Hub : Genes

Rtp3

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	ENSRNOG00000037167	0.7	0.11	0.0e+00	0.18	0.31	0.31	0.3	3.1e-19	1.5e-35	5.5e-35	2.3e-33
2	Liver	gene expression	ENSRNOG00000037167	0.04	0.05	8.5e-04	0.02	0.02	0.02	0.02	3.0e-03	1.7e-03	4.6e-03	2.6e-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	0.3	1.0	2.0	-0.2	-1.4
BMI without tail	1.3	2.7	4.4	1.0	-2.1
Body weight	5.7	24.1	31.8	4.0	-5.6
Epididymis fat weight	0.3	0.7	0.7	0.8	-0.8
Glucose	0.2	0.3	0.4	0.4	-0.6
Heart weight	2.0	2.9	3.5	1.5	-1.9
Left kidney weight	0.4	1.1	2.1	0.3	-1.5
Right kidney weight	0.1	0.3	0.6	-0.1	-0.8
Tail length	6.7	20.2	21.5	4.4	-4.6
Length with tail	9.1	33.3	36.6	5.5	-6.0
Length without tail	6.1	13.4	15.0	3.4	-3.9
Liver weight, left	0.1	0.2	0.4	0.7	-0.1
Liver weight, right	1.0	1.7	2.1	1.1	-1.4
Parametrial fat weight	0.8	1.7	2.0	1.2	-1.4
Retroperitoneal fat weight	0.5	1.7	2.0	1.1	-1.4
Intraocular pressure	1.7	2.4	3.6	1.9	-1.1
Extensor digitorum longus weight	0.1	0.6	0.6	-0.8	0.8
Soleus weight	3.3	9.6	12.5	2.6	-3.5
Tibialis anterior weight	0.0	0.0	0.0	0.0	-0.2
Tibia length	5.4	15.1	21.7	2.9	-4.7
Number of licking bursts	0.1	0.1	0.2	-0.2	0.4
Food consumed during 24 hour testing period	1.2	1.5	1.9	1.1	-1.4
Times rat made contact with spout	0.4	0.5	0.6	0.8	-0.6
Mean time between licks in bursts	1.1	1.5	1.7	-1.3	1.2
Mean num. licks in bursts	0.4	0.5	0.7	0.6	-0.8
Std. dev. time between licks in bursts	3.5	4.2	4.3	-2.1	2.0
Water consumed over 24 hours	0.0	0.0	0.0	-0.2	0.1
Indifference point 0 sec	1.1	1.8	1.8	1.4	-1.3
Indifference point AUC	0.0	0.0	0.1	0.0	-0.3
Indifference point function ln k	0.4	0.5	0.9	-1.0	0.3
Indifference point function log k	0.4	0.5	0.9	-1.0	0.3
Delay discounting total patch changes 0 sec	1.3	2.1	2.2	1.5	-1.5
Delay discounting total patch changes 12 sec	0.8	1.1	1.1	1.1	-1.0
Delay discounting total patch changes 18 sec	3.0	3.9	4.3	2.1	-1.9
Delay discounting total patch changes 24 sec	2.7	3.4	4.0	1.7	-2.0
Delay discounting total patch changes 6 sec	0.1	0.2	0.3	0.5	-0.4
Delay discounting time to switch 0 sec	0.1	0.2	0.3	-0.1	0.6
Delay discounting water rate 0 sec	0.1	0.2	0.3	0.3	-0.6
Delay discounting water rate 12 sec	0.2	0.3	0.6	0.4	-0.7
Delay discounting water rate 18 sec	0.1	0.1	0.2	-0.5	-0.3
Delay discounting water rate 24 sec	0.7	0.9	1.0	1.0	-0.9
Delay discounting water rate 6 sec	0.2	0.3	0.5	0.1	-0.7
Locomotor activity	5.6	8.9	10.3	2.7	-3.2
Locomotor testing distance	5.3	8.8	10.5	2.7	-3.2
Locomotor testing rearing	0.4	0.6	0.7	0.9	-0.7
Light reinforcement 1	0.5	0.9	1.2	0.8	-1.1
Light reinforcement 2	0.3	0.3	0.6	-0.8	0.3
Reaction time number correct	0.2	0.3	0.4	-0.4	0.7
Reaction time mean minus median	0.0	0.0	0.0	-0.1	-0.2
Reaction time mean minus median AUC	0.1	0.2	0.3	0.3	-0.5
Reaction time num false alarms	0.2	0.2	0.4	-0.2	0.6
Reaction time num false alarms AUC	0.0	0.1	0.1	0.1	0.3
Reaction time trials correct on left	0.2	0.3	0.4	-0.4	0.7
Reaction time trials on left	0.2	0.3	0.5	-0.4	0.7
Reaction time mean	0.0	0.0	0.1	0.2	-0.1
Reaction time mean AUC	0.0	0.0	0.0	0.2	0.0
Median of all reaction times	0.0	0.1	0.1	0.4	-0.0
Reaction time omissions	0.2	0.3	0.6	0.2	0.8
Reaction time false alarm rate	0.0	0.0	0.0	0.1	0.2
Reaction time premature initiation rate	1.8	2.4	2.5	1.6	-1.6
Reaction time premature initiations	0.9	1.2	1.4	1.2	-1.1
Std. dev. reaction times	0.1	0.1	0.2	0.4	-0.3
Reaction time trials completed	0.2	0.3	0.5	-0.4	0.7
Reaction time trials AUC	0.3	0.4	0.6	-0.4	0.8
Social response proportion	0.5	0.6	0.9	0.9	-0.5
Social responses	0.3	0.4	0.4	0.5	-0.7
Social time	0.6	0.8	0.9	-0.8	0.9
Conditioned locomotion	2.5	3.0	3.9	-1.5	2.0
Cocaine response after cond. corrected	0.3	0.3	0.5	0.7	-0.5
Cocaine response after cond. not corrected	1.7	1.9	2.0	1.3	-1.4
Cocaine response before conditioning	0.8	1.0	1.6	0.5	-1.3
Saline control response	1.6	2.1	2.4	1.5	-1.3
Condit. Reinf. active minus inactive responses	1.8	2.2	3.1	1.2	-1.8
Condit. Reinf. active-inactive response ratio	1.4	1.4	2.0	0.9	-1.4
Condit. Reinf. active responses	1.6	2.2	2.7	1.3	-1.6
Condit. Reinf. inactive responses	0.0	0.0	0.0	-0.0	0.1
Condit. Reinf. lever presses	1.9	2.7	3.9	1.2	-2.0
Condit. Reinf. lever reinforcers received	1.8	2.5	3.1	1.4	-1.8
Pavlov. Cond. lever latency	0.3	0.4	0.8	-0.2	0.9
Pavlov. Cond. magazine entry latency	0.5	0.5	1.0	-1.0	0.2
Pavlov. Cond. change in total contacts	2.0	2.8	4.2	1.2	-2.0
Pavlov. Cond. index score	0.2	0.2	0.2	-0.4	-0.5
Pavlov. Cond. latency score	0.2	0.2	0.2	-0.5	-0.4
Pavlov. Cond. lever contacts	0.7	1.0	1.7	0.5	-1.3
Pavlov. Cond. magazine entry number	0.6	0.8	1.3	1.1	-0.5
Pavlov. Cond. intertrial magazine entries	0.2	0.3	0.6	0.1	0.8
Pavlov. Cond. lever-magazine prob. diff.	0.2	0.2	0.3	-0.5	-0.5
Pavlov. Cond. response bias	0.1	0.2	0.2	-0.4	-0.5
Conditioned reinforcement - actives	0.3	0.3	0.4	-0.6	0.4
Conditioned reinforcement - inactives	0.8	0.9	0.9	-1.0	0.9
Conditioned locomotion	0.3	0.4	0.5	-0.7	0.6
Intermittent access intake day 1-15 change	0.4	0.4	0.4	-0.6	0.7
Intermittent access intake escalation	0.3	0.3	0.3	-0.5	0.5
Intermittent access intake escalation 2	0.0	0.0	0.0	0.1	-0.2
Intermitt. access day 1 inactive lever presses	0.0	0.0	0.0	-0.2	0.0
Intermitt. access day 15 inactive lever presses	0.7	0.8	0.9	-0.8	0.9
Intermitt. access escalation Index	0.0	0.0	0.0	0.0	-0.0
Intermittent access day 1 total infusions	0.0	0.0	0.0	-0.2	0.1
Intermittent access day 15 total infusions	0.2	0.2	0.3	-0.5	0.4
Intermittent access terminal intake (last 3 days)	0.1	0.1	0.1	-0.3	0.2
Intermittent access total infusions	0.4	0.4	0.5	-0.7	0.5
Intermittent access day 1 locomotion	0.1	0.1	0.1	-0.4	0.3
Intermittent access day 15 total locomotion	0.5	0.5	0.5	-0.7	0.7
Intermittent access total locomotion	1.1	1.2	1.2	-1.1	1.1
Intermittent access standard deviation	0.2	0.2	0.3	0.4	-0.5
Cocaine induced anxiety	0.5	0.6	0.7	-0.7	0.8
Post-drug Anxiety	0.2	0.3	0.4	-0.4	0.6
Baseline Anxiety	0.1	0.1	0.2	-0.3	0.4
Lifetime Intake	0.3	0.3	0.4	-0.6	0.5
Incentive Sensitization - Responses	1.8	1.8	1.8	-1.3	1.4
Incentive Sensitization - Breakpoint	1.7	1.7	1.8	-1.3	1.3
Progressive ratio test 1 active lever presses	0.0	0.0	0.0	-0.1	-0.0
Progressive ratio test 1 breakpoint	0.0	0.0	0.0	-0.2	0.1
Progressive ratio test 1 inactive lever presses	0.3	0.4	0.4	-0.6	0.6
Progressive ratio test 2 active lever presses	0.9	0.9	1.0	-1.0	0.9
Progressive ratio test 2 breakpoint	0.7	0.8	0.8	-0.9	0.9
Progressive ratio test 2 inactive lever presses	1.9	2.2	2.4	-1.5	1.4
Total sessions with >9 infusions	0.0	0.0	0.0	-0.1	0.2
Short access day 1 total inactive lever presses	3.1	3.4	3.5	-1.9	1.8
Short access day 10 total inactive lever presses	0.0	0.0	0.0	-0.1	0.1
Short access day 1 total infusions	0.8	0.8	0.9	-0.9	0.9
Short access day 10 total infusions	0.0	0.0	0.1	-0.2	0.1
Short access total infusions	0.4	0.4	0.5	-0.7	0.6
Short access day 1 locomotion	0.0	0.0	0.0	-0.2	0.1
Short access day 10 total locomotion	0.0	0.0	0.0	0.2	-0.2
Short access total locomotion	0.0	0.0	0.0	-0.1	0.0
Compulsive drug intake	0.0	0.0	0.0	-0.0	0.1
One hour access (0.3 mA shock)	0.1	0.1	0.1	-0.4	0.2
One hour access (shock baseline)	0.0	0.1	0.1	-0.3	0.1
Number of responses in last shaping day	0.6	0.6	0.6	-0.8	0.8
Context. condit. distance diff. score	0.0	0.0	0.0	-0.1	-0.1
Locomotion velocity, session 1	0.1	0.1	0.2	-0.4	0.2
Locomotion distance, session 1	0.6	0.7	1.4	0.2	-1.2
Locomotion velocity, session 2	0.5	0.6	0.9	-1.0	0.5
Locomotion distance, session 2	0.2	0.4	0.7	-0.8	-0.1
Locomotion velocity, session 3	0.1	0.2	0.2	-0.4	-0.4
Locomotion distance, session 3	1.5	1.7	2.6	-1.6	0.9
Stereotopy head waving bouts, day 3	0.1	0.1	0.2	0.4	-0.2
Stereotopy head waving duration, day 3	0.5	0.6	0.9	1.0	-0.5
Locomotion velocity, session 7	0.3	0.3	0.4	0.5	-0.6
Locomotion distance, session 7	0.5	0.7	0.8	-0.9	0.8
Stereotopy head waving bouts, day 7	0.1	0.1	0.1	-0.2	0.3
Stereotopy head waving duration, day 7	0.2	0.2	0.2	0.4	-0.5
Locomotion velocity, session 8	0.3	0.3	0.5	-0.4	-0.7
Locomotion distance, session 8	0.3	0.4	0.6	-0.5	-0.8
Degree of sensitization distance	1.7	1.8	2.4	1.5	-1.1
Degree of sensitization stereotypy	0.0	0.0	0.0	0.1	0.1
Condit. Reinf. active minus inactive responses	0.3	0.3	0.5	0.7	-0.2
Condit. Reinf. active-inactive response ratio	0.5	0.5	0.9	0.9	-0.4
Condit. Reinf. active responses	0.0	0.0	0.1	0.2	0.2
Condit. Reinf. inactive responses	0.7	0.8	0.9	-0.9	0.9
Incentive salience index mean	0.0	0.0	0.1	-0.2	0.3
Condit. Reinf. lever presses	1.7	2.2	2.6	-1.6	1.4
Time in familiar zone, hab. session 1	0.8	0.8	1.3	-0.5	1.2
Time in novel zone, hab. session 1	0.4	0.4	0.5	0.5	-0.7
Total zone transitions, hab. session 1	0.4	0.5	1.1	0.1	-1.0
Total locomotion distance, hab. session 1	0.1	0.2	0.4	0.1	-0.6
Locomotion velocity, hab. session 1	0.2	0.2	0.4	0.1	-0.7
Time in familiar zone, hab. session 2	0.4	0.4	0.4	-0.6	0.6
Time in novel zone, hab. session 2	0.1	0.1	0.1	0.4	-0.1
Total zone transitions, hab. session 2	0.2	0.3	0.4	-0.6	-0.4
Total locomotion distance, hab. session 2	0.2	0.2	0.4	-0.1	-0.6
Locomotion velocity, hab. session 2	0.1	0.2	0.3	-0.2	-0.5
Novel to familiar place preference ratio	0.8	0.8	1.0	0.8	-1.0
Novelty place preference	0.8	0.8	0.9	0.9	-1.0
Time in novel zone, NPP test	1.1	1.2	1.2	1.1	-1.1
Total zone transitions, NPP test	1.5	2.1	4.1	0.4	-2.0
Total locomotion distance, NPP test	0.6	0.8	1.5	0.4	-1.2
Locomotion velocity, NPP test	0.6	0.9	1.7	0.4	-1.3
Pavlov. Cond. lever latency	6.0	7.7	8.9	3.0	-2.5
Pavlov. Cond. magazine entry latency	6.7	8.7	8.9	-3.0	2.9
Pavlov. Cond. change in total contacts	1.5	1.6	1.8	-1.2	1.4
Pavlov. Cond. index score	6.7	8.6	8.9	-3.0	2.9
Pavlov. Cond. latency score	6.8	8.7	9.3	-3.1	2.8
Pavlov. Cond. lever contacts	3.7	4.4	5.3	-2.3	1.9
Pavlov. Cond. magazine entry number	7.4	9.2	9.5	3.0	-3.1
Pavlov. Cond. intertrial magazine entries	0.5	0.6	0.6	0.8	-0.7
Pavlov. Cond. lever-magazine prob. diff.	6.0	7.5	7.8	-2.8	2.7
Pavlov. Cond. response bias	7.3	9.0	9.2	-3.0	3.0
Bone: apparent density	0.0	0.0	0.0	0.0	-0.2
Bone surface	0.1	0.2	0.4	-0.6	0.2
Bone volume	0.1	0.1	0.2	-0.4	0.0
Bone: connectivity density	0.2	0.2	0.4	-0.3	0.6
Bone: cortical apparent density	0.2	0.3	0.4	-0.4	0.7
Bone: cortical area	0.1	0.2	0.2	-0.4	0.4
Bone: cortical porosity	0.1	0.1	0.1	0.4	0.3
Bone: cortical porosity	0.1	0.1	0.2	0.2	0.5
Bone: cortical thickness	0.1	0.1	0.2	0.2	-0.4
Bone: cortical thickness	0.0	0.0	0.0	0.1	-0.1
Bone: cortical tissue density	0.2	0.3	0.4	-0.4	0.7
Bone: elastic displacement	0.0	0.1	0.1	0.2	-0.2
Bone: elastic work	0.4	0.5	0.9	0.3	-0.9
Bone: endosteal estimation	0.1	0.3	0.4	0.6	-0.4
Bone: endosteal perimeter	1.1	2.2	2.4	-1.4	1.5
Bone: final force	0.7	1.1	1.4	0.9	-1.2
Bone: final moment	0.9	1.5	1.9	1.0	-1.4
Bone: marrow area	0.1	0.3	0.4	0.6	-0.5
Bone: maximum diameter	0.4	0.8	0.8	-0.9	0.9
Bone: maximum force	0.7	1.2	1.2	1.0	-1.1
Bone: maximum moment	0.8	1.3	1.5	1.1	-1.2
Bone: minimum diameter	0.3	0.6	0.7	-0.8	0.7
Bone: periosteal estimation	0.0	0.0	0.0	0.1	-0.2
Bone: periosteal perimeter	1.1	1.8	2.0	-1.3	1.4
Bone: post-yield work	0.0	0.0	0.1	0.1	-0.2
Bone: stiffness	0.2	0.3	0.4	0.6	-0.4
Bone: tissue strength	3.0	2.9	3.3	1.6	-1.8
Bone: trabecular number	0.7	1.0	1.2	-1.1	0.9
Bone: trabecular spacing	1.4	1.8	1.9	1.4	-1.3
Bone: trabecular thickness	0.1	0.1	0.1	-0.3	-0.2
Bone: trabecular tissue density	0.2	0.2	0.3	0.4	-0.6
Breakpoint value in progressive ratio session	0.1	0.1	0.1	0.3	-0.2
Distance traveled before self-admin	0.0	0.0	0.0	0.2	-0.2
Distance traveled after self-admin	0.2	0.2	0.2	-0.5	0.4
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	0.2	0.2	0.3	0.5	-0.5
Diff in mean of infusions in LGA sessions	0.0	0.0	0.0	-0.1	0.1
Extinction: sum of active levers before priming	0.0	0.0	0.0	0.2	-0.2
Active lever presses in extinction session 6	0.4	0.4	0.4	0.6	-0.6
Delta distance traveled before/after self-admin	0.3	0.3	0.3	-0.6	0.5
Delta ambulatory time before/after self-admin	0.2	0.2	0.2	0.4	-0.5
Time in closed arm before self-admin	1.8	2.0	2.2	1.4	-1.5
Time in closed arm after self-admin	0.0	0.0	0.0	0.2	-0.2
Time in open arm before self-admin	1.3	1.3	1.5	-1.1	1.2
Time in open arm after self-admin	0.2	0.2	0.2	-0.4	0.5
Sum of active levers in priming session hrs 5-6	0.4	0.4	0.4	0.7	-0.6
Time to tail flick, vehicle, before self-admin	2.0	2.0	2.0	1.4	-1.4
Time to tail flick, vehicle, after self-admin	0.4	0.4	0.5	0.5	-0.7
Time to tail flick, test, before self-admin	0.0	0.0	0.0	0.1	0.0
Time to tail flick, test, after self-admin	0.2	0.2	0.2	-0.4	0.4
Delta time to tail flick, vehicle, before/after SA	0.6	0.6	0.7	-0.8	0.7
Delta time to tail flick, test, before/after SA	0.2	0.2	0.2	-0.5	0.3
Ambulatory time before self-admin	0.0	0.0	0.0	-0.1	0.1
Ambulatory time after self-admin	0.0	0.0	0.0	-0.1	0.1
Total heroin consumption	1.1	1.3	1.4	1.1	-1.2
Area under the delay curve	2.1	2.3	2.4	-1.4	1.6
Delay disc. indifference point, 0s delay	0.0	0.0	0.0	-0.2	0.1
Delay disc. indifference point, 16s delay	1.1	1.1	1.1	-1.1	1.1
Delay disc. indifference point, 2s delay	0.3	0.3	0.3	-0.6	0.6
Delay disc. indifference point, 24s delay	0.9	0.8	0.9	-0.9	1.0
Delay disc. indifference point, 4s delay	2.2	2.3	2.4	-1.5	1.6
Delay disc. indifference point, 8s delay	2.0	2.1	2.3	-1.4	1.5
Delay discount exponential model param	2.5	2.6	2.8	1.6	-1.7
Delay discount hyperbolic model param	2.4	2.6	2.8	1.5	-1.7
Fecal boli incidents, locomotor time 1	0.4	0.4	0.5	0.5	-0.7
Change in fecal boli incidents, locomotor task	0.0	0.0	0.0	0.2	-0.2
Time >=10cm from walls, locomotor time 1	0.1	0.1	0.2	-0.2	0.4
Bouts of movement, locomotor time 1	0.0	0.0	0.0	0.2	-0.1
Total resting periods, locomotor time 1	0.0	0.0	0.0	0.1	-0.1
Rest time, locomotor task time 1	0.4	0.5	0.6	-0.6	0.8
Distance moved, locomotor task time 1	1.4	1.6	1.8	1.1	-1.3
Vertical activity count, locomotor time 1	0.7	0.7	0.7	0.8	-0.8
Time >=10cm from walls, locomotor time 2	1.4	1.5	1.7	1.2	-1.3
Bouts of movement, locomotor time 2	0.0	0.0	0.0	-0.0	-0.2
Total resting periods, locomotor time 2	0.0	0.0	0.1	-0.3	0.0
Rest time, locomotor task time 2	0.0	0.0	0.0	-0.2	0.1
Distance moved, locomotor task time 2	0.8	0.9	0.9	0.9	-1.0
Vertical activity count, locomotor time 2	0.0	0.0	0.0	0.2	-0.2
Weight adjusted by age	0.3	0.3	0.3	0.5	-0.5
Seeking ratio, delayed vs. immediate footshock	2.2	2.5	2.7	-1.5	1.7
Locomotion in novel chamber	0.2	0.2	0.2	-0.5	0.4
Locomotion in novel chamber post-restriction	0.7	0.8	1.0	0.8	-1.0
Progressive ratio	3.3	3.9	4.5	1.8	-2.1
Food seeking constrained by brief footshock	0.7	0.8	0.9	-0.9	0.9
Seeking ratio, punishment vs. effort	5.3	6.5	6.9	-2.5	2.6
Run reversals in cocaine runway, females	1.7	1.7	2.1	-1.2	1.4
Run reversals in cocaine runway, males	0.3	0.3	0.3	0.6	-0.6
Latency to leave start box in cocaine runway	0.2	0.2	0.3	0.4	-0.5
Latency to leave start box in cocaine runway, F	1.0	1.1	1.4	0.9	-1.2
Latency to leave start box in cocaine runway, M	0.4	0.4	0.4	-0.6	0.6
Cd content in liver	3.3	3.6	4.9	2.2	-1.5
Co content in liver	0.0	0.0	0.0	0.2	-0.1
Cu content in liver	4.1	5.0	5.1	2.2	-2.3
Fe content in liver	2.7	3.2	4.8	2.2	-1.3
K content in liver	0.5	0.5	0.9	0.1	-0.9
Mg content in liver	0.4	0.4	0.7	-0.8	-0.2
Mn content in liver	0.5	0.5	1.0	0.1	-1.0
Na content in liver	0.6	0.6	1.0	1.0	-0.5
Rb content in liver	2.6	3.3	5.6	2.4	-1.0
Se content in liver	0.0	0.0	0.0	-0.2	-0.1
Sr content in liver	0.4	0.4	0.7	-0.8	-0.2
Zn content in liver	3.9	4.3	5.4	1.8	-2.3