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Table 2 Differential methylation patterns by gene location

From: Epigenetics may characterize asymptomatic COVID-19 infection

Gene

Chromosomal location (hg19)

Gene function

Hypothetical clinical implications

β-coefficient

Difference in methylation (asymptomatic – symptomatic)

Q value*

F-box only protein 16 (FBXO16)

8.28302736

Promotes phosphorylation-dependent ubiquination and degradation, involved in controlling amount of protein in eukaryotes

Degradation of beta-catenin leads to decreased cell adherent protein expression, leading to disruption of cardiac electrical and mechanical communication between myocytes

− 0.23

− 0.07

0.004

Pleckstrin and Sec7 domain containing 3 (PSD3)

8.18663702

Codes protein, involved in endocytosis, implicated in tumor suppression

Increases signal transduction targeting proteins to subcellular compartments to respond to viral infection

− 0.14

− 0.13

0.009

Ribonucleic acid export 1 (RAE1)

20.55953214

Nucleocytoplasmic transport, mitotic checkpoint regulator

This tumor suppressor gene may be important for cell division in immune cells

-0.20

-0.11

0.009

NIPA like domain containing 2 (NIPAL2)

8.99306708

Autosomal recessive gene associated with congenital ichthyosis

Involved in transport of glucose and other sugars, likely in response to increased metabolic demands of infection

− 0.12

− 0.13

0.019

SH3 and multiple ankyrin repeat domains 2 (SHANK2)

11.70681592

Codes postsynaptic proteins at excitatory synapses, disruption may predispose to autism or developmental delay

May play a role in SARS-CoV-2 induced altered mental status

− 0.22

− 0.05

0.023

Phosphoglucomutase 1 (PGM1)

1.64117325

Codes isozyme of phosphoglucomutase (PGM), mutations cause glycogen storage disease type 14, highly polymorphic, mutations causes glycogen storage disease

Associated with breakdown and synthesis of glucose, upregulated during acute infection due to metabolic demands

− 0.15

− 0.11

0.029

  1. *We report q-values rather than p values. Q-values are adjusted using the Benjamini–Hochberg Procedure, which controls the false discovery rate (FDR). The raw p values do not account for the number of statistical tests being performed and, without correcting for multiple tests, there would be many false positives due to chance