Table 2.
Top 15 inferred oncogenes of LUSC. η S TCGA and η S HPA are the average similarity ratios for reconstructed GSMNs based on the data from the TCGA and HPA databases, respectively. η E TCGA and η E HPA are the membership grades of the fuzzy equal function for reconstructed GSMNs based on the data from the TCGA and HPA databases, respectively. Higher η E values indicate higher consistency of the flux alterations with the template. DEG and P value were calculated in sas® software. The pathway for each gene was found from the GeneCards (https://www.genecards.org/) and VMH (https://www.vmh.life/) databases. A gene is biological significant if |DEG| > 2 and P value < 0.05.
| Gene | DEG a | P value b | (η S TCGA , η E TCGA ) | (η S HPA , η E HPA ) | Pathway | Disease (score) c |
|---|---|---|---|---|---|---|
| SLCO2B1 | −2.22 | 8.80E−20 | (0.917, 0.829) | (0.871, 0.842) | Atenolol pathway | Ileum cancer (1.31) |
| SLC9A1 | −0.22 | 3.08E−03 | (0.911, 0.822) | (0.847, 0.826) | Osteoclast signaling | Gastroesophageal reflux (1.00) |
| SLC7A10 | 2.68 | 1.14E−02 | (0.911, 0.819) | (0.862, 0.835) | Differentiation of white and brown adipocyte | Follicular lymphoma (0.91) |
| SLC20A1 | 0.42 | 3.45E−04 | (0.904, 0.822) | (0.870, 0.843) | Glucose/energy metabolism | Leukemia (0.86) |
| AQP8 | −1.27 | 1.85E−05 | (0.906, 0.817) | (0.878, 0.854) | Detoxification of reactive oxygen species | Colorectal adenoma (0.89) |
| AGL | 0.42 | 1.49E−12 | (0.908, 0.814) | NA | Glycogen metabolism | Bladder lateral wall cancer (1.26) |
| SLC12A4 | −1.11 | 8.74E−40 | (0.906, 0.815) | (0.871, 0.841) | Transport of glucose and other sugars | Fish‐eye disease (1.50) |
| KYAT1 | 0.74 | 2.25E−36 | (0.909, 0.812) | (0.865, 0.838) | Selenocompound metabolism | Schizophrenia (0.74) |
| SLC6A2 | 4.35 | 1.46E−16 | (0.897, 0.818) | NA | Methylphenidate pathway | Adrenal medulla cancer (1.21) |
| SLC5A12 | 4.93 | 1.70E−63 | (0.898, 0.816) | (0.867, 0.631) | NRF2 pathway | Follicular lymphoma (0.91) |
| SLC4A2 | −0.32 | 3.49E−07 | (0.903, 0.810) | (0.867, 0.631) | Bile secretion | Hepatocellular carcinoma (0.68) |
| SLCO1C1 | −0.91 | 1.11E−04 | (0.898, 0.813) | (0.867, 0.631) | Transport of vitamins and nucleosides | Allan–Herndon–Dudley syndrome (1.20) |
| SLC23A2 | −0.26 | 1.75E−04 | (0.897, 0.814) | (0.866, 0.839) | Metabolism of water‐soluble vitamins and cofactors | Hepatitis C virus (0.87) |
| ACE2 | 0.77 | 2.46E−06 | (0.896, 0.815) | (0.867, 0.631) | A‐beta plaque formation and APP metabolism | Renal oncocytoma (0.72) |
| SLC43A1 | −0.97 | 9.28E−14 | (0.897, 0.810) | (0.866, 0.840) | Amino acid transport across the plasma membrane | Seminoma (1.07) |
DEG = log2(CA/HT) denotes a differential expression gene and is computed from cancer and healthy samples of TCGA datasets.
P value is computed from cancerous and healthy samples of TCGA datasets.
Diseases and scores are obtained from the GeneCards database.