Table 1. Lasso regression coefficients and molecular function information of seventeen GRGPs based on TCGA-HCC data.
| Gene1 | Encoding protein | Function | Gene2 | Encoding protein | Function | Coefficient |
|---|---|---|---|---|---|---|
| IDUA | hydrolyzes the terminal alpha-L-iduronic acid residues of two glycosaminoglycans, dermatan sulfate and heparan sulfate | Chondroitin sulfate/dermatan sulfate metabolism and Glycosaminoglycan metabolism | GNPDA1 | An allosteric enzyme | The reversible conversion of D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium | −0.294 |
| IDUA | hydrolyzes the terminal alpha-L-iduronic acid residues of two glycosaminoglycans, dermatan sulfate and heparan sulfate | Chondroitin sulfate/dermatan sulfate metabolism and Glycosaminoglycan metabolism | ME2 | A mitochondrial NAD-dependent malic enzyme | Catalyzes the oxidative decarboxylation of malate to pyruvate | −0.145 |
| IDUA | hydrolyzes the terminal alpha-L-iduronic acid residues of two glycosaminoglycans, dermatan sulfate and heparan sulfate | Chondroitin sulfate/dermatan sulfate metabolism and Glycosaminoglycan metabolism | G6PD | A cytosolic enzyme encoded by a housekeeping X-linked gene | Produce NADPH | −0.160 |
| IDUA | hydrolyzes the terminal alpha-L-iduronic acid residues of two glycosaminoglycans, dermatan sulfate and heparan sulfate | Chondroitin sulfate/dermatan sulfate metabolism and Glycosaminoglycan metabolism | GPC1 | Disease related genes belongs to the glypican family | Play a role in the control of cell division and growth regulation | −0.345 |
| HMMR | Involved in cell motility | Regulation of PLK1 activity at G2/M transition and metabolism | PFKFB1 | A member of the family of bifunctional 6-phosphofructo-2-kinase | An activator of the glycolysis pathway and an inhibitor of the gluconeogenesis pathway/participate in hepatocellular carcinoma tumorigenesis | 0.049 |
| MPI | Phosphomannose isomerase catalyzes the interconversion of fructose-6-phosphate and mannose-6-phosphate | Metabolism of proteins and amino sugar and nucleotide sugar metabolism | GPC1 | Disease related genes belongs to the glypican family | Play a role in the control of cell division and growth regulation | −0.343 |
| SDC2 | A transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family | Microglia activation during neuroinflammation: overview and cell surface interactions at the vascular wall | LDHA | Cancer-related protein belongs to the LDH/MDH superfamily | Catalyzes the conversion of L-lactate and NAD to pyruvate and NADH in the final step of anaerobic glycolysis | −0.291 |
| PRPS1 | Catalyzes the phosphoribosylation of ribose 5-phosphate to 5-phosphoribosyl-1-pyrophosphate | Thiopurine pathway, pharmacokinetics/pharmacodynamics and carbon metabolism | PLOD2 | A membrane-bound homodimeric enzyme | Participate in collagen chain trimerization and degradation of the extracellular matrix | −0.085 |
| GALK1 | Galactokinase is a major enzyme for the metabolism of galactose | Galactokinase is a major enzyme for the metabolism of galactose | IER3 | A predicted intracellular protein belongs to the IER3 family | Protect cells from Fas- or tumor necrosis factor type alpha-induced apoptosis | −0.061 |
| CHST1 | A member of the keratin sulfotransferase family of proteins. The encoded enzyme catalyzes the sulfation of the proteoglycan keratin | Among its related pathways are Keratan sulfate/keratin metabolism and metabolism | GYS2 | Liver glycogen synthase | Participate in galactose metabolism and glycogen metabolism | 0.019 |
| MET | A member of the receptor tyrosine kinase family of proteins and the product of the proto-oncogene MET | Hepatocyte growth factor, induces dimerization and activation of the receptor | PLOD2 | A membrane-bound homodimeric enzyme | Participate in collagen chain trimerization and degradation of the extracellular matrix | −0.265 |
| MERTK | A member of the MER/AXL/TYRO3 receptor kinase family | Regulate cell survival, migration, differentiation, and phagocytosis of apoptotic cells | GYS2 | Liver glycogen synthase | Participate in galactose metabolism and glycogen metabolism | 0.334 |
| GPC1 | Disease related genes belongs to the glypican family | Play a role in the control of cell division and growth regulation | GYS2 | Liver glycogen synthase | Participate in galactose metabolism and glycogen metabolism | 0.198 |
| IL13RA1 | A subunit of the interleukin 13 receptor | Bind tyrosine kinase TYK2 and mediate the signaling processes | IGFBP3 | Encodes a protein with an IGFBP domain and a thyroglobulin type-I domain | Prolonging the half-life of insulin-like growth factor (IGF) and altering their interaction with cell surface receptors | −0.308 |
| LDHA | Cancer-related protein belongs to the LDH/MDH superfamily | Catalyzes the conversion of L-lactate and NAD to pyruvate and NADH in the final step of anaerobic glycolysis | GOT2 | A pyridoxal phosphate-dependent enzyme | Play a role in amino acid metabolism and the urea and tricarboxylic acid cycles. | 0.171 |
| CYB5A | A membrane-bound cytochrome | Reduces ferric hemoglobin (methemoglobin) to ferrous hemoglobin | IGFBP3 | Encodes a protein with an IGFBP domain and a thyroglobulin type-I domain | Prolonging the half-life of insulin-like growth factor (IGF) and altering their interaction with cell surface receptors | −0.116 |
Note:
PLK1, Polo-like kinase 1; MET, Mesenchymal Epithelial Transition; MER/AXL/TYRO3 receptor, TAM receptors; TYK2, Tyrosine Kinase 2; LDH/MDH, lactate and Malate dehydrogenases; NAD, Nicotinamide adenine dinucleotide; NADH, Nicotinamide adenine dinucleotide; IGFBP, insulin-like growth factor-binding protein; IGF, insulin-like growth factor; IER3, Immediate Early Response 3; NADPH, nicotinamide adenine dinucleotide phosphate.