2	0.2	0.4	-0.4
Bone: endosteal estimation	15.1	32.5	34.5	-5.9	5.5
Bone: endosteal perimeter	18.3	37.6	40.1	-6.3	5.9
Bone: final force	0.0	0.0	0.1	-0.3	-0.0
Bone: final moment	0.0	0.0	0.1	-0.3	-0.0
Bone: marrow area	14.7	31.6	33.5	-5.8	5.4
Bone: maximum diameter	3.7	6.7	7.7	-2.8	2.4
Bone: maximum force	0.5	0.9	1.1	-1.1	0.8
Bone: maximum moment	0.5	0.8	1.1	-1.1	0.8
Bone: minimum diameter	13.1	24.2	25.7	-5.1	4.8
Bone: periosteal estimation	7.9	16.1	17.6	-4.2	3.8
Bone: periosteal perimeter	4.5	7.5	8.5	-2.9	2.6
Bone: post-yield work	3.1	4.3	4.5	-2.1	2.0
Bone: stiffness	0.3	0.5	0.7	-0.8	0.5
Bone: tissue strength	1.7	1.6	1.8	1.2	-1.3
Bone: trabecular number	0.1	0.2	0.3	-0.6	0.1
Bone: trabecular spacing	0.1	0.1	0.2	-0.2	0.5
Bone: trabecular thickness	0.4	0.5	0.6	-0.8	0.5
Bone: trabecular tissue density	2.6	3.7	4.0	1.8	-2.0
Breakpoint value in progressive ratio session	1.4	1.6	1.6	-1.2	1.2
Distance traveled before self-admin	0.0	0.0	0.0	-0.1	-0.0
Distance traveled after self-admin	0.4	0.4	0.4	-0.6	0.6
Delta time in closed arm before/after self-admin	0.1	0.1	0.1	0.2	-0.4
Delta time in open arm before/after self-admin	0.1	0.1	0.1	0.3	-0.1
Diff in mean of infusions in LGA sessions	0.3	0.3	0.4	0.7	-0.5
Extinction: sum of active levers before priming	0.8	0.8	0.9	-0.9	0.9
Active lever presses in extinction session 6	3.4	3.3	3.4	-1.8	1.8
Delta distance traveled before/after self-admin	0.1	0.1	0.1	0.3	-0.2
Delta ambulatory time before/after self-admin	0.0	0.0	0.0	0.0	-0.0
Time in closed arm before self-admin	1.3	1.5	1.6	1.2	-1.2
Time in closed arm after self-admin	1.1	1.2	1.3	1.0	-1.1
Time in open arm before self-admin	0.0	0.0	0.0	0.2	-0.2
Time in open arm after self-admin	0.9	1.0	1.2	-0.9	1.1
Sum of active levers in priming session hrs 5-6	0.0	0.0	0.0	-0.0	0.1
Time to tail flick, vehicle, before self-admin	0.3	0.3	0.4	0.4	-0.6
Time to tail flick, vehicle, after self-admin	0.3	0.3	0.4	-0.6	0.5
Time to tail flick, test, before self-admin	0.1	0.1	0.2	0.4	-0.3
Time to tail flick, test, after self-admin	0.2	0.3	0.3	0.5	-0.5
Delta time to tail flick, vehicle, before/after SA	1.2	1.2	1.2	-1.1	1.1
Delta time to tail flick, test, before/after SA	0.2	0.1	0.2	0.3	-0.4
Ambulatory time before self-admin	0.1	0.1	0.1	-0.3	0.3
Ambulatory time after self-admin	0.4	0.4	0.4	-0.7	0.6
Total heroin consumption	0.2	0.2	0.3	-0.6	0.4
Area under the delay curve	0.0	0.0	0.0	-0.0	-0.1
Delay disc. indifference point, 0s delay	0.9	1.0	1.0	0.9	-1.0
Delay disc. indifference point, 16s delay	0.3	0.3	0.3	-0.6	0.5
Delay disc. indifference point, 2s delay	0.1	0.2	0.3	0.2	-0.5
Delay disc. indifference point, 24s delay	1.9	1.8	1.9	-1.4	1.3
Delay disc. indifference point, 4s delay	0.9	0.9	1.0	0.9	-1.0
Delay disc. indifference point, 8s delay	0.8	0.8	0.9	0.8	-1.0
Delay discount exponential model param	0.0	0.1	0.1	0.3	-0.1
Delay discount hyperbolic model param	0.0	0.0	0.0	0.0	0.1
Fecal boli incidents, locomotor time 1	0.3	0.3	0.3	-0.5	0.6
Change in fecal boli incidents, locomotor task	0.2	0.2	0.2	0.5	-0.4
Time >=10cm from walls, locomotor time 1	1.7	1.7	1.8	1.3	-1.3
Bouts of movement, locomotor time 1	0.4	0.4	0.5	0.7	-0.6
Total resting periods, locomotor time 1	0.6	0.6	0.8	0.9	-0.7
Rest time, locomotor task time 1	0.7	0.8	0.8	0.9	-0.9
Distance moved, locomotor task time 1	0.6	0.7	0.7	-0.8	0.8
Vertical activity count, locomotor time 1	0.2	0.3	0.3	-0.5	0.5
Time >=10cm from walls, locomotor time 2	0.1	0.1	0.1	0.3	-0.3
Bouts of movement, locomotor time 2	0.0	0.0	0.1	0.3	-0.1
Total resting periods, locomotor time 2	0.2	0.2	0.3	0.6	-0.4
Rest time, locomotor task time 2	3.0	3.5	3.6	1.9	-1.8
Distance moved, locomotor task time 2	0.3	0.4	0.4	-0.6	0.6
Vertical activity count, locomotor time 2	2.3	2.5	2.6	-1.6	1.6
Weight adjusted by age	0.1	0.1	0.1	0.3	-0.2
Seeking ratio, delayed vs. immediate footshock	0.3	0.4	0.5	-0.5	0.7
Locomotion in novel chamber	0.0	0.0	0.0	-0.1	-0.0
Locomotion in novel chamber post-restriction	1.0	1.2	1.5	-1.2	0.9
Progressive ratio	0.0	0.0	0.1	0.1	-0.3
Food seeking constrained by brief footshock	4.7	5.7	5.7	-2.4	2.4
Seeking ratio, punishment vs. effort	1.9	2.3	2.5	-1.5	1.6
Run reversals in cocaine runway, females	0.1	0.1	0.2	0.4	-0.2
Run reversals in cocaine runway, males	0.0	0.0	0.0	0.1	-0.1
Latency to leave start box in cocaine runway	0.2	0.2	0.2	0.5	-0.4
Latency to leave start box in cocaine runway, F	0.4	0.4	0.5	0.7	-0.7
Latency to leave start box in cocaine runway, M	0.0	0.0	0.0	0.2	-0.1
Cd content in liver	2.0	2.2	2.5	1.6	-1.4
Co content in liver	0.0	0.0	0.0	-0.0	0.2
Cu content in liver	0.1	0.1	0.1	-0.3	0.3
Fe content in liver	0.4	0.4	0.4	0.6	-0.7
K content in liver	0.3	0.3	0.4	-0.6	0.3
Mg content in liver	0.1	0.1	0.2	0.3	-0.4
Mn content in liver	1.2	1.3	1.8	1.0	-1.3
Na content in liver	0.2	0.2	0.3	-0.6	0.4
Rb content in liver	4.1	5.1	5.3	2.2	-2.3
Se content in liver	0.9	1.1	1.2	1.0	-1.1
Sr content in liver	0.2	0.2	0.2	-0.5	0.4
Zn content in liver	0.1	0.1	0.2	0.2	-0.4