Table 4.
Top Up-regulated Gene Ontology Biological Processes and selected genes found in circulating lymphocytes and monocytes of each group comparison.
| Group Comparison | Top Up-regulated Gene Ontology Biological Process | Number of genes in this category | Represented genes found only in this comparison (Name/ Function) |
|---|---|---|---|
| * T2DMpoorly-DL-P versus H | immune response/ chemotaxis/ inflammatory response/innate immune response/ apoptosis / caspase activation/ | 37 | CXCL10 (chemokine (C-X-C motif) ligand 10), IL7 (Interleukin 7), CCR1 (chemokine (C-C motif) receptor 1), NLRC4 (NLR family, CARD domain containing 4/ interleukin-1 beta secretion) SERPING1 (serpin peptidase inhibitor, clade G (C1 inhibitor), member 1/ innate immune response), OAS1, OAS3 (2’,5’-oligoadenylate synthetase 1; and 3), GBP1 (guanylate binding protein 1, interferon-inducible) |
| signal transduction/defense response /response to virus | 11 | STAT1 (signal transducer and activator of transcription 1), MX1 (Interferon-Inducible Protein P78), IFI6 (interferon, alpha-inducible protein 6), RSAD2 (radical S-adenosyl methionine domain containing 2) | |
| glucose/ carbohydrate/ lipid metabolic processes | 8 | INSIG1 (insulin induced gene 1), FKFB3 (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3), ACSL1 (acyl-CoA synthetase long-chain family member 1), GBA (glucosidase, beta; acid) | |
| metabolic processes | 5 | DHRS9 (dehydrogenase/reductase (SDR family) member 9), ATP9A (ATPase, class II, type 9A), HGD (homogentisate 1,2-dioxygenase) | |
| # T2DMwell-DL-P versus H | innate immune response/ immune response/ defense response/ apoptosis / inflammatory response | 17 | CLEC12A; CLEC12B (C-type lectin domain family 12, member A; member B), ITGB1 (integrin, beta 1), SERGN (serglycin/platelet degranulation/ negative regulation of cytokine secretion), IL2RA (interleukin 2 receptor, alpha), ELANE (elastase 2, neutrophil) |
| glucose/ lipid/ metabolic processes | 6 | PFKP (phosphofructokinase, platelet), CPT1A (carnitine palmitoyltransferase 1A (liver), PLCB1 (phospholipase C, beta 1) | |
| metabolic processes | 4 | ENPP4 (ectonucleotide pyrophosphatase/phosphodiesterase 4), CEBPD (CCAAT/enhancer binding protein (C/EBP), delta), SMAD5 (SMAD family member 5) | |
| & DL-P versus H | immune response | 2 | IL1R2 (interleukin 1 receptor, type II), GBP5 (guanylate binding protein 5) |
| glucose/ lipid/ metabolic processes | 2 | AKR1C3 (aldo-keto reductase family 1, member C3), PTGDS (prostaglandin D2 synthase) | |
| @ P versus H | innate immune response/ immune response/ chemotaxis/ defense response | 10 | FTH1 (ferritin, heavy polypeptide 1), FCGR2B (Fc fragment of IgG, low affinity IIb, receptor (CD32)), CXCL16 (chemokine (C-X-C motif) ligand 16), NLRP2 (NLR family, pyrin domain containing 2) |
| carbohydrate metabolic processes | 3 | GK (glycerol kinase), ST8SIA1 (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1), B3GALTL (beta 1,3-galactosyltransferase-like), | |
| metabolic processes/ signaling pathway | 8 | SEL1L (SEL1L Adaptor Subunit Of ERAD E3 Ubiquitin Ligase), DUSP2 (dual specificity phosphatase 2), KYNU (kynureninase (L-kynurenine hydrolase) | |
|
§ T2DMpoorly-DL-P versus H + T2DMwell-DL-P versus H (T2DM groups, independent of glycemic control) |
innate immune system/ chemotaxis/ | 7 | CTSL1 (cathepsin L1), RETN (resistin), CLU (clusterin), OASL (2’−5’-oligoadenylate synthetase-like), CXCL5 (chemokine (C-X-C motif) ligand 5), CRISP3 (cysteine-rich secretory protein 30, FCGR1A (Fc fragment of IgG, high affinity Ia, receptor (CD64) |
| lipid metabolic processes | 1 | FAR2 (Fatty Acyl-CoA Reductase 2) | |
| metabolic processes | 7 | MMP9 (matrix metallopeptidase 9), MMP8 (matrix metallopeptidase 8 -neutrophil collagenase), ARG1 (arginase, liver), B4GALT5 (Beta-1,4-Galactosyltransferase 5) | |
|
€ T2DMpoorly-DL-P versus H + T2DMwell-DL-P versus H + DL-P versus H (DL-P groups) |
defense response/ immune response/ innate immune response/ apoptosis | 10 | DEFA1, DEFA3, DEFA4 (defensin, alpha 1; alpha 3; alpha 4), MPO (myeloperoxidase), BPI (bactericidal/permeability-increasing protein), CAMP (cathelicidin antimicrobial peptide) |
| carbohydrate and lipid metabolic processes | 6 | PTGS1 (prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase), NRG1 (neuregulin 1), BPGM (2,3-bisphosphoglycerate mutase), PDK4 (pyruvate dehydrogenase kinase, isozyme 4), MGLL (monoglyceride lipase) | |
| protein amino acid phosphorylation/ signaling transduction processes | 7 | MYLK (myosin light chain kinase),PRKAR2B (protein kinase, cAMP-dependent, regulatory, type II, beta), RHOBTB1 (Rho-related BTB domain containing 1), PDE5A (phosphodiesterase 5 A, cGMP-specific) | |
| All comparisons | defense response/ immune response | 3 | CLEC4D (C-type lectin domain family 4, member D), LTF (lactotransferrin) |
| lipid biosynthetic process | 1 | ELOVL7 (ELOVL family member 7, elongation of long chain fatty acids) | |
| metabolic processes | 5 | ALAS2 (aminolevulinate, delta-, synthase 20), ENOSF1 (enolase superfamily member 1) |
Symbols refer to the group comparisons showed in the Fig. 4 (Venn diagram). Example: * In the T2DMpoorly-DL-P versus H were found 292 genes up-regulated, being 37 of them belonging to the immune system (Number of genes in this category of the Gene Ontology Biological Processes), in which some of the selected genes were mentioned.