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Table 1 LRpath analysis reveals that cytokine and hormone activity, immune response, and metabolic processes among the top enriched concepts within differentially methylated genes

From: Bisphenol A-associated epigenomic changes in prepubescent girls: a cross-sectional study in Gharbiah, Egypt

Dichotomous model - pathway (FDR <0.2, P-value <0.02)
Name Concept type #Genes Coeff Odds ratio P-Value FDR Enriched
Cytokine-cytokine receptor interaction KEGG Pathway 229 −0.200253028 0.288086617 3.06E-06 5.69E-04 Down
Metabolism of xenobiotics by cytochrome P450 KEGG Pathway 61 −0.287221818 0.167801921 1.58E-04 0.014739788 Down
Vitamin A (retinol) metabolism EHMN Pathway Gene 25 −0.428286702 0.069834019 3.14E-04 0.015401391 Down
N-Glycan biosynthesis KEGG Pathway 44 0.359631955 9.346216996 0.001289861 0.079971357 Up
Proteogylcan biosynthesis EHMN Pathway Gene 21 −0.40681778 0.079801493 0.001359963 0.0333191 Down
Oxidative phosphorylation KEGG Pathway 101 0.206370232 3.605679051 0.004079267 0.176257686 Up
C21-Steroid hormone metabolism KEGG Pathway 12 −0.42731737 0.07025597 0.00473811 0.176257686 Down
Proteasome KEGG Pathway 21 0.442939628 15.68486443 0.006686061 0.18372292 Up
Ribosome KEGG Pathway 59 0.255415299 4.890555948 0.006914303 0.18372292 Up
Natural killer cell mediated cytotoxicity KEGG Pathway 116 −0.157029295 0.376862256 0.008222671 0.188057588 Down
Dichotomous model - GO (FDR <0.01, P-value <5e-4, Odds ratio >5)
Name Concept type #Genes Coeff Odds ratio P-value FDR Enriched
Epidermis development GO Biological Process 120 −0.288785876 0.166178787 7.22E-08 2.83E-05 Down
Ectoderm development GO Biological Process 130 −0.27220051 0.184220938 1.69E-07 4.41E-05 Down
Sensory perception of chemical stimulus GO Biological Process 81 −0.326598184 0.131377584 2.59E-07 5.80E-05 Down
Digestion GO Biological Process 85 −0.314243619 0.141861941 4.72E-07 8.22E-05 Down
Ribonucleoprotein complex biogenesis and assembly GO Biological Process 161 0.282212002 5.776725456 5.25E-07 8.23E-05 Up
Regulation of homeostatic process GO Biological Process 18 −0.534094322 0.03618224 2.19E-06 3.12E-04 Down
G-protein-couples receptor binding GO Molecular Function 69 −0.298251857 0.156684914 1.91E-05 0.001995771 Down
Chemokine binding GO Molecular Function 26 −0.431856927 0.068301636 2.48E-05 0.002021324 Down
Sensory perception of smell GO Biological Process 56 −0.318324204 0.138309662 2.90E-05 0.002387889 Down
Serine-type endopeptidase inhibitor activity GO Molecular Function 73 −0.285841884 0.169247136 2.90E-05 0.002021324 Down
Continuous model - pathway (FDR <0.2, P-value <0.02)
Name Concept type #Genes Coeff Odds ratio P-Value FDR Enriched
Cytokine-cytokine receptor interation KEGG Pathway 229 −0.205604496 0.278663207 9.68E-09 1.80E-06 Down
Metabolism of xenobiotics by cytochrome P450 KEGG Pathway 61 −0.2927432 0.162141761 4.33E-06 4.03E-04 Down
Complement and coagulation cascades KEGG Pathway 66 0.25256689 0.208127535 5.11E-05 0.003167145 Down
Plaminogen activating cascade Panther Pathway 13 −0.497645229 0.045380623 6.32E-05 0.114613557 Down
Cytokines and Inflammatory Response Biocarta Pathway 29 −0.33471697 0.124913374 195E-04 0.035217055 Down
Ribosome KEGG Pathway 59 0.287062223 5.953499593 2.21E-04 0.010264183 Up
Vitamin A (retinol) metabolism EHMN Pathway Gene 25 −0.385600917 0.091048898 2.51E-04 0.012317017 Down
Autoimmune thyroid disease KEGG Pathway 47 −0.26174305 0.196590877 3.38E-04 0.012575822 Down
Oxidative phosphorylation KEGG Pathway 101 0.209255664 3.670918657 4.30E-04 0.013316379 Up
Asthma KEGG Pathway 26 −0.321259111 0.135809858 6.79E-04 0.015209508 Down
Continuous model - GO (FDR <0.01, P-value <5e-4, Odds ratio >5)
Name Concept type #Genes Coeff Odds ratio P-Value FDR Enriched
Sensory perception of chemical stimulus GO Biological Process 81 −0.378994195 0.094865006 8.35E-14 6.54E-11 Down
Digestion GO Biological Process 85 −0.332578826 0.126584265 6.03E-11 2.10E-08 Down
Epidermis development GO Biological Process 120 −0.281910372 0.17343325 2.06E-10 5.38E-08 Down
Ectoderm development GO Biological Process 130 −0.26538019 0.192197099 7.20E-10 1.34E-07 Down
Sensory perception of smell GO Biological Process 56 −0.372825845 0.09857215 7.72E-10 1.34E-07 Down
Acute inflammatory response GO Biological Process 69 −0.321398071 0.135692626 1.28E-08 1.55E-06 Down
Serine-type endopeptidase inhibitor activity GO Molecular Function 73 −0.304550109 0.150670556 3.09E-08 2.71E-06 Down
olfactory receptor activity GO Molecular Function 42 −0.377710874 0.095624611 3.89E-08 2.71E-06 Down
Immunoglobulin mediated immune response GO Biological Process 50 −0.352071918 0.11214204 5.47E-08 5.72E-06 Down
B cell mediated immunity GO Biological Process 51 −0.34665743 0.115979703 7.23E-08 7.08E-06 Down
Continuous model - metabolite
Progesterone Metabolite 34 −0.456431331 0.058628061 2.25E-07 1.04E-04 Down
Testerone Metabolite 53 −0.364806957 0.103608877 5.41E-07 1.25E-04 Down
Trichloroethanol Metabolite 46 −0.365998732 0.102844341 2.20E-06 2.59E-04 Down
Estradiol-17beta Metabolite 47 −0.362340859 0.105208999 2.25E-06 2.59E-04 Down
  1. This table depicts the top 10 GO and pathway concepts in both the dichotomous and continuous analyses.