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