Tnf

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 PL gene expression Tnf 0.07 0.04 9.0e-04 0.02 0.03 0.03 0.02 4.1e-03 6.4e-04 3.9e-04 2.1e-03
2 Adipose gene expression Tnf 0.06 0.03 6.2e-04 0 0.02 0.02 0.02 1.7e-01 1.7e-03 2.5e-03 6.0e-03
3 Brain gene expression Tnf 0.05 0.03 6.4e-03 0.02 0 0 0.01 5.1e-03 1.1e-01 2.5e-01 8.0e-02

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 density0.81.42.30.7-1.51.2
Area under the delay curve0.00.00.10.40.10.1
BMI with tail1.65.48.1-2.80.5-2.8
BMI without tail1.64.78.4-2.90.4-2.4
Body weight4.118.128.7-5.43.0-4.0
Weight adjusted by age3.96.08.3-2.22.2-2.9
Bone surface0.10.30.4-0.60.6-0.2
Bone volume0.10.10.3-0.6-0.2-0.1
Breakpoint value in progressive ratio session0.50.61.00.8-0.31.0
Number of licking bursts0.60.91.11.00.91.0
Context. condit. distance diff. score1.51.83.31.80.91.1
Locomotion velocity, session 10.60.71.31.2-0.10.8
Locomotion distance, session 10.81.11.21.1-1.10.9
Locomotion velocity, session 20.40.40.91.0-0.10.6
Locomotion distance, session 20.30.51.01.0-0.30.5
Locomotion velocity, session 30.30.30.90.3-0.9-0.0
Locomotion distance, session 31.61.82.51.6-1.21.2
Stereotopy head waving bouts, day 30.91.02.1-0.81.4-0.6
Stereotopy head waving duration, day 30.50.61.1-0.81.0-0.5
Locomotion velocity, session 71.61.83.21.8-1.01.1
Locomotion distance, session 73.24.16.22.5-1.81.7
Stereotopy head waving bouts, day 70.20.20.50.0-0.40.7
Stereotopy head waving duration, day 70.10.20.2-0.5-0.10.4
Locomotion velocity, session 81.21.43.30.91.80.5
Locomotion distance, session 81.01.42.91.70.80.8
Degree of sensitization distance0.30.30.70.30.8-0.2
Degree of sensitization stereotypy0.91.01.70.6-0.91.3
Conditioned locomotion1.31.52.0-1.21.4-1.1
Cocaine response after cond. corrected0.20.20.40.20.6-0.6
Cocaine response after cond. not corrected0.70.81.8-0.31.3-0.7
Cocaine response before conditioning0.91.11.7-1.31.3-0.3
Saline control response1.52.03.1-1.8-0.9-1.4
Bone: connectivity density0.10.20.30.3-0.60.3
Bone: cortical apparent density0.60.81.1-1.1-0.6-1.0
Bone: cortical area0.20.30.4-0.60.5-0.3
Bone: cortical porosity1.21.31.61.2-1.01.3
Bone: cortical porosity0.70.71.11.0-0.41.0
Bone: cortical thickness0.40.61.4-0.7-1.2-0.3
Bone: cortical thickness0.70.81.6-0.8-1.2-0.5
Bone: cortical tissue density0.60.81.1-1.0-0.5-1.0
Condit. Reinf. active minus inactive responses1.71.92.91.7-1.11.2
Condit. Reinf. active-inactive response ratio0.40.40.80.5-0.90.3
Condit. Reinf. active responses1.31.62.41.5-1.21.0
Condit. Reinf. inactive responses1.51.82.31.2-1.51.3
Incentive salience index mean1.41.83.71.9-0.21.3
Condit. Reinf. lever presses1.01.52.21.51.01.1
Condit. Reinf. active minus inactive responses0.20.30.4-0.60.6-0.5
Condit. Reinf. active-inactive response ratio0.80.91.6-0.81.3-0.8
Condit. Reinf. active responses0.00.00.0-0.10.0-0.1
Condit. Reinf. inactive responses0.20.30.60.3-0.80.2
Condit. Reinf. lever presses0.30.40.80.9-0.60.2
Condit. Reinf. lever reinforcers received0.00.00.10.3-0.10.1
Conditioned reinforcement - actives0.10.20.3-0.5-0.4-0.3
Conditioned reinforcement - inactives0.00.10.1-0.2-0.4-0.1
Conditioned locomotion0.10.10.1-0.40.3-0.3
Patch foraging indifference point 0 sec0.51.01.3-1.1-0.7-1.2
Patch foraging indifference point AUC0.10.10.20.1-0.20.5
Delay disc. indifference point, 0s delay0.20.20.60.20.80.0
Delay disc. indifference point, 16s delay0.30.30.80.5-0.9-0.0
Delay disc. indifference point, 2s delay0.30.30.80.20.9-0.1
Delay disc. indifference point, 24s delay0.20.20.40.4-0.2-0.6
Delay disc. indifference point, 4s delay0.20.20.4-0.50.6-0.2
Delay disc. indifference point, 8s delay0.30.30.50.6-0.20.7
Indifference point function ln k0.40.71.01.00.31.0
Indifference point function log k0.40.71.01.00.31.0
Patch foraging total patch changes 0 sec0.61.11.3-1.1-0.8-1.1
Patch foraging total patch changes 12 sec0.60.81.1-0.7-0.8-1.0
Patch foraging total patch changes 18 sec0.81.22.3-0.9-1.5-0.6
Patch foraging total patch changes 24 sec0.71.33.80.1-1.90.2
Patch foraging total patch changes 6 sec0.71.11.5-0.8-1.0-1.2
Patch foraging time to switch 0 sec0.81.63.1-1.30.3-1.8
Patch foraging water rate 0 sec0.10.10.2-0.40.3-0.3
Patch foraging water rate 12 sec0.30.71.20.4-1.10.9
Patch foraging water rate 18 sec0.20.30.6-0.8-0.0-0.6
Patch foraging water rate 24 sec0.20.20.6-0.8-0.30.1
Patch foraging water rate 6 sec0.30.40.80.1-0.60.9
Seeking ratio, delayed vs. immediate footshock0.20.20.4-0.3-0.40.6
Distance traveled before self-admin1.11.41.7-1.31.3-1.0
Distance traveled after self-admin1.21.41.9-1.41.0-1.1
Extensor digitorum longus weight0.20.91.8-0.71.4-0.7
Bone: elastic displacement0.60.71.40.3-1.20.7
Bone: elastic work0.10.10.3-0.5-0.1-0.1
Bone: endosteal estimation3.57.713.7-2.33.7-2.0
Bone: endosteal perimeter1.53.28.6-0.72.9-0.8
Epididymis fat weight1.86.27.3-2.6-2.7-2.2
Delta time in closed arm before/after self-admin1.11.01.5-0.81.0-1.2
Delta time in open arm before/after self-admin0.20.20.3-0.5-0.5-0.0
Diff in mean of infusions in LGA sessions1.51.93.01.7-0.71.4
Delay discount exponential model param0.00.10.2-0.4-0.0-0.1
Extinction: sum of active levers before priming0.40.51.11.00.50.2
Active lever presses in extinction session 60.20.20.50.3-0.70.1
Bone: final force2.13.36.1-2.50.7-1.9
Bone: final moment1.82.95.4-2.30.6-1.7
Food consumed during 24 hour testing period1.72.42.9-1.41.7-1.5
Glucose1.52.46.01.02.5-0.1
Heart weight0.71.11.3-0.91.1-1.1
Delay discount hyperbolic model param0.10.10.2-0.5-0.0-0.2
Intermittent access intake day 1-15 change0.10.20.30.1-0.50.4
Intermittent access intake escalation0.30.71.6-0.1-1.30.6
Intermittent access intake escalation 20.20.20.40.1-0.40.7
Intermitt. access day 1 inactive lever presses0.31.33.3-0.21.8-0.8
Intermitt. access day 15 inactive lever presses0.50.91.1-1.00.8-1.1
Intermitt. access escalation Index1.41.93.31.6-0.21.8
Intermittent access day 1 total infusions0.61.01.21.1-1.10.9
Intermittent access day 15 total infusions0.71.12.30.4-1.50.9
Intermittent access terminal intake (last 3 days)0.40.51.30.3-1.10.5
Intermittent access total infusions0.50.61.20.4-1.10.7
Intermittent access day 1 locomotion0.10.10.1-0.4-0.4-0.0
Intermittent access day 15 total locomotion0.51.02.0-1.40.3-0.9
Intermittent access total locomotion0.40.51.2-1.1-0.3-0.4
Intermittent access standard deviation0.91.82.8-1.7-0.0-1.6
Left kidney weight2.612.221.5-4.61.8-3.4
Right kidney weight3.114.125.1-5.02.2-3.5
Cocaine induced anxiety0.20.20.60.10.8-0.3
Post-drug Anxiety0.20.20.4-0.20.6-0.2
Baseline Anxiety0.10.20.20.5-0.10.5
Tail length1.66.28.3-2.82.9-1.5
Length with tail3.414.618.0-4.24.1-3.0
Length without tail5.718.220.9-4.64.2-4.1
Times rat made contact with spout3.33.86.71.5-2.61.6
Lifetime Intake0.30.30.70.2-0.90.5
Liver weight, left2.74.47.7-1.62.8-1.7
Liver weight, right2.44.17.5-1.42.7-1.7
Locomotor activity0.50.91.4-1.21.1-0.2
Locomotor testing distance0.40.71.2-0.71.1-0.5
Locomotor testing rearing1.02.02.3-1.51.4-1.3
Locomotion in novel chamber0.10.10.2-0.5-0.10.3
Locomotion in novel chamber post-restriction0.71.21.8-1.30.5-1.2
Fecal boli incidents, locomotor time 10.00.10.1-0.20.1-0.3
Change in fecal boli incidents, locomotor task0.90.92.1-0.11.5-0.8
Time >=10cm from walls, locomotor time 14.44.75.8-1.92.4-2.1
Bouts of movement, locomotor time 10.50.50.90.9-0.50.7
Total resting periods, locomotor time 10.20.20.50.7-0.20.5
Rest time, locomotor task time 10.10.20.3-0.30.6-0.2
Distance moved, locomotor task time 10.00.10.1-0.40.1-0.2
Vertical activity count, locomotor time 10.10.20.6-0.8-0.0-0.1
Time >=10cm from walls, locomotor time 21.72.54.4-1.12.1-1.4
Bouts of movement, locomotor time 20.10.10.3-0.2-0.20.5
Total resting periods, locomotor time 20.10.20.50.1-0.00.7
Rest time, locomotor task time 20.70.92.3-0.41.5-0.3
Distance moved, locomotor task time 20.50.60.9-0.9-0.1-0.9
Vertical activity count, locomotor time 20.40.61.2-0.70.2-1.1
Light reinforcement 10.20.50.7-0.90.5-0.7
Light reinforcement 21.11.71.9-1.21.3-1.4
Bone: marrow area3.78.113.8-2.43.7-2.2
Bone: maximum diameter0.61.13.2-0.01.80.0
Bone: maximum force1.62.94.8-2.20.9-1.7
Bone: maximum moment1.42.54.3-2.10.9-1.6
Mean time between licks in bursts0.40.91.60.51.31.0
Mean num. licks in bursts0.91.44.2-0.2-2.1-0.2
Cd content in liver0.40.40.6-0.8-0.0-0.8
Co content in liver1.41.73.2-1.30.2-1.8
Cu content in liver3.13.65.91.8-2.41.3
Fe content in liver0.60.71.6-1.3-0.4-0.7
K content in liver0.40.30.70.8-0.40.4
Mg content in liver0.90.91.81.40.80.5
Mn content in liver1.31.53.90.82.00.1
Na content in liver1.31.41.71.0-1.31.2
Rb content in liver0.20.30.80.10.3-0.9
Se content in liver1.41.63.01.70.71.2
Sr content in liver1.21.01.1-1.01.0-1.0
Zn content in liver0.40.40.7-0.20.7-0.8
Bone: minimum diameter1.52.76.4-1.02.5-0.9
Time in familiar zone, hab. session 13.43.37.01.3-2.61.0
Time in novel zone, hab. session 12.72.75.1-1.32.3-1.1
Total zone transitions, hab. session 10.30.41.01.0-0.30.5
Total locomotion distance, hab. session 10.20.20.60.8-0.30.2
Locomotion velocity, hab. session 10.20.30.60.8-0.30.2
Time in familiar zone, hab. session 20.40.41.30.0-1.1-0.2
Time in novel zone, hab. session 20.10.10.3-0.30.50.0
Total zone transitions, hab. session 20.00.00.00.00.0-0.0
Total locomotion distance, hab. session 20.20.20.50.7-0.30.4
Locomotion velocity, hab. session 20.40.51.11.0-0.30.7
Novel to familiar place preference ratio0.40.40.50.6-0.50.7
Novelty place preference0.30.30.50.5-0.40.7
Time in novel zone, NPP test0.20.20.30.4-0.30.6
Total zone transitions, NPP test0.30.40.91.0-0.30.6
Total locomotion distance, NPP test0.10.10.40.6-0.20.1
Locomotion velocity, NPP test0.30.40.90.9-0.30.4
Intraocular pressure0.20.30.6-0.4-0.8-0.1
Delta distance traveled before/after self-admin0.00.00.0-0.2-0.1-0.2
Delta ambulatory time before/after self-admin0.00.00.1-0.30.1-0.2
Parametrial fat weight2.45.610.1-3.20.5-2.5
Pavlov. Cond. lever latency2.32.94.4-2.0-0.6-2.1
Pavlov. Cond. magazine entry latency2.73.56.02.1-0.22.5
Pavlov. Cond. change in total contacts1.01.12.21.00.21.5
Pavlov. Cond. index score2.83.65.92.20.42.4
Pavlov. Cond. latency score2.83.66.02.10.42.5
Pavlov. Cond. lever contacts1.61.92.41.41.01.6
Pavlov. Cond. magazine entry number1.92.43.9-1.90.1-2.0
Pavlov. Cond. intertrial magazine entries0.40.50.9-0.4-1.0-0.6
Pavlov. Cond. lever-magazine prob. diff.3.03.76.02.20.32.4
Pavlov. Cond. response bias2.22.74.21.90.32.1
Pavlov. Cond. lever latency0.50.61.5-0.61.20.2
Pavlov. Cond. magazine entry latency0.00.10.1-0.00.2-0.4
Pavlov. Cond. change in total contacts0.10.20.50.2-0.7-0.2
Pavlov. Cond. index score0.10.20.20.3-0.5-0.5
Pavlov. Cond. latency score0.20.20.40.2-0.5-0.6
Pavlov. Cond. lever contacts0.30.41.00.4-1.0-0.3
Pavlov. Cond. magazine entry number0.20.20.50.3-0.00.7
Pavlov. Cond. intertrial magazine entries0.81.32.11.30.21.5
Pavlov. Cond. lever-magazine prob. diff.0.10.20.30.3-0.5-0.5
Pavlov. Cond. response bias0.20.30.50.6-0.7-0.0
Time in closed arm before self-admin0.20.30.60.10.5-0.7
Time in closed arm after self-admin0.20.20.4-0.30.3-0.7
Time in open arm before self-admin1.21.32.21.2-0.61.5
Time in open arm after self-admin0.10.20.20.3-0.40.5
Bone: periosteal estimation2.14.46.8-2.02.6-1.6
Bone: periosteal perimeter0.61.13.0-0.51.7-0.3
Bone: post-yield work1.62.34.4-0.92.1-1.3
Progressive ratio test 1 active lever presses0.00.00.10.3-0.2-0.1
Progressive ratio test 1 breakpoint0.00.00.10.3-0.1-0.2
Progressive ratio test 1 inactive lever presses0.10.20.3-0.2-0.5-0.6
Progressive ratio test 2 active lever presses0.91.01.30.8-1.11.1
Progressive ratio test 2 breakpoint1.11.21.70.8-1.31.1
Progressive ratio test 2 inactive lever presses0.00.10.10.20.40.1
Incentive Sensitization - Responses1.21.82.51.2-1.11.6
Incentive Sensitization - Breakpoint1.31.72.31.1-1.21.5
Sum of active levers in priming session hrs 5-60.20.10.40.60.10.0
Progressive ratio2.53.97.6-2.80.4-1.9
Food seeking constrained by brief footshock0.10.10.40.0-0.60.1
Seeking ratio, punishment vs. effort2.33.36.62.6-0.61.7
Retroperitoneal fat weight0.31.42.2-1.50.2-1.4
Reaction time number correct0.40.71.0-1.0-0.5-0.9
Reaction time mean minus median0.20.40.80.20.50.9
Reaction time mean minus median AUC0.10.30.50.50.40.7
Reaction time num false alarms0.40.51.10.60.21.1
Reaction time num false alarms AUC0.40.61.30.70.21.1
Reaction time trials correct on left0.40.71.0-1.0-0.5-0.9
Reaction time trials on left0.40.71.1-1.1-0.4-1.0
Reaction time mean0.50.82.20.21.5-0.1
Reaction time mean AUC0.40.61.90.21.4-0.1
Median of all reaction times0.60.92.40.01.5-0.4
Reaction time omissions0.30.51.4-0.21.2-0.0
Reaction time false alarm rate1.11.52.51.30.51.6
Reaction time premature initiation rate1.01.41.8-1.21.0-1.3
Reaction time premature initiations1.32.43.5-1.80.7-1.9
Std. dev. reaction times0.30.51.00.51.00.5
Reaction time trials completed0.40.71.1-1.1-0.4-1.0
Reaction time trials AUC0.40.71.1-1.1-0.4-0.9
Run reversals in cocaine runway, females0.20.20.3-0.4-0.5-0.5
Run reversals in cocaine runway, males0.40.40.6-0.70.80.3
Latency to leave start box in cocaine runway0.30.40.60.80.60.2
Latency to leave start box in cocaine runway, F0.20.30.50.70.30.4
Latency to leave start box in cocaine runway, M0.20.20.4-0.00.6-0.3
Std. dev. time between licks in bursts1.11.54.30.22.1-0.1
Total sessions with >9 infusions0.30.30.50.3-0.70.6
Short access day 1 total inactive lever presses0.30.41.0-0.51.00.1
Short access day 10 total inactive lever presses0.10.10.20.50.10.4
Short access day 1 total infusions0.20.20.50.7-0.20.3
Short access day 10 total infusions0.30.30.80.2-0.90.3
Short access total infusions0.20.20.30.3-0.60.4
Short access day 1 locomotion1.01.31.91.4-0.51.3
Short access day 10 total locomotion1.01.92.6-0.71.6-1.6
Short access total locomotion0.30.40.8-0.10.9-0.5
One hour access (0.3 mA shock)2.12.43.31.6-1.21.8
Compulsive drug intake1.31.62.21.51.01.2
One hour access (shock baseline)0.71.02.7-0.3-1.70.5
Social response proportion0.80.91.9-0.41.4-0.7
Social responses0.20.20.60.00.8-0.1
Social time0.60.92.30.21.50.5
Soleus weight1.95.715.3-0.83.9-1.1
Bone: stiffness0.50.81.7-1.30.1-0.9
Tibialis anterior weight0.10.40.9-0.3-0.9-0.5
Time to tail flick, vehicle, before self-admin0.30.30.80.3-0.40.9
Time to tail flick, vehicle, after self-admin0.20.30.60.80.20.5
Time to tail flick, test, before self-admin0.70.71.10.3-1.01.0
Time to tail flick, test, after self-admin2.22.33.71.0-1.51.9
Delta time to tail flick, vehicle, before/after SA0.50.50.60.8-0.70.5
Delta time to tail flick, test, before/after SA0.10.10.20.3-0.50.2
Tibia length3.28.811.8-2.83.4-2.6
Ambulatory time before self-admin0.10.20.4-0.60.4-0.1
Ambulatory time after self-admin0.70.81.2-1.10.8-0.7
Bone: tissue strength1.01.01.7-1.30.6-0.9
Total heroin consumption0.00.00.10.00.20.3
Bone: trabecular number1.22.03.40.8-1.81.4
Bone: trabecular spacing2.02.63.9-1.42.0-1.4
Bone: trabecular thickness0.50.71.50.3-1.20.7
Bone: trabecular tissue density0.10.20.5-0.0-0.40.7
Water consumed over 24 hours0.10.10.30.30.5-0.0
Number of responses in last shaping day0.60.71.70.61.30.0