AKT/PKB	serine/threonine kinase/protein kinase B
AMBRA1	Autophagy and beclin 1 regulator 1
AMPK	5′ Adenosine-monophosphate-activated protein kinase
APC	Adenomatous polyposis coli
ATG	Autophagy-related genes or proteins
BAX	Bcl-2-associated X protein
BECN1	Beclin1, a mammalian ortholog of the yeast Atg6
BEST4	Bestrophin 4
BNIP3	Bcl-2-interacting protein 3
BNIP3L	Bcl-2/adenovirus E1B 19kDa protein-interacting protein 3-like
BRAF	Proto-oncogene B-Raf; encodes protein called B-Raf
CCL2/MCP-1	Chemokine (C-C Motif) ligand 2/monocyte chemoattractant protein 1
CCL8/MCP-2	Chemokine (C-C Motif) ligand 8/monocyte chemoattractant protein 2
C/E/I/M(SCs)	Cancer/embryonic/intestinal/mesenchymal stem cells
CD	Crohn’s disease
CI	Confidence interval
CIMP	CpG island methylator phenotype
CIN	Chromosomal instability
c-MET	Tyrosine-protein kinase Met/hepatocyte growth factor receptor (HGFR)
c-Myc	Proto-oncogene protein; transcription factor
CQ	Chloroquine
CRC	Colorectal cancer
CSCs	Cancer stem cells
c-Src	Src proto-oncogene, non-receptor tyrosine kinase
DECP1	Double FYVE-containing protein 1 or ZFYVE1 protein
EGF/EGFR	Epidermal growth factor/EGF receptor (HER1 in humans)
eIF4A3	Eukaryotic initiation factor 4A-III
ERK1/2	Extracellular signal-regulated kinase 1/2
FAK	Focal adhesion kinase or protein tyrosine kinase 2
FOXO	Forkhead box protein class O
GAPs	Goblet cell-associated antigen passage
GH/GH-R	Growth hormone/GH-receptor
GLP-2	Glucagon-like peptide 2
GNPTAB	N-acetylglucosamine-1-phosphotransferase subunits alpha/beta
GSK-3β	Glycogen synthase kinase-3β
HIF-1	Hypoxia-inducible factor 1
IBD	Inflammatory bowel diseases
IECs	Intestinal epithelial cells
IGF-1, -2	Insulin growth factor 1, -2
IGF-1R, -2R	IGF receptor type I, type II
IGF-BPs	IGF-binding proteins
IR-A	Isoform A of the insulin receptor
IRS-1/2	Insulin receptor substrate 1/2
JAK	Janus kinase
KLF4	Gut-enriched Kruppel-like factor 4; zinc-finger transcription factor
KRAS	Kirsten rat sarcoma virus; encodes protein called K-Ras
LAMP2	Lysosome-associated membrane protein 2
(M)LC3B/MAP2	Microtubule-associated protein 1A/1B light chain 3B/protein 2
LKB1	Liver kinase B1; serine/threonine protein kinase (STK11)
lncRNAs	Long non-coding RNAs
LOI	Loss of imprinting
MAPK	Mitogen-activated protein kinase
MEFs	Mouse embryonic fibroblasts
MEK1/2	Mitogen-activated protein kinase (MAP2K, MEK, MAPKK)
MetS	Metabolic syndrome
MOI	Maintenance of imprinting
MSI-H	High microsatellite instability
MSS	Microsatellite stable
mTORC1/2	Mammalian target of rapamycin complex 1/complex 2
NADPH	Nicotinamide adenine dinucleotide phosphate oxidase
NANOG	Homebox protein, transcription factor
NF-κB	Nuclear factor-kappa B
NRF-1/2	Nuclear respiratory factor 1/2
OCT-4	Octamer-binding transcription factor 4
OS	Overall survival
PARP1	Poly [ADP-ribose] polymerase 1
PGDF	Platelet-derived growth factor
PI3K	Phosphatidylinositol-3-kinase
PIK3CA	Gene encoding phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha
PINK1	PTEN-induced kinase 1
PLCs	Paneth-like cells
PKCα/PRKCA	Protein kinase Cα
PPAR	Peroxisome proliferator-activated receptor
PSCs	Pluripotent stem cells
PTEN	Phosphatase and tensin homolog deleted on chromosome ten
Raf-1	Proto-oncogene serine/threonine protein kinase
Raptor	Regulatory-associated protein of mTOR
RAS	Oncogene “Rat sarcoma virus” from three Ras genes: HRAS, KRAS and NRAS
ROS	Reactive oxygen species
SATB2	SATB homeobox 2; DNA-binding protein
SGK-1	Serine/threonine-protein kinase/serum and glucocorticoid-regulated kinase 1
SHC	SHC-transforming protein 1 encoded by the SHC gene
SIRT1	NAD-dependent deacetylase sirtuin 1, a mammalian homologue of silent information regulator 2 of the yeast Saccharomyces cerevisiae
SLITs/ROBOs	SLIT glycoproteins and their roundabout receptors
SNP	Single nucleotide polymorphism
SNX9, -18,-33	Sorting nexin9, -18, -33
SOD3	Superoxide dismutase 3
SOX2	Transcription factor 2, known also as sex-determining region Y (SRY)-box 2
STAT3	Signal transducer and activator of transcription 3
TCGA	The cancer genome atlas
TGF-α, β	Tumor growth factor α, β
TLRs	Toll-like receptors
TME	Tumor microenvironment
TP53	Tumor gene/protein 53
UC	Ulcerative colitis
ULK1/2	Unc-51 like autophagy activating kinase
uPA/uPAR	Urokinase-type plasminogen activator/receptor
Wnt	Gene wingless + integrated or int-1