Gene symbol* | Gene title | FC† | FC‡ | CoQ10§ | Q-RT-PCR¶ | CoQ10** |
---|---|---|---|---|---|---|
Mitochondrial metabolism | ||||||
C7orf55 | Chromosome 7 open reading frame 55 | −2.1 | nc | – | ||
BRP44 | Brain protein 44 | 2.0 | 2.3 | U | 8.0 | –2-fold |
C10orf58 | Chromosome 10 open reading frame 58 | −19.5 | −1.6 | pR | ||
NADH mobilisation | ||||||
CYB561 | Cytochrome b561 | −1.3 | nc | O | ||
CYB5A | Cytochrome b5-A | −1.4 | −1.5 | U | ||
CYB5R1 | Cytochrome b5 reductase 1 | −1.3 | nc | U | ||
CYB5R2 | Cytochrome b5 reductase 2 | −1.4 | −1.9 | U | ||
CYB5R3 | Cytochrome b5 reductase 3 | −1.4 | −1.6 | R | ||
CYB5R4 | Cytochrome b5 reductase 4 | −1.3 | −1.6 | R | ||
Lipid metabolism | ||||||
FDFT1 | Farnesyl-diphosphate farnesyltransferase 1 | −2.3 | −1.5 | U | −4.3 | +2-fold |
IDI1 | Isopentenyl-diphosphate δ isomerase 1 | −2.1 | nc | U | ||
CH25H | Cholesterol 25-hydroxylase | −10.8 | −3.2 | O | −1.3 | –3-fold |
RSAD2 | Radical S-adenosyl methionine domain containing 2 | −6.8 | 1.4 | pR | ||
INSIG1 | Insulin-induced gene 1 | −2.6 | 1.7 | O | ||
LDLR | Low density lipoprotein receptor | −3.0 | −1.8 | pR | ||
SQLE | Squalene epoxidase | −2.5 | nc | U | ||
SCD | Stearoyl-coenzyme A desaturase (δ-9-desaturase) | −3.3 | nc | U | ||
Insulin metabolism | ||||||
CPE | Carboxypeptidase E | 10.0 | 2.5 | pR | ||
PAPPA | Pregnancy-associated plasma protein A, pappalysin | 2.5 | 1.7 | R | 4.8 | –5-fold |
PCSK2 | Proprotein convertase subtilisin/kexin type 2 | −75.5 | −4.3 | O | ||
Other metabolism | ||||||
SCIN | Scinderin | −5.4 | −1.4 | O | ||
PYGL | Phosphorylase, glycogen; liver | −2.5 | −1.6 | R | ||
SLC40A1 | Solute carrier family 40 (iron-regulated transporter) | 7.6 | 2.9 | R | ||
QPRT | Quinolinate phosphoribosyltransferase | −3.4 | nc | R | ||
ATP8B1 | ATPase, class I, type 8B and member 1 | 2.4 | nc | pR | ||
Cell cycle | ||||||
POSTN | Periostin, osteoblast specific factor | 73.8 | 153.9 | U | 238.2 | –20% |
VEGFA | Vascular endothelial growth factor A | 2.9 | nc | – | ||
SEMA5A | Semaphorin 5A, receptor for cell growth | 3.6 | 1.6 | pR | ||
AEBP1 | AE binding protein 1 | 66.1 | nc | R | ||
CSRP2 | Cysteine and glycine-rich protein 2 | 5.3 | 1.5 | R | ||
DOK5 | Docking protein 5 | 6.5 | 1.6 | U | ||
MID1 | Midline 1 (Opitz/BBB syndrome) | 3.9 | 4.4 | U | ||
CHURC1 | Churchill domain containing 1 | 3.5 | nc | – | ||
CREG1 | Repressor 1 of E1A-stimulated genes | 3.0 | 1.3 | R | ||
RUNX1 | Runt-related transcription factor 1 (aml1 oncogene) | 1.9 | 1.6 | – | ||
BHLHB5 | Basic helix-loop-helix domain containing; class B, 5 | −6.1 | −1.4 | – | ||
IFITM1 | Interferon induced transmembrane protein 1 (9–27) | −3.8 | −3.7 | O | ||
EDN1 | Endothelin 1 | −3.0 | nc | U | ||
MATN2 | Matrilin 2 | −9.2 | nc | U | ||
MCAM | Melanoma cell adhesion molecule | −6.7 | −3.0 | R | −10.9 | +10% |
MKX | Mohawk homeobox | −4.5 | −1.5 | – | ||
PSG6 | Pregnancy specific β-1-glycoprotein 6 | 2.6 | nc | – | ||
DCN | Decorin | 2.0 | −1.6 | – | ||
PKP4 | Plakophilin 4 | 2.0 | 1.4 | U | ||
EFEMP1 | EGF-containing fibulin-like extracellular matrix protein 1 | 13.2 | 2.2 | pR | ||
VCAN | Versican | 2.8 | 2.7 | – | 4.6 | +10% |
SMARCA1 | Component of SWI/SNF chromatin complex, member A1 | −1.3 | nc | pR | ||
SMARCA4 | Component of SWI/SNF chromatin complex, member A4 | −1.9 | nc | pR | ||
CDK6 | Cyclin-dependent kinase 6, overexpressed in tumour | 1.4 | 2.9 | U | ||
CDKN1A | P21, inhibitor of CDK | −9.2 | −2.1 | U | ||
CDKN1C | P57, inhibitor of CDK | −2.6 | −1.3 | R | ||
CDKN3 | Inhibitor of CDK, overexpressed in cancer cells | 1.9 | 2.7 | U | ||
CD31 | Cell surface antigen | −1.8 | −1.5 | R | ||
RB1 | Retinoblastoma protein | −1.4 | nc | R | ||
E2F7 | E2F transcription factor 7 | 3.6 | nc | U | ||
E2F8 | E2F transcription factor 8 | 2.2 | nc | U | ||
FST | Follistatin | 2.6 | 1.4 | O | ||
Development and differentiation | ||||||
BDNF | Brain-derived neurotrophic factor | −2.9 | nc | pR | ||
GRP | Gastrin-releasing peptide | −263.6 | nc | – | ||
NTNG1 | Netrin G1 | −8.3 | 1.8 | U | ||
PTN | Pleiotrophin (neurite growth-promoting factor 1) | −2.7 | nc | R | ||
FOXQ1 | Forkhead box Q1 | −6.5 | nc | – | ||
HOXA11 | Homeobox A11 | −4.3 | −2.4 | U | ||
HOXC9 | Homeobox C9 | −4.8 | −2.0 | U | ||
LHX9 | LIM homeobox 9 | −93.0 | −1.5 | U | ||
SP110 | SP110 nuclear body protein | −2.5 | nc | pR | ||
P2RY5 | Purinergic receptor P2Y; G-protein coupled, 5 | −4.4 | −1.3 | pR | ||
TSPAN10 | Tetraspanin 10 | −10.1 | nc | – | ||
EPSTI1 | Epithelial stromal interaction 1 | −5.2 | −1.4 | R | ||
TSHZ1 | Teashirt zinc finger homeobox 1 | −2.8 | nc | R | ||
KRT34 | Keratin 34 | −5.3 | −7.6 | R | −5.7 | –60% |
TPM1 | Tropomyosin 1 (α) | −1.8 | 1.7 | – | ||
FOXP1 | Forkhead box P1 | 2.3 | nc | – | ||
LMCD1 | LIM and cysteine-rich domains 1 | 3.8 | nc | U | ||
Cell resistance to stress | ||||||
CYP1B1 | Cytochrome P450, family 1B and polypeptide 1 | 4.5 | 1.5 | – | 7.0 | –5-fold |
MGC87042 | Similar to six epithelial antigen of prostate | 12.2 | – | R | ||
TMEM49 | Transmembrane protein 49/microRNA 21 | 1.9 | nc | – | ||
RAD23B | RAD23 homologue B (Saccharomyces cerevisiae) | 2.2 | nc | R | ||
TXNIP | Thioredoxin-interacting protein | 2.0 | −4.9 | – | ||
SGK1 | Serum/glucocorticoid regulated kinase 1 | 3.4 | 1.5 | – | ||
SOCS3 | Suppressor of cytokine signalling 3 | −3.6 | nc | R | ||
RHOU | Ras homologue gene family. member U | −8.3 | nc | O | ||
Apoptosis | ||||||
AIM1 | Absent in melanoma 1 | −4.5 | −1.4 | O | ||
APCDD1 | Adenomatosis polyposis coli down-regulated 1 | −6.4 | −1.8 | O | ||
MAGED1 | Melanoma antigen family D, 1 | −1.7 | nc | U | ||
MAGED4/4B | Melanoma antigen family D, 4/4B | −5.0 | −1.6 | U | ||
RAC2 | Small GTP-binding protein Rac2 (rho family) | −2.3 | −1.3 | U | ||
TRIM55 | Tripartite motif-containing 55 | −11.7 | −1.6 | U | ||
IFI6 | Interferon, α-inducible protein 6 | −4.9 | −1.3 | R | ||
XAF1 | XIAP associated factor-1 | −3.0 | −1.5 | R | ||
TNFRSF10D | Tumour necrosis factor receptor superfamily 10D | 2.4 | 2.6 | U | 15.1 | +20% |
SFRP1 | Secreted frizzled-related protein 1 | 8.7 | 2.5 | U | 11.8 | –2-fold |
Signalling | ||||||
ARL4C | ADP-ribosylation factor-like 4C | 3.8 | 1.6 | pR | ||
USP53 | Ubiquitin specific peptidase 53 | 4.2 | 1.7 | – | ||
GABBR2 | γ-aminobutyric acid B receptor, 2 | 13.8 | 2.0 | U | ||
CNGA3 | Cyclic nucleotide gated channel α-3 | −67.3 | nc | – | ||
GNG2 | G-protein, γ-2 | −4.2 | 1.4 | pR | ||
HERC6 | Hect domain and RLD 6 | −7.4 | −1.4 | R | ||
MLPH | Melanophilin | −8.5 | −1.9 | R | ||
NCK2 | NCK adaptor protein 2 | −1.7 | nc | – | ||
PARP14 | Poly (ADP-ribose) polymerase family, member 14 | −3.1 | −1.5 | – | ||
Immunity | ||||||
CDC42SE2 | CDC42 small effector 2 | −2.8 | nc | – | ||
LY6K | Lymphocyte antigen 6 complex, locus K | −4.7 | 1.4 | – | ||
GALNAC4S-6ST | B cell RAG associated protein | −17.3 | −2.5 | O | ||
TNFSF4 | Tumour necrosis factor superfamily, member 4 | −5.9 | nc | – | ||
TRIM14 | Tripartite motif-containing 14 | −4.5 | nc | – | ||
BTN3(A2/A3) | Butyrophilin 3 (A2/A3) | −2.0 | −1.3 | R | ||
IFI27 | Interferon, α-inducible protein 27 | −9.8 | nc | O | ||
IFI44 | Interferon-induced protein 44 | −3.3 | −2.3 | R | ||
IFI44L | Interferon-induced protein 44-like | −15.0 | −1.9 | R | ||
IFIT1 | Interferon-induced protein (tetratricopeptide repeats 1) | −5.3 | nc | – | ||
IFIT3 | Interferon-induced protein (tetratricopeptide repeats 3) | −3.5 | −1.7 | R | ||
GBP1 | Guanylate binding protein 1, interferon-inducible | −2.7 | – | – | ||
ISG15 | ISG15 ubiquitin-like modifier | −6.4 | nc | R | ||
MX1 | Myxovirus resistance 1 | −7.4 | −1.8 | pR | ||
MX2 | Myxovirus resistance 2 | −6.1 | −3.0 | pR | ||
OAS1 | 2′,5′-oligoadenylate synthetase 1, 40/46 kDa | −5.1 | −4.9 | R | ||
OAS2 | 2′-5′-oligoadenylate synthetase 2, 69/71 kDa | −6.2 | −1.6 | R | ||
OAS3 | 2′-5′-oligoadenylate synthetase 3, 100 kDa | −3.6 | −1.3 | R | ||
OASL | 2′-5′-oligoadenylate synthetase-like | −3.1 | −2.6 | R | ||
PSMB9 | Proteasome subunit, β-type, 9 | −1.8 | nc | U |
*In italic letter, biomarkers used in several types of cancer as described by Yoo and collaborators.28 See the text for more information.
†Full change (FC) in the comparative analysis ran with Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Values represent the FC (mean) for each gene corresponding to different patient samples (SAM analysis; R=1.5; false discovery rate (FDR)=0%). In parenthesis, FC of non-significant genes by the statistical threshold used, which were selected owing to their role in specific processes and pathways (see the text for full details). In the case of different probes selected for one gene, values represent the mean of FC for each probe (see online supplementary table S1 for full details).
‡FC in the comparative analysis ran with Affymetrix Gene Chip Human Gene 1.0 ST Array. In parenthesis, FC of non-significant genes by the statistical threshold used. Genes with no change (nc).
§Effect of coenzyme Q10 (CoQ10) supplementation on gene expression in CoQ10 deficiency: unaffected genes by CoQ10 treatment (U); genes that restored the expression either partially (pR) or completely (R); genes with opposite regulation than in CoQ10 deficiency (O); and specifically regulated genes only after CoQ10 supplementation (S). Genes non-affected by CoQ10 supplementation (−). See the text and online supplementary table S8 for full details.
¶FC in gene expression analysed by quantitative real time PCR (Q-RT-PCR). See supplementary material and table S11 for primer sequence.
**Effect of CoQ10 supplementation on mRNA levels analysed by Q-RT-PCR. Positive values, increase on gene expression; negative values, decrease on gene expression.
AE binding protein 1, adipocyte enhancer binding protein 1; aml1 oncogene, acute myeloid leukaemia 1 oncogene; EGF-containing fibulin-like extracellular matrix protein 1, elongation factor G-containing fibulin-like extracellular matrix protein 1; small GTP-binding protein Rac2 (rho family), small guanosine triphosphate-binding protein Rac2 (rho family); SP110 nuclear body protein, specificity protein-110 nuclear body protein.