Table 3: List of underexpressed genes in HT29 cells upon incubation with instant coffee.

Gene symbolGene title valueFC absoluteRegulation

ACBD5Acyl-coenzyme A binding domain containing 50.0171.3Down
CXADRCoxsackie virus and adenovirus receptor0.0151.3Down
FANCD2Fanconi anemia, complementation group D20.0471.3Down
FRYLFRY-like0.0391.3Down
NUB1Negative regulator of ubiquitin-like proteins 10.0291.3Down
PBRM1Polybromo 10.0041.3Down
PRKACBProtein kinase, cAMP-dependent, catalytic, beta0.0331.3Down
RIF1RAP1 interacting factor homolog (yeast)0.0121.3Down
SLC39A6Solute carrier family 39 (zinc transporter), member 60.0221.3Down
TMEM170Transmembrane protein 1700.0321.3Down
WDR26WD repeat domain 260.0281.3Down
RNGTTRNA guanylyltransferase and 5-phosphatase0.041.3Down
CTDSPL2CTD small phosphatase like 20.031.3Down
ZC3H11AZinc finger CCCH-type containing 11A0.0141.3Down
TMOD3Tropomodulin 3 (ubiquitous)0.01711.3Down
CPDCarboxypeptidase D0.0021.31Down
CBLCas-Br-M ecotropic retroviral transforming sequence0.0081.31Down
CDC42SE2CDC42 small effector 20.0221.31Down
CLN5Ceroid-lipofuscinosis, neuronal 50.0011.31Down
DDX3XDEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked0.0271.31Down
FGFR1OP2FGFR1 oncogene partner 20.0491.31Down
LRRFIP1Leucine-rich repeat (in FLII) interacting protein 10.0261.31Down
PDCD4Programmed cell death 40.0051.31Down
REPS2RALBP1-associated Eps domain containing 20.0461.31Down
SLC7A6Solute carrier family 7, member 60.0021.31Down
TFRCTransferrin receptor (p90, CD71)0.0381.31Down
TMEM19Transmembrane protein 190.0241.31Down
AGPSAlkylglycerone phosphate synthase0.0011.31Down
SLC4A7Solute carrier family 4, member 70.0281.31Down
SPTAN1Spectrin, alpha, nonerythrocytic 1 (alpha-fodrin)0.021.31Down
GPD2Glycerol-3-phosphate dehydrogenase 2 (mitochondrial)0.0331.31Down
BICD1Bicaudal D homolog 1 (Drosophila)0.0081.31Down
FBXW11F-box and WD repeat domain containing 110.0251.31Down
BCLAF1BCL2-associated transcription factor 10.0251.32Down
CDH1Cadherin 1, type 1, E-cadherin (epithelial)0.0111.32Down
CLK4CDC-like kinase 40.0491.32Down
PTAR1Protein prenyltransferase alpha subunit repeat containing 10.0271.32Down
SMEK2SMEK homolog 2, suppressor of mek1 (Dictyostelium)0.0121.32Down
CEPT1Choline/ethanolamine phosphotransferase 10.0381.32Down
SAR1ASAR1 gene homolog A (S. cerevisiae)0.0331.32Down
PDGFCPlatelet-derived growth factor C0.021.32Down
NFAT5Nuclear factor of activated T-cells 5, tonicity responsive0.0451.32Down
FRS2Fibroblast growth factor receptor substrate 20.031.32Down
BMS1P5BMS1 pseudogene 50.0361.33Down
GLSGlutaminase5.00E-041.33Down
LMAN1Lectin, mannose binding, 17.00E-041.33Down
ARHGAP18Rho GTPase-activating protein 188.00E-041.33Down
ARHGAP5Rho GTPase-activating protein 50.0061.33Down
CCNE2Cyclin E20.0361.33Down
SPCS3Signal peptidase complex subunit 3 homolog (S. cerevisiae)0.0081.33Down
NCOA2Nuclear receptor coactivator 20.0051.33Down
SRPRBSignal recognition particle receptor, B subunit0.0181.33Down
TLK1Tousled-like kinase 10.041.33Down
NCOA3Nuclear receptor coactivator 30.0481.33Down
STRN3Striatin, calmodulin-binding protein 32.00E-041.33Down
AP1G1Adaptor-related protein complex 1, gamma 1 subunit0.0041.34Down
B3GALNT2Beta-1,3-N-acetylgalactosaminyltransferase 20.0341.34Down
PPHLN1Periphilin 12.00E-041.34Down
SNX13Sorting nexin 130.0011.34Down
TMED2Transmembrane emp24 domain-trafficking protein 20.0411.34Down
BRWD1Bromodomain and WD repeat domain containing 10.0111.34Down
HLA-BMajor histocompatibility complex, class I, B0.0281.34Down
CHPCalcium-binding protein P220.0021.34Down
MTMR9Myotubularin-related protein 90.0261.34Down
DCUN1D4DCN1, defective in cullin neddylation 1, domain containing 40.0311.34Down
ARL6IP2ADP-ribosylation factor-like 6 interacting protein 20.021.35Down
GLIS3GLIS family zinc finger 30.011.35Down
LARP4La ribonucleoprotein domain family, member 40.0191.35Down
PTPLBProtein tyrosine phosphatase-like member b0.0361.35Down
TRAM1Translocation-associated membrane protein 10.0021.35Down
TMEM64Transmembrane protein 640.0011.35Down
CBFBCore-binding factor, beta subunit0.0051.35Down
SELTSelenoprotein T0.0021.35Down
PEX13Peroxisome biogenesis factor 130.0111.35Down
TNKS2TRF1-interacting ankyrin-related ADP-ribose polymerase 20.0341.35Down
TMPOThymopoietin0.0011.35Down
LIN7CLin-7 homolog C (C. elegans)0.0071.35Down
MTA2Metastasis-associated 1 family, member 20.0131.36Down
TMEM168Transmembrane protein 1680.0351.36Down
CREBZFCREB/ATF bZIP transcription factor0.0161.36Down
OSTF1Osteoclast-stimulating factor 10.0021.36Down
WDR57WD repeat domain 57 (U5 snRNP specific)0.0011.36Down
GLT25D1Glycosyltransferase 25 domain containing 10.0081.36Down
NAPGN-ethylmaleimide-sensitive factor attachment protein, gamma0.0151.36Down
CCDC126Coiled-coil domain containing 1260.0391.37Down
LASS6LAG1 homolog, ceramide synthase 60.0051.37Down
MYSM1Myb-like, SWIRM and MPN domains 10.0211.37Down
CYP51A1Cytochrome P450, family 51, subfamily A, polypeptide 10.0071.37Down
PDE4DIPPhosphodiesterase 4D interacting protein (myomegalin)0.0241.37Down
SAP30LSAP30-like0.0121.37Down
PTPRJProtein tyrosine phosphatase, receptor type, J0.0111.37Down
PGGT1BProtein geranylgeranyltransferase type I, beta subunit9.00E-041.37Down
ASPHAspartate beta-hydroxylase0.0111.37Down
SEMA3CSema domain, (semaphorin) 3C0.0361.38Down
WDR76WD repeat domain 760.0161.38Down
ATP13A3ATPase-type 13A30.0021.38Down
LMBR1Limb region 1 homolog (mouse)0.0141.38Down
GLUD1Glutamate dehydrogenase 10.0011.39Down
GSTCDGlutathione S-transferase, C-terminal domain containing0.0291.39Down
SPTLC1Serine palmitoyltransferase, subunit 10.021.39Down
U2AF1U2 small nuclear RNA auxiliary factor 19.00E-041.39Down
UHMK1U2AF homology motif (UHM) kinase 10.0071.39Down
ARGLU1Arginine and glutamate-rich 16.00E-041.39Down
ANKRD12Ankyrin repeat domain 120.031.39Down
PPP3R1Protein phosphatase 3, regulatory subunit B, alpha isoform0.0231.39Down
XRN15-3 exoribonuclease 10.0191.4Down
CLSPNClaspin homolog (Xenopus laevis)0.0131.4Down
CXADRP1Coxsackie virus and adenovirus receptor pseudogene 10.0341.4Down
G3BP1GTPase-activating protein- (SH3 domain) binding protein 10.0021.4Down
TMEM30ATransmembrane protein 30A0.011.4Down
CLCN3Chloride channel 30.0351.41Down
STK4Serine/threonine kinase 40.0391.41Down
ZNF644Zinc finger protein 6440.021.41Down
TCP11L1T-complex 11 (mouse)-like 10.0141.41Down
SFRS6Splicing factor, arginine/serine-rich 60.0311.41Down
NPLN-acetylneuraminate pyruvate lyase0.0061.41Down
G3BP2GTPase-activating protein- (SH3 domain) binding protein 20.0011.42Down
HNRNPUHeterogeneous nuclear ribonucleoprotein U0.011.42Down
TBL1XR1Transducin (beta)-like 1 X-linked receptor 10.0011.42Down
PHTF2Putative homeodomain transcription factor 20.0021.42Down
ADAM10ADAM metallopeptidase domain 100.0111.43Down
ADAM9ADAM metallopeptidase domain 9 (meltrin gamma)0.011.43Down
MALAT1Metastasis-associated lung adenocarcinoma transcript 10.041.43Down
SCARB2Scavenger receptor class B, member 20.0011.43Down
CANXCalnexin0.0431.43Down
CASP2Caspase 2, apoptosis-related cysteine peptidase0.0331.43Down
TRPS1Trichorhinophalangeal syndrome I0.0051.44Down
ZFXZinc finger protein, X-linked0.0331.44Down
SGPL1Sphingosine-1-phosphate lyase 10.041.44Down
PTPN11Protein tyrosine phosphatase, nonreceptor type 110.0451.44Down
SFRS11Splicing factor, arginine/serine-rich 110.0451.45Down
B3GNT5Beta-1,3-N-acetylglucosaminyltransferase 50.0211.45Down
MAP3K1Mitogen-activated protein kinase kinase kinase 10.0191.45Down
SNHG4Small nucleolar RNA host gene (nonprotein coding) 40.0041.46Down
PARD6BPar-6 partitioning defective 6 homolog beta (C. elegans)0.041.46Down
ROD1ROD1 regulator of differentiation 1 (S. pombe)0.0011.46Down
SPTBN1Spectrin, beta, nonerythrocytic 10.021.48Down
TXNDC1Thioredoxin domain containing 10.0131.48Down
ATF2Activating transcription factor 20.0051.48Down
RDXRadixin0.0431.48Down
SCAMP1Secretory carrier membrane protein 10.0091.48Down
PTAR1Protein prenyltransferase alpha subunit repeat containing 10.0181.49Down
RC3H2Ring finger and CCCH-type zinc finger domains 20.00371.49Down
ADAM17ADAM metallopeptidase domain 170.0071.49Down
FAM76BFamily with sequence similarity 76, member B0.0141.5Down
ITGB8Integrin, beta 81.00E-041.5Down
TRIM23Tripartite motif-containing 230.0051.5Down
CASC5Cancer susceptibility candidate 50.0191.52Down
SLC16A1Solute carrier family 16, member 10.0021.52Down
FNBP1Formin-binding protein 10.0371.53Down
PRKAR1AProtein kinase, cAMP-dependent, regulatory, type I, alpha9.00E-041.53Down
B4GALT1Beta 1,4-galactosyltransferase, polypeptide 10.0351.55Down
MDM4Mdm4 p53-binding protein homolog (mouse)0.0111.58Down
FGD4FYVE, RhoGEF, and PH domain containing 40.0011.59Down
UBA6Ubiquitin-like modifier activating enzyme 68.00E-041.62Down
ZDHHC21Zinc finger, DHHC-type containing 210.0361.64Down
REEP3Receptor accessory protein 37.00E-041.65Down
SSR3Signal sequence receptor, gamma0.0141.65Down
ZDHHC20Zinc finger, DHHC-type containing 200.0031.66Down
EIF2S3Eukaryotic translation initiation factor 2, subunit 3 gamma0.0011.7Down
HNRNPH1Heterogeneous nuclear ribonucleoprotein H10.0111.79Down
ATL3Atlastin 30.0012.02Down

The table shows the list of underexpressed genes by 1.3-fold with a value obtained in cells treated with instant caffeinated coffee and includes the gene symbol for all genes, and their associated description. The ratio columns correspond to the absolute fold change in expression relative to the control group and the type of regulation (down: downregulation).