Ssh3

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 LHb alternative polyA XM_039085534.1 0.18 0.13 2.9e-03 0.1 0.01 0.09 0 2.0e-03 1.5e-01 3.7e-03 2.4e-01
2 NAcc intron excision ratio chr1_201561649_201561831 0.02 0.02 5.9e-03 0.02 0.02 0.01 0.02 2.4e-03 3.6e-03 5.9e-03 2.9e-03
3 LHb alternative polyA XM_039085520.1 0.17 0.12 5.0e-03 0.02 0 0.07 -0.01 1.1e-01 2.7e-01 8.2e-03 5.7e-01

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 density1.62.63.41.51.5-1.8
Area under the delay curve1.41.51.91.01.4-1.2
BMI with tail0.30.81.80.20.8-1.3
BMI without tail0.10.20.70.10.2-0.8
Body weight0.83.45.2-2.3-2.01.1
Weight adjusted by age1.01.11.9-0.9-1.40.8
Bone surface0.30.51.00.60.4-1.0
Bone volume0.81.41.81.11.1-1.3
Breakpoint value in progressive ratio session0.60.71.0-0.8-1.00.7
Number of licking bursts0.00.00.00.2-0.0-0.1
Context. condit. distance diff. score0.70.80.90.90.9-0.9
Locomotion velocity, session 10.10.10.4-0.1-0.6-0.0
Locomotion distance, session 10.50.71.30.60.6-1.1
Locomotion velocity, session 20.91.11.6-1.3-1.00.9
Locomotion distance, session 20.00.00.1-0.2-0.0-0.3
Locomotion velocity, session 31.01.22.21.00.6-1.5
Locomotion distance, session 30.10.10.10.1-0.0-0.4
Stereotopy head waving bouts, day 31.92.23.01.71.0-1.7
Stereotopy head waving duration, day 31.82.22.71.61.3-1.5
Locomotion velocity, session 71.01.11.50.91.0-1.2
Locomotion distance, session 70.00.00.0-0.1-0.1-0.2
Stereotopy head waving bouts, day 71.82.02.31.51.2-1.5
Stereotopy head waving duration, day 70.50.61.10.70.6-1.0
Locomotion velocity, session 80.70.81.4-0.9-1.20.4
Locomotion distance, session 80.40.50.70.60.7-0.9
Degree of sensitization distance0.10.10.20.30.3-0.4
Degree of sensitization stereotypy0.20.20.40.40.3-0.6
Conditioned locomotion4.35.05.9-2.4-2.02.3
Cocaine response after cond. corrected0.20.20.30.40.3-0.6
Cocaine response after cond. not corrected0.60.71.00.70.7-1.0
Cocaine response before conditioning0.10.10.10.20.3-0.3
Saline control response0.81.11.6-1.3-1.00.7
Bone: connectivity density0.60.91.80.70.7-1.3
Bone: cortical apparent density0.50.71.0-1.0-0.80.6
Bone: cortical area1.01.51.6-1.2-1.21.3
Bone: cortical porosity0.10.20.40.20.6-0.2
Bone: cortical porosity0.10.10.1-0.30.10.2
Bone: cortical thickness6.310.411.1-3.3-3.33.0
Bone: cortical thickness2.93.45.0-1.8-2.21.4
Bone: cortical tissue density0.70.91.2-1.1-0.90.7
Condit. Reinf. active minus inactive responses0.20.20.30.40.5-0.6
Condit. Reinf. active-inactive response ratio0.30.30.40.40.6-0.6
Condit. Reinf. active responses0.10.10.10.10.4-0.1
Condit. Reinf. inactive responses0.00.00.1-0.10.20.2
Incentive salience index mean0.10.10.10.10.3-0.4
Condit. Reinf. lever presses0.10.10.2-0.4-0.20.4
Condit. Reinf. active minus inactive responses2.12.62.81.61.5-1.7
Condit. Reinf. active-inactive response ratio2.42.52.81.71.6-1.4
Condit. Reinf. active responses1.72.42.81.51.5-1.7
Condit. Reinf. inactive responses0.20.30.50.20.5-0.7
Condit. Reinf. lever presses0.10.10.10.2-0.1-0.4
Condit. Reinf. lever reinforcers received1.31.92.51.31.2-1.6
Conditioned reinforcement - actives0.10.10.1-0.10.20.4
Conditioned reinforcement - inactives2.83.14.22.11.9-1.2
Conditioned locomotion1.11.42.01.41.4-0.4
Patch foraging indifference point 0 sec0.40.60.80.80.9-0.5
Patch foraging indifference point AUC2.12.52.9-1.5-1.71.5
Delay disc. indifference point, 0s delay1.61.82.71.30.9-1.6
Delay disc. indifference point, 16s delay2.02.13.81.31.9-0.9
Delay disc. indifference point, 2s delay0.91.01.31.20.8-1.0
Delay disc. indifference point, 24s delay0.20.20.4-0.6-0.00.6
Delay disc. indifference point, 4s delay0.50.50.70.50.8-0.8
Delay disc. indifference point, 8s delay0.40.40.60.40.7-0.8
Indifference point function ln k2.02.73.21.81.8-1.4
Indifference point function log k2.02.73.21.81.8-1.4
Patch foraging total patch changes 0 sec0.00.00.10.20.20.1
Patch foraging total patch changes 12 sec1.21.51.8-1.2-1.41.0
Patch foraging total patch changes 18 sec0.00.00.0-0.1-0.20.2
Patch foraging total patch changes 24 sec1.31.62.0-1.2-1.41.1
Patch foraging total patch changes 6 sec0.00.10.1-0.0-0.3-0.2
Patch foraging time to switch 0 sec0.40.61.30.60.5-1.1
Patch foraging water rate 0 sec0.20.41.0-0.10.21.0
Patch foraging water rate 12 sec0.20.20.50.20.40.7
Patch foraging water rate 18 sec0.20.20.40.50.6-0.3
Patch foraging water rate 24 sec0.20.20.6-0.20.10.8
Patch foraging water rate 6 sec0.20.30.7-0.4-0.30.8
Seeking ratio, delayed vs. immediate footshock0.80.91.10.80.9-1.0
Distance traveled before self-admin0.00.00.00.1-0.20.0
Distance traveled after self-admin0.00.00.0-0.1-0.0-0.1
Extensor digitorum longus weight3.714.517.7-4.2-3.93.2
Bone: elastic displacement1.71.92.6-1.3-1.21.6
Bone: elastic work3.14.14.9-2.0-2.21.8
Bone: endosteal estimation2.55.56.12.52.5-2.1
Bone: endosteal perimeter5.010.511.73.43.3-2.9
Epididymis fat weight1.73.94.92.22.2-1.4
Delta time in closed arm before/after self-admin1.41.31.7-1.3-1.11.0
Delta time in open arm before/after self-admin0.20.20.40.60.0-0.3
Diff in mean of infusions in LGA sessions0.50.50.7-0.6-0.70.8
Delay discount exponential model param1.01.11.5-0.8-1.21.0
Extinction: sum of active levers before priming0.50.50.9-1.0-0.70.3
Active lever presses in extinction session 63.02.92.9-1.7-1.71.7
Bone: final force0.40.61.1-0.7-1.10.5
Bone: final moment0.30.50.9-0.7-1.00.4
Food consumed during 24 hour testing period0.00.00.1-0.0-0.00.3
Glucose3.45.05.62.22.4-2.2
Heart weight1.11.61.91.41.3-1.1
Delay discount hyperbolic model param0.91.01.2-0.8-1.11.1
Intermittent access intake day 1-15 change0.10.10.10.4-0.30.3
Intermittent access intake escalation0.20.20.50.7-0.0-0.1
Intermittent access intake escalation 20.10.10.20.1-0.40.2
Intermitt. access day 1 inactive lever presses1.31.41.81.31.2-1.0
Intermitt. access day 15 inactive lever presses1.82.02.91.71.2-1.3
Intermitt. access escalation Index1.21.02.40.81.6-0.3
Intermittent access day 1 total infusions9.611.112.63.43.5-3.1
Intermittent access day 15 total infusions6.57.39.63.12.8-2.2
Intermittent access terminal intake (last 3 days)6.36.88.83.02.6-2.2
Intermittent access total infusions6.26.88.42.72.9-2.2
Intermittent access day 1 locomotion6.56.88.22.52.9-2.4
Intermittent access day 15 total locomotion3.94.25.12.22.3-1.6
Intermittent access total locomotion9.110.312.73.33.6-2.7
Intermittent access standard deviation0.10.10.30.60.2-0.2
Left kidney weight0.00.10.20.40.20.2
Right kidney weight0.10.30.8-0.2-0.40.9
Cocaine induced anxiety0.00.00.1-0.1-0.30.1
Post-drug Anxiety1.61.82.1-1.4-1.41.2
Baseline Anxiety2.22.32.8-1.7-1.61.3
Tail length1.75.27.0-2.2-2.61.9
Length with tail2.69.310.8-3.2-3.32.6
Length without tail1.63.54.4-2.1-1.91.6
Times rat made contact with spout0.10.10.20.10.0-0.4
Lifetime Intake5.46.17.62.52.7-2.1
Liver weight, left0.10.10.20.4-0.3-0.1
Liver weight, right0.10.10.2-0.3-0.30.5
Locomotor activity0.00.00.10.30.00.1
Locomotor testing distance0.00.10.20.50.1-0.1
Locomotor testing rearing1.01.52.21.50.9-1.2
Locomotion in novel chamber3.74.66.72.62.0-1.8
Locomotion in novel chamber post-restriction1.01.21.81.41.2-0.7
Fecal boli incidents, locomotor time 10.10.10.10.3-0.3-0.2
Change in fecal boli incidents, locomotor task0.10.10.3-0.10.5-0.2
Time >=10cm from walls, locomotor time 14.95.06.02.22.4-2.1
Bouts of movement, locomotor time 11.41.62.1-1.5-0.71.4
Total resting periods, locomotor time 10.91.01.5-1.2-0.41.2
Rest time, locomotor task time 10.10.20.30.00.60.4
Distance moved, locomotor task time 10.70.71.10.90.6-1.0
Vertical activity count, locomotor time 11.21.32.01.40.6-1.2
Time >=10cm from walls, locomotor time 20.10.10.4-0.20.60.2
Bouts of movement, locomotor time 20.30.40.6-0.8-0.30.6
Total resting periods, locomotor time 20.10.10.2-0.4-0.00.3
Rest time, locomotor task time 22.02.33.31.81.1-1.5
Distance moved, locomotor task time 20.91.01.4-1.2-0.71.1
Vertical activity count, locomotor time 22.12.32.7-1.5-1.31.7
Light reinforcement 10.00.10.10.30.20.2
Light reinforcement 20.40.50.80.80.9-0.0
Bone: marrow area2.65.66.22.52.5-2.1
Bone: maximum diameter0.00.00.10.10.00.2
Bone: maximum force0.20.30.60.4-0.1-0.8
Bone: maximum moment0.10.20.50.3-0.0-0.7
Mean time between licks in bursts0.40.61.0-1.0-0.70.5
Mean num. licks in bursts0.10.10.20.20.3-0.4
Cd content in liver0.20.20.30.60.5-0.1
Co content in liver0.50.50.6-0.7-0.70.8
Cu content in liver0.10.20.2-0.5-0.20.5
Fe content in liver0.10.10.2-0.2-0.50.2
K content in liver0.20.20.50.20.0-0.7
Mg content in liver2.82.83.51.61.5-1.9
Mn content in liver0.40.50.6-0.7-0.80.5
Na content in liver0.70.70.9-0.7-0.90.9
Rb content in liver3.64.45.42.31.7-2.2
Se content in liver0.91.11.21.11.0-1.0
Sr content in liver3.22.93.2-1.8-1.71.7
Zn content in liver0.40.40.6-0.8-0.40.6
Bone: minimum diameter3.05.66.12.32.5-2.3
Time in familiar zone, hab. session 11.01.01.31.01.2-0.8
Time in novel zone, hab. session 10.30.30.6-0.5-0.70.2
Total zone transitions, hab. session 10.00.10.1-0.2-0.40.1
Total locomotion distance, hab. session 10.50.71.11.00.7-0.7
Locomotion velocity, hab. session 10.10.20.40.60.3-0.3
Time in familiar zone, hab. session 21.21.21.7-1.3-0.91.1
Time in novel zone, hab. session 21.21.21.51.10.8-1.2
Total zone transitions, hab. session 21.21.62.61.01.1-1.6
Total locomotion distance, hab. session 21.31.82.11.31.2-1.4
Locomotion velocity, hab. session 21.72.22.41.51.4-1.5
Novel to familiar place preference ratio0.10.10.20.30.4-0.4
Novelty place preference0.30.40.40.50.6-0.7
Time in novel zone, NPP test0.40.40.50.50.6-0.7
Total zone transitions, NPP test0.10.10.20.1-0.2-0.5
Total locomotion distance, NPP test0.30.50.70.80.4-0.8
Locomotion velocity, NPP test0.20.30.50.70.3-0.6
Intraocular pressure0.20.30.7-0.5-0.10.8
Delta distance traveled before/after self-admin0.00.00.0-0.2-0.1-0.0
Delta ambulatory time before/after self-admin0.10.10.2-0.5-0.20.1
Parametrial fat weight2.03.94.12.02.0-1.9
Pavlov. Cond. lever latency0.00.00.00.10.20.1
Pavlov. Cond. magazine entry latency1.01.21.51.11.0-1.2
Pavlov. Cond. change in total contacts0.70.80.91.00.8-0.9
Pavlov. Cond. index score0.00.00.00.20.1-0.1
Pavlov. Cond. latency score0.10.10.10.30.1-0.3
Pavlov. Cond. lever contacts0.00.00.00.0-0.1-0.2
Pavlov. Cond. magazine entry number0.00.00.0-0.10.1-0.2
Pavlov. Cond. intertrial magazine entries0.20.20.5-0.3-0.00.7
Pavlov. Cond. lever-magazine prob. diff.0.00.00.00.10.0-0.1
Pavlov. Cond. response bias0.00.00.00.1-0.1-0.1
Pavlov. Cond. lever latency0.00.00.0-0.10.2-0.0
Pavlov. Cond. magazine entry latency0.10.10.1-0.3-0.2-0.3
Pavlov. Cond. change in total contacts0.20.20.30.50.3-0.5
Pavlov. Cond. index score0.00.00.00.0-0.1-0.2
Pavlov. Cond. latency score0.00.00.00.0-0.1-0.2
Pavlov. Cond. lever contacts0.10.20.2-0.3-0.40.5
Pavlov. Cond. magazine entry number0.10.20.30.40.50.2
Pavlov. Cond. intertrial magazine entries0.20.30.50.70.6-0.2
Pavlov. Cond. lever-magazine prob. diff.0.00.00.1-0.1-0.3-0.1
Pavlov. Cond. response bias0.00.10.1-0.2-0.30.1
Time in closed arm before self-admin0.40.40.50.70.7-0.5
Time in closed arm after self-admin0.20.20.3-0.4-0.10.5
Time in open arm before self-admin0.20.20.5-0.7-0.10.4
Time in open arm after self-admin0.10.10.2-0.4-0.30.2
Bone: periosteal estimation0.20.30.50.70.6-0.4
Bone: periosteal perimeter0.50.81.01.00.8-0.8
Bone: post-yield work8.111.011.73.23.3-3.4
Progressive ratio test 1 active lever presses1.31.32.71.01.6-0.6
Progressive ratio test 1 breakpoint0.91.02.00.91.4-0.4
Progressive ratio test 1 inactive lever presses0.90.91.60.81.3-0.7
Progressive ratio test 2 active lever presses2.62.84.61.62.2-1.1
Progressive ratio test 2 breakpoint1.92.13.91.42.0-0.7
Progressive ratio test 2 inactive lever presses7.18.210.83.03.3-2.2
Incentive Sensitization - Responses0.40.40.90.50.9-0.5
Incentive Sensitization - Breakpoint0.50.50.90.60.9-0.5
Sum of active levers in priming session hrs 5-63.43.34.1-1.9-1.52.0
Progressive ratio0.91.01.90.90.6-1.4
Food seeking constrained by brief footshock0.20.20.6-0.2-0.80.0
Seeking ratio, punishment vs. effort0.50.60.9-0.6-0.61.0
Retroperitoneal fat weight2.79.011.33.33.4-2.3
Reaction time number correct1.21.71.9-1.4-1.11.4
Reaction time mean minus median0.20.30.6-0.5-0.80.1
Reaction time mean minus median AUC0.91.22.0-1.1-1.40.7
Reaction time num false alarms0.71.01.3-1.1-0.91.0
Reaction time num false alarms AUC1.21.72.1-1.5-1.31.1
Reaction time trials correct on left1.21.71.9-1.4-1.11.4
Reaction time trials on left1.52.12.4-1.5-1.31.5
Reaction time mean0.20.30.50.70.3-0.7
Reaction time mean AUC0.40.50.70.80.4-0.8
Median of all reaction times0.60.81.11.00.6-1.0
Reaction time omissions1.11.52.0-1.4-1.30.9
Reaction time false alarm rate0.20.30.5-0.7-0.60.4
Reaction time premature initiation rate1.62.13.0-1.6-1.70.9
Reaction time premature initiations3.85.36.3-2.5-2.51.9
Std. dev. reaction times0.00.00.1-0.1-0.3-0.2
Reaction time trials completed1.52.12.4-1.5-1.31.5
Reaction time trials AUC1.01.51.8-1.3-1.11.3
Run reversals in cocaine runway, females0.30.30.70.30.0-0.8
Run reversals in cocaine runway, males1.71.62.5-1.1-1.61.1
Latency to leave start box in cocaine runway1.21.21.41.11.1-1.2
Latency to leave start box in cocaine runway, F0.60.60.90.70.7-1.0
Latency to leave start box in cocaine runway, M0.10.10.10.30.3-0.1
Std. dev. time between licks in bursts1.72.02.6-1.6-1.31.4
Total sessions with >9 infusions1.51.62.31.21.5-1.1
Short access day 1 total inactive lever presses2.42.73.41.81.9-1.3
Short access day 10 total inactive lever presses1.01.11.61.30.8-1.0
Short access day 1 total infusions4.64.96.42.22.5-1.9
Short access day 10 total infusions5.76.47.42.42.7-2.4
Short access total infusions2.93.34.01.72.0-1.7
Short access day 1 locomotion3.84.15.71.92.4-1.7
Short access day 10 total locomotion2.52.84.11.52.0-1.4
Short access total locomotion2.52.64.01.42.0-1.4
One hour access (0.3 mA shock)5.15.97.32.72.6-1.9
Compulsive drug intake3.73.74.6-2.2-2.01.5
One hour access (shock baseline)5.46.38.02.82.8-1.7
Social response proportion0.10.10.1-0.20.3-0.4
Social responses0.50.61.1-1.1-0.40.7
Social time0.20.30.4-0.7-0.60.3
Soleus weight0.61.92.81.61.7-0.6
Bone: stiffness0.40.61.10.70.4-1.0
Tibialis anterior weight8.729.833.0-5.7-5.55.1
Time to tail flick, vehicle, before self-admin1.11.12.01.40.1-1.2
Time to tail flick, vehicle, after self-admin0.40.40.9-0.9-0.60.2
Time to tail flick, test, before self-admin2.12.12.71.41.2-1.6
Time to tail flick, test, after self-admin0.10.10.1-0.4-0.10.3
Delta time to tail flick, vehicle, before/after SA0.80.81.8-1.3-0.20.7
Delta time to tail flick, test, before/after SA4.84.45.1-2.1-1.82.3
Tibia length0.92.63.7-1.5-1.41.9
Ambulatory time before self-admin0.00.00.10.30.1-0.2
Ambulatory time after self-admin1.31.41.41.21.2-1.2
Bone: tissue strength0.30.30.40.60.6-0.4
Total heroin consumption1.82.22.7-1.7-1.51.2
Bone: trabecular number1.11.82.31.21.2-1.5
Bone: trabecular spacing0.20.30.5-0.5-0.40.7
Bone: trabecular thickness2.53.03.21.61.8-1.8
Bone: trabecular tissue density0.50.71.01.01.0-0.1
Water consumed over 24 hours0.10.10.2-0.2-0.4-0.1
Number of responses in last shaping day0.10.10.20.30.4-0.1