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. Author manuscript; available in PMC: 2017 Oct 4.
Published in final edited form as: Nat Genet. 2016 Oct 10;48(11):1396–1406. doi: 10.1038/ng.3695

Table 3.

Gene set and tissue enrichment results for associations with individual bacterial traits

Top 20 enriched gene sets
Top 20 Enriched Tissues
Original gene
set ID		 Original gene set description Nominal P Name MeSH
first-level
term		 MeSH
second-level
term		 Nominal P MeSH term
GO:0007566 Embryo implantation 2.29 × 10−5 Keratinocytes Cells Epithelial cells 2.85 × 10−3 A11.436.397
MP:0009402 Decreased skeletal muscle fber diameter 4.09 × 10−5 Intestines Digestive system Gastrointestinal tract 5.57 × 10−3 A03.556.124
GO:0033273 Response to vitamin 4.77 × 10−5 Gastrointestinal tract Digestive system Gastrointestinal tract 6.7 × 10−3 A03.556
GO:0033280 Response to vitamin D 8.8 × 10−5 Lower
gastrointestinal
tract		 Digestive system Gastrointestinal tract 6.92 × 10−3 A03.556.249
MP:0006317 Decreased urine sodium level 1.19 × 10−4 Colon Digestive system Gastrointestinal tract 7.07 × 10−3 A03.556.249.249.356
GO:0071496 Cellular response to external stimulus 1.73 × 10−4 Intestine, large Digestive system Gastrointestinal tract 7.27 × 10−3 A03.556.249.249
MP:0010027 Increased liver cholesterol level 1.73 × 10−4 Hepatocytes Cells Epithelial cells 9.19 × 10−3 A11.436.348
MP:0000221 Digestive system 1.75 × 10−4 Ileum Digestive system Gastrointestinal tract 9.96 × 10−3 A03.556.249.124
GO:0007229 Integrin-mediated signaling pathway 1.97 × 10−4 Rectum Digestive system Gastrointestinal tract 0.01 A03.556.124.526.767
GO:0031668 Cellular response to extracellular stimulus 2.33 × 10−4 Intestinal mucosa Digestive system Gastrointestinal tract 0.02 A03.556.124.369
GO:0033189 Response to vitamin A 2.5 × 10−4 Mucous membrane Tissues Membranes 0.02 A10.615.550
GO:0031669 Cellular response to nutrient levels 3.03 × 10−4 Colon, sigmoid Digestive system Gastrointestinal tract 0.02 A03.556.249.249.356.668
GO:0055093 Response to hyperoxia 3.09 × 10−4 Epithelial cells Cells Epithelial cells 0.03 A11.436
ENSG00000215328 HSPA1A PPI subnetwork 3.27 × 10−4 Hypothalamo hypophyseal system Nervous system Central nervous system 0.03 A08.186.211.730.317.357. 352.435
ENSG00000143393 PI4KB PPI subnetwork 3.37 × 10−4 Neurosecretory systems Nervous system Neurosecretory systems 0.03 A08.713
MP:0005266 Abnormal metabolism 3.51 × 10−4 Hypothalamus, middle Nervous system Central nervous system 0.03 A08.186.211.730.317.35 7.352
GO:0048545 Response to steroid hormone stimulus 3.54 × 10−4 Membranes Tissues Membranes 0.04 A10.615
GO:0009991 Response to extracellular stimulus 3.7 × 10−4 Monocyte macrophage precursor cells Cells Myeloid cells 0.04 A11.627.624.249
GO:0033143 Regulation of intracellular steroid hormone receptor signaling pathway 4.29 × 10−4 Urinary bladder Urogenital system Urinary tract 0.04 A05.810.890
GO:0031490 Chromatin DNA binding 4.59 × 10−4 Intestine, small Digestive system Gastrointestinal tract 0.04 A03.556.124.684

Enrichment analysis was performed using DEPICT for the 40 loci associated with individual bacterial traits. The table shows the 20 most enriched gene sets (three left columns) and the 20 most enriched tissues or cell types (fve right columns). For tissue and cell type enrichment, headings are given for minimum two MeSH levels: frst- and second-level terms. The “Name” column contains the name for the lowest level term with enrichment. The MeSH codes for the hierarchical branch are given in the “MeSH term” column. Analysis for enriched genes and analysis for enriched tissues were independent of each other.