Table 3.
List of underexpressed genes in HT29 cells upon incubation with instant coffee.
| Gene symbol | Gene title | P value | FC absolute | Regulation |
|---|---|---|---|---|
| ACBD5 | Acyl-coenzyme A binding domain containing 5 | 0.017 | 1.3 | Down |
| CXADR | Coxsackie virus and adenovirus receptor | 0.015 | 1.3 | Down |
| FANCD2 | Fanconi anemia, complementation group D2 | 0.047 | 1.3 | Down |
| FRYL | FRY-like | 0.039 | 1.3 | Down |
| NUB1 | Negative regulator of ubiquitin-like proteins 1 | 0.029 | 1.3 | Down |
| PBRM1 | Polybromo 1 | 0.004 | 1.3 | Down |
| PRKACB | Protein kinase, cAMP-dependent, catalytic, beta | 0.033 | 1.3 | Down |
| RIF1 | RAP1 interacting factor homolog (yeast) | 0.012 | 1.3 | Down |
| SLC39A6 | Solute carrier family 39 (zinc transporter), member 6 | 0.022 | 1.3 | Down |
| TMEM170 | Transmembrane protein 170 | 0.032 | 1.3 | Down |
| WDR26 | WD repeat domain 26 | 0.028 | 1.3 | Down |
| RNGTT | RNA guanylyltransferase and 5′-phosphatase | 0.04 | 1.3 | Down |
| CTDSPL2 | CTD small phosphatase like 2 | 0.03 | 1.3 | Down |
| ZC3H11A | Zinc finger CCCH-type containing 11A | 0.014 | 1.3 | Down |
| TMOD3 | Tropomodulin 3 (ubiquitous) | 0.0171 | 1.3 | Down |
| CPD | Carboxypeptidase D | 0.002 | 1.31 | Down |
| CBL | Cas-Br-M ecotropic retroviral transforming sequence | 0.008 | 1.31 | Down |
| CDC42SE2 | CDC42 small effector 2 | 0.022 | 1.31 | Down |
| CLN5 | Ceroid-lipofuscinosis, neuronal 5 | 0.001 | 1.31 | Down |
| DDX3X | DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked | 0.027 | 1.31 | Down |
| FGFR1OP2 | FGFR1 oncogene partner 2 | 0.049 | 1.31 | Down |
| LRRFIP1 | Leucine-rich repeat (in FLII) interacting protein 1 | 0.026 | 1.31 | Down |
| PDCD4 | Programmed cell death 4 | 0.005 | 1.31 | Down |
| REPS2 | RALBP1-associated Eps domain containing 2 | 0.046 | 1.31 | Down |
| SLC7A6 | Solute carrier family 7, member 6 | 0.002 | 1.31 | Down |
| TFRC | Transferrin receptor (p90, CD71) | 0.038 | 1.31 | Down |
| TMEM19 | Transmembrane protein 19 | 0.024 | 1.31 | Down |
| AGPS | Alkylglycerone phosphate synthase | 0.001 | 1.31 | Down |
| SLC4A7 | Solute carrier family 4, member 7 | 0.028 | 1.31 | Down |
| SPTAN1 | Spectrin, alpha, nonerythrocytic 1 (alpha-fodrin) | 0.02 | 1.31 | Down |
| GPD2 | Glycerol-3-phosphate dehydrogenase 2 (mitochondrial) | 0.033 | 1.31 | Down |
| BICD1 | Bicaudal D homolog 1 (Drosophila) | 0.008 | 1.31 | Down |
| FBXW11 | F-box and WD repeat domain containing 11 | 0.025 | 1.31 | Down |
| BCLAF1 | BCL2-associated transcription factor 1 | 0.025 | 1.32 | Down |
| CDH1 | Cadherin 1, type 1, E-cadherin (epithelial) | 0.011 | 1.32 | Down |
| CLK4 | CDC-like kinase 4 | 0.049 | 1.32 | Down |
| PTAR1 | Protein prenyltransferase alpha subunit repeat containing 1 | 0.027 | 1.32 | Down |
| SMEK2 | SMEK homolog 2, suppressor of mek1 (Dictyostelium) | 0.012 | 1.32 | Down |
| CEPT1 | Choline/ethanolamine phosphotransferase 1 | 0.038 | 1.32 | Down |
| SAR1A | SAR1 gene homolog A (S. cerevisiae) | 0.033 | 1.32 | Down |
| PDGFC | Platelet-derived growth factor C | 0.02 | 1.32 | Down |
| NFAT5 | Nuclear factor of activated T-cells 5, tonicity responsive | 0.045 | 1.32 | Down |
| FRS2 | Fibroblast growth factor receptor substrate 2 | 0.03 | 1.32 | Down |
| BMS1P5 | BMS1 pseudogene 5 | 0.036 | 1.33 | Down |
| GLS | Glutaminase | 5.00E-04 | 1.33 | Down |
| LMAN1 | Lectin, mannose binding, 1 | 7.00E-04 | 1.33 | Down |
| ARHGAP18 | Rho GTPase-activating protein 18 | 8.00E-04 | 1.33 | Down |
| ARHGAP5 | Rho GTPase-activating protein 5 | 0.006 | 1.33 | Down |
| CCNE2 | Cyclin E2 | 0.036 | 1.33 | Down |
| SPCS3 | Signal peptidase complex subunit 3 homolog (S. cerevisiae) | 0.008 | 1.33 | Down |
| NCOA2 | Nuclear receptor coactivator 2 | 0.005 | 1.33 | Down |
| SRPRB | Signal recognition particle receptor, B subunit | 0.018 | 1.33 | Down |
| TLK1 | Tousled-like kinase 1 | 0.04 | 1.33 | Down |
| NCOA3 | Nuclear receptor coactivator 3 | 0.048 | 1.33 | Down |
| STRN3 | Striatin, calmodulin-binding protein 3 | 2.00E-04 | 1.33 | Down |
| AP1G1 | Adaptor-related protein complex 1, gamma 1 subunit | 0.004 | 1.34 | Down |
| B3GALNT2 | Beta-1,3-N-acetylgalactosaminyltransferase 2 | 0.034 | 1.34 | Down |
| PPHLN1 | Periphilin 1 | 2.00E-04 | 1.34 | Down |
| SNX13 | Sorting nexin 13 | 0.001 | 1.34 | Down |
| TMED2 | Transmembrane emp24 domain-trafficking protein 2 | 0.041 | 1.34 | Down |
| BRWD1 | Bromodomain and WD repeat domain containing 1 | 0.011 | 1.34 | Down |
| HLA-B | Major histocompatibility complex, class I, B | 0.028 | 1.34 | Down |
| CHP | Calcium-binding protein P22 | 0.002 | 1.34 | Down |
| MTMR9 | Myotubularin-related protein 9 | 0.026 | 1.34 | Down |
| DCUN1D4 | DCN1, defective in cullin neddylation 1, domain containing 4 | 0.031 | 1.34 | Down |
| ARL6IP2 | ADP-ribosylation factor-like 6 interacting protein 2 | 0.02 | 1.35 | Down |
| GLIS3 | GLIS family zinc finger 3 | 0.01 | 1.35 | Down |
| LARP4 | La ribonucleoprotein domain family, member 4 | 0.019 | 1.35 | Down |
| PTPLB | Protein tyrosine phosphatase-like member b | 0.036 | 1.35 | Down |
| TRAM1 | Translocation-associated membrane protein 1 | 0.002 | 1.35 | Down |
| TMEM64 | Transmembrane protein 64 | 0.001 | 1.35 | Down |
| CBFB | Core-binding factor, beta subunit | 0.005 | 1.35 | Down |
| SELT | Selenoprotein T | 0.002 | 1.35 | Down |
| PEX13 | Peroxisome biogenesis factor 13 | 0.011 | 1.35 | Down |
| TNKS2 | TRF1-interacting ankyrin-related ADP-ribose polymerase 2 | 0.034 | 1.35 | Down |
| TMPO | Thymopoietin | 0.001 | 1.35 | Down |
| LIN7C | Lin-7 homolog C (C. elegans) | 0.007 | 1.35 | Down |
| MTA2 | Metastasis-associated 1 family, member 2 | 0.013 | 1.36 | Down |
| TMEM168 | Transmembrane protein 168 | 0.035 | 1.36 | Down |
| CREBZF | CREB/ATF bZIP transcription factor | 0.016 | 1.36 | Down |
| OSTF1 | Osteoclast-stimulating factor 1 | 0.002 | 1.36 | Down |
| WDR57 | WD repeat domain 57 (U5 snRNP specific) | 0.001 | 1.36 | Down |
| GLT25D1 | Glycosyltransferase 25 domain containing 1 | 0.008 | 1.36 | Down |
| NAPG | N-ethylmaleimide-sensitive factor attachment protein, gamma | 0.015 | 1.36 | Down |
| CCDC126 | Coiled-coil domain containing 126 | 0.039 | 1.37 | Down |
| LASS6 | LAG1 homolog, ceramide synthase 6 | 0.005 | 1.37 | Down |
| MYSM1 | Myb-like, SWIRM and MPN domains 1 | 0.021 | 1.37 | Down |
| CYP51A1 | Cytochrome P450, family 51, subfamily A, polypeptide 1 | 0.007 | 1.37 | Down |
| PDE4DIP | Phosphodiesterase 4D interacting protein (myomegalin) | 0.024 | 1.37 | Down |
| SAP30L | SAP30-like | 0.012 | 1.37 | Down |
| PTPRJ | Protein tyrosine phosphatase, receptor type, J | 0.011 | 1.37 | Down |
| PGGT1B | Protein geranylgeranyltransferase type I, beta subunit | 9.00E-04 | 1.37 | Down |
| ASPH | Aspartate beta-hydroxylase | 0.011 | 1.37 | Down |
| SEMA3C | Sema domain, (semaphorin) 3C | 0.036 | 1.38 | Down |
| WDR76 | WD repeat domain 76 | 0.016 | 1.38 | Down |
| ATP13A3 | ATPase-type 13A3 | 0.002 | 1.38 | Down |
| LMBR1 | Limb region 1 homolog (mouse) | 0.014 | 1.38 | Down |
| GLUD1 | Glutamate dehydrogenase 1 | 0.001 | 1.39 | Down |
| GSTCD | Glutathione S-transferase, C-terminal domain containing | 0.029 | 1.39 | Down |
| SPTLC1 | Serine palmitoyltransferase, subunit 1 | 0.02 | 1.39 | Down |
| U2AF1 | U2 small nuclear RNA auxiliary factor 1 | 9.00E-04 | 1.39 | Down |
| UHMK1 | U2AF homology motif (UHM) kinase 1 | 0.007 | 1.39 | Down |
| ARGLU1 | Arginine and glutamate-rich 1 | 6.00E-04 | 1.39 | Down |
| ANKRD12 | Ankyrin repeat domain 12 | 0.03 | 1.39 | Down |
| PPP3R1 | Protein phosphatase 3, regulatory subunit B, alpha isoform | 0.023 | 1.39 | Down |
| XRN1 | 5′-3′ exoribonuclease 1 | 0.019 | 1.4 | Down |
| CLSPN | Claspin homolog (Xenopus laevis) | 0.013 | 1.4 | Down |
| CXADRP1 | Coxsackie virus and adenovirus receptor pseudogene 1 | 0.034 | 1.4 | Down |
| G3BP1 | GTPase-activating protein- (SH3 domain) binding protein 1 | 0.002 | 1.4 | Down |
| TMEM30A | Transmembrane protein 30A | 0.01 | 1.4 | Down |
| CLCN3 | Chloride channel 3 | 0.035 | 1.41 | Down |
| STK4 | Serine/threonine kinase 4 | 0.039 | 1.41 | Down |
| ZNF644 | Zinc finger protein 644 | 0.02 | 1.41 | Down |
| TCP11L1 | T-complex 11 (mouse)-like 1 | 0.014 | 1.41 | Down |
| SFRS6 | Splicing factor, arginine/serine-rich 6 | 0.031 | 1.41 | Down |
| NPL | N-acetylneuraminate pyruvate lyase | 0.006 | 1.41 | Down |
| G3BP2 | GTPase-activating protein- (SH3 domain) binding protein 2 | 0.001 | 1.42 | Down |
| HNRNPU | Heterogeneous nuclear ribonucleoprotein U | 0.01 | 1.42 | Down |
| TBL1XR1 | Transducin (beta)-like 1 X-linked receptor 1 | 0.001 | 1.42 | Down |
| PHTF2 | Putative homeodomain transcription factor 2 | 0.002 | 1.42 | Down |
| ADAM10 | ADAM metallopeptidase domain 10 | 0.011 | 1.43 | Down |
| ADAM9 | ADAM metallopeptidase domain 9 (meltrin gamma) | 0.01 | 1.43 | Down |
| MALAT1 | Metastasis-associated lung adenocarcinoma transcript 1 | 0.04 | 1.43 | Down |
| SCARB2 | Scavenger receptor class B, member 2 | 0.001 | 1.43 | Down |
| CANX | Calnexin | 0.043 | 1.43 | Down |
| CASP2 | Caspase 2, apoptosis-related cysteine peptidase | 0.033 | 1.43 | Down |
| TRPS1 | Trichorhinophalangeal syndrome I | 0.005 | 1.44 | Down |
| ZFX | Zinc finger protein, X-linked | 0.033 | 1.44 | Down |
| SGPL1 | Sphingosine-1-phosphate lyase 1 | 0.04 | 1.44 | Down |
| PTPN11 | Protein tyrosine phosphatase, nonreceptor type 11 | 0.045 | 1.44 | Down |
| SFRS11 | Splicing factor, arginine/serine-rich 11 | 0.045 | 1.45 | Down |
| B3GNT5 | Beta-1,3-N-acetylglucosaminyltransferase 5 | 0.021 | 1.45 | Down |
| MAP3K1 | Mitogen-activated protein kinase kinase kinase 1 | 0.019 | 1.45 | Down |
| SNHG4 | Small nucleolar RNA host gene (nonprotein coding) 4 | 0.004 | 1.46 | Down |
| PARD6B | Par-6 partitioning defective 6 homolog beta (C. elegans) | 0.04 | 1.46 | Down |
| ROD1 | ROD1 regulator of differentiation 1 (S. pombe) | 0.001 | 1.46 | Down |
| SPTBN1 | Spectrin, beta, nonerythrocytic 1 | 0.02 | 1.48 | Down |
| TXNDC1 | Thioredoxin domain containing 1 | 0.013 | 1.48 | Down |
| ATF2 | Activating transcription factor 2 | 0.005 | 1.48 | Down |
| RDX | Radixin | 0.043 | 1.48 | Down |
| SCAMP1 | Secretory carrier membrane protein 1 | 0.009 | 1.48 | Down |
| PTAR1 | Protein prenyltransferase alpha subunit repeat containing 1 | 0.018 | 1.49 | Down |
| RC3H2 | Ring finger and CCCH-type zinc finger domains 2 | 0.0037 | 1.49 | Down |
| ADAM17 | ADAM metallopeptidase domain 17 | 0.007 | 1.49 | Down |
| FAM76B | Family with sequence similarity 76, member B | 0.014 | 1.5 | Down |
| ITGB8 | Integrin, beta 8 | 1.00E-04 | 1.5 | Down |
| TRIM23 | Tripartite motif-containing 23 | 0.005 | 1.5 | Down |
| CASC5 | Cancer susceptibility candidate 5 | 0.019 | 1.52 | Down |
| SLC16A1 | Solute carrier family 16, member 1 | 0.002 | 1.52 | Down |
| FNBP1 | Formin-binding protein 1 | 0.037 | 1.53 | Down |
| PRKAR1A | Protein kinase, cAMP-dependent, regulatory, type I, alpha | 9.00E-04 | 1.53 | Down |
| B4GALT1 | Beta 1,4-galactosyltransferase, polypeptide 1 | 0.035 | 1.55 | Down |
| MDM4 | Mdm4 p53-binding protein homolog (mouse) | 0.011 | 1.58 | Down |
| FGD4 | FYVE, RhoGEF, and PH domain containing 4 | 0.001 | 1.59 | Down |
| UBA6 | Ubiquitin-like modifier activating enzyme 6 | 8.00E-04 | 1.62 | Down |
| ZDHHC21 | Zinc finger, DHHC-type containing 21 | 0.036 | 1.64 | Down |
| REEP3 | Receptor accessory protein 3 | 7.00E-04 | 1.65 | Down |
| SSR3 | Signal sequence receptor, gamma | 0.014 | 1.65 | Down |
| ZDHHC20 | Zinc finger, DHHC-type containing 20 | 0.003 | 1.66 | Down |
| EIF2S3 | Eukaryotic translation initiation factor 2, subunit 3 gamma | 0.001 | 1.7 | Down |
| HNRNPH1 | Heterogeneous nuclear ribonucleoprotein H1 | 0.011 | 1.79 | Down |
| ATL3 | Atlastin 3 | 0.001 | 2.02 | Down |
The table shows the list of underexpressed genes by 1.3-fold with a P value <0.05 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).