Hub : Genes

Klf1

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	Klf1	0.04	0.02	1.4e-03	0.03	0.02	0.03	0.03	1.6e-04	4.0e-03	3.6e-04	2.6e-04
2	Brain	gene expression	Klf1	0.05	0.03	7.9e-04	0.01	0.02	0.02	0.02	1.2e-02	1.1e-02	7.0e-03	5.9e-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 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	3.6	6.6	8.3	2.2	-2.9
Area under the delay curve	0.2	0.3	0.6	-0.3	-0.8
BMI with tail	1.2	4.1	4.7	-2.2	1.9
BMI without tail	0.0	0.1	0.2	-0.1	-0.5
Body weight	0.1	0.4	0.7	0.2	0.8
Weight adjusted by age	0.2	0.5	0.7	-0.9	0.5
Bone surface	3.0	6.0	6.5	2.3	-2.6
Bone volume	3.0	5.9	6.6	2.3	-2.6
Breakpoint value in progressive ratio session	0.6	1.0	1.9	0.2	1.4
Number of licking bursts	0.2	0.6	0.6	0.8	-0.8
Context. condit. distance diff. score	1.1	1.3	1.5	-1.0	1.2
Locomotion velocity, session 1	1.0	1.1	1.4	1.2	-1.0
Locomotion distance, session 1	0.2	0.2	0.4	0.6	-0.1
Locomotion velocity, session 2	0.8	0.9	1.0	0.9	-1.0
Locomotion distance, session 2	0.2	0.2	0.4	0.2	0.7
Locomotion velocity, session 3	0.0	0.0	0.1	-0.2	-0.2
Locomotion distance, session 3	2.1	2.4	3.4	1.2	-1.8
Stereotopy head waving bouts, day 3	0.4	0.5	0.9	-1.0	-0.2
Stereotopy head waving duration, day 3	0.3	0.4	0.8	-0.9	0.1
Locomotion velocity, session 7	0.0	0.0	0.0	0.1	-0.1
Locomotion distance, session 7	0.3	0.3	0.6	0.8	-0.2
Stereotopy head waving bouts, day 7	0.8	1.0	1.9	0.2	-1.4
Stereotopy head waving duration, day 7	1.3	1.6	2.9	0.6	-1.7
Locomotion velocity, session 8	0.3	0.3	0.5	0.4	0.7
Locomotion distance, session 8	0.3	0.4	0.8	-0.1	0.9
Degree of sensitization distance	1.0	1.1	2.1	-0.1	1.4
Degree of sensitization stereotypy	0.6	0.7	1.2	0.3	-1.1
Conditioned locomotion	0.1	0.1	0.2	0.4	0.0
Cocaine response after cond. corrected	0.7	1.0	2.1	-0.1	1.4
Cocaine response after cond. not corrected	0.6	0.9	1.8	-0.2	1.3
Cocaine response before conditioning	0.5	0.6	1.0	0.4	-1.0
Saline control response	2.0	2.8	5.3	2.3	-0.6
Bone: connectivity density	7.0	11.1	14.0	2.9	-3.7
Bone: cortical apparent density	0.3	0.5	0.8	-0.2	-0.9
Bone: cortical area	0.2	0.3	0.5	0.7	0.2
Bone: cortical porosity	1.6	1.8	2.9	-0.8	1.7
Bone: cortical porosity	1.0	1.1	2.0	-0.4	1.4
Bone: cortical thickness	0.8	1.4	1.8	-1.0	1.3
Bone: cortical thickness	0.3	0.3	0.3	-0.5	0.6
Bone: cortical tissue density	0.3	0.5	1.0	-0.1	-1.0
Condit. Reinf. active minus inactive responses	0.2	0.2	0.4	-0.6	-0.3
Condit. Reinf. active-inactive response ratio	0.4	0.4	0.4	-0.6	0.7
Condit. Reinf. active responses	0.4	0.5	0.8	-0.4	-0.9
Condit. Reinf. inactive responses	2.3	2.9	4.2	1.3	-2.1
Incentive salience index mean	0.7	0.9	1.8	0.0	-1.3
Condit. Reinf. lever presses	1.4	2.0	3.8	0.5	-2.0
Condit. Reinf. active minus inactive responses	0.1	0.2	0.3	0.6	-0.1
Condit. Reinf. active-inactive response ratio	0.2	0.3	0.5	-0.5	0.7
Condit. Reinf. active responses	0.1	0.2	0.4	0.7	0.0
Condit. Reinf. inactive responses	0.1	0.2	0.3	0.2	0.5
Condit. Reinf. lever presses	0.0	0.0	0.0	-0.1	0.1
Condit. Reinf. lever reinforcers received	0.1	0.1	0.2	0.5	0.0
Conditioned reinforcement - actives	0.0	0.0	0.0	-0.1	0.1
Conditioned reinforcement - inactives	0.0	0.1	0.1	-0.3	0.2
Conditioned locomotion	0.0	0.0	0.0	-0.1	-0.1
Patch foraging indifference point 0 sec	0.0	0.0	0.1	0.3	-0.0
Patch foraging indifference point AUC	0.5	1.2	1.7	1.3	-0.8
Delay disc. indifference point, 0s delay	1.0	1.1	1.5	0.9	-1.2
Delay disc. indifference point, 16s delay	0.6	0.9	0.9	-1.0	0.9
Delay disc. indifference point, 2s delay	0.6	0.7	1.4	-1.2	-0.0
Delay disc. indifference point, 24s delay	0.0	0.0	0.1	-0.1	0.3
Delay disc. indifference point, 4s delay	1.5	1.6	3.2	0.2	-1.8
Delay disc. indifference point, 8s delay	0.3	0.4	0.8	-0.2	-0.9
Indifference point function ln k	0.3	0.9	1.7	-1.3	0.4
Indifference point function log k	0.3	0.9	1.7	-1.3	0.4
Patch foraging total patch changes 0 sec	0.0	0.1	0.1	-0.1	0.4
Patch foraging total patch changes 12 sec	1.3	1.7	2.3	1.5	-1.1
Patch foraging total patch changes 18 sec	1.5	3.5	4.8	2.2	-1.5
Patch foraging total patch changes 24 sec	0.7	2.6	3.2	1.8	-1.4
Patch foraging total patch changes 6 sec	0.3	0.6	0.7	0.8	-0.7
Patch foraging time to switch 0 sec	0.0	0.0	0.0	0.2	-0.0
Patch foraging water rate 0 sec	0.0	0.2	0.3	-0.0	0.6
Patch foraging water rate 12 sec	0.2	0.6	0.7	-0.8	-0.8
Patch foraging water rate 18 sec	0.7	1.7	3.3	0.2	-1.8
Patch foraging water rate 24 sec	0.3	0.4	0.9	-0.1	-0.9
Patch foraging water rate 6 sec	2.8	4.1	5.1	2.3	-1.7
Seeking ratio, delayed vs. immediate footshock	0.9	1.2	2.4	-1.5	0.3
Distance traveled before self-admin	0.6	1.3	1.8	-1.3	0.9
Distance traveled after self-admin	0.7	1.2	1.8	-1.4	0.8
Extensor digitorum longus weight	0.4	1.8	3.1	-0.7	1.8
Bone: elastic displacement	0.2	0.3	0.4	-0.6	0.5
Bone: elastic work	1.8	2.3	2.6	-1.4	1.6
Bone: endosteal estimation	0.2	0.6	1.1	1.1	0.1
Bone: endosteal perimeter	0.7	1.7	3.3	1.8	-0.4
Epididymis fat weight	0.0	0.1	0.2	0.4	0.2
Delta time in closed arm before/after self-admin	0.2	0.2	0.4	-0.6	-0.0
Delta time in open arm before/after self-admin	1.6	1.9	3.8	1.9	0.1
Diff in mean of infusions in LGA sessions	0.1	0.2	0.3	0.6	-0.2
Delay discount exponential model param	0.3	0.4	0.8	0.3	0.9
Extinction: sum of active levers before priming	0.6	1.0	1.9	-1.4	-0.1
Active lever presses in extinction session 6	0.4	0.4	0.5	-0.7	-0.6
Bone: final force	0.2	0.3	0.4	0.3	0.6
Bone: final moment	0.1	0.2	0.4	0.1	0.7
Food consumed during 24 hour testing period	2.8	5.7	7.8	2.8	-1.9
Glucose	0.6	0.9	1.4	0.6	1.2
Heart weight	0.3	0.6	0.6	-0.8	-0.7
Delay discount hyperbolic model param	0.5	0.7	1.3	0.2	1.1
Intermittent access intake day 1-15 change	0.6	3.0	3.4	1.8	-1.6
Intermittent access intake escalation	0.3	1.9	2.0	1.4	-1.3
Intermittent access intake escalation 2	1.4	2.3	2.7	1.6	-1.4
Intermitt. access day 1 inactive lever presses	0.0	0.5	0.8	0.4	-0.9
Intermitt. access day 15 inactive lever presses	0.2	1.3	1.3	-1.1	1.1
Intermitt. access escalation Index	0.1	0.2	0.2	-0.4	-0.5
Intermittent access day 1 total infusions	1.1	3.3	3.9	-2.0	1.7
Intermittent access day 15 total infusions	0.3	0.7	1.0	-1.0	0.6
Intermittent access terminal intake (last 3 days)	0.4	0.8	1.0	-1.0	0.8
Intermittent access total infusions	1.3	1.6	1.7	-1.3	1.2
Intermittent access day 1 locomotion	0.9	1.6	2.6	-1.6	0.9
Intermittent access day 15 total locomotion	0.5	1.8	2.1	-1.2	1.5
Intermittent access total locomotion	2.3	2.8	3.2	-1.6	1.8
Intermittent access standard deviation	0.1	0.7	0.8	0.8	-0.9
Left kidney weight	0.5	4.4	6.3	2.5	-1.6
Right kidney weight	0.4	3.0	5.6	2.4	-0.6
Cocaine induced anxiety	0.1	0.2	0.3	-0.6	-0.4
Post-drug Anxiety	0.2	0.3	0.5	-0.7	0.2
Baseline Anxiety	0.1	0.2	0.5	0.1	0.7
Tail length	1.7	9.2	10.3	3.2	-2.9
Length with tail	0.6	2.6	4.5	2.1	-0.8
Length without tail	0.3	1.3	2.7	-0.1	1.6
Times rat made contact with spout	0.2	0.2	0.4	-0.3	-0.6
Lifetime Intake	0.9	1.1	1.1	-1.1	1.0
Liver weight, left	0.4	0.7	1.3	1.2	-0.0
Liver weight, right	0.9	1.6	2.9	1.7	-0.5
Locomotor activity	0.4	0.7	1.1	-0.5	1.0
Locomotor testing distance	0.3	0.8	1.2	-0.6	1.1
Locomotor testing rearing	0.3	1.2	2.0	1.4	-0.7
Locomotion in novel chamber	0.3	0.3	0.5	-0.4	0.7
Locomotion in novel chamber post-restriction	0.2	0.5	0.6	0.8	-0.7
Fecal boli incidents, locomotor time 1	0.4	1.1	2.1	1.4	-0.4
Change in fecal boli incidents, locomotor task	2.0	2.1	4.0	0.5	-2.0
Time >=10cm from walls, locomotor time 1	0.1	0.1	0.2	0.1	-0.5
Bouts of movement, locomotor time 1	0.3	0.3	0.6	-0.8	-0.3
Total resting periods, locomotor time 1	0.6	0.7	1.2	-1.1	-0.3
Rest time, locomotor task time 1	0.3	0.5	0.9	-1.0	0.3
Distance moved, locomotor task time 1	0.1	0.3	0.5	0.2	0.7
Vertical activity count, locomotor time 1	0.4	2.4	4.8	2.2	-0.2
Time >=10cm from walls, locomotor time 2	0.5	1.3	1.6	-1.1	1.3
Bouts of movement, locomotor time 2	0.1	0.5	0.8	-0.9	-0.5
Total resting periods, locomotor time 2	0.1	0.3	0.4	-0.6	-0.5
Rest time, locomotor task time 2	0.1	0.2	0.3	0.3	-0.5
Distance moved, locomotor task time 2	2.1	2.8	3.9	-1.3	2.0
Vertical activity count, locomotor time 2	0.4	0.9	1.5	1.2	0.4
Light reinforcement 1	3.9	17.6	28.7	5.4	-2.6
Light reinforcement 2	3.7	8.4	14.9	3.9	-1.4
Bone: marrow area	0.2	0.5	1.1	1.0	0.1
Bone: maximum diameter	0.1	0.2	0.4	0.7	0.2
Bone: maximum force	0.2	0.4	0.8	0.2	0.9
Bone: maximum moment	0.2	0.4	0.8	0.0	0.9
Mean time between licks in bursts	0.1	0.7	0.8	0.7	-0.9
Mean num. licks in bursts	0.2	0.5	1.0	-1.0	0.0
Cd content in liver	1.1	1.3	1.5	-1.0	1.2
Co content in liver	1.3	1.5	2.2	-1.5	0.9
Cu content in liver	0.3	0.4	0.8	-0.2	0.9
Fe content in liver	0.2	0.2	0.4	0.1	-0.6
K content in liver	0.7	0.7	1.0	-0.7	1.0
Mg content in liver	0.2	0.2	0.4	-0.1	0.6
Mn content in liver	0.5	0.6	1.2	1.1	-0.2
Na content in liver	0.0	0.0	0.0	-0.1	-0.0
Rb content in liver	0.6	0.7	1.0	1.0	-0.6
Se content in liver	0.3	0.4	0.8	0.9	-0.0
Sr content in liver	0.7	0.6	0.8	-0.7	0.9
Zn content in liver	1.0	1.2	1.6	-0.9	1.2
Bone: minimum diameter	0.8	1.5	2.6	1.6	-0.7
Time in familiar zone, hab. session 1	1.6	1.7	1.9	1.2	-1.4
Time in novel zone, hab. session 1	1.5	1.7	2.6	-1.6	0.9
Total zone transitions, hab. session 1	0.0	0.1	0.1	0.3	-0.1
Total locomotion distance, hab. session 1	0.0	0.0	0.0	-0.1	0.0
Locomotion velocity, hab. session 1	0.0	0.0	0.0	0.2	0.1
Time in familiar zone, hab. session 2	1.8	2.0	2.9	1.7	-1.1
Time in novel zone, hab. session 2	3.1	3.4	3.7	-1.9	1.7
Total zone transitions, hab. session 2	0.9	1.2	1.4	1.0	-1.2
Total locomotion distance, hab. session 2	0.2	0.2	0.4	0.6	-0.0
Locomotion velocity, hab. session 2	0.2	0.2	0.4	0.6	0.1
Novel to familiar place preference ratio	0.6	0.8	1.3	-1.2	0.4
Novelty place preference	0.6	0.8	1.3	-1.1	0.6
Time in novel zone, NPP test	0.9	1.1	1.9	-1.4	0.6
Total zone transitions, NPP test	0.6	1.0	1.7	1.3	-0.5
Total locomotion distance, NPP test	0.0	0.0	0.1	0.2	-0.2
Locomotion velocity, NPP test	0.1	0.1	0.2	0.4	0.2
Intraocular pressure	1.2	1.9	3.0	-1.7	0.9
Delta distance traveled before/after self-admin	0.1	0.1	0.1	0.2	-0.4
Delta ambulatory time before/after self-admin	0.5	0.9	1.2	0.8	-1.1
Parametrial fat weight	0.5	1.1	2.0	1.4	0.5
Pavlov. Cond. lever latency	0.2	0.2	0.4	0.7	-0.2
Pavlov. Cond. magazine entry latency	0.5	0.6	1.2	-1.1	0.1
Pavlov. Cond. change in total contacts	0.2	0.2	0.4	0.1	-0.6
Pavlov. Cond. index score	0.4	0.5	1.0	-1.0	0.2
Pavlov. Cond. latency score	0.3	0.4	0.7	-0.8	0.2
Pavlov. Cond. lever contacts	0.5	0.6	1.1	-1.0	0.3
Pavlov. Cond. magazine entry number	1.1	1.4	2.3	1.5	-0.6
Pavlov. Cond. intertrial magazine entries	0.5	0.5	1.1	1.0	-0.2
Pavlov. Cond. lever-magazine prob. diff.	0.9	1.1	1.9	-1.4	0.6
Pavlov. Cond. response bias	0.7	0.9	1.8	-1.3	0.1
Pavlov. Cond. lever latency	0.2	0.3	0.5	-0.4	0.7
Pavlov. Cond. magazine entry latency	0.0	0.0	0.0	-0.0	-0.1
Pavlov. Cond. change in total contacts	0.2	0.4	0.7	0.2	-0.9
Pavlov. Cond. index score	0.2	0.2	0.4	0.2	-0.7
Pavlov. Cond. latency score	0.2	0.3	0.5	0.2	-0.7
Pavlov. Cond. lever contacts	0.3	0.4	0.6	0.4	-0.8
Pavlov. Cond. magazine entry number	0.0	0.0	0.1	-0.2	0.0
Pavlov. Cond. intertrial magazine entries	1.2	2.6	3.3	1.8	-1.3
Pavlov. Cond. lever-magazine prob. diff.	0.1	0.2	0.3	0.1	-0.6
Pavlov. Cond. response bias	0.0	0.1	0.1	0.2	-0.2
Time in closed arm before self-admin	0.9	1.5	2.5	0.8	-1.6
Time in closed arm after self-admin	0.6	0.6	1.3	0.2	-1.1
Time in open arm before self-admin	0.5	0.6	1.1	-1.0	0.5
Time in open arm after self-admin	0.5	0.5	0.9	-0.2	1.0
Bone: periosteal estimation	0.3	0.8	1.6	1.3	-0.0
Bone: periosteal perimeter	0.6	1.3	2.5	1.6	-0.3
Bone: post-yield work	0.0	0.1	0.1	0.4	-0.2
Progressive ratio test 1 active lever presses	1.0	1.8	1.9	-1.3	1.4
Progressive ratio test 1 breakpoint	1.2	2.0	2.1	-1.4	1.5
Progressive ratio test 1 inactive lever presses	0.3	0.8	0.9	-0.8	0.9
Progressive ratio test 2 active lever presses	1.2	1.6	1.6	-1.3	1.3
Progressive ratio test 2 breakpoint	1.4	1.8	1.8	-1.3	1.3
Progressive ratio test 2 inactive lever presses	0.9	2.7	3.1	-1.8	1.5
Incentive Sensitization - Responses	0.1	0.2	0.2	-0.5	0.5
Incentive Sensitization - Breakpoint	0.1	0.1	0.2	-0.4	0.4
Sum of active levers in priming session hrs 5-6	0.0	0.0	0.1	0.2	0.3
Progressive ratio	0.2	0.6	1.1	1.1	-0.1
Food seeking constrained by brief footshock	2.1	2.7	4.0	2.0	-1.2
Seeking ratio, punishment vs. effort	0.1	0.3	0.4	0.6	-0.4
Retroperitoneal fat weight	0.3	1.2	1.5	1.2	0.9
Reaction time number correct	0.2	0.7	1.3	-1.2	-0.0
Reaction time mean minus median	0.3	1.6	2.3	-1.0	1.5
Reaction time mean minus median AUC	0.4	2.9	3.6	-1.5	1.9
Reaction time num false alarms	0.9	1.5	1.5	-1.2	1.2
Reaction time num false alarms AUC	0.5	1.0	1.7	-1.3	0.6
Reaction time trials correct on left	0.2	0.7	1.3	-1.2	-0.0
Reaction time trials on left	0.2	0.8	1.5	-1.2	0.1
Reaction time mean	2.8	6.2	6.7	-2.4	2.6
Reaction time mean AUC	2.4	5.7	6.1	-2.3	2.5
Median of all reaction times	3.8	6.0	6.1	-2.5	2.4
Reaction time omissions	2.3	3.8	5.2	-1.6	2.3
Reaction time false alarm rate	0.2	0.3	0.3	-0.5	0.5
Reaction time premature initiation rate	5.2	8.1	9.5	3.1	-2.6
Reaction time premature initiations	1.6	4.9	5.1	2.2	-2.3
Std. dev. reaction times	0.8	2.6	3.2	-1.4	1.8
Reaction time trials completed	0.2	0.8	1.5	-1.2	0.1
Reaction time trials AUC	0.3	0.9	1.8	-1.3	0.3
Run reversals in cocaine runway, females	3.1	3.5	6.2	-0.8	2.5
Run reversals in cocaine runway, males	0.8	0.9	1.5	-1.2	0.6
Latency to leave start box in cocaine runway	1.1	1.6	2.7	-0.6	1.7
Latency to leave start box in cocaine runway, F	1.6	2.0	3.1	-0.9	1.8
Latency to leave start box in cocaine runway, M	0.1	0.1	0.2	0.5	0.2
Std. dev. time between licks in bursts	0.8	1.6	1.6	1.2	-1.3
Total sessions with >9 infusions	1.1	1.4	2.4	-1.6	0.6
Short access day 1 total inactive lever presses	0.5	0.9	1.8	-0.2	1.3
Short access day 10 total inactive lever presses	0.4	2.4	2.7	1.5	-1.6
Short access day 1 total infusions	0.9	1.9	2.8	-1.7	0.9
Short access day 10 total infusions	0.5	0.8	1.2	-1.1	0.7
Short access total infusions	0.9	1.3	1.7	-1.3	1.0
Short access day 1 locomotion	1.7	2.8	3.9	-2.0	1.3
Short access day 10 total locomotion	0.2	0.8	1.6	-1.3	0.1
Short access total locomotion	1.2	1.9	3.1	-1.8	0.8
One hour access (0.3 mA shock)	0.8	1.0	1.1	-1.1	0.9
Compulsive drug intake	0.6	0.9	1.7	0.1	-1.3
One hour access (shock baseline)	0.6	1.5	2.1	-1.0	1.4
Social response proportion	0.7	0.8	1.6	-0.2	1.3
Social responses	0.1	0.1	0.1	0.3	-0.2
Social time	0.7	1.1	1.8	0.7	-1.3
Soleus weight	0.0	0.0	0.0	-0.2	0.2
Bone: stiffness	0.4	0.7	1.4	0.3	1.2
Tibialis anterior weight	0.1	0.3	0.3	-0.5	0.5
Time to tail flick, vehicle, before self-admin	0.3	0.4	0.5	0.7	-0.4
Time to tail flick, vehicle, after self-admin	0.2	0.4	0.7	0.9	-0.2
Time to tail flick, test, before self-admin	3.6	4.2	5.4	-1.7	2.3
Time to tail flick, test, after self-admin	0.0	0.0	0.0	0.2	0.1
Delta time to tail flick, vehicle, before/after SA	0.0	0.0	0.0	0.2	0.2
Delta time to tail flick, test, before/after SA	0.5	0.6	1.1	0.4	-1.0
Tibia length	0.0	0.0	0.1	-0.0	0.3
Ambulatory time before self-admin	0.7	2.0	2.4	-1.5	1.3
Ambulatory time after self-admin	0.2	0.3	0.5	-0.7	0.4
Bone: tissue strength	0.9	0.9	1.4	-0.6	1.2
Total heroin consumption	0.1	0.1	0.2	-0.1	0.4
Bone: trabecular number	4.9	9.2	13.5	2.2	-3.7
Bone: trabecular spacing	3.8	5.5	7.1	-2.0	2.7
Bone: trabecular thickness	0.5	0.6	0.9	0.6	-0.9
Bone: trabecular tissue density	2.6	4.5	6.0	-1.7	2.5
Water consumed over 24 hours	0.4	0.7	1.0	0.7	-1.0
Number of responses in last shaping day	0.3	0.4	0.6	-0.8	-0.4