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. 2018 Aug 10;33(1):965–977. doi: 10.1096/fj.201800554RR

TABLE 2.

Top 10 enriched gene sets (pathways) that are associated with aging and epicatechin supplementation in SkM

Gene Gene set name (pathway)a K Gene description k k/Kb P FDR q
YC vs. OC (791 genes applied)c NABA_MATRISOME 1028 Ensemble of genes encoding ECM and ECM-associated proteins 137 0.1333 9.44E−85 1.25E−81
NABA_CORE_MATRISOME 275 Ensemble of genes encoding core ECM, including ECM glycoproteins, collagens, and proteoglycans 68 0.2473 2.00E−60 1.33E−57
NABA_ECM_GLYCOPROTEINS 196 Genes encoding structural ECM glycoproteins 42 0.2143 7.28E−35 3.22E−32
NABA_MATRISOME_ASSOCIATED 753 Ensemble of genes encoding ECM-associated proteins, including ECM-affiliated proteins, ECM regulators, and secreted factors 69 0.0916 6.64E−32 2.21E−29
NABA_ECM_REGULATORS 238 Genes encoding enzymes and their regulators involved in the remodeling of the ECM 39 0.1639 8.52E−28 2.26E−25
KEGG_COMPLEMENT_AND_COAGULATION_CASCADES 69 Complement and coagulation cascades 25 0.3623 1.24E−27 2.35E−25
KEGG_PPAR_SIGNALING_PATHWAY 69 PPAR-signaling pathway 25 0.3623 1.24E−27 2.35E−25
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS 478 Genes involved in metabolism of lipids and lipoproteins 51 0.1067 7.24E−27 1.20E−24
KEGG_FOCAL_ADHESION 201 Focal adhesion 35 0.1741 5.28E−26 7.80E−24
PID_INTEGRIN1_PATHWAY 66 Beta1-integrin cell surface interactions 21 0.3182 4.81E−22 6.39E−20
OC vs. EC (222 genes applied)d NABA_CORE_MATRISOME 275 Ensemble of genes encoding core ECM, including ECM glycoproteins, collagens, and proteoglycans 20 0.0727 1.58E−18 2.10E−15
NABA_MATRISOME 1028 Ensemble of genes encoding ECM and ECM-associated proteins 29 0.0282 3.03E−15 2.01E−12
REACTOME_DEVELOPMENTAL_BIOLOGY 396 Genes involved in developmental biology 19 0.048 2.38E−14 1.05E−11
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS 478 Genes involved in metabolism of lipids and lipoproteins 20 0.0418 6.23E−14 2.07E−11
NABA_COLLAGENS 44 Genes encoding collagen proteins 9 0.2045 3.47E−13 8.96E−11
PID_INTEGRIN1_PATHWAY 66 Beta1-integrin cell surface interactions 10 0.1515 4.04E−13 8.96E−11
KEGG_PPAR_SIGNALING_PATHWAY 69 PPAR-signaling pathway 10 0.1449 6.44E−13 1.22E−10
REACTOME_NEURONAL_SYSTEM 279 Genes involved in neuronal system 15 0.0538 2.75E−12 4.44E−10
REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES 186 Genes involved in transmission across chemical synapses 13 0.0699 3.01E−12 4.44E−10
KEGG_ECM_RECEPTOR_INTERACTION 84 ECM–receptor interaction 10 0.119 4.94E−12 5.97E−10
Both YC vs. OC and OC vs. EC (92 genes applied)e NABA_CORE_MATRISOME 275 Ensemble of genes encoding core ECM, including ECM glycoproteins, collagens, and proteoglycans 18 0.0655 1.14E−22 1.52E−19
NABA_MATRISOME 1028 Ensemble of genes encoding ECM and ECM-associated proteins 23 0.0224 2.51E−18 1.67E−15
PID_INTEGRIN1_PATHWAY 66 Beta1-integrin cell surface interactions 10 0.1515 8.50E−17 3.76E−14
KEGG_ECM_RECEPTOR_INTERACTION 84 ECM–receptor interaction 10 0.119 1.08E−15 3.59E−13
REACTOME_DEVELOPMENTAL_BIOLOGY 396 Genes involved in developmental biology 15 0.0379 1.76E−15 4.68E−13
NABA_COLLAGENS 44 Genes encoding collagen proteins 8 0.1818 2.40E−14 5.31E−12
KEGG_FOCAL_ADHESION 201 Focal adhesion 11 0.0547 2.31E−13 4.22E−11
REACTOME_COLLAGEN_FORMATION 58 Genes involved in collagen formation 8 0.1379 2.54E−13 4.22E−11
KEGG_PPAR_SIGNALING_PATHWAY 69 PPAR-signaling pathway 8 0.1159 1.09E−12 1.56E−10
REACTOME_NCAM1_INTERACTIONS 39 Genes involved in NCAM1 interactions 7 0.1795 1.17E−12 1.56E−10

FDR, false discovery rate; K, genes in gene set (n); k, genes shared (n); NCAM, neural cell adhesion molecule. aAssociated pathways with differential gene expressions were identified by using Gene Set Enrichment Analysis (http://software.broadinstitute.org/gsea/msigdb). The list of top 100 pathways is provided in Supplemental Tables 2–4. bk/K = proportion of identified differential expression genes for a given gene set (pathway). cTop 10 enriched pathways that were associated with aging in SkM. dTop 10 enriched pathways that were associated with epicatechin supplementation in SkM of OC mice. eTop 10 enriched pathways that were associated with aging and epicatechin supplementation in SkM.