Table 5.
Top-ranking biomarker candidates identified through the ML framework.
|
Previously Reported in | ||||||||
|---|---|---|---|---|---|---|---|---|
| Gene Symbol | ILMN ID | Prediction | Rank (Importance Level) | Conventional DEG Analysis* | Radiation Biomarker Reviews§ | No. of References from Gene-Specific Literature Searches (String 1; String 2) |
Main Biological Function | Novelty Score† |
| Brf2 | ILMN_1258583 | Dose Medulla | 5 (0.0) | No | No | 1; 2 | Transcriptional initiation | 2 |
| Ccng1 | ILMN_2702233 | Dose Medulla | 4 (13.6) | No | Yes | 19; 33 | Cell cycle regulation | 0 |
| Cdkn1a | ILMN_2634083 | Dose Cortex | 2 (91.3) | Yes | Yes | 426; 1,151 | Cell cycle regulation | 0 |
| Dose Medulla | 5 (100) | |||||||
| ILMN_2846775 | Dose Cortex | 1 (0.0) | ||||||
| Ddit4l | ILMN_2695819 | Dose Medulla | 2 (44.8) | No | No | 0; 2 | Stress response (pro-apoptotic) |
2 |
| Gria3 | ILMN_2638066 | Dose Cortex | 3 (19.2) | No | No | 0; 1 | Neurotransmission (glutamate receptor) | 2 |
| ILMN_2638066 | Dose Medulla | 3 (19.4) | ||||||
| Mdm2 | ILMN_1250774 | Dose Cortex | 4 (5.2) | No | Yes | 212; 926 | Negative regulator of p53 (oncogene) | 0 |
| Plk2 | ILMN_1260448 | Dose Cortex | 1 (100) | No | No | 6; 10 | Cell division (serine/threonine-protein kinase) | 1 |
List of biomarker candidates (microarray probes) identified in the datasets (GSE44762) from murine kidney cortex and medulla irradiated with 0.13 – 13 Gy absorbed dose from i.v. injected 177Lu-octreotate over 24 hours including unirradiated controls. To determine the novelty of KNN-based biomarker candidates, the gene symbols were searched within previous conventional DEG analysis, within literature reviews on radiation biomarker candidates, and additional gene-specific literature searches in context with radiation and biodosimetry to determine whether the genes have been proposed for biodosimetry in previous work.
Relative importance levels scaled between 0 and 100.
No., number; ILMN, Illumina probe identifier; IR, ionizing radiation.
*As reported in Schüler et al., 2014 (22).
†Novelty score: 0, reported as IR biomarker candidate in vast literature; 1, proposed as IR biomarker candidate in some literature; 2, not yet proposed as IR biomarker candidate in the literature.