Hub : Genes

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 ENSRNOG00000070745 0.05 0.04 2.4e-03 0.02 0.02 0.02 0.02 1.6e-02 5.7e-03 2.1e-02 1.6e-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 strong Z-scores (below -2 or above 2): lower negative Z-scores are darker blue, higher positive Z-scores are darker red.

Trait Avg chi2 ratio Avg chi2 Max chi2 1
BMI with tail2.06.46.4-2.5
BMI without tail2.34.74.7-2.2
Body weight6.427.127.1-5.2
Epididymis fat weight0.20.50.5-0.7
Glucose0.10.10.1-0.3
Heart weight0.40.50.5-0.7
Left kidney weight3.19.09.0-3.0
Right kidney weight3.39.39.3-3.0
Tail length2.78.28.2-2.9
Length with tail3.111.311.3-3.4
Length without tail3.27.07.0-2.7
Liver weight, left1.72.72.7-1.6
Liver weight, right1.62.62.6-1.6
Parametrial fat weight0.91.71.7-1.3
Retroperitoneal fat weight0.41.41.4-1.2
Intraocular pressure0.20.30.30.6
Extensor digitorum longus weight0.21.01.0-1.0
Soleus weight1.33.73.7-1.9
Tibialis anterior weight0.00.10.10.4
Tibia length4.111.611.6-3.4
Number of licking bursts0.10.10.10.3
Food consumed during 24 hour testing period1.41.71.7-1.3
Times rat made contact with spout3.23.63.61.9
Mean time between licks in bursts0.00.00.0-0.1
Mean num. licks in bursts0.20.30.30.5
Std. dev. time between licks in bursts0.50.60.6-0.7
Water consumed over 24 hours0.00.00.0-0.0
Indifference point 0 sec0.60.90.9-1.0
Indifference point AUC0.00.10.1-0.2
Indifference point function ln k0.10.20.20.4
Indifference point function log k0.10.20.20.4
Delay discounting total patch changes 0 sec0.50.80.8-0.9
Delay discounting total patch changes 12 sec0.20.30.3-0.5
Delay discounting total patch changes 18 sec0.00.00.00.1
Delay discounting total patch changes 24 sec0.91.11.11.1
Delay discounting total patch changes 6 sec0.20.30.3-0.5
Delay discounting time to switch 0 sec0.20.30.3-0.6
Delay discounting water rate 0 sec0.10.20.2-0.4
Delay discounting water rate 12 sec0.50.70.70.8
Delay discounting water rate 18 sec0.10.10.1-0.3
Delay discounting water rate 24 sec0.10.10.1-0.3
Delay discounting water rate 6 sec0.10.10.10.3
Locomotor activity1.22.02.0-1.4
Locomotor testing distance0.71.11.1-1.0
Locomotor testing rearing1.72.62.6-1.6
Light reinforcement 10.20.40.4-0.6
Light reinforcement 20.81.11.1-1.0
Reaction time number correct0.40.60.6-0.8
Reaction time mean minus median0.30.40.40.6
Reaction time mean minus median AUC0.60.70.70.9
Reaction time num false alarms0.00.00.00.2
Reaction time num false alarms AUC0.00.00.00.0
Reaction time trials correct on left0.40.60.6-0.8
Reaction time trials on left0.50.70.7-0.8
Reaction time mean0.00.10.10.3
Reaction time mean AUC0.10.10.10.3
Median of all reaction times0.00.00.0-0.0
Reaction time omissions0.10.10.10.3
Reaction time false alarm rate0.20.20.20.5
Reaction time premature initiation rate1.01.31.3-1.1
Reaction time premature initiations1.92.82.8-1.7
Std. dev. reaction times0.10.20.20.4
Reaction time trials completed0.50.70.7-0.8
Reaction time trials AUC0.40.60.6-0.8
Social response proportion1.51.61.6-1.3
Social responses0.60.70.7-0.9
Social time0.00.00.0-0.1
Conditioned locomotion1.51.71.7-1.3
Cocaine response after cond. corrected0.10.10.10.3
Cocaine response after cond. not corrected0.40.50.5-0.7
Cocaine response before conditioning3.54.34.3-2.1
Saline control response1.31.81.8-1.3
Condit. Reinf. active minus inactive responses0.80.90.9-1.0
Condit. Reinf. active-inactive response ratio1.71.81.8-1.3
Condit. Reinf. active responses0.10.10.1-0.3
Condit. Reinf. inactive responses0.10.10.10.4
Condit. Reinf. lever presses0.20.30.30.6
Condit. Reinf. lever reinforcers received0.00.00.0-0.1
Pavlov. Cond. lever latency0.30.40.4-0.7
Pavlov. Cond. magazine entry latency0.00.00.00.1
Pavlov. Cond. change in total contacts0.10.10.10.3
Pavlov. Cond. index score0.10.20.20.4
Pavlov. Cond. latency score0.00.00.00.2
Pavlov. Cond. lever contacts0.30.50.50.7
Pavlov. Cond. magazine entry number0.00.00.0-0.1
Pavlov. Cond. intertrial magazine entries0.30.30.30.6
Pavlov. Cond. lever-magazine prob. diff.0.10.10.10.3
Pavlov. Cond. response bias0.70.90.91.0
Conditioned reinforcement - actives0.40.40.4-0.6
Conditioned reinforcement - inactives0.10.10.1-0.3
Conditioned locomotion0.20.20.2-0.4
Intermittent access intake day 1-15 change0.10.10.10.4
Intermittent access intake escalation0.10.10.10.3
Intermittent access intake escalation 20.40.40.40.6
Intermitt. access day 1 inactive lever presses1.31.41.4-1.2
Intermitt. access day 15 inactive lever presses1.21.31.3-1.1
Intermitt. access escalation Index1.41.21.21.1
Intermittent access day 1 total infusions0.91.11.11.0
Intermittent access day 15 total infusions0.40.50.50.7
Intermittent access terminal intake (last 3 days)0.00.00.00.2
Intermittent access total infusions0.10.10.10.4
Intermittent access day 1 locomotion0.10.10.1-0.2
Intermittent access day 15 total locomotion0.80.90.9-0.9
Intermittent access total locomotion0.40.40.4-0.6
Intermittent access standard deviation1.61.71.7-1.3
Cocaine induced anxiety0.30.30.30.6
Post-drug Anxiety0.10.10.1-0.4
Baseline Anxiety0.30.30.3-0.6
Lifetime Intake0.00.00.00.2
Incentive Sensitization - Responses1.51.51.51.2
Incentive Sensitization - Breakpoint1.51.61.61.2
Progressive ratio test 1 active lever presses0.10.10.10.3
Progressive ratio test 1 breakpoint0.00.00.00.1
Progressive ratio test 1 inactive lever presses0.00.00.00.1
Progressive ratio test 2 active lever presses0.80.90.90.9
Progressive ratio test 2 breakpoint1.41.61.61.3
Progressive ratio test 2 inactive lever presses0.00.00.00.2
Total sessions with >9 infusions0.00.00.0-0.1
Short access day 1 total inactive lever presses0.10.10.1-0.3
Short access day 10 total inactive lever presses0.00.00.0-0.2
Short access day 1 total infusions0.10.10.10.3
Short access day 10 total infusions0.00.00.0-0.1
Short access total infusions0.00.00.0-0.0
Short access day 1 locomotion0.91.01.01.0
Short access day 10 total locomotion2.02.22.2-1.5
Short access total locomotion0.80.80.8-0.9
Compulsive drug intake0.90.90.90.9
One hour access (0.3 mA shock)1.51.81.81.3
One hour access (shock baseline)0.00.00.0-0.2
Number of responses in last shaping day0.20.20.2-0.4
Context. condit. distance diff. score1.41.71.71.3
Locomotion velocity, session 10.50.60.60.7
Locomotion distance, session 11.62.02.01.4
Locomotion velocity, session 20.40.50.50.7
Locomotion distance, session 21.11.61.61.2
Locomotion velocity, session 30.10.10.10.3
Locomotion distance, session 33.03.23.21.8
Stereotopy head waving bouts, day 31.41.61.6-1.3
Stereotopy head waving duration, day 31.51.91.9-1.4
Locomotion velocity, session 74.55.05.02.2
Locomotion distance, session 77.29.29.23.0
Stereotopy head waving bouts, day 70.00.00.00.0
Stereotopy head waving duration, day 70.30.30.3-0.6
Locomotion velocity, session 80.00.00.0-0.0
Locomotion distance, session 81.72.62.61.6
Degree of sensitization distance0.00.00.0-0.0
Degree of sensitization stereotypy0.30.40.40.6
Condit. Reinf. active minus inactive responses1.41.61.61.3
Condit. Reinf. active-inactive response ratio0.10.10.10.3
Condit. Reinf. active responses1.62.02.01.4
Condit. Reinf. inactive responses2.63.03.01.7
Incentive salience index mean1.62.02.01.4
Condit. Reinf. lever presses1.21.61.61.3
Time in familiar zone, hab. session 14.24.04.02.0
Time in novel zone, hab. session 14.03.93.9-2.0
Total zone transitions, hab. session 10.50.70.70.8
Total locomotion distance, hab. session 10.40.60.60.8
Locomotion velocity, hab. session 10.30.50.50.7
Time in familiar zone, hab. session 20.20.20.20.4
Time in novel zone, hab. session 20.30.30.3-0.5
Total zone transitions, hab. session 20.10.10.10.3
Total locomotion distance, hab. session 20.81.01.01.0
Locomotion velocity, hab. session 21.21.61.61.3
Novel to familiar place preference ratio0.40.40.40.6
Novelty place preference0.20.20.20.5
Time in novel zone, NPP test0.10.10.10.3
Total zone transitions, NPP test1.01.51.51.2
Total locomotion distance, NPP test0.81.11.11.1
Locomotion velocity, NPP test1.42.02.01.4
Pavlov. Cond. lever latency1.82.32.3-1.5
Pavlov. Cond. magazine entry latency1.11.41.41.2
Pavlov. Cond. change in total contacts0.30.30.30.5
Pavlov. Cond. index score1.72.12.11.5
Pavlov. Cond. latency score1.72.12.11.5
Pavlov. Cond. lever contacts0.81.01.01.0
Pavlov. Cond. magazine entry number0.81.11.1-1.0
Pavlov. Cond. intertrial magazine entries0.00.00.00.2
Pavlov. Cond. lever-magazine prob. diff.1.82.22.21.5
Pavlov. Cond. response bias1.01.31.31.1
Bone: apparent density1.83.03.01.7
Bone surface0.10.10.1-0.4
Bone volume0.00.00.00.1
Bone: connectivity density0.81.31.31.1
Bone: cortical apparent density0.20.30.3-0.5
Bone: cortical area0.40.60.6-0.8
Bone: cortical porosity0.40.40.40.6
Bone: cortical porosity0.10.10.10.3
Bone: cortical thickness0.00.00.0-0.2
Bone: cortical thickness0.00.00.0-0.2
Bone: cortical tissue density0.30.40.4-0.6
Bone: elastic displacement0.50.50.50.7
Bone: elastic work0.10.10.1-0.3
Bone: endosteal estimation5.211.211.2-3.4
Bone: endosteal perimeter1.42.92.9-1.7
Bone: final force2.64.34.3-2.1
Bone: final moment2.33.83.8-1.9
Bone: marrow area5.612.012.0-3.5
Bone: maximum diameter0.30.50.5-0.7
Bone: maximum force1.93.33.3-1.8
Bone: maximum moment1.73.03.0-1.7
Bone: minimum diameter1.52.82.8-1.7
Bone: periosteal estimation3.87.97.9-2.8
Bone: periosteal perimeter1.11.81.8-1.4
Bone: post-yield work1.01.41.4-1.2
Bone: stiffness0.61.01.0-1.0
Bone: tissue strength0.50.50.5-0.7
Bone: trabecular number2.94.54.52.1
Bone: trabecular spacing3.95.15.1-2.2
Bone: trabecular thickness1.41.71.71.3
Bone: trabecular tissue density0.10.10.1-0.3
Breakpoint value in progressive ratio session0.40.50.50.7
Distance traveled before self-admin0.60.70.7-0.8
Distance traveled after self-admin1.82.02.0-1.4
Delta time in closed arm before/after self-admin1.61.51.5-1.2
Delta time in open arm before/after self-admin0.20.10.10.4
Diff in mean of infusions in LGA sessions3.43.83.82.0
Extinction: sum of active levers before priming0.30.30.30.5
Active lever presses in extinction session 60.00.00.0-0.0
Delta distance traveled before/after self-admin0.30.30.3-0.6
Delta ambulatory time before/after self-admin0.20.20.2-0.5
Time in closed arm before self-admin0.00.00.0-0.1
Time in closed arm after self-admin0.20.20.2-0.4
Time in open arm before self-admin0.70.70.70.9
Time in open arm after self-admin0.50.60.60.8
Sum of active levers in priming session hrs 5-60.10.10.10.2
Time to tail flick, vehicle, before self-admin0.40.40.40.6
Time to tail flick, vehicle, after self-admin0.10.10.10.3
Time to tail flick, test, before self-admin0.40.40.40.7
Time to tail flick, test, after self-admin2.82.82.81.7
Delta time to tail flick, vehicle, before/after SA0.40.40.40.6
Delta time to tail flick, test, before/after SA0.40.40.40.6
Ambulatory time before self-admin0.00.00.0-0.1
Ambulatory time after self-admin0.70.80.8-0.9
Total heroin consumption0.00.00.00.1
Area under the delay curve0.00.00.0-0.1
Delay disc. indifference point, 0s delay0.00.00.0-0.2
Delay disc. indifference point, 16s delay0.20.20.20.5
Delay disc. indifference point, 2s delay0.50.60.6-0.8
Delay disc. indifference point, 24s delay0.00.00.0-0.2
Delay disc. indifference point, 4s delay1.01.11.1-1.0
Delay disc. indifference point, 8s delay0.20.20.20.4
Delay discount exponential model param0.00.00.00.1
Delay discount hyperbolic model param0.00.00.00.2
Fecal boli incidents, locomotor time 10.00.00.0-0.0
Change in fecal boli incidents, locomotor task0.30.30.3-0.6
Time >=10cm from walls, locomotor time 14.64.64.6-2.1
Bouts of movement, locomotor time 11.01.11.11.0
Total resting periods, locomotor time 10.50.60.60.8
Rest time, locomotor task time 10.10.10.1-0.3
Distance moved, locomotor task time 10.20.20.2-0.4
Vertical activity count, locomotor time 10.30.30.3-0.6
Time >=10cm from walls, locomotor time 23.13.33.3-1.8
Bouts of movement, locomotor time 20.00.00.0-0.2
Total resting periods, locomotor time 20.00.00.0-0.1
Rest time, locomotor task time 20.20.20.2-0.5
Distance moved, locomotor task time 20.20.20.2-0.5
Vertical activity count, locomotor time 20.40.40.4-0.6
Weight adjusted by age6.57.37.3-2.7
Seeking ratio, delayed vs. immediate footshock0.30.30.3-0.6
Locomotion in novel chamber0.00.10.1-0.2
Locomotion in novel chamber post-restriction1.11.31.3-1.1
Progressive ratio4.24.94.9-2.2
Food seeking constrained by brief footshock0.00.00.00.0
Seeking ratio, punishment vs. effort2.83.43.41.9
Run reversals in cocaine runway, females0.00.00.00.1
Run reversals in cocaine runway, males0.00.00.0-0.1
Latency to leave start box in cocaine runway0.10.10.10.3
Latency to leave start box in cocaine runway, F0.30.30.30.6
Latency to leave start box in cocaine runway, M0.00.00.0-0.2
Cd content in liver0.10.10.1-0.3
Co content in liver1.72.02.0-1.4
Cu content in liver5.06.16.12.5
Fe content in liver0.40.40.4-0.7
K content in liver0.60.60.60.7
Mg content in liver1.31.31.31.2
Mn content in liver0.10.10.1-0.3
Na content in liver0.60.70.70.8
Rb content in liver0.00.00.00.0
Se content in liver1.01.21.21.1
Sr content in liver1.41.21.2-1.1
Zn content in liver0.20.20.2-0.4