ART	antiretroviral therapy
DANCR	differentiation antagonizing non-protein coding RNA
FC	fold change
FIRRE	functional intergenic repeating RNA element
GBP1P1	guanylate binding protein 1 pseudogene 1
GO_BP	Gene Ontology Biological Process
GS	gene significance
HCV	hepatitis C
HIV-1	human immunodeficiency virus type I
IFN	interferon
ISGs	interferon stimulated genes
JAK-STAT	Janus kinase/signal transducer and activator of transcription
KEGG	Kyoto Encyclopedia of Genes and Genomes
lncRNAs	long non-coding RNAs
LPS	lipopolysaccharides
MDA5	melanoma differentiation-associated protein 5
MDMs	monocyte-derived macrophages
MM	module membership
ncRNAs	non-coding RNAs
NF-κB	nuclear factor kappa-light-chain-enhancer of activated B cells
NRIR	negative regulator of interferon response
PAMP	pathogen-associated molecular pattern
PBMCs	peripheral blood mononuclear cells
qPCR	quantitative reverse transcription polymerase chain reaction
RIG-I	retinoic acid-inducible gene I
ROS	reactive oxygen species
STAT	signal transducer and activator of transcription proteins
TNK2-AS1	TNK2 antisense RNA 1
WGCNA	Weighted gene co-expression network analysis