Table 3.
List of hub genes specific for the endemic cohort derived using different methodologies along with their corresponding functional roles and regulators (as identified from TRRUST database).
| Source | Hub genes* | Biological process | Role | Key regulators |
|---|---|---|---|---|
|
Network Topological Analysis of DEGs |
HRAS | GO:0000165: MAPK cascade |
Housekeeping | N/A |
| SOS1 | GO:0002260: Lymphocyte homeostasis |
Housekeeping | N/A | |
| KRAS | GO:0000165: MAPK cascade |
Housekeeping | N/A | |
| SRC | GO:0002376: Immune system processes |
Responsive | SP1, TAF1 | |
| EGFR | GO:0038134: ERBB2- EGFR signaling |
Responsive | AR, BCL3 BRAC1, CREBBP, EGR1, ESR1, HDAC1/3, HOXB7, JUN, JUNB, KLF10, LRRFIP1, MTA1, NFKB1, NR3C2, PGR, PML, PPARG, RELA, SP1 |
|
| MAPK1 | GO:0000165: MAPK cascade | Housekeeping | N/A | |
| MAPK14 | GO:0000165: MAPK cascade |
Housekeeping | N/A | |
| PTK2 | GO:0001932: Regulation of protein phosphorylation |
Responsive | N/A | |
| UBB | GO:0016567: Protein ubiquitination |
Housekeeping | N/A | |
| Hybrid Clustering based on LogFC values (Cluster 2) | GRB2 | GO:0007173: EGFR signaling | Responsive | N/A |
| ERBB2 | GO:0004714: Transmembrane receptor protein tyrosine kinase activity |
Responsive | AR, ATF, CREB1, DENND4A, ELF1, EP300, ETV4, FOXP3, GATA4, JUND, MYB, NCOA3, PAX2, PGR, PURA, SP1, TFAP2A, VDR, XRCC5, YBX1, YY1 |
|
| PTPN11 | GO:0000077: DNA damage checkpoint signaling |
Housekeeping | N/A | |
| SOCS1 | GO:001817: Regulation of cytokine production | Responsive | GL1/2, HIF1A,IRF1, SP1, STAT3/6 | |
| PIK3CD | GO:0002250: Adaptive immune response |
Responsive |
RUNX1 |
|
| SOCS3 | GO:001817: Regulation of cytokine production GO:0000082: |
Responsive | CEBPA, NFKB1, RELA, SP3, STAT1/3/4 | |
| CCND1 | G1/S transition mitotic cell cycle | Housekeeping | N/A | |
| PDGFRA | GO:0001775: Cell activation |
Housekeeping | N/A | |
| CSF3R | HSA:9674555: Signaling by CSF3 | Responsive | CEBPA, ETS1, MYB, SPI1 | |
| LCK | HAS:389356: CD28 co-stimulation | Responsive | MYB | |
| FGF13 | GO:0000165: MAPK cascade |
Housekeeping | N/A | |
| WT1 | HAS:9675108: Nervous system development |
Responsive | CTCF, EP300, ETS1, GATA1/2, HDAC4/5, HOXA10, IFI6, MYB, NFKB1, PAX2/8, RELA, SP1, TFCP2 |
|
| PHGDH | GO0006541: Glutamine metabolic process GO:0033209: |
Responsive | HOXA10, SP1 | |
| KRT18 | Tumor necrosis Factor-mediated signaling pathway |
Responsive | BRCA1, CTBP1, SP1 | |
| PTPN1 | HAS:163615: PKA activation |
Housekeeping | N/A | |
|
Hybrid Clustering
based on LogFC values (Cluster 4) |
RPS16 | GO:0006364: rRNA processing |
Housekeeping | N/A |
| RPL6 | Same as above | Housekeeping | N/A | |
| RPS9 | Same as above | Housekeeping | N/A | |
| RPL22 | Same as above | Housekeeping | N/A | |
| RPS15 | Same as above | Housekeeping | N/A | |
| ETF1 | GO:0006415: Translational Termination | Housekeeping | N/A | |
| SOX2 | HAS-452271: Signaling by WNT | Responsive | ID4, KDM2A, POU5F1 | |
| FN1 | GO:0006953: Acute-phase response |
Responsive | AR, ATF2, CEBPA, EGR1, KLF8, NFKB1, PARP1, RELA, SNAI1, SOX17, TWIST1/2 |
|
| HSP90AA1 | GO:0002218: Activation of innate immune response |
Housekeeping | N/A | |
| EEF1D | GO:0009299: Translational elongation |
Housekeeping | N/A | |
| WNT2B | HAS:3238698: WNT ligand biogenesis and trafficking | Responsive | GLI2 | |
| JAG1 | HAS:2979096:NOTCH2 activation and transcriptional signal to the Nucleus | Responsive | KDM4C, PPARG, RUNX3, SNAI2 | |
| TLR6 | Responsive | HIF1A | ||
| Features from Wrapper Algorithm with Random Forest | GRB2 | GO:0007173: EGFR signaling | Responsive | |
| ERBB2 | See above | Responsive | See above | |
| ERBB4 | GO: 0006916: Apoptotic process | Responsive | WWP1 | |
| ERBB3 | GO:0007162: Negative regulation of cell adhesion | Responsive | AR, TWIST1/2, YBX1 | |
| PIK3R1 | GO:0002687: Positive regulation of leukocyte migration | Responsive | N/A | |
| RET | GO:0000165: MAPK cascade | Responsive | ESR1, FOXA1, SOX10, NKX2-1, TFAP2C | |
| TXK | GO0001819: Positive regulation of cytokine production |
Housekeeping | N/A | |
| MST1R | GO:0002376: Immune system processes |
Responsive | N/A |
Functional roles identified from: https://housekeeping.unicamp.br/.
N/A, Not Available.