Table 3 Top enriched tissue-based gene sets in complex traits

From: Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes

Phenotype

Tissue (method)

log10BF

Select top driving genes (# of signals)

Alzheimer’s disease

Adrenal gland

(SE)

45.6

APOE, APOC1

(2)

Neuroticism

Brain

(SE)

26.3

LINGO1, KCNC2

(2)

Adult height

Nerve tibial

(DE)

25.2b

PTCH1, SFRP4, FLNB

(59)

Crohn’s disease

Cluster 1a

(DE)

15.4

SMAD3, ZMIZ1, NUPR1

(6)

Inflammatory bowel disease

Cluster 1a

(DE)

15.8

SMAD3, ZMIZ1, NUPR1

(10)

Ulcerative colitis

Heart

(HE)

7.0

PLA2G2A, TCAP, ALDOA

(4)

Age at natural menopause

Brain

(DE)

1053.2

BRSK1, PPP1R1B, NPTXR

(6)

Coronary artery disease

Brain

(DE)

8.5

PSRC1, ZEB2, PTPN11

(3)

Fasting glucose

Pancreas

(SE)

2396.8

G6PC2, PDX1, SLC30A8

(5)

Fasting insulin

Testis

(SE)

866.7

ABHD1, PRR30, C2orf16

(3)

Heart rate

Heart

(HE)

4.1

MYH6, PLN

(5)

High-density lipoprotein

Liver

(HE)

20.2

APOA1, APOE, MT1G, FTH1

(10)

Low-density lipoprotein

Liver

(SE)

33.4

ABCG5, LPA, ANGPTL3, HP

(13)

Total cholesterol

Liver

(DE)

56.0

APOA1, APOE, HP

(9)

Triglycerides

Liver

(HE)

93.2

APOA1, APOE, FTH1

(7)

Serum urate

Kidney

(SE)

210.8b

SLC17A1, SLC22A11, PDZK1

(7)

Hemoglobin (HB)

Whole blood

(DE)

2078.1

HIST1H1E, HIST1H1C

(4)

Mean cell HB

Whole blood

(DE)

1363.0

NPRL3, FBXO7, UBXN6

(11)

Mean cell volume

Whole blood

(DE)

1019.6b

UBXN6, RBM38, NPRL3

(11)

Packed cell volume

Heart

(HE)

945.4

RPL19, TCAP

(2)

Red blood cell count

Breast

(SE)

141.7

OBP2B, STAC2

(2)

  1. Each tissue-based gene set contains 100 transcribed genes used in the Genotype-Tissue Expression project. For each trait we report the most enriched tissue-based gene set (if any) that has a Bayes factor (BF) greater than 1000 and has more than two member genes with enrichment P1 > 0.9 (denoted as “signals”). All trait-tissue pairs reported above pass the sanity checks (Supplementary Fig. 17) The corresponding baseline and enrichment parameter estimates are provided in online results (Methods). P1: posterior probability that at least one SNP within 100 kb of the transcribed region of a given gene has nonzero effect on the target trait; HE: highly expressed; SE: selectively expressed; DE: distinctively expressed
  2. a Multiple tissues show partial membership in “Cluster 1”, including ovary, thyroid, spleen, breast, and stomach47
  3. b These three BFs are smaller than corresponding BFs that SNPs within 100 kb of transcribed regions of all genes are enriched (Supplementary Fig. 19)
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