Hub : Genes

Prph

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	ENSRNOG00000052880	0.09	0.08	2.6e-08	0.07	0.06	0.06	0.06	5.7e-08	2.9e-07	1.0e-07	1.2e-07
2	LHb	gene expression	ENSRNOG00000052880	0.41	0.21	3.4e-08	0.25	0.29	0.27	0.27	1.4e-06	1.6e-07	3.2e-07	3.5e-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 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	4.9	15.9	17.7	-4.2	3.8
BMI without tail	0.1	0.2	0.4	-0.6	-0.2
Body weight	6.7	28.5	31.3	-5.6	5.1
Epididymis fat weight	0.2	0.5	0.6	-0.7	0.6
Glucose	0.2	0.3	0.6	-0.8	0.2
Heart weight	0.0	0.1	0.1	-0.1	0.3
Left kidney weight	0.2	0.7	1.0	-0.6	1.0
Right kidney weight	2.7	7.6	7.8	-2.8	2.7
Tail length	0.1	0.2	0.3	0.1	-0.6
Length with tail	2.0	7.5	7.9	-2.8	2.7
Length without tail	7.6	16.6	17.0	-4.0	4.1
Liver weight, left	2.3	3.7	4.3	-2.1	1.7
Liver weight, right	1.8	3.0	3.5	-1.9	1.6
Parametrial fat weight	2.1	4.1	4.3	2.0	-2.1
Retroperitoneal fat weight	0.4	1.3	1.8	0.9	-1.3
Intraocular pressure	7.2	10.1	10.9	3.1	-3.3
Extensor digitorum longus weight	4.5	17.9	20.9	-4.6	3.9
Soleus weight	0.7	2.0	2.1	-1.5	1.3
Tibialis anterior weight	1.5	5.1	7.8	-2.8	1.6
Tibia length	8.3	23.5	26.5	-5.1	4.5
Number of licking bursts	0.2	0.3	0.6	0.1	-0.8
Food consumed during 24 hour testing period	1.7	2.0	2.1	-1.4	1.4
Times rat made contact with spout	0.1	0.1	0.1	0.2	-0.3
Mean time between licks in bursts	0.2	0.3	0.6	0.7	-0.2
Mean num. licks in bursts	0.1	0.1	0.3	0.5	0.2
Std. dev. time between licks in bursts	0.9	1.1	1.5	0.8	-1.2
Water consumed over 24 hours	0.0	0.0	0.0	-0.0	0.1
Indifference point 0 sec	2.0	3.3	3.6	1.7	-1.9
Indifference point AUC	0.2	0.2	0.3	0.2	-0.6
Indifference point function ln k	3.5	4.9	5.6	-2.0	2.4
Indifference point function log k	3.5	4.9	5.6	-2.0	2.4
Delay discounting total patch changes 0 sec	1.9	3.1	3.4	1.7	-1.9
Delay discounting total patch changes 12 sec	1.6	2.2	2.9	1.2	-1.7
Delay discounting total patch changes 18 sec	3.6	4.7	5.6	2.0	-2.4
Delay discounting total patch changes 24 sec	1.8	2.2	2.7	1.3	-1.7
Delay discounting total patch changes 6 sec	2.1	3.2	3.9	1.6	-2.0
Delay discounting time to switch 0 sec	2.2	3.4	3.5	1.8	-1.9
Delay discounting water rate 0 sec	2.7	4.3	4.5	-2.0	2.1
Delay discounting water rate 12 sec	3.5	5.2	5.8	-2.1	2.4
Delay discounting water rate 18 sec	0.3	0.4	0.5	-0.7	0.6
Delay discounting water rate 24 sec	3.0	4.1	4.5	-1.9	2.1
Delay discounting water rate 6 sec	3.3	4.8	5.4	-2.1	2.3
Locomotor activity	1.1	1.7	2.0	1.2	-1.4
Locomotor testing distance	2.9	4.9	5.3	2.1	-2.3
Locomotor testing rearing	1.9	3.0	3.8	1.5	-2.0
Light reinforcement 1	2.4	4.4	5.6	1.8	-2.4
Light reinforcement 2	0.9	1.1	1.3	1.0	-1.1
Reaction time number correct	1.1	1.6	2.4	-0.8	1.6
Reaction time mean minus median	8.1	10.5	11.3	3.1	-3.4
Reaction time mean minus median AUC	5.8	7.4	7.9	2.6	-2.8
Reaction time num false alarms	1.7	2.4	2.5	1.6	-1.5
Reaction time num false alarms AUC	2.4	3.3	3.4	1.8	-1.8
Reaction time trials correct on left	1.1	1.6	2.4	-0.8	1.6
Reaction time trials on left	0.8	1.2	1.9	-0.7	1.4
Reaction time mean	0.6	0.8	1.0	0.7	-1.0
Reaction time mean AUC	0.3	0.4	0.5	0.5	-0.7
Median of all reaction times	0.0	0.1	0.1	-0.3	0.1
Reaction time omissions	10.2	13.8	13.8	3.7	-3.7
Reaction time false alarm rate	2.4	3.4	4.0	1.7	-2.0
Reaction time premature initiation rate	5.5	7.3	9.4	2.3	-3.1
Reaction time premature initiations	2.6	3.7	4.4	1.8	-2.1
Std. dev. reaction times	6.0	8.3	8.8	2.8	-3.0
Reaction time trials completed	0.8	1.2	1.9	-0.7	1.4
Reaction time trials AUC	1.4	2.0	3.0	-1.0	1.7
Social response proportion	0.1	0.1	0.2	0.2	-0.4
Social responses	6.8	8.8	10.7	2.6	-3.3
Social time	0.0	0.0	0.0	0.2	0.0
Conditioned locomotion	0.0	0.0	0.0	0.0	0.2
Cocaine response after cond. corrected	0.0	0.0	0.0	0.2	-0.1
Cocaine response after cond. not corrected	0.6	0.7	0.8	0.9	-0.8
Cocaine response before conditioning	3.3	4.0	4.1	2.0	-2.0
Saline control response	0.1	0.2	0.2	-0.4	0.4
Condit. Reinf. active minus inactive responses	0.0	0.0	0.0	-0.0	-0.1
Condit. Reinf. active-inactive response ratio	0.3	0.3	0.4	0.5	-0.6
Condit. Reinf. active responses	0.1	0.1	0.3	0.2	-0.5
Condit. Reinf. inactive responses	0.4	0.5	0.7	0.6	-0.9
Condit. Reinf. lever presses	0.0	0.1	0.1	-0.3	-0.0
Condit. Reinf. lever reinforcers received	0.3	0.5	0.7	0.5	-0.9
Pavlov. Cond. lever latency	0.0	0.0	0.0	0.1	0.1
Pavlov. Cond. magazine entry latency	1.2	1.4	1.4	-1.1	1.2
Pavlov. Cond. change in total contacts	1.8	2.5	3.2	-1.8	1.3
Pavlov. Cond. index score	0.6	0.8	1.0	-1.0	0.8
Pavlov. Cond. latency score	0.6	0.8	0.9	-1.0	0.8
Pavlov. Cond. lever contacts	0.1	0.1	0.2	0.1	-0.4
Pavlov. Cond. magazine entry number	2.5	3.1	3.4	1.9	-1.7
Pavlov. Cond. intertrial magazine entries	5.8	7.5	7.8	2.8	-2.7
Pavlov. Cond. lever-magazine prob. diff.	1.1	1.4	1.7	-1.3	1.1
Pavlov. Cond. response bias	0.0	0.0	0.1	-0.2	-0.1
Conditioned reinforcement - actives	1.4	1.4	1.7	1.0	-1.3
Conditioned reinforcement - inactives	1.9	2.2	2.5	1.3	-1.6
Conditioned locomotion	0.2	0.3	0.5	0.3	-0.7
Intermittent access intake day 1-15 change	1.2	1.2	1.8	0.8	-1.3
Intermittent access intake escalation	0.9	0.8	1.3	0.6	-1.1
Intermittent access intake escalation 2	1.5	1.4	2.0	0.9	-1.4
Intermitt. access day 1 inactive lever presses	2.6	2.8	3.0	1.7	-1.6
Intermitt. access day 15 inactive lever presses	1.2	1.3	1.4	1.1	-1.2
Intermitt. access escalation Index	0.1	0.1	0.2	0.2	-0.4
Intermittent access day 1 total infusions	1.3	1.4	1.5	1.2	-1.2
Intermittent access day 15 total infusions	2.5	2.7	3.5	1.4	-1.9
Intermittent access terminal intake (last 3 days)	2.9	3.2	3.7	1.6	-1.9
Intermittent access total infusions	2.7	3.0	3.4	1.6	-1.8
Intermittent access day 1 locomotion	0.8	0.9	0.9	0.9	-0.9
Intermittent access day 15 total locomotion	1.2	1.3	1.9	0.9	-1.4
Intermittent access total locomotion	2.9	3.2	4.0	1.6	-2.0
Intermittent access standard deviation	0.5	0.5	0.7	0.6	-0.8
Cocaine induced anxiety	1.3	1.5	1.9	-1.4	1.1
Post-drug Anxiety	5.4	6.0	6.2	-2.5	2.4
Baseline Anxiety	0.8	0.9	1.0	-0.8	1.0
Lifetime Intake	2.5	2.8	3.4	1.5	-1.8
Incentive Sensitization - Responses	0.1	0.1	0.1	-0.4	-0.0
Incentive Sensitization - Breakpoint	0.0	0.0	0.0	-0.2	-0.1
Progressive ratio test 1 active lever presses	4.6	4.7	5.2	2.0	-2.3
Progressive ratio test 1 breakpoint	4.1	4.2	4.8	1.9	-2.2
Progressive ratio test 1 inactive lever presses	3.3	3.5	4.1	1.7	-2.0
Progressive ratio test 2 active lever presses	2.2	2.3	3.0	1.3	-1.7
Progressive ratio test 2 breakpoint	2.9	3.2	3.9	1.6	-2.0
Progressive ratio test 2 inactive lever presses	2.3	2.7	3.2	1.5	-1.8
Total sessions with >9 infusions	0.9	1.0	1.4	0.7	-1.2
Short access day 1 total inactive lever presses	1.4	1.5	1.9	1.1	-1.4
Short access day 10 total inactive lever presses	0.1	0.2	0.2	0.4	-0.4
Short access day 1 total infusions	0.1	0.1	0.1	0.2	-0.3
Short access day 10 total infusions	0.9	1.0	1.3	0.8	-1.1
Short access total infusions	0.5	0.5	0.9	0.5	-0.9
Short access day 1 locomotion	0.1	0.1	0.2	0.0	-0.4
Short access day 10 total locomotion	0.1	0.1	0.1	0.3	-0.3
Short access total locomotion	0.3	0.3	0.5	0.3	-0.7
Compulsive drug intake	0.9	0.9	1.2	-0.8	1.1
One hour access (0.3 mA shock)	0.2	0.3	0.5	0.1	-0.7
One hour access (shock baseline)	0.2	0.2	0.4	-0.1	-0.6
Number of responses in last shaping day	0.2	0.2	0.4	-0.6	0.0
Context. condit. distance diff. score	0.3	0.4	0.5	-0.7	0.5
Locomotion velocity, session 1	1.4	1.5	1.9	1.4	-1.0
Locomotion distance, session 1	3.7	4.8	6.2	2.5	-1.8
Locomotion velocity, session 2	0.6	0.7	1.2	1.1	-0.5
Locomotion distance, session 2	3.1	4.4	5.8	2.4	-1.8
Locomotion velocity, session 3	4.6	5.4	6.1	2.5	-2.2
Locomotion distance, session 3	6.1	6.6	7.3	2.7	-2.4
Stereotopy head waving bouts, day 3	0.9	1.1	1.3	-0.9	1.2
Stereotopy head waving duration, day 3	0.4	0.5	0.8	-0.4	0.9
Locomotion velocity, session 7	0.3	0.3	0.3	0.5	-0.6
Locomotion distance, session 7	1.5	2.0	2.4	1.2	-1.6
Stereotopy head waving bouts, day 7	0.9	1.0	1.0	-1.0	1.0
Stereotopy head waving duration, day 7	1.2	1.5	1.5	-1.2	1.2
Locomotion velocity, session 8	0.0	0.0	0.0	0.2	0.1
Locomotion distance, session 8	1.3	1.9	2.2	1.5	-1.3
Degree of sensitization distance	0.9	0.9	1.4	-1.2	0.7
Degree of sensitization stereotypy	0.2	0.2	0.3	-0.5	0.4
Condit. Reinf. active minus inactive responses	0.2	0.2	0.4	0.6	-0.2
Condit. Reinf. active-inactive response ratio	0.1	0.1	0.3	-0.1	0.5
Condit. Reinf. active responses	0.8	1.0	1.4	1.2	-0.8
Condit. Reinf. inactive responses	2.7	3.2	3.3	1.8	-1.8
Incentive salience index mean	0.0	0.0	0.0	0.0	0.1
Condit. Reinf. lever presses	0.1	0.1	0.1	-0.3	0.3
Time in familiar zone, hab. session 1	0.5	0.4	0.6	0.8	-0.5
Time in novel zone, hab. session 1	0.4	0.4	0.5	-0.7	0.5
Total zone transitions, hab. session 1	0.4	0.6	0.8	0.9	-0.7
Total locomotion distance, hab. session 1	0.0	0.0	0.1	0.3	0.1
Locomotion velocity, hab. session 1	0.0	0.0	0.0	0.1	0.2
Time in familiar zone, hab. session 2	0.2	0.2	0.4	-0.3	0.6
Time in novel zone, hab. session 2	0.2	0.2	0.2	0.3	-0.5
Total zone transitions, hab. session 2	0.5	0.7	1.0	1.0	-0.6
Total locomotion distance, hab. session 2	0.2	0.3	0.5	0.7	-0.3
Locomotion velocity, hab. session 2	0.1	0.2	0.3	0.6	-0.1
Novel to familiar place preference ratio	2.3	2.4	3.0	-1.7	1.4
Novelty place preference	1.8	1.9	2.4	-1.5	1.2
Time in novel zone, NPP test	1.5	1.6	2.1	-1.5	1.1
Total zone transitions, NPP test	1.7	2.4	3.1	1.8	-1.3
Total locomotion distance, NPP test	2.1	3.0	3.7	1.9	-1.5
Locomotion velocity, NPP test	1.3	1.8	2.4	1.5	-1.1
Pavlov. Cond. lever latency	0.1	0.1	0.2	-0.0	0.5
Pavlov. Cond. magazine entry latency	0.0	0.0	0.0	-0.0	0.0
Pavlov. Cond. change in total contacts	0.1	0.1	0.1	-0.3	0.0
Pavlov. Cond. index score	0.1	0.1	0.2	-0.5	-0.0
Pavlov. Cond. latency score	0.1	0.1	0.1	-0.4	-0.1
Pavlov. Cond. lever contacts	0.4	0.4	0.8	0.3	-0.9
Pavlov. Cond. magazine entry number	0.0	0.0	0.0	0.0	0.2
Pavlov. Cond. intertrial magazine entries	0.7	0.8	1.4	1.2	-0.5
Pavlov. Cond. lever-magazine prob. diff.	0.2	0.3	0.5	-0.7	0.3
Pavlov. Cond. response bias	0.1	0.1	0.1	0.1	-0.4
Bone: apparent density	10.2	16.8	17.6	-4.0	4.2
Bone surface	12.0	21.0	21.7	-4.5	4.7
Bone volume	8.7	14.7	15.5	-3.7	3.9
Bone: connectivity density	7.3	11.5	12.2	-3.3	3.5
Bone: cortical apparent density	0.2	0.3	0.4	0.4	-0.6
Bone: cortical area	10.1	15.2	16.1	-4.0	3.8
Bone: cortical porosity	1.0	1.1	1.4	1.2	-0.9
Bone: cortical porosity	1.5	1.6	2.0	1.4	-1.1
Bone: cortical thickness	3.5	5.8	6.2	-2.5	2.3
Bone: cortical thickness	0.3	0.3	0.5	-0.7	0.3
Bone: cortical tissue density	0.3	0.4	0.5	0.5	-0.7
Bone: elastic displacement	4.9	5.6	6.5	2.6	-2.1
Bone: elastic work	0.1	0.1	0.2	0.4	0.1
Bone: endosteal estimation	8.1	17.4	17.4	-4.2	4.2
Bone: endosteal perimeter	7.6	15.6	17.2	-4.2	3.7
Bone: final force	9.8	16.0	17.0	-3.9	4.1
Bone: final moment	10.1	16.7	18.2	-3.9	4.3
Bone: marrow area	7.9	17.0	17.0	-4.1	4.1
Bone: maximum diameter	4.3	7.9	9.3	-3.1	2.5
Bone: maximum force	14.4	25.0	26.1	-4.9	5.1
Bone: maximum moment	14.7	25.5	27.4	-4.9	5.2
Bone: minimum diameter	9.5	17.6	18.2	-4.3	4.1
Bone: periosteal estimation	12.6	25.8	27.0	-5.2	5.0
Bone: periosteal perimeter	10.8	17.9	18.7	-4.3	4.1
Bone: post-yield work	8.9	12.1	12.5	-3.4	3.5
Bone: stiffness	17.5	27.7	27.9	-5.3	5.2
Bone: tissue strength	1.0	0.9	1.3	-0.8	1.2
Bone: trabecular number	6.2	9.7	10.6	-3.0	3.3
Bone: trabecular spacing	2.3	3.0	3.3	1.6	-1.8
Bone: trabecular thickness	0.1	0.1	0.1	0.3	-0.4
Bone: trabecular tissue density	0.1	0.1	0.1	0.2	-0.3
Breakpoint value in progressive ratio session	0.2	0.3	0.3	-0.5	0.5
Distance traveled before self-admin	1.3	1.4	1.5	1.2	-1.1
Distance traveled after self-admin	0.3	0.3	0.5	0.7	-0.4
Delta time in closed arm before/after self-admin	0.2	0.2	0.3	-0.4	0.5
Delta time in open arm before/after self-admin	4.6	4.4	4.6	2.1	-2.1
Diff in mean of infusions in LGA sessions	1.4	1.5	1.9	-1.1	1.4
Extinction: sum of active levers before priming	0.4	0.4	0.5	-0.4	0.7
Active lever presses in extinction session 6	0.3	0.3	0.4	-0.5	0.7
Delta distance traveled before/after self-admin	0.1	0.1	0.1	-0.2	0.3
Delta ambulatory time before/after self-admin	0.0	0.0	0.1	-0.2	0.0
Time in closed arm before self-admin	1.9	2.1	2.6	-1.6	1.3
Time in closed arm after self-admin	0.8	0.9	1.0	-1.0	0.9
Time in open arm before self-admin	0.6	0.7	0.8	-0.8	0.9
Time in open arm after self-admin	0.4	0.4	0.6	0.8	-0.5
Sum of active levers in priming session hrs 5-6	0.1	0.1	0.1	0.3	-0.1
Time to tail flick, vehicle, before self-admin	1.1	1.1	1.4	1.2	-0.9
Time to tail flick, vehicle, after self-admin	0.2	0.2	0.2	-0.5	0.5
Time to tail flick, test, before self-admin	0.5	0.5	0.8	0.9	-0.5
Time to tail flick, test, after self-admin	0.2	0.2	0.3	-0.5	0.5
Delta time to tail flick, vehicle, before/after SA	0.5	0.5	0.6	-0.8	0.6
Delta time to tail flick, test, before/after SA	0.3	0.3	0.4	-0.6	0.3
Ambulatory time before self-admin	4.0	4.2	4.3	2.1	-2.0
Ambulatory time after self-admin	1.8	2.0	2.1	1.4	-1.5
Total heroin consumption	2.0	2.4	2.5	-1.6	1.5
Area under the delay curve	0.9	1.0	1.0	-1.0	1.0
Delay disc. indifference point, 0s delay	1.1	1.2	1.4	-1.0	1.2
Delay disc. indifference point, 16s delay	1.1	1.1	1.3	-1.2	0.9
Delay disc. indifference point, 2s delay	1.3	1.4	1.7	-1.1	1.3
Delay disc. indifference point, 24s delay	1.5	1.5	1.6	-1.3	1.2
Delay disc. indifference point, 4s delay	0.2	0.2	0.3	-0.4	0.5
Delay disc. indifference point, 8s delay	2.7	2.8	2.9	-1.7	1.6
Delay discount exponential model param	0.9	0.9	1.0	1.0	-0.9
Delay discount hyperbolic model param	0.8	0.9	0.9	0.9	-0.9
Fecal boli incidents, locomotor time 1	2.7	2.9	3.4	1.8	-1.5
Change in fecal boli incidents, locomotor task	1.3	1.2	1.5	-0.9	1.2
Time >=10cm from walls, locomotor time 1	0.2	0.2	0.2	-0.5	0.4
Bouts of movement, locomotor time 1	0.0	0.0	0.1	0.3	0.1
Total resting periods, locomotor time 1	0.3	0.4	0.6	0.8	-0.4
Rest time, locomotor task time 1	0.5	0.6	0.8	0.9	-0.6
Distance moved, locomotor task time 1	0.1	0.2	0.3	-0.5	0.2
Vertical activity count, locomotor time 1	1.7	1.8	2.2	-1.5	1.2
Time >=10cm from walls, locomotor time 2	0.8	0.9	1.1	1.0	-0.8
Bouts of movement, locomotor time 2	2.7	3.0	3.0	-1.7	1.7
Total resting periods, locomotor time 2	3.2	3.4	3.7	-1.9	1.8
Rest time, locomotor task time 2	0.0	0.0	0.1	-0.3	0.1
Distance moved, locomotor task time 2	0.1	0.1	0.2	0.4	-0.2
Vertical activity count, locomotor time 2	0.0	0.0	0.0	-0.2	0.0
Weight adjusted by age	2.5	2.8	3.3	-1.8	1.5
Seeking ratio, delayed vs. immediate footshock	0.2	0.3	0.3	-0.5	0.6
Locomotion in novel chamber	0.5	0.6	0.7	-0.8	0.8
Locomotion in novel chamber post-restriction	0.0	0.0	0.0	-0.2	0.1
Progressive ratio	0.0	0.0	0.1	0.1	-0.2
Food seeking constrained by brief footshock	0.3	0.3	0.4	0.4	-0.7
Seeking ratio, punishment vs. effort	0.0	0.0	0.0	-0.0	-0.0
Run reversals in cocaine runway, females	0.0	0.0	0.0	-0.2	0.0
Run reversals in cocaine runway, males	1.7	1.6	1.7	1.3	-1.2
Latency to leave start box in cocaine runway	0.0	0.0	0.0	-0.2	-0.1
Latency to leave start box in cocaine runway, F	1.6	1.8	2.0	1.2	-1.4
Latency to leave start box in cocaine runway, M	2.3	2.2	2.3	-1.5	1.4
Cd content in liver	0.6	0.6	0.9	0.6	-0.9
Co content in liver	0.4	0.5	0.9	0.4	-0.9
Cu content in liver	0.5	0.6	0.8	-0.6	0.9
Fe content in liver	0.2	0.2	0.4	0.2	-0.7
K content in liver	0.2	0.2	0.2	-0.5	0.4
Mg content in liver	0.0	0.0	0.0	0.2	-0.1
Mn content in liver	0.1	0.1	0.1	0.1	0.3
Na content in liver	0.0	0.0	0.1	0.1	-0.2
Rb content in liver	0.2	0.3	0.5	0.2	-0.7
Se content in liver	0.6	0.7	0.8	0.7	-0.9
Sr content in liver	0.3	0.3	0.5	-0.7	0.4
Zn content in liver	1.8	2.0	2.3	1.3	-1.5