Hub : Genes

Hoxb3

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 alternative TSS XM_039086074.2 0.02 0.02 2.4e-03 0.01 0.01 0.01 0 1.4e-02 2.7e-02 2.7e-02 1.3e-01
2 Adipose mRNA stability Hoxb3 0.07 0.08 7.6e-03 0.01 0 0 0.01 1.6e-02 1.3e-01 1.7e-01 2.8e-02
3 Adipose gene expression Hoxb3 0.06 0.04 7.4e-09 0.05 0.03 0.06 0.02 3.5e-06 1.1e-04 2.0e-07 1.5e-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 3
Bone: apparent density1.52.62.71.7-1.6-1.5
Area under the delay curve0.20.20.7-0.10.20.8
BMI with tail19.567.469.18.2-8.3-8.1
BMI without tail1.54.75.22.3-2.3-1.9
Body weight1.04.44.82.1-2.0-2.2
Weight adjusted by age0.10.20.6-0.30.20.7
Bone surface0.50.91.11.0-1.0-0.8
Bone volume1.32.32.41.5-1.6-1.5
Breakpoint value in progressive ratio session2.73.23.3-1.81.71.8
Number of licking bursts0.60.91.2-1.11.10.6
Context. condit. distance diff. score0.91.11.41.1-1.2-0.8
Locomotion velocity, session 10.00.00.1-0.10.1-0.3
Locomotion distance, session 14.75.96.6-2.62.52.2
Locomotion velocity, session 21.21.41.6-1.11.11.3
Locomotion distance, session 26.18.59.6-3.13.02.6
Locomotion velocity, session 30.10.20.30.5-0.5-0.1
Locomotion distance, session 31.81.93.0-1.11.21.7
Stereotopy head waving bouts, day 33.94.56.31.9-1.9-2.5
Stereotopy head waving duration, day 33.33.95.21.8-1.8-2.3
Locomotion velocity, session 71.51.71.9-1.21.41.3
Locomotion distance, session 76.78.58.9-3.03.02.8
Stereotopy head waving bouts, day 70.20.20.40.3-0.4-0.6
Stereotopy head waving duration, day 70.20.20.30.4-0.5-0.6
Locomotion velocity, session 80.40.50.70.8-0.8-0.3
Locomotion distance, session 80.60.91.2-0.90.81.1
Degree of sensitization distance0.20.20.3-0.60.50.1
Degree of sensitization stereotypy0.20.20.3-0.60.40.3
Conditioned locomotion2.12.53.21.8-1.6-1.3
Cocaine response after cond. corrected5.97.17.32.6-2.7-2.7
Cocaine response after cond. not corrected3.33.94.31.9-2.1-1.9
Cocaine response before conditioning3.03.63.7-1.91.81.9
Saline control response0.10.10.2-0.10.10.5
Bone: connectivity density0.30.50.70.8-0.8-0.3
Bone: cortical apparent density5.77.89.7-2.62.63.1
Bone: cortical area0.40.60.90.9-0.9-0.5
Bone: cortical porosity0.30.30.50.5-0.5-0.7
Bone: cortical porosity0.40.50.70.6-0.6-0.8
Bone: cortical thickness0.10.10.20.5-0.30.4
Bone: cortical thickness0.60.71.4-0.60.61.2
Bone: cortical tissue density6.58.810.5-2.82.83.2
Condit. Reinf. active minus inactive responses1.01.21.6-1.31.20.6
Condit. Reinf. active-inactive response ratio0.10.10.20.1-0.1-0.5
Condit. Reinf. active responses1.31.62.1-1.51.40.7
Condit. Reinf. inactive responses1.01.31.5-1.21.21.0
Incentive salience index mean1.72.12.7-1.71.61.0
Condit. Reinf. lever presses2.12.93.5-1.91.91.3
Condit. Reinf. active minus inactive responses0.00.00.1-0.30.2-0.1
Condit. Reinf. active-inactive response ratio0.10.10.2-0.30.2-0.4
Condit. Reinf. active responses0.00.00.0-0.20.10.1
Condit. Reinf. inactive responses0.10.10.30.0-0.10.5
Condit. Reinf. lever presses0.30.40.8-0.40.40.9
Condit. Reinf. lever reinforcers received0.10.10.1-0.30.20.4
Conditioned reinforcement - actives0.50.91.4-1.21.1-0.2
Conditioned reinforcement - inactives0.00.00.1-0.30.00.0
Conditioned locomotion0.70.92.50.4-0.3-1.6
Patch foraging indifference point 0 sec1.12.12.71.5-1.6-1.1
Patch foraging indifference point AUC0.00.10.1-0.10.40.3
Delay disc. indifference point, 0s delay0.30.31.00.00.11.0
Delay disc. indifference point, 16s delay0.70.71.11.0-1.0-0.4
Delay disc. indifference point, 2s delay0.10.10.2-0.00.10.5
Delay disc. indifference point, 24s delay0.50.50.6-0.70.70.8
Delay disc. indifference point, 4s delay2.12.24.0-1.11.12.0
Delay disc. indifference point, 8s delay0.10.10.3-0.20.30.5
Indifference point function ln k0.00.00.1-0.20.10.2
Indifference point function log k0.00.00.1-0.20.10.2
Patch foraging total patch changes 0 sec1.22.22.81.6-1.7-1.2
Patch foraging total patch changes 12 sec0.00.00.00.2-0.0-0.1
Patch foraging total patch changes 18 sec1.52.32.51.6-1.6-1.4
Patch foraging total patch changes 24 sec0.71.11.21.1-1.0-1.1
Patch foraging total patch changes 6 sec0.60.91.01.0-1.0-0.9
Patch foraging time to switch 0 sec0.00.00.1-0.20.10.0
Patch foraging water rate 0 sec1.02.12.31.5-1.5-1.3
Patch foraging water rate 12 sec0.10.20.30.5-0.6-0.1
Patch foraging water rate 18 sec0.00.00.1-0.10.00.4
Patch foraging water rate 24 sec1.11.51.71.1-1.3-1.2
Patch foraging water rate 6 sec0.00.00.1-0.1-0.00.2
Seeking ratio, delayed vs. immediate footshock2.32.83.71.9-1.8-1.1
Distance traveled before self-admin0.91.11.8-1.31.10.6
Distance traveled after self-admin0.10.10.20.0-0.1-0.5
Extensor digitorum longus weight0.72.73.71.9-1.7-1.1
Bone: elastic displacement0.10.10.20.2-0.2-0.4
Bone: elastic work0.00.00.00.1-0.0-0.0
Bone: endosteal estimation0.10.30.50.3-0.5-0.7
Bone: endosteal perimeter0.51.01.20.9-0.9-1.1
Epididymis fat weight0.10.51.20.4-0.4-1.1
Delta time in closed arm before/after self-admin0.30.20.30.5-0.5-0.5
Delta time in open arm before/after self-admin1.11.11.7-0.80.91.3
Diff in mean of infusions in LGA sessions1.31.62.3-1.51.30.9
Delay discount exponential model param0.30.30.90.3-0.3-0.9
Extinction: sum of active levers before priming0.70.71.1-1.00.70.8
Active lever presses in extinction session 60.10.10.10.3-0.3-0.4
Bone: final force0.20.30.40.5-0.4-0.7
Bone: final moment0.30.40.50.7-0.6-0.7
Food consumed during 24 hour testing period2.02.73.0-1.71.71.5
Glucose2.03.13.51.9-1.7-1.8
Heart weight1.21.93.40.9-1.1-1.8
Delay discount hyperbolic model param0.30.30.80.2-0.3-0.9
Intermittent access intake day 1-15 change0.00.10.1-0.20.2-0.3
Intermittent access intake escalation0.00.00.1-0.20.1-0.3
Intermittent access intake escalation 20.40.50.90.6-0.4-1.0
Intermitt. access day 1 inactive lever presses0.00.00.0-0.10.20.2
Intermitt. access day 15 inactive lever presses1.02.02.31.4-1.5-1.3
Intermitt. access escalation Index0.30.40.8-0.70.90.1
Intermittent access day 1 total infusions0.00.00.1-0.20.30.1
Intermittent access day 15 total infusions0.10.10.1-0.40.40.1
Intermittent access terminal intake (last 3 days)0.00.00.1-0.10.1-0.3
Intermittent access total infusions0.00.00.0-0.0-0.0-0.1
Intermittent access day 1 locomotion0.20.30.5-0.60.70.3
Intermittent access day 15 total locomotion0.10.20.4-0.70.5-0.1
Intermittent access total locomotion0.10.10.1-0.40.2-0.3
Intermittent access standard deviation0.61.21.51.0-1.1-1.2
Left kidney weight0.00.00.00.0-0.2-0.0
Right kidney weight0.31.31.61.1-1.1-1.3
Cocaine induced anxiety0.10.10.20.2-0.2-0.5
Post-drug Anxiety0.50.50.7-0.90.80.4
Baseline Anxiety1.11.31.5-1.21.11.0
Tail length19.174.676.7-8.68.88.5
Length with tail7.532.833.9-5.75.85.7
Length without tail0.10.30.40.6-0.6-0.5
Times rat made contact with spout0.70.81.2-1.11.00.4
Lifetime Intake0.00.00.00.1-0.1-0.1
Liver weight, left0.00.00.00.2-0.0-0.1
Liver weight, right0.10.10.2-0.40.20.4
Locomotor activity0.10.10.20.2-0.2-0.5
Locomotor testing distance0.51.01.20.9-1.0-1.1
Locomotor testing rearing0.10.10.20.4-0.40.1
Locomotion in novel chamber0.20.20.3-0.50.20.6
Locomotion in novel chamber post-restriction1.72.83.11.6-1.8-1.7
Fecal boli incidents, locomotor time 13.04.44.92.0-2.0-2.2
Change in fecal boli incidents, locomotor task2.72.72.8-1.71.71.6
Time >=10cm from walls, locomotor time 10.10.10.3-0.10.10.5
Bouts of movement, locomotor time 10.10.10.20.4-0.3-0.3
Total resting periods, locomotor time 10.40.50.50.7-0.7-0.6
Rest time, locomotor task time 10.30.40.70.5-0.5-0.8
Distance moved, locomotor task time 11.32.02.1-1.51.41.3
Vertical activity count, locomotor time 10.20.60.7-0.80.80.6
Time >=10cm from walls, locomotor time 20.30.40.6-0.60.50.7
Bouts of movement, locomotor time 20.10.10.10.3-0.4-0.1
Total resting periods, locomotor time 20.10.10.20.4-0.4-0.1
Rest time, locomotor task time 20.70.80.9-1.01.00.8
Distance moved, locomotor task time 20.20.20.2-0.40.40.5
Vertical activity count, locomotor time 20.00.00.0-0.20.20.0
Light reinforcement 10.00.10.10.1-0.3-0.3
Light reinforcement 20.10.10.2-0.40.50.1
Bone: marrow area0.10.20.30.3-0.4-0.6
Bone: maximum diameter0.50.91.10.9-0.9-1.1
Bone: maximum force0.61.01.11.0-1.0-1.0
Bone: maximum moment0.71.31.51.2-1.1-1.1
Mean time between licks in bursts0.61.52.11.3-1.4-0.9
Mean num. licks in bursts0.00.00.00.2-0.2-0.0
Cd content in liver0.00.00.0-0.00.0-0.1
Co content in liver0.00.00.0-0.20.10.0
Cu content in liver7.99.411.5-3.43.32.4
Fe content in liver0.50.60.7-0.80.70.8
K content in liver0.90.91.5-1.21.10.1
Mg content in liver5.75.87.3-2.72.61.9
Mn content in liver5.15.76.3-2.32.42.5
Na content in liver0.30.30.6-0.40.4-0.8
Rb content in liver1.11.32.0-1.41.10.8
Se content in liver0.30.30.40.6-0.4-0.6
Sr content in liver1.41.21.9-0.81.01.4
Zn content in liver0.20.20.4-0.50.6-0.3
Bone: minimum diameter0.00.00.10.1-0.2-0.3
Time in familiar zone, hab. session 10.20.20.4-0.20.20.6
Time in novel zone, hab. session 11.81.82.51.2-1.1-1.6
Total zone transitions, hab. session 17.310.210.7-3.33.13.2
Total locomotion distance, hab. session 14.05.76.3-2.52.42.2
Locomotion velocity, hab. session 14.97.07.8-2.82.72.4
Time in familiar zone, hab. session 21.01.11.31.2-1.1-0.8
Time in novel zone, hab. session 20.10.10.1-0.40.30.3
Total zone transitions, hab. session 24.05.16.2-2.52.32.0
Total locomotion distance, hab. session 20.81.11.6-1.31.20.6
Locomotion velocity, hab. session 21.01.42.0-1.41.30.7
Novel to familiar place preference ratio0.20.20.5-0.40.30.7
Novelty place preference0.20.30.6-0.30.20.8
Time in novel zone, NPP test0.10.20.4-0.20.10.7
Total zone transitions, NPP test5.57.98.0-2.82.82.8
Total locomotion distance, NPP test1.72.32.4-1.61.61.5
Locomotion velocity, NPP test2.33.23.3-1.81.81.8
Intraocular pressure0.91.31.7-1.11.01.3
Delta distance traveled before/after self-admin1.11.11.51.2-1.1-0.8
Delta ambulatory time before/after self-admin1.11.31.51.2-1.1-1.1
Parametrial fat weight0.10.10.20.3-0.3-0.4
Pavlov. Cond. lever latency1.31.61.71.2-1.3-1.3
Pavlov. Cond. magazine entry latency0.10.10.2-0.40.40.1
Pavlov. Cond. change in total contacts3.63.84.1-2.02.01.8
Pavlov. Cond. index score0.81.01.2-1.11.00.9
Pavlov. Cond. latency score0.81.11.3-1.11.10.9
Pavlov. Cond. lever contacts2.53.03.1-1.71.81.7
Pavlov. Cond. magazine entry number0.50.60.80.9-0.9-0.6
Pavlov. Cond. intertrial magazine entries1.11.31.5-1.21.21.0
Pavlov. Cond. lever-magazine prob. diff.0.81.01.1-1.11.00.9
Pavlov. Cond. response bias0.91.11.2-1.11.11.0
Pavlov. Cond. lever latency1.41.92.4-1.61.51.0
Pavlov. Cond. magazine entry latency0.20.30.4-0.50.60.5
Pavlov. Cond. change in total contacts0.40.60.80.9-0.9-0.5
Pavlov. Cond. index score0.40.50.60.8-0.7-0.6
Pavlov. Cond. latency score0.10.20.20.5-0.4-0.3
Pavlov. Cond. lever contacts1.21.72.21.5-1.4-1.0
Pavlov. Cond. magazine entry number0.00.00.0-0.20.10.2
Pavlov. Cond. intertrial magazine entries1.62.52.8-1.71.41.6
Pavlov. Cond. lever-magazine prob. diff.0.40.50.70.8-0.7-0.7
Pavlov. Cond. response bias1.21.61.81.4-1.3-1.1
Time in closed arm before self-admin2.53.23.92.0-1.9-1.4
Time in closed arm after self-admin3.03.33.82.0-1.9-1.6
Time in open arm before self-admin0.20.20.4-0.70.50.3
Time in open arm after self-admin2.12.32.7-1.51.41.6
Bone: periosteal estimation0.40.80.90.9-0.9-0.9
Bone: periosteal perimeter1.42.42.81.6-1.7-1.3
Bone: post-yield work0.50.81.01.0-1.0-0.6
Progressive ratio test 1 active lever presses1.01.21.5-1.21.20.8
Progressive ratio test 1 breakpoint0.70.91.1-1.11.10.7
Progressive ratio test 1 inactive lever presses0.30.40.40.7-0.6-0.6
Progressive ratio test 2 active lever presses0.40.50.8-0.90.80.3
Progressive ratio test 2 breakpoint0.40.50.7-0.80.80.3
Progressive ratio test 2 inactive lever presses0.00.00.10.1-0.2-0.2
Incentive Sensitization - Responses0.00.00.0-0.1-0.0-0.1
Incentive Sensitization - Breakpoint0.00.00.00.0-0.2-0.2
Sum of active levers in priming session hrs 5-64.44.14.4-2.12.11.9
Progressive ratio0.10.20.30.6-0.50.2
Food seeking constrained by brief footshock0.00.00.1-0.10.2-0.3
Seeking ratio, punishment vs. effort0.60.91.3-1.11.10.3
Retroperitoneal fat weight0.41.82.01.4-1.3-1.3
Reaction time number correct0.61.11.71.3-1.30.0
Reaction time mean minus median0.71.72.2-1.51.31.1
Reaction time mean minus median AUC0.92.43.1-1.81.61.2
Reaction time num false alarms1.01.51.9-1.41.30.8
Reaction time num false alarms AUC1.11.82.3-1.51.40.9
Reaction time trials correct on left0.61.11.71.3-1.30.0
Reaction time trials on left0.51.01.61.2-1.20.1
Reaction time mean0.50.81.2-1.11.00.3
Reaction time mean AUC0.60.91.5-1.21.10.4
Median of all reaction times0.30.40.6-0.80.7-0.1
Reaction time omissions1.11.61.9-1.41.41.1
Reaction time false alarm rate1.52.13.1-1.81.70.7
Reaction time premature initiation rate0.20.30.5-0.40.50.7
Reaction time premature initiations0.10.20.70.2-0.10.8
Std. dev. reaction times0.91.62.3-1.51.30.9
Reaction time trials completed0.51.01.61.2-1.20.1
Reaction time trials AUC0.51.01.61.2-1.30.1
Run reversals in cocaine runway, females0.10.10.2-0.30.30.4
Run reversals in cocaine runway, males1.71.71.81.3-1.3-1.3
Latency to leave start box in cocaine runway5.76.57.52.7-2.6-2.2
Latency to leave start box in cocaine runway, F7.99.010.83.3-3.1-2.6
Latency to leave start box in cocaine runway, M0.30.30.40.4-0.4-0.6
Std. dev. time between licks in bursts1.01.31.51.1-1.2-1.1
Total sessions with >9 infusions0.00.00.10.10.0-0.3
Short access day 1 total inactive lever presses0.91.23.0-0.60.51.7
Short access day 10 total inactive lever presses0.61.31.71.3-1.3-0.9
Short access day 1 total infusions0.00.10.10.3-0.2-0.1
Short access day 10 total infusions0.10.10.40.1-0.1-0.6
Short access total infusions0.20.20.20.5-0.4-0.5
Short access day 1 locomotion0.60.71.40.6-0.5-1.2
Short access day 10 total locomotion0.20.41.30.0-0.0-1.1
Short access total locomotion0.40.51.10.4-0.3-1.1
One hour access (0.3 mA shock)0.60.70.8-0.90.80.8
Compulsive drug intake3.44.14.4-2.12.02.0
One hour access (shock baseline)0.81.31.71.0-1.1-1.3
Social response proportion2.12.42.6-1.61.61.4
Social responses0.10.10.2-0.00.00.5
Social time0.10.10.20.3-0.4-0.2
Soleus weight1.44.24.42.1-2.0-2.1
Bone: stiffness0.00.10.10.2-0.2-0.4
Tibialis anterior weight0.10.40.6-0.50.50.8
Time to tail flick, vehicle, before self-admin3.43.64.1-1.81.82.0
Time to tail flick, vehicle, after self-admin1.11.42.11.3-1.5-0.7
Time to tail flick, test, before self-admin0.40.40.50.7-0.7-0.4
Time to tail flick, test, after self-admin0.70.71.10.8-1.0-0.5
Delta time to tail flick, vehicle, before/after SA5.85.56.32.5-2.5-2.0
Delta time to tail flick, test, before/after SA0.30.30.3-0.60.50.6
Tibia length0.61.72.21.5-1.4-0.9
Ambulatory time before self-admin0.30.50.9-0.90.70.3
Ambulatory time after self-admin0.20.20.50.1-0.2-0.7
Bone: tissue strength0.90.91.31.1-1.0-0.6
Total heroin consumption1.11.31.5-1.21.11.2
Bone: trabecular number0.30.50.80.6-0.5-0.9
Bone: trabecular spacing0.00.00.00.1-0.1-0.0
Bone: trabecular thickness4.05.06.12.5-2.4-1.7
Bone: trabecular tissue density0.00.00.1-0.10.00.3
Water consumed over 24 hours0.10.10.2-0.30.40.4
Number of responses in last shaping day0.91.01.11.0-1.1-0.9