Table 1.
Top ten genes evaluated in the PPI networks using five ranking methods (MCC, MNC, Degree, EPC and EcCentricity) by the Cytoscape App CytoHubba.
| Calculation method | Degree | MNC | MCC | EPC | EcCentricity |
|---|---|---|---|---|---|
| (A) Upregulated | |||||
| Gene symbol | AURKA | AURKA | AURKA | AURKA | AURKA |
| MAD2L1 | MAD2L1 | MAD2L1 | TRIP13 | TRIP13 | |
| CCNB2 | CCNB2 | CCNB2 | CCNB2 | CCNB2 | |
| BIRC5 | BIRC5 | BIRC5 | PHGDH | PHGDH | |
| BUB1 | BUB1 | BUB1 | BUB1 | BUB1 | |
| UBE2C | UBE2C | UBE2C | UBE2C | UBE2C | |
| TYMS | TYMS | PTTG1 | CDC45 | CDC45 | |
| CDK1 | CDK1 | CDK1 | CDK1 | CDK1 | |
| MYC | MYC | CDC45 | MYC | MYC | |
| CDC20 | CDC20 | CDC20 | CDC20 | CDC20 | |
| (B) Downregulated | |||||
| Gene symbol | ESR1 | ESR1 | ESR1 | FOXA1 | PIP |
| CCND1 | CCND1 | FOXA1 | ESR1 | AR | |
| AR | TFF1 | TFF1 | GATA3 | ESR1 | |
| TFF1 | AR | GATA3 | TFF1 | GATA3 | |
| FOXA1 | FOXA1 | TFF3 | CCND1 | MUC1 | |
| GATA3 | GATA3 | CCND1 | AR | AZGP1 | |
| AGR2 | MUC1 | AGR2 | AGR2 | FOXA1 | |
| MUC1 | TFF3 | XBP1 | MUC1 | IGF1R | |
| PIP | AGR2 | AGR3 | TFF3 | TFF1 | |
| TFF3 | PIP | SLC39A6 | XBP1 | MYB | |
| (C) Upregulated | |||||
| Gene symbol | HIST2H2AC | ERBB2 | HIST2H2AC | HIST2H2BE | KLK6 |
| HIST1H4H | HIST2H2BE | HIST1H4E | HIST2H2AC | RBP1 | |
| ERBB2 | HIST2H2AC | HIST2H4A | HIST1H4E | CX3CL1 | |
| HIST2H2BE | CDH1 | HIST1H2BD | HIST1H2BK | CCL2 | |
| HIST1H4E | HIST1H4E | HIST2H2AA3 | CDH1 | SDC1 | |
| CCL2 | HIST2H4A | HIST1H4H | HIST2H4A | MYC | |
| MYC | MYC | HIST1H3D | HIST1H2BD | FOS | |
| HIST2H4A | HIST1H4H | HIST1H3H | MYC | CDH1 | |
| FOS | FOS | HIST1H2AE | HIST1H4H | LTF | |
| CDH1 | CCL2 | HIST1H1C | FOS | APP | |
A/B: Hub genes detected for the DEGs in the up- and downregulated PPI networks, respectively. C: Hub genes detected for the PPI network with DEGs expressed in hormone-positive (HR+) breast cancer patients only.