KSHV	Kaposi’s sarcoma-associated herpesvirus
HHV8	Human herpesvirus-8
EBV	Epstein–Barr virus
TRN	Transcription factor or transcriptional regulatory network
IEGs	Immediate-early genes
TFs	Transcription factors
IL-8	Interleukin 8
CXCL8	Chemokine (C-X-C motif) ligand 8
CXCL7	Chemokine (C-X-C motif) ligand 7
CCL19	Chemokine (C-C motif) ligand 19
CXCL13	Chemokine (C-X-C motif) ligand 13
MSI	Microsatellite instability
MSS	Microsatellite stability
APC	Adenomatous polyposis coli
KRAS	Kirsten rat sarcoma virus
PIK3CA	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha
SMAD4	Mothers against decapentaplegic homolog 4
TP53	Tumor protein P53
DCC	Netrin receptor
SMAD	Mothers against decapentaplegic
BRAF	B-Raf Proto-Oncogene
Wnt	Wingless-related integration site
BMP	Bone morphogenetic protein
TGFβ	Transforming growth factor-beta
Ras	Rat sarcoma virus
ST6GALNAC1	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1
CDH1	Cadherin 1
STK11	Serine/threonine kinase 11
MLH1	mutL homolog 1
MSH2	mutS homolog 2
EPCAM	Epithelial cell adhesion molecule
MSH6	mutS homolog 6
PMS2	PMS1 homolog 2, mismatch repair system component
FAP	Familial adenomatous polyposis
BRCA2	BReast CAncer gene 2
PALB2	Partner and localizer of BRCA2
CLDN18-ARHGAP	Fusion Gene_Claudin 18-Rho GTPase-activating protein
ARID1A	AT-rich interaction domain 1A
PD-L1/2	Programmed cell death ligand ½
ICIs	Immune checkpoint inhibitors
CTLA-4	Cytotoxic T-lymphocyte associated protein 4
PD-1	Programmed cell death 1
LAG-3	Lymphocyte activating 3
TIM-3	Hepatitis A virus cellular receptor 2
PD-L1	CD274 molecule
ERBB2	erb-b2 receptor tyrosine kinase 2
MET	Methoprene-tolerant proto-oncogene, receptor tyrosine kinase
NKX2	Ventral nervous system defective
DOK2	Docking protein 2
ALK	Anaplastic lymphoma receptor tyrosine kinase
ROS1	ROS proto-oncogene 1, receptor tyrosine kinase
RET	Ret proto-oncogene
ALK/EML4	Anaplastic lymphoma receptor tyrosine kinase–Echinoderm microtubule-associated protein-like 4
TTN	titin
CSMD3	CUB and Sushi multiple domains 3
MUT16	MUTator 16
RYR2	Ryanodine receptor 2
BRINP3	BMP/retinoic acid inducible neural specific 3
COL11A1	Collagen type XI alpha 1 chain
GRIN2B	Glutamate ionotropic receptor NMDA type subunit 2B
MUC5B	Mucin 5B, oligomeric mucus/gel-forming
NLRP3	NLR family pyrin domain containing 3
TENM3	Teneurin transmembrane protein 3
NSCLC	Non-small cell lung cancer
LUAD	Lung adenocarcinoma
LUSC	Lung squamous cell carcinoma
TCGA-STAD	The Cancer Genome Atlas Stomach Adenocarcinoma
RUNX2	Runt-related transcription factor 2
SOX4	SRY-box transcription factor 4
SOX17	SRY-box transcription factor 17
BZW2	Basic leucine zipper and W2 domains 2
FOXM1	Forkhead box M1
ZBTB16	Zinc finger and BTB domain containing 16
TAL1	T-cell acute lymphocytic leukemia 1 bHLH transcription factor 1, erythroid differentiation factor
KLF4	Kruppel-like transcription factor 4
EPAS1	Endothelial PAS domain protein 1
HOXC6	Homeobox C6
ID4	Inhibitor of DNA binding 4
KLF2	Kruppel-like transcription factor 2
MEIS1	Meis homeobox 1
NR2F1	Nuclear receptor subfamily 2 group F member 1
TBX4	T-box transcription factor 4
TCF21	Transcription factor 21
TFAP2C	Transcription factor AP-2 gamma
LMO2	LIM domain only 2
MNDA	Myeloid cell nuclear differentiation antigen
FOXF1	Forkhead box F1
HLF	HLF transcription factor, PAR bZIP family member
RFX2	Regulatory factor X2
DLX5	Distal-less homeobox 5
MYBL2	MYB proto-oncogene like 2
NR4A3	Nuclear receptor subfamily 4 group A member 3
PKNOX2	PBX/knotted 1 homeobox 2
GPRASP1	G protein-coupled receptor associated sorting protein 1
PAH	Pulmonary arterial hypertension
DEGs	Differentially expressed genes
CpG	Cytosine–guanine dinucleotides
DNMT1	DNA methyltransferase 1
DNMT3A	DNA methyltransferase 3 Alpha
DNMT3B	DNA methyltransferase 3 Beta
TET	Ten-eleven translocation family
FIGN	Fidgetin, microtubule severing factor
HTRA3	HtrA serine peptidase 3
BDNF	Brain-derived neurotrophic factor
HCN4	Hyperpolarization activated cyclic nucleotide gated potassium channel 4
STAC2	SH3- and cysteine-rich domain 2
SEPT9	Septin 9
SDC2	Syndecan 2
MGMT	O-6-methylguanine-DNA methyltransferase
NDGR4	N-Myc Downstream-Regulated Gene 4 Protein
BMP3	Bone morphogenetic protein 3
VIM	Vimentin
SFRP	Secreted frizzled-related protein
p16	Cyclin-dependent kinase inhibitor 2A
LINE-1	Long interspersed nuclear element 1
BCAT1/IKZF1	Branched-chain amino acid transaminase 1-IKAROS family zinc finger 1
RASSF1A	Ras-association domain family member 1
Wnt5A	Wnt family member 5A
SFRP2	Secreted frizzled-related protein 2
DKK2	Dickkopf WNT signaling pathway inhibitor 2
PCDH10	Protocadherin 10
TMEFF2	Transmembrane protein with EGF-like and two follistatin-like domains 2
SFRP1	Secreted frizzled-related protein 1
HS3ST2	Heparan sulfate-glucosamine 3-sulfotransferase 2
CDH1/RHOA	Cadherin 1-ras homolog family member A
RPRM	Reprimo, TP53-dependent G2 arrest mediator homolog
ZNF793	Zinc finger protein 793
RUNX3	Runt-related transcription factor 3
PTEN	Phosphatase and tensin homolog
CXXC4	CXXC finger protein 4
TIMP2	TIMP metallopeptidase inhibitor 2
COL9A2	Collagen type IX alpha 2 chain
EYA1	EYA transcriptional coactivator and phosphatase 1
ZNF365	Zinc finger protein 365
AMPH	Amphiphysin
SORCS3	Sortilin-related VPS10 domain containing receptor 3
AJAP1	Adherens junctions-associated protein 1
TGFβ2	Transforming growth factor beta 2
SHOX2	Short stature homeobox 2
RASSF1A	Ras-association domain family member 1
RASSF1A-RARβ2	Ras-association domain family member 1–retinoic acid receptor beta 2
SHOX2-PTGER4	Short stature homeobox 2-prostaglandin E receptor 4
p16-RARβ2	Cyclin=dependent kinase inhibitor 2A–retinoic acid receptor beta 2
DAL-1	Erythrocyte membrane protein band 4.1 like 3
EPHB6	EPH receptor B6
HS3ST2	Heparan sulfate-glucosamine 3-sulfotransferase 2
TMEM88	Transmembrane protein 88
ELMO3	Engulfment and cell motility 3
HOXA9	Homeobox A9
RARβ2	Retinoic acid receptor beta 2
CDH13	Cadherin 13
CDKN2A/P16	Cyclin-dependent kinase inhibitor 2A
CASP8	Caspase 8
TNFRSF6/Fas	Fas cell surface death receptor
TRAIL-R1/DR4	TNF receptor superfamily member 10a
SCLC	Small-cell carcinoma
cfDNA	Cell-free DNA
ANK1	Ankyrin 1
CCND2	Cyclin D2
GATA3	GATA-binding protein 3
KCNH5	Potassium voltage gated channel subfamily H member 5
RARβ	Retinoic acid receptor beta
RASSF1	Ras-association domain family member 1
CLDN1	Claudin 1
TP63	Tumor protein p63
TPX5	T-box transcription factor 5
ADHFE1	Alcohol dehydrogenase iron containing 1
HNF1B	HNF1 homeobox B
EZH2	Enhancer of zeste 2 polycomb-repressive complex 2 subunit
IBD	Inflammatory bowel disease
COPD	Chronic obstructive pulmonary disease
PAH-LTRS	PAH associated with the congenital left-to-right shunt
CSCs	Cancer stem cells
NF-kB	Nuclear factor kappaB
STAT3	Signal transducer and activator of transcription 3
SCFAs	Short-chain fatty acids
MUC2	Mucin 2, oligomeric mucus/gel-forming
IL-6	Interleukin 6
MUC5B	Mucin 5B, oligomeric mucus/gel-forming
MUC7	Mucin 7, secreted
IL-1	Interleukin 1
IL-8	Interleukin 8
TNF α	Tumor necrosis factor alpha-like
GRHL2	Grainyhead-like 2 transcription factor
RhoG	Ras homology growth
ZEB1	Zinc finger E-box binding homeobox 1
MHC	Major histocompatibility complex
TLR	Toll-like receptors
HLA-A	Major histocompatibility complex, class I, A
HLA-B	Major histocompatibility complex, class I, B
HLA-C	Major histocompatibility complex, class I, C
CD8+ T cells	Cytotoxic T lymphocytes
HLA-DP	Major histocompatibility complex, class II, DP
HLA-DQ	Major histocompatibility complex, class II, DQ
HLA-DR	Major histocompatibility complex, class II, DR
CD4+ T cells	Helper T lymphocytes
TSA	Tumor-specific antigen
CTLA4	Cytotoxic T-lymphocyte-associated protein 4
APOBEC	Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide 3
PAMPs	Pathogen-associated molecular patterns
PRRs	Pattern-recognition receptors
RLRs	Retinoic acid-inducible gene-I (RIG-I)-like receptors
ALRs	Melanoma-2 (AIM2)-like receptors
CLRs	C-type lectin receptors
NLRs	Nucleotide oligomerization domain (NOD)-like receptors
MAVS	Mitochondrial antiviral-signaling protein
TBK1	TANK-binding kinase 1
IKKε	Nuclear factor kappaB kinase-ε
IRF3	Interferon regulatory factor 3
IRF7	Interferon regulatory factor 7
CRD	Carbohydrate-recognition domain
CTLD	C-type lectin-like domain
Dectin-1	C-type lectin 1
ITAM	Immunoreceptor tyrosine-based activation motif
DC-SIGN	DC-specific ICAM3-grabbing non-integrin
NAIP	NLR family apoptosis inhibitory protein
CIITA	Class II major histocompatibility complex transactivator
HETE	Cytochrome P450 family 4 subfamily F member 2
TP1	Transition protein 1
TIR	Toll/IL-1R domain