Hub : Traits

Mg content in liver

Tags: Physiology · Liver

Project: vulpe_liver_2014

2 significantly associated models · 2 unique genes

Significant Loci

# chr p0 p1 # assoc genes # joint models best TWAS P best SNP P cond SNP P % var exp joint genes
1 10 46789397 48185455 1 1 4.6e-08 4.0e-01 0.22 -118 Trim16
2 18 3105227 4504638 1 1 4.5e-08 3.7e-05 0.45 97 Ttc39c

p0: physical position of the start of the locus. p1: physical position of the end of the locus. # joint models: number of models selected by step-wise conditional analysis.

Pleiotropic Associations

Trait chisq ratio # genes+ # genes++ % genes++ corr corr P genes
BMI with tail 1.8 1 0 0 0 1 Ttc39c
Heart weight 7.8 1 0 0 0 1 Trim16
Liver weight, left 7.8 1 0 0 0 1 Trim16
Intraocular pressure 22.7 2 1 50 0 1 Trim16 Ttc39c
Extensor digitorum longus weight 1.5 1 0 0 0 1 Ttc39c
Tibia length 3.0 1 0 0 0 1 Ttc39c
Number of licking bursts 19.2 1 0 0 0 1 Trim16
Food consumed during 24 hour testing period 18.6 1 0 0 0 1 Trim16
Times rat made contact with spout 16.5 1 0 0 0 1 Trim16
Mean num. licks in bursts 46.0 1 1 50 0 1 Trim16
Std. dev. time between licks in bursts 5.4 1 0 0 0 1 Trim16
Water consumed over 24 hours 23.8 1 1 50 0 1 Trim16
Indifference point 0 sec 6.1 2 0 0 0 1 Trim16 Ttc39c
Delay discounting total patch changes 0 sec 6.4 2 0 0 0 1 Trim16 Ttc39c
Delay discounting total patch changes 18 sec 45.7 1 1 50 0 1 Trim16
Delay discounting total patch changes 24 sec 4.2 1 0 0 0 1 Ttc39c
Delay discounting total patch changes 6 sec 5.5 2 0 0 0 1 Trim16 Ttc39c
Delay discounting water rate 0 sec 15.1 1 0 0 0 1 Trim16
Delay discounting water rate 6 sec 7.2 1 0 0 0 1 Trim16
Locomotor activity 4.9 1 0 0 0 1 Trim16
Reaction time number correct 7.5 1 0 0 0 1 Trim16
Reaction time trials correct on left 7.5 1 0 0 0 1 Trim16
Reaction time trials on left 6.9 1 0 0 0 1 Trim16
Reaction time premature initiation rate 5.0 2 0 0 0 1 Trim16 Ttc39c
Reaction time premature initiations 5.0 1 0 0 0 1 Ttc39c
Reaction time trials completed 6.9 1 0 0 0 1 Trim16
Reaction time trials AUC 6.0 1 0 0 0 1 Trim16
Social responses 4.0 1 0 0 0 1 Trim16
Social time 25.9 1 1 50 0 1 Trim16
Cocaine response after cond. corrected 14.6 1 0 0 0 1 Trim16
Cocaine response after cond. not corrected 16.0 1 0 0 0 1 Trim16
Saline control response 8.8 1 0 0 0 1 Ttc39c
Condit. Reinf. inactive responses 6.1 1 0 0 0 1 Ttc39c
Condit. Reinf. lever presses 7.4 1 0 0 0 1 Trim16
Intermitt. access day 1 inactive lever presses 36.6 1 1 50 0 1 Trim16
Intermitt. access escalation Index 27.6 1 0 0 0 1 Trim16
Intermittent access day 1 locomotion 12.8 1 0 0 0 1 Trim16
Intermittent access total locomotion 9.9 1 0 0 0 1 Trim16
Cocaine induced anxiety 31.7 1 1 50 0 1 Trim16
Post-drug Anxiety 7.8 2 0 0 0 1 Trim16 Ttc39c
Baseline Anxiety 29.9 1 1 50 0 1 Trim16
Progressive ratio test 1 inactive lever presses 10.6 1 0 0 0 1 Trim16
Total sessions with >9 infusions 13.7 1 0 0 0 1 Trim16
Short access day 1 total inactive lever presses 13.8 1 0 0 0 1 Trim16
Short access day 1 total infusions 62.7 1 1 50 0 1 Trim16
Short access total infusions 5.0 1 0 0 0 1 Trim16
Short access day 1 locomotion 33.1 1 1 50 0 1 Trim16
Short access day 10 total locomotion 14.3 1 0 0 0 1 Trim16
Short access total locomotion 10.1 1 0 0 0 1 Trim16
Compulsive drug intake 11.9 1 0 0 0 1 Trim16
Number of responses in last shaping day 25.6 1 1 50 0 1 Trim16
Context. condit. distance diff. score 5.0 1 0 0 0 1 Trim16
Locomotion distance, session 1 31.9 1 1 50 0 1 Trim16
Locomotion distance, session 2 15.7 1 0 0 0 1 Trim16
Locomotion velocity, session 7 5.0 1 0 0 0 1 Trim16
Stereotopy head waving bouts, day 7 25.4 1 1 50 0 1 Trim16
Stereotopy head waving duration, day 7 6.5 1 0 0 0 1 Trim16
Degree of sensitization stereotypy 7.4 1 0 0 0 1 Trim16
Condit. Reinf. active minus inactive responses 5.1 1 0 0 0 1 Trim16
Condit. Reinf. active-inactive response ratio 5.1 1 0 0 0 1 Trim16
Incentive salience index mean 5.9 1 0 0 0 1 Trim16
Time in familiar zone, hab. session 1 6.6 1 0 0 0 1 Trim16
Time in novel zone, hab. session 1 5.6 1 0 0 0 1 Trim16
Total zone transitions, hab. session 1 37.4 1 1 50 0 1 Trim16
Total locomotion distance, hab. session 1 38.5 1 1 50 0 1 Trim16
Locomotion velocity, hab. session 1 30.2 1 1 50 0 1 Trim16
Time in familiar zone, hab. session 2 8.6 1 0 0 0 1 Trim16
Total locomotion distance, hab. session 2 11.5 1 0 0 0 1 Trim16
Locomotion velocity, hab. session 2 10.0 1 0 0 0 1 Trim16
Time in novel zone, NPP test 5.2 1 0 0 0 1 Trim16
Total zone transitions, NPP test 3.6 1 0 0 0 1 Trim16
Total locomotion distance, NPP test 4.5 1 0 0 0 1 Trim16
Locomotion velocity, NPP test 4.0 1 0 0 0 1 Trim16
Pavlov. Cond. lever latency 4.8 1 0 0 0 1 Ttc39c
Pavlov. Cond. magazine entry latency 30.9 1 1 50 0 1 Trim16
Pavlov. Cond. index score 10.8 1 0 0 0 1 Trim16
Pavlov. Cond. latency score 5.9 1 0 0 0 1 Trim16
Pavlov. Cond. magazine entry number 28.0 1 1 50 0 1 Trim16
Pavlov. Cond. intertrial magazine entries 14.4 1 0 0 0 1 Trim16
Pavlov. Cond. lever-magazine prob. diff. 10.2 1 0 0 0 1 Trim16
Pavlov. Cond. response bias 8.3 1 0 0 0 1 Trim16
Bone: cortical apparent density 18.1 1 0 0 0 1 Trim16
Bone: cortical porosity 21.5 1 0 0 0 1 Trim16
Bone: cortical porosity 27.4 1 1 50 0 1 Trim16
Bone: cortical tissue density 19.6 1 0 0 0 1 Trim16
Bone: elastic work 5.8 1 0 0 0 1 Trim16
Bone: post-yield work 16.2 1 0 0 0 1 Trim16
Bone: tissue strength 7.4 1 0 0 0 1 Trim16
Delta ambulatory time before/after self-admin 4.7 1 0 0 0 1 Ttc39c
Delay disc. indifference point, 16s delay 6.6 1 0 0 0 1 Trim16
Distance moved, locomotor task time 2 6.6 1 0 0 0 1 Trim16
Food seeking constrained by brief footshock 4.2 1 0 0 0 1 Trim16
Run reversals in cocaine runway, females 11.6 1 0 0 0 1 Trim16
Run reversals in cocaine runway, males 6.2 1 0 0 0 1 Trim16
Latency to leave start box in cocaine runway 10.7 1 0 0 0 1 Trim16
Latency to leave start box in cocaine runway, F 7.3 1 0 0 0 1 Trim16
Cu content in liver 6.2 1 0 0 0 1 Trim16
K content in liver 12.6 2 0 0 0 1 Trim16 Ttc39c
Mn content in liver 6.2 2 0 0 0 1 Trim16 Ttc39c
Na content in liver 5.1 1 0 0 0 1 Ttc39c
Rb content in liver 24.8 1 1 50 0 1 Trim16
Se content in liver 13.6 2 0 0 0 1 Trim16 Ttc39c
Zn content in liver 5.5 1 0 0 0 1 Ttc39c

chisq ratio: Average Chi2 statistic for the selected genes in the secondary trait, divided by the average statistic for all genes in the secondary trait. # genes+: Shared significant genes at Bonferroni correction. # genes++: Shared significant genes at transcriptome-wide significance. % genes++: Number of [++] genes as a percentage of primary trait’s total joint genes. corr: Correlation of effect sizes across the [+] genes.

Associations by panel

tissue modality # hits % hits/tests avg chisq
Adipose alternative polyA 0 0.000 1.00
Adipose alternative TSS 0 0.000 0.99
Adipose gene expression 0 0.000 1.03
Adipose isoform ratio 0 0.000 1.05
Adipose intron excision ratio 0 0.000 1.05
Adipose mRNA stability 0 0.000 1.03
BLA alternative polyA 0 0.000 1.01
BLA alternative TSS 0 0.000 0.94
BLA gene expression 0 0.000 1.00
BLA isoform ratio 0 0.000 1.02
BLA intron excision ratio 0 0.000 1.12
BLA mRNA stability 0 0.000 0.97
Brain alternative polyA 0 0.000 1.05
Brain alternative TSS 0 0.000 1.02
Brain gene expression 0 0.000 1.03
Brain isoform ratio 0 0.000 1.00
Brain intron excision ratio 0 0.000 1.05
Brain mRNA stability 0 0.000 1.01
Eye alternative polyA 0 0.000 1.13
Eye alternative TSS 0 0.000 0.92
Eye gene expression 0 0.000 1.10
Eye isoform ratio 0 0.000 1.01
Eye intron excision ratio 1 0.163 1.15
Eye mRNA stability 0 0.000 1.04
IL alternative polyA 0 0.000 0.97
IL alternative TSS 0 0.000 0.99
IL gene expression 0 0.000 1.03
IL isoform ratio 0 0.000 1.05
IL intron excision ratio 0 0.000 1.10
IL mRNA stability 0 0.000 0.96
LHb alternative polyA 0 0.000 1.09
LHb alternative TSS 0 0.000 0.94
LHb gene expression 0 0.000 1.02
LHb isoform ratio 0 0.000 1.11
LHb intron excision ratio 0 0.000 1.19
LHb mRNA stability 0 0.000 0.96
Liver alternative polyA 0 0.000 1.11
Liver alternative TSS 0 0.000 0.92
Liver gene expression 0 0.000 1.03
Liver isoform ratio 0 0.000 1.07
Liver intron excision ratio 0 0.000 1.07
Liver mRNA stability 0 0.000 1.07
NAcc alternative polyA 0 0.000 1.04
NAcc alternative TSS 0 0.000 0.91
NAcc gene expression 0 0.000 1.03
NAcc isoform ratio 0 0.000 1.03
NAcc intron excision ratio 0 0.000 1.09
NAcc mRNA stability 0 0.000 0.97
OFC alternative polyA 0 0.000 1.08
OFC alternative TSS 0 0.000 0.86
OFC gene expression 0 0.000 1.03
OFC isoform ratio 0 0.000 1.09
OFC intron excision ratio 0 0.000 1.28
OFC mRNA stability 0 0.000 0.98
PL alternative polyA 0 0.000 1.02
PL alternative TSS 0 0.000 0.85
PL gene expression 1 0.014 1.03
PL isoform ratio 0 0.000 1.08
PL intron excision ratio 0 0.000 1.15
PL mRNA stability 0 0.000 1.01

avg chisq: Average Chi2 (squared Z-score) across all models in this panel for this trait.