Derived from data made available by the Genotype Tissue Expression (GTEx) project (Lonsdale et al. 2013), which provides \(z\)-scores for assessing the significance of effects of genetic variants (single nucleotide polymorphisms, or SNPs) on gene expression across 44 human tissues. To reduce the data to a more manageable size, Urbut et al. (2019) chose the "top" SNP for each gene --- that is, the SNP associated with the largest (absolute) \(z\)-score over all 44 tissues. This yields a \(16,069 \times 44\) matrix of \(z\)-scores, with rows corresponding to SNP-gene pairs and columns corresponding to tissues. The dataset included here is further subsampled down to 1000 rows.
gtex is a matrix with 1000 rows and 44 columns, with rows
corresponding to SNP-gene pairs and columns corresponding to tissues.
https://github.com/stephenslab/gtexresults/blob/master/data/MatrixEQTLSumStats.Portable.Z.rds
Lonsdale et al. (2013). "The Genotype-Tissue Expression (GTEx) project." Nature Genetics 45(6), 580--585.
Urbut, Wang, Carbonetto, and Stephens (2019). "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions." Nature Genetics 51(1), 187--195.
data(gtex)
summary(gtex)
#> Adipose_Subcutaneous Adipose_Visceral_Omentum Adrenal_Gland
#> Min. :-22.19423 Min. :-14.87582 Min. :-12.57593
#> 1st Qu.: -1.84280 1st Qu.: -1.57162 1st Qu.: -1.26369
#> Median : -0.06988 Median : -0.05287 Median : -0.01588
#> Mean : -0.27107 Mean : -0.16151 Mean : -0.16142
#> 3rd Qu.: 1.48032 3rd Qu.: 1.19198 3rd Qu.: 0.93398
#> Max. : 21.08357 Max. : 16.43779 Max. : 13.65782
#> Artery_Aorta Artery_Coronary Artery_Tibial
#> Min. :-17.62629 Min. :-12.74545 Min. :-23.307430
#> 1st Qu.: -1.45706 1st Qu.: -1.11132 1st Qu.: -1.598985
#> Median : -0.01537 Median : -0.06018 Median : 0.008435
#> Mean : -0.15449 Mean : -0.11235 Mean : -0.134894
#> 3rd Qu.: 1.27376 3rd Qu.: 1.03352 3rd Qu.: 1.497730
#> Max. : 18.06622 Max. : 11.14108 Max. : 22.814513
#> Brain_Anterior_cingulate_cortex_BA24 Brain_Caudate_basal_ganglia
#> Min. :-8.99940 Min. :-12.12301
#> 1st Qu.:-1.08092 1st Qu.: -1.16093
#> Median :-0.03334 Median : 0.05487
#> Mean :-0.07624 Mean : 0.00441
#> 3rd Qu.: 0.96140 3rd Qu.: 1.06846
#> Max. : 7.90574 Max. : 11.00090
#> Brain_Cerebellar_Hemisphere Brain_Cerebellum Brain_Cortex
#> Min. :-12.144353 Min. :-12.86501 Min. :-10.85760
#> 1st Qu.: -1.098736 1st Qu.: -1.19935 1st Qu.: -1.14260
#> Median : 0.020778 Median : -0.03972 Median : -0.03468
#> Mean : 0.000413 Mean : -0.01722 Mean : -0.05909
#> 3rd Qu.: 1.107743 3rd Qu.: 1.10800 3rd Qu.: 1.01669
#> Max. : 10.897779 Max. : 11.67528 Max. : 11.59038
#> Brain_Frontal_Cortex_BA9 Brain_Hippocampus Brain_Hypothalamus
#> Min. :-11.80390 Min. :-11.232401 Min. :-10.031394
#> 1st Qu.: -1.14363 1st Qu.: -1.023547 1st Qu.: -0.905895
#> Median : -0.07074 Median : 0.005028 Median : -0.007766
#> Mean : -0.05440 Mean : 0.005987 Mean : -0.043437
#> 3rd Qu.: 1.02602 3rd Qu.: 1.007408 3rd Qu.: 0.879970
#> Max. : 10.35621 Max. : 8.075452 Max. : 8.981126
#> Brain_Nucleus_accumbens_basal_ganglia Brain_Putamen_basal_ganglia
#> Min. :-10.8223 Min. :-9.46936
#> 1st Qu.: -1.1396 1st Qu.:-1.10615
#> Median : -0.1130 Median :-0.04910
#> Mean : -0.1048 Mean :-0.06563
#> 3rd Qu.: 0.9185 3rd Qu.: 1.00442
#> Max. : 9.5235 Max. : 8.90531
#> Breast_Mammary_Tissue Cells_EBV-transformed_lymphocytes
#> Min. :-15.6587 Min. :-10.57911
#> 1st Qu.: -1.4741 1st Qu.: -1.25969
#> Median : -0.0223 Median : -0.03338
#> Mean : -0.1313 Mean : -0.10913
#> 3rd Qu.: 1.2819 3rd Qu.: 1.02339
#> Max. : 16.8237 Max. : 14.77698
#> Cells_Transformed_fibroblasts Colon_Sigmoid Colon_Transverse
#> Min. :-17.0952 Min. :-13.33327 Min. :-15.36002
#> 1st Qu.: -1.7708 1st Qu.: -1.34944 1st Qu.: -1.36955
#> Median : -0.1495 Median : -0.06941 Median : -0.03634
#> Mean : -0.3416 Mean : -0.16364 Mean : -0.20777
#> 3rd Qu.: 1.2835 3rd Qu.: 1.04081 3rd Qu.: 1.06871
#> Max. : 19.2887 Max. : 13.37116 Max. : 15.64862
#> Esophagus_Gastroesophageal_Junction Esophagus_Mucosa Esophagus_Muscularis
#> Min. :-13.42037 Min. :-19.5164 Min. :-18.61334
#> 1st Qu.: -1.27899 1st Qu.: -1.5160 1st Qu.: -1.71632
#> Median : -0.03443 Median : -0.1147 Median : -0.06828
#> Mean : -0.13436 Mean : -0.1280 Mean : -0.25893
#> 3rd Qu.: 1.05542 3rd Qu.: 1.3108 3rd Qu.: 1.35094
#> Max. : 12.27858 Max. : 19.6146 Max. : 18.45721
#> Heart_Atrial_Appendage Heart_Left_Ventricle Liver
#> Min. :-14.16783 Min. :-15.2517 Min. :-11.116238
#> 1st Qu.: -1.45627 1st Qu.: -1.3879 1st Qu.: -0.921782
#> Median : -0.07628 Median : -0.0378 Median : 0.007326
#> Mean : -0.18849 Mean : -0.2160 Mean : -0.012890
#> 3rd Qu.: 1.10405 3rd Qu.: 1.0856 3rd Qu.: 0.965711
#> Max. : 14.05779 Max. : 15.3510 Max. : 8.653149
#> Lung Muscle_Skeletal Nerve_Tibial Ovary
#> Min. :-20.4296 Min. :-23.1101 Min. :-20.97164 Min. :-10.31093
#> 1st Qu.: -1.6291 1st Qu.: -1.7727 1st Qu.: -1.88211 1st Qu.: -1.10607
#> Median : -0.1825 Median : -0.1185 Median : -0.02156 Median : 0.02842
#> Mean : -0.2045 Mean : -0.3323 Mean : -0.21575 Mean : -0.05246
#> 3rd Qu.: 1.3875 3rd Qu.: 1.3392 3rd Qu.: 1.52011 3rd Qu.: 1.02720
#> Max. : 21.4307 Max. : 20.0308 Max. : 22.36088 Max. : 10.35619
#> Pancreas Pituitary Prostate
#> Min. :-13.85419 Min. :-11.0648 Min. :-10.15243
#> 1st Qu.: -1.36881 1st Qu.: -1.2287 1st Qu.: -1.13629
#> Median : -0.07797 Median : -0.1005 Median : -0.12194
#> Mean : -0.17514 Mean : -0.1267 Mean : -0.07537
#> 3rd Qu.: 1.10445 3rd Qu.: 1.0129 3rd Qu.: 0.97536
#> Max. : 15.43049 Max. : 10.3997 Max. : 10.83603
#> Skin_Not_Sun_Exposed_Suprapubic Skin_Sun_Exposed_Lower_leg
#> Min. :-16.80919 Min. :-23.10359
#> 1st Qu.: -1.41420 1st Qu.: -1.72428
#> Median : 0.03397 Median : -0.08678
#> Mean : -0.04676 Mean : -0.15531
#> 3rd Qu.: 1.30838 3rd Qu.: 1.41275
#> Max. : 15.69632 Max. : 22.23993
#> Small_Intestine_Terminal_Ileum Spleen Stomach
#> Min. :-8.719451 Min. :-10.6512 Min. :-14.36215
#> 1st Qu.:-1.079962 1st Qu.: -1.2765 1st Qu.: -1.35343
#> Median : 0.001343 Median : -0.1641 Median : -0.05671
#> Mean :-0.102133 Mean : -0.1566 Mean : -0.17118
#> 3rd Qu.: 0.971632 3rd Qu.: 0.9506 3rd Qu.: 1.19389
#> Max. : 8.807607 Max. : 11.4742 Max. : 14.75691
#> Testis Thyroid Uterus Vagina
#> Min. :-12.4311 Min. :-20.74476 Min. :-8.33238 Min. :-8.60648
#> 1st Qu.: -1.4523 1st Qu.: -1.81461 1st Qu.:-1.12685 1st Qu.:-1.04414
#> Median : -0.1939 Median : -0.01762 Median :-0.01644 Median :-0.02833
#> Mean : -0.1863 Mean : -0.11999 Mean :-0.10482 Mean :-0.05341
#> 3rd Qu.: 1.1162 3rd Qu.: 1.55465 3rd Qu.: 0.87098 3rd Qu.: 0.96256
#> Max. : 16.4308 Max. : 22.27820 Max. : 9.66800 Max. : 9.45592
#> Whole_Blood
#> Min. :-23.1985
#> 1st Qu.: -1.4820
#> Median : -0.1303
#> Mean : -0.1078
#> 3rd Qu.: 1.1960
#> Max. : 19.4720