Decision Trees for the Analysis of Gene Expression Levels of COVID-19: An Association with Alzheimer’s Disease
Abstract
:1. Introduction
2. Materials and Methods
2.1. Microarray Collection
2.2. Data Processing
2.3. Statistical Analysis
2.4. Decision Tree
- Accuracy: the total number of correct classifications divided by the size of the corresponding test set.
- Sensitivity: ability to correctly identify patients with asymptomatic and symptomatic COVID-19.
- Specificity: ability to correctly identify patients who do not have COVID-19.
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Genes/Groups | Symptomatic Mean | Symptomatic std.dev | Asymptomatic Mean | Asymptomatic std.dev | Healthy Controls Mean | Healthy Controls std.dev | F Ratio |
---|---|---|---|---|---|---|---|
TMEM106A | 5.816394 | 0.3775489 | 7.4241314 | 0.23304962 | 7.463178 | 0.2478398 | 144.75156 |
TNFAIP3 | 11.618307 | 0.4019925 | 8.287449 | 0.50382364 | 8.084149 | 0.38873255 | 257.89365 |
IER3 | 10.167634 | 0.5320755 | 7.5864162 | 0.3664378 | 7.700342 | 0.31561947 | 173.8846 |
ZNF394 | 7.964314 | 0.2556696 | 6.6509304 | 0.27549538 | 6.463861 | 0.2902587 | 110.72787 |
ABCA13 | 8.67961 | 0.5993782 | 4.191325 | 1.152125 | 4.047996 | 0.5659465 | 122.08616 |
FBXL14 | 6.397647 | 0.2234289 | 8.146227 | 0.26870775 | 8.219295 | 0.25515413 | 208.84077 |
CD63 | 9.559783 | 0.4696372 | 7.531043 | 0.17533515 | 7.447514 | 0.3454388 | 167.34497 |
DUSP1 | 11.526863 | 0.3501923 | 8.561377 | 0.7014648 | 8.818249 | 0.5148774 | 106.75434 |
PLK3 | 7.3127217 | 0.4593841 | 5.3107634 | 0.29284862 | 5.438676 | 0.36669925 | 119.47468 |
PPP1R15A | 8.71425 | 0.6500824 | 6.556414 | 0.32009986 | 6.7638645 | 0.3106922 | 103.9078 |
a | b | c | Classification |
---|---|---|---|
10 | 0 | 1 | a = symptomatic |
0 | 9 | 9 | b = asymptomatic |
0 | 3 | 15 | c = healthy controls |
a | b | c | Classification |
---|---|---|---|
9 | 0 | 2 | a = symptomatic |
0 | 8 | 10 | b = asymptomatic |
0 | 8 | 10 | c = healthy controls |
a | b | c | Classification |
---|---|---|---|
10 | 1 | 0 | a = symptomatic |
3 | 6 | 9 | b = asymptomatic |
0 | 1 | 17 | c = healthy controls |
Description | p Value | p Adjust | Gene ID | log_p Value |
---|---|---|---|---|
L-aspartate transmembrane transport | 0.00174788 | 0.04632427 | UCP2 | 2.75748815 |
Neutrophil-mediated killing of bacterium | 0.00174788 | 0.04632427 | TREM1 | 2.75748815 |
Neutrophil-mediated killing of symbiont cell | 0.00190668 | 0.04632427 | TREM1 | 2.71972261 |
Neutrophil-mediated cytotoxicity | 0.00222422 | 0.04632427 | TREM1 | 2.65282186 |
Phosphate ion transmembrane transport | 0.0025417 | 0.04632427 | UCP2 | 2.59487596 |
Sulfate transmembrane transport | 0.0025417 | 0.04632427 | UCP2 | 2.59487596 |
Sulfate transport | 0.00270041 | 0.04632427 | UCP2 | 2.56857004 |
Aspartate transmembrane transport | 0.00301779 | 0.04632427 | UCP2 | 2.52031141 |
Response to lead ion | 0.0033351 | 0.04632427 | UCP2 | 2.47689177 |
Glutamine metabolic process | 0.00428662 | 0.04632427 | UCP2 | 2.36788545 |
Phosphate ion transport | 0.00428662 | 0.04632427 | UCP2 | 2.36788545 |
C4-dicarboxylate transport | 0.00428662 | 0.04632427 | UCP2 | 2.36788545 |
Response to superoxide | 0.00444514 | 0.04632427 | UCP2 | 2.35211421 |
Killing by host of symbiont cells | 0.00444514 | 0.04632427 | TREM1 | 2.35211421 |
Response to oxygen radical | 0.00460365 | 0.04632427 | UCP2 | 2.33689727 |
Liver regeneration | 0.00460365 | 0.04632427 | UCP2 | 2.33689727 |
Neutrophil mediated immunity | 0.00555437 | 0.05188886 | TREM1 | 2.2553654 |
Mitochondrial fission | 0.00634617 | 0.05188886 | UCP2 | 2.19748861 |
Negative regulation of insulin secretion | 0.00634617 | 0.05188886 | UCP2 | 2.19748861 |
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Torres-Sosa, J.A.; Aranda-Abreu, G.E.; Cruz-Ramírez, N.; Mestizo-Gutiérrez, S.L. Decision Trees for the Analysis of Gene Expression Levels of COVID-19: An Association with Alzheimer’s Disease. BioMedInformatics 2025, 5, 26. https://doi.org/10.3390/biomedinformatics5020026
Torres-Sosa JA, Aranda-Abreu GE, Cruz-Ramírez N, Mestizo-Gutiérrez SL. Decision Trees for the Analysis of Gene Expression Levels of COVID-19: An Association with Alzheimer’s Disease. BioMedInformatics. 2025; 5(2):26. https://doi.org/10.3390/biomedinformatics5020026
Chicago/Turabian StyleTorres-Sosa, Jesús Alberto, Gonzalo Emiliano Aranda-Abreu, Nicandro Cruz-Ramírez, and Sonia Lilia Mestizo-Gutiérrez. 2025. "Decision Trees for the Analysis of Gene Expression Levels of COVID-19: An Association with Alzheimer’s Disease" BioMedInformatics 5, no. 2: 26. https://doi.org/10.3390/biomedinformatics5020026
APA StyleTorres-Sosa, J. A., Aranda-Abreu, G. E., Cruz-Ramírez, N., & Mestizo-Gutiérrez, S. L. (2025). Decision Trees for the Analysis of Gene Expression Levels of COVID-19: An Association with Alzheimer’s Disease. BioMedInformatics, 5(2), 26. https://doi.org/10.3390/biomedinformatics5020026