Hub : Genes

Hoxb2

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	Liver	gene expression	Hoxb2	0.11	0.07	5.7e-04	0.02	0.01	0.03	0.02	5.4e-03	2.0e-02	3.0e-04	4.7e-03
2	Adipose	gene expression	Hoxb2	0.12	0.07	1.2e-15	0.13	0.03	0.13	0.04	6.9e-14	1.8e-04	4.0e-14	8.4e-06

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	1.7	2.9	3.1	1.7	-1.8
Area under the delay curve	0.6	0.7	1.2	-0.4	1.1
BMI with tail	15.4	53.1	54.9	7.2	-7.4
BMI without tail	1.1	3.3	3.6	1.9	-1.7
Body weight	1.1	4.7	4.8	2.1	-2.2
Weight adjusted by age	1.2	1.8	2.5	-1.6	1.1
Bone surface	0.9	1.7	2.3	1.5	-1.0
Bone volume	2.1	3.8	4.6	2.1	-1.8
Breakpoint value in progressive ratio session	2.1	2.6	3.3	-1.8	1.4
Number of licking bursts	0.1	0.1	0.2	0.4	0.2
Context. condit. distance diff. score	0.2	0.2	0.4	0.2	-0.6
Locomotion velocity, session 1	0.4	0.4	0.4	0.6	-0.6
Locomotion distance, session 1	1.7	2.1	3.1	-1.1	1.8
Locomotion velocity, session 2	1.4	1.6	1.8	-1.2	1.3
Locomotion distance, session 2	2.1	3.0	3.6	-1.6	1.9
Locomotion velocity, session 3	0.3	0.3	0.7	-0.8	0.1
Locomotion distance, session 3	3.7	4.1	4.6	-2.2	1.9
Stereotopy head waving bouts, day 3	4.2	4.9	7.3	1.6	-2.7
Stereotopy head waving duration, day 3	3.4	4.0	5.2	1.7	-2.3
Locomotion velocity, session 7	0.4	0.4	0.8	-0.2	0.9
Locomotion distance, session 7	2.1	2.6	4.5	-0.9	2.1
Stereotopy head waving bouts, day 7	0.2	0.2	0.4	0.1	-0.6
Stereotopy head waving duration, day 7	0.1	0.1	0.2	-0.2	-0.4
Locomotion velocity, session 8	0.4	0.5	0.8	-0.9	-0.3
Locomotion distance, session 8	0.8	1.2	1.4	-1.2	1.0
Degree of sensitization distance	0.6	0.6	1.2	1.1	-0.3
Degree of sensitization stereotypy	0.1	0.1	0.1	-0.2	0.3
Conditioned locomotion	0.6	0.6	1.1	0.5	-1.0
Cocaine response after cond. corrected	4.4	5.3	5.8	2.2	-2.4
Cocaine response after cond. not corrected	2.3	2.7	2.8	1.7	-1.6
Cocaine response before conditioning	2.0	2.4	3.3	-1.2	1.8
Saline control response	0.4	0.5	0.8	0.4	0.9
Bone: connectivity density	0.2	0.3	0.4	0.6	-0.4
Bone: cortical apparent density	6.4	8.7	9.6	-2.8	3.1
Bone: cortical area	0.4	0.7	1.4	1.2	-0.0
Bone: cortical porosity	0.3	0.4	0.7	0.8	-0.3
Bone: cortical porosity	0.7	0.8	1.4	1.2	-0.4
Bone: cortical thickness	0.2	0.4	0.8	0.0	0.9
Bone: cortical thickness	0.9	1.0	1.4	-0.8	1.2
Bone: cortical tissue density	6.8	9.3	10.3	-2.9	3.2
Condit. Reinf. active minus inactive responses	0.4	0.4	0.8	0.9	0.1
Condit. Reinf. active-inactive response ratio	1.5	1.6	3.0	1.7	-0.5
Condit. Reinf. active responses	0.0	0.0	0.0	-0.1	0.0
Condit. Reinf. inactive responses	1.7	2.1	3.9	-2.0	0.5
Incentive salience index mean	0.1	0.1	0.2	0.1	0.5
Condit. Reinf. lever presses	0.7	0.9	1.0	-1.0	0.9
Condit. Reinf. active minus inactive responses	0.3	0.4	0.8	0.9	-0.2
Condit. Reinf. active-inactive response ratio	1.0	1.1	1.7	1.3	-0.8
Condit. Reinf. active responses	0.2	0.3	0.6	0.8	0.3
Condit. Reinf. inactive responses	0.4	0.6	1.0	-0.3	1.0
Condit. Reinf. lever presses	1.9	2.6	2.8	-1.7	1.5
Condit. Reinf. lever reinforcers received	0.2	0.3	0.4	0.5	0.6
Conditioned reinforcement - actives	0.1	0.2	0.2	0.5	-0.3
Conditioned reinforcement - inactives	1.1	1.5	3.1	1.8	-0.1
Conditioned locomotion	1.1	1.5	1.7	1.1	-1.3
Patch foraging indifference point 0 sec	0.1	0.3	0.4	-0.3	-0.7
Patch foraging indifference point AUC	0.7	1.0	2.0	-1.4	0.4
Delay disc. indifference point, 0s delay	1.1	1.3	1.6	-1.0	1.3
Delay disc. indifference point, 16s delay	0.0	0.0	0.0	0.1	-0.1
Delay disc. indifference point, 2s delay	0.3	0.3	0.3	-0.5	0.5
Delay disc. indifference point, 24s delay	0.4	0.4	0.5	0.5	0.7
Delay disc. indifference point, 4s delay	2.8	3.0	4.7	-1.1	2.2
Delay disc. indifference point, 8s delay	0.4	0.5	0.6	-0.6	0.7
Indifference point function ln k	0.0	0.0	0.1	0.1	0.2
Indifference point function log k	0.0	0.0	0.1	0.1	0.2
Patch foraging total patch changes 0 sec	0.1	0.2	0.4	-0.1	-0.7
Patch foraging total patch changes 12 sec	0.2	0.3	0.5	-0.7	0.2
Patch foraging total patch changes 18 sec	0.2	0.2	0.4	0.1	-0.7
Patch foraging total patch changes 24 sec	0.3	0.5	0.8	0.4	-0.9
Patch foraging total patch changes 6 sec	0.1	0.1	0.2	0.1	-0.4
Patch foraging time to switch 0 sec	0.1	0.3	0.5	0.7	-0.3
Patch foraging water rate 0 sec	0.3	0.7	1.1	0.5	-1.0
Patch foraging water rate 12 sec	0.1	0.2	0.3	-0.1	0.6
Patch foraging water rate 18 sec	0.1	0.2	0.3	0.2	0.5
Patch foraging water rate 24 sec	0.6	0.8	0.9	0.9	-0.9
Patch foraging water rate 6 sec	0.6	0.8	1.7	-1.3	0.1
Seeking ratio, delayed vs. immediate footshock	0.6	0.7	0.7	0.8	-0.8
Distance traveled before self-admin	0.4	0.6	0.9	0.9	0.5
Distance traveled after self-admin	0.1	0.2	0.3	0.6	-0.1
Extensor digitorum longus weight	0.0	0.0	0.0	0.1	-0.2
Bone: elastic displacement	0.2	0.2	0.4	-0.0	-0.6
Bone: elastic work	0.1	0.2	0.3	-0.6	0.1
Bone: endosteal estimation	0.4	0.8	1.1	1.1	-0.7
Bone: endosteal perimeter	0.7	1.5	1.7	1.3	-1.1
Epididymis fat weight	0.8	2.7	4.9	2.2	-0.7
Delta time in closed arm before/after self-admin	0.1	0.1	0.1	0.4	-0.2
Delta time in open arm before/after self-admin	1.7	1.6	1.7	-1.3	1.3
Diff in mean of infusions in LGA sessions	0.6	0.8	1.5	1.2	-0.0
Delay discount exponential model param	0.7	0.8	1.4	0.3	-1.2
Extinction: sum of active levers before priming	0.5	0.5	0.9	0.4	0.9
Active lever presses in extinction session 6	0.0	0.0	0.0	0.1	-0.2
Bone: final force	0.8	1.2	2.3	1.5	-0.4
Bone: final moment	0.4	0.7	1.3	1.1	-0.4
Food consumed during 24 hour testing period	1.4	1.9	2.2	-1.3	1.5
Glucose	1.0	1.5	2.8	0.5	-1.7
Heart weight	4.8	7.4	11.4	3.4	-1.9
Delay discount hyperbolic model param	0.7	0.7	1.3	0.3	-1.2
Intermittent access intake day 1-15 change	0.2	0.4	0.4	-0.6	-0.6
Intermittent access intake escalation	0.2	0.5	0.6	-0.8	-0.6
Intermittent access intake escalation 2	1.1	1.2	2.3	-0.4	-1.5
Intermitt. access day 1 inactive lever presses	0.0	0.1	0.1	0.3	-0.3
Intermitt. access day 15 inactive lever presses	0.8	1.6	2.2	1.0	-1.5
Intermitt. access escalation Index	0.6	0.8	1.6	-1.3	-0.0
Intermittent access day 1 total infusions	0.5	0.9	1.6	1.3	0.3
Intermittent access day 15 total infusions	0.0	0.0	0.1	0.2	0.0
Intermittent access terminal intake (last 3 days)	0.2	0.3	0.5	0.7	-0.4
Intermittent access total infusions	0.6	0.7	1.5	1.2	-0.1
Intermittent access day 1 locomotion	0.3	0.4	0.8	0.9	0.0
Intermittent access day 15 total locomotion	0.3	0.5	1.0	1.0	-0.0
Intermittent access total locomotion	0.6	0.7	1.1	1.0	-0.6
Intermittent access standard deviation	1.0	2.2	2.7	1.3	-1.6
Left kidney weight	0.0	0.0	0.0	0.2	-0.1
Right kidney weight	0.2	1.0	1.7	0.4	-1.3
Cocaine induced anxiety	0.2	0.3	0.5	0.3	-0.7
Post-drug Anxiety	0.2	0.2	0.3	0.6	-0.1
Baseline Anxiety	0.3	0.4	0.7	0.0	0.9
Tail length	15.5	60.4	62.9	-7.9	7.6
Length with tail	6.0	26.1	28.0	-5.3	4.9
Length without tail	0.1	0.3	0.3	0.6	-0.5
Times rat made contact with spout	0.0	0.0	0.0	0.2	0.1
Lifetime Intake	0.1	0.1	0.1	0.4	-0.1
Liver weight, left	0.0	0.0	0.0	0.1	0.1
Liver weight, right	0.2	0.3	0.5	-0.3	0.7
Locomotor activity	0.3	0.5	0.8	0.9	-0.5
Locomotor testing distance	0.4	0.7	1.0	0.5	-1.0
Locomotor testing rearing	0.1	0.2	0.3	-0.6	0.3
Locomotion in novel chamber	0.3	0.3	0.3	0.6	0.6
Locomotion in novel chamber post-restriction	2.8	4.6	7.7	2.8	-1.2
Fecal boli incidents, locomotor time 1	2.6	3.7	5.7	1.3	-2.4
Change in fecal boli incidents, locomotor task	1.3	1.3	2.6	0.1	1.6
Time >=10cm from walls, locomotor time 1	0.6	0.6	1.0	0.5	1.0
Bouts of movement, locomotor time 1	0.4	0.4	0.8	-0.9	-0.2
Total resting periods, locomotor time 1	0.3	0.3	0.3	-0.6	-0.5
Rest time, locomotor task time 1	0.4	0.5	0.9	-0.4	-0.9
Distance moved, locomotor task time 1	0.6	0.8	1.7	0.2	1.3
Vertical activity count, locomotor time 1	0.3	0.8	1.3	0.4	1.2
Time >=10cm from walls, locomotor time 2	0.6	0.9	0.9	1.0	0.9
Bouts of movement, locomotor time 2	0.0	0.0	0.0	0.2	-0.2
Total resting periods, locomotor time 2	0.0	0.0	0.1	0.0	-0.3
Rest time, locomotor task time 2	1.1	1.4	2.5	-1.6	0.6
Distance moved, locomotor task time 2	0.2	0.3	0.4	0.4	0.6
Vertical activity count, locomotor time 2	0.4	0.5	0.8	0.9	0.5
Light reinforcement 1	0.1	0.2	0.3	-0.5	-0.5
Light reinforcement 2	0.3	0.4	0.8	-0.9	-0.2
Bone: marrow area	0.3	0.6	0.9	0.9	-0.6
Bone: maximum diameter	0.9	1.6	2.3	1.5	-1.0
Bone: maximum force	0.8	1.5	2.6	1.6	-0.6
Bone: maximum moment	0.5	0.9	1.3	1.2	-0.6
Mean time between licks in bursts	0.3	0.6	1.2	1.1	-0.2
Mean num. licks in bursts	0.1	0.1	0.2	-0.5	0.2
Cd content in liver	0.0	0.0	0.1	0.3	0.0
Co content in liver	0.2	0.2	0.4	-0.6	-0.2
Cu content in liver	1.7	2.0	3.6	0.6	1.9
Fe content in liver	1.3	1.5	2.1	1.4	1.0
K content in liver	2.2	2.1	4.1	2.0	-0.4
Mg content in liver	1.8	1.9	2.0	1.3	1.4
Mn content in liver	4.5	5.0	6.3	-2.5	1.9
Na content in liver	3.0	3.2	4.2	2.0	-1.5
Rb content in liver	0.5	0.5	0.9	0.4	0.9
Se content in liver	0.7	0.9	1.0	0.9	-1.0
Sr content in liver	4.0	3.5	5.3	-2.3	1.3
Zn content in liver	2.4	2.7	5.1	2.3	-0.5
Bone: minimum diameter	0.3	0.6	1.1	1.1	0.0
Time in familiar zone, hab. session 1	0.2	0.2	0.3	-0.2	0.6
Time in novel zone, hab. session 1	1.9	1.9	3.5	0.6	-1.9
Total zone transitions, hab. session 1	3.4	4.7	7.4	-1.4	2.7
Total locomotion distance, hab. session 1	1.0	1.5	2.8	-0.4	1.7
Locomotion velocity, hab. session 1	1.5	2.1	4.2	-0.3	2.1
Time in familiar zone, hab. session 2	0.4	0.4	0.5	0.5	-0.7
Time in novel zone, hab. session 2	0.1	0.1	0.1	-0.3	0.3
Total zone transitions, hab. session 2	1.1	1.4	2.5	-0.5	1.6
Total locomotion distance, hab. session 2	0.2	0.2	0.5	0.7	0.1
Locomotion velocity, hab. session 2	0.2	0.2	0.4	0.6	0.2
Novel to familiar place preference ratio	0.4	0.5	0.8	-0.3	0.9
Novelty place preference	0.6	0.7	1.1	-0.5	1.0
Time in novel zone, NPP test	0.5	0.5	0.8	-0.4	0.9
Total zone transitions, NPP test	3.6	5.1	6.3	-2.0	2.5
Total locomotion distance, NPP test	0.7	0.9	1.5	-0.6	1.2
Locomotion velocity, NPP test	1.1	1.5	2.3	-0.8	1.5
Intraocular pressure	1.7	2.4	3.5	-1.1	1.9
Delta distance traveled before/after self-admin	0.1	0.1	0.1	-0.3	-0.3
Delta ambulatory time before/after self-admin	0.2	0.3	0.5	0.1	-0.7
Parametrial fat weight	0.2	0.4	0.8	0.9	-0.1
Pavlov. Cond. lever latency	1.5	1.9	2.0	1.4	-1.3
Pavlov. Cond. magazine entry latency	0.0	0.0	0.0	0.1	-0.0
Pavlov. Cond. change in total contacts	1.4	1.5	2.3	-0.8	1.5
Pavlov. Cond. index score	0.4	0.5	0.7	-0.5	0.8
Pavlov. Cond. latency score	0.6	0.7	0.8	-0.8	0.9
Pavlov. Cond. lever contacts	2.0	2.4	2.4	-1.5	1.6
Pavlov. Cond. magazine entry number	0.2	0.2	0.3	-0.3	-0.5
Pavlov. Cond. intertrial magazine entries	0.2	0.2	0.4	-0.1	0.6
Pavlov. Cond. lever-magazine prob. diff.	0.4	0.5	0.8	-0.6	0.9
Pavlov. Cond. response bias	0.4	0.5	0.7	-0.4	0.9
Pavlov. Cond. lever latency	0.7	0.9	1.2	1.1	0.8
Pavlov. Cond. magazine entry latency	1.2	1.4	2.8	-1.7	0.3
Pavlov. Cond. change in total contacts	0.6	1.0	1.9	-1.4	-0.2
Pavlov. Cond. index score	0.4	0.6	0.9	-1.0	-0.5
Pavlov. Cond. latency score	0.5	0.7	1.3	-1.2	-0.3
Pavlov. Cond. lever contacts	0.6	0.9	1.3	-1.1	-0.7
Pavlov. Cond. magazine entry number	0.5	0.6	1.2	1.1	0.2
Pavlov. Cond. intertrial magazine entries	1.0	1.5	2.9	-0.1	1.7
Pavlov. Cond. lever-magazine prob. diff.	0.5	0.7	1.1	-1.0	-0.5
Pavlov. Cond. response bias	0.5	0.7	0.8	-0.8	-0.9
Time in closed arm before self-admin	2.9	3.8	4.9	2.2	-1.6
Time in closed arm after self-admin	3.8	4.1	5.2	2.3	-1.7
Time in open arm before self-admin	0.5	0.6	0.7	-0.7	0.8
Time in open arm after self-admin	3.3	3.6	4.1	-1.8	2.0
Bone: periosteal estimation	0.7	1.4	2.4	1.5	-0.7
Bone: periosteal perimeter	0.8	1.3	1.7	1.3	-1.0
Bone: post-yield work	0.1	0.1	0.2	0.2	-0.4
Progressive ratio test 1 active lever presses	0.9	1.1	1.3	-1.1	1.0
Progressive ratio test 1 breakpoint	0.8	0.9	1.1	-1.0	0.9
Progressive ratio test 1 inactive lever presses	0.2	0.3	0.3	0.5	-0.5
Progressive ratio test 2 active lever presses	0.6	0.8	1.0	1.0	0.7
Progressive ratio test 2 breakpoint	0.7	0.8	1.1	1.0	0.7
Progressive ratio test 2 inactive lever presses	0.5	0.8	1.5	1.2	-0.2
Incentive Sensitization - Responses	1.5	2.2	4.2	2.1	0.3
Incentive Sensitization - Breakpoint	1.6	2.0	4.0	2.0	0.2
Sum of active levers in priming session hrs 5-6	4.4	4.1	4.4	-2.1	1.9
Progressive ratio	1.7	2.6	5.2	-2.3	0.1
Food seeking constrained by brief footshock	1.7	2.1	3.9	-2.0	-0.5
Seeking ratio, punishment vs. effort	0.2	0.2	0.3	0.6	0.4
Retroperitoneal fat weight	0.4	1.5	1.7	1.2	-1.3
Reaction time number correct	0.2	0.3	0.4	-0.6	0.5
Reaction time mean minus median	0.5	1.3	1.9	-0.8	1.4
Reaction time mean minus median AUC	0.5	1.3	2.3	-0.6	1.5
Reaction time num false alarms	0.4	0.5	0.7	-0.8	0.6
Reaction time num false alarms AUC	0.6	0.9	1.4	-1.2	0.7
Reaction time trials correct on left	0.2	0.3	0.4	-0.6	0.5
Reaction time trials on left	0.2	0.4	0.5	-0.7	0.5
Reaction time mean	0.4	0.7	1.2	1.1	0.4
Reaction time mean AUC	0.5	0.8	1.3	1.2	0.5
Median of all reaction times	0.9	1.3	2.5	1.6	-0.2
Reaction time omissions	0.7	1.0	1.1	-1.0	1.0
Reaction time false alarm rate	0.2	0.3	0.6	-0.8	0.2
Reaction time premature initiation rate	0.5	0.7	0.8	-0.9	0.7
Reaction time premature initiations	1.0	1.8	2.2	-1.5	1.2
Std. dev. reaction times	0.3	0.6	1.2	0.1	1.1
Reaction time trials completed	0.2	0.4	0.5	-0.7	0.5
Reaction time trials AUC	0.2	0.5	0.6	-0.8	0.6
Run reversals in cocaine runway, females	0.4	0.4	0.4	-0.7	0.6
Run reversals in cocaine runway, males	0.7	0.7	0.9	0.6	-1.0
Latency to leave start box in cocaine runway	4.1	4.6	5.3	2.0	-2.3
Latency to leave start box in cocaine runway, F	3.3	3.7	6.2	1.1	-2.5
Latency to leave start box in cocaine runway, M	3.7	3.4	5.9	2.4	-1.0
Std. dev. time between licks in bursts	0.5	0.6	1.2	0.1	-1.1
Total sessions with >9 infusions	0.5	0.6	1.1	-1.1	-0.3
Short access day 1 total inactive lever presses	3.2	4.2	4.3	-2.0	2.1
Short access day 10 total inactive lever presses	0.7	1.8	3.0	1.7	-0.8
Short access day 1 total infusions	0.7	1.0	1.9	-1.4	0.1
Short access day 10 total infusions	0.4	0.5	0.7	0.5	-0.9
Short access total infusions	0.3	0.4	0.6	-0.8	-0.5
Short access day 1 locomotion	1.2	1.4	2.4	0.7	-1.5
Short access day 10 total locomotion	0.7	1.2	2.1	0.7	-1.4
Short access total locomotion	1.0	1.2	2.2	0.4	-1.5
One hour access (0.3 mA shock)	0.3	0.3	0.6	0.2	0.8
Compulsive drug intake	2.5	3.0	4.3	-1.3	2.1
One hour access (shock baseline)	1.7	2.6	3.0	1.7	-1.5
Social response proportion	0.3	0.4	0.7	-0.3	0.8
Social responses	0.1	0.1	0.2	-0.4	0.1
Social time	0.3	0.4	0.7	0.9	-0.1
Soleus weight	0.9	2.6	3.4	1.3	-1.8
Bone: stiffness	1.0	1.6	3.1	1.8	0.1
Tibialis anterior weight	0.8	2.6	3.2	-1.8	1.4
Time to tail flick, vehicle, before self-admin	1.6	1.6	2.9	-0.6	1.7
Time to tail flick, vehicle, after self-admin	0.9	1.2	2.2	1.5	-0.4
Time to tail flick, test, before self-admin	0.3	0.4	0.5	0.7	-0.5
Time to tail flick, test, after self-admin	0.4	0.5	0.9	0.9	-0.2
Delta time to tail flick, vehicle, before/after SA	2.4	2.3	3.0	1.3	-1.7
Delta time to tail flick, test, before/after SA	0.5	0.5	0.6	-0.5	0.8
Tibia length	0.1	0.2	0.2	0.4	-0.5
Ambulatory time before self-admin	0.9	1.3	2.5	1.6	0.3
Ambulatory time after self-admin	1.0	1.2	2.3	1.5	-0.2
Bone: tissue strength	0.0	0.0	0.0	-0.1	-0.1
Total heroin consumption	0.8	0.9	1.2	-0.8	1.1
Bone: trabecular number	1.1	1.9	2.1	1.3	-1.5
Bone: trabecular spacing	0.1	0.1	0.2	-0.1	0.4
Bone: trabecular thickness	1.2	1.5	2.0	1.1	-1.4
Bone: trabecular tissue density	0.3	0.4	0.4	-0.6	0.6
Water consumed over 24 hours	0.4	0.5	0.9	-0.9	0.4
Number of responses in last shaping day	1.3	1.4	2.4	1.6	-0.6