Decoding Diabetes Biomarkers and Related Molecular Mechanisms by Using Machine Learning, Text Mining, and Gene Expression Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Text Mining Analysis
2.2. Gene Expression Analysis and Correlation Analysis
2.3. Enrichment Analysis and Protein–Protein Interactions
2.4. Machine Learning Analysis and Correlation Analyses
3. Results
3.1. Diabetes-Related Genes Occurring Frequently in the Literature
3.2. Differential Gene Expression and Correlation Analyses
3.3. Text Mining versus Gene Expression
3.4. Machine Learning Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
DEG | Differential expressed genes |
ER | Endoplasmic reticulum |
GEO | Gene Expression Omnibus |
IDF | International Diabetes Federation |
PPI | Protein-protein interaction |
TCA | Tricarboxylic acid |
TCR | T-Cell antigen Receptor |
References
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Term Name | FDR | Share | Intersection | Term Name | FDR | Share | Intersection |
---|---|---|---|---|---|---|---|
response to nitrogen compound | 33.3 | 47.27% | 4.73% | positive regulation of macromolecule metabolic process | 19.3 | 58.18% | 1.85% |
response to organonitrogen compound | 32.6 | 45.45% | 4.95% | positive regulation of multicellular organismal process | 19.3 | 40.00% | 3.07% |
regulation of multicellular organismal process | 30.9 | 62.73% | 2.59% | apoptotic process | 19.2 | 44.55% | 2.63% |
cellular response to chemical stimulus | 30.6 | 65.45% | 2.38% | localization | 19.1 | 76.36% | 1.31% |
response to endogenous stimulus | 28 | 49.09% | 3.47% | signaling | 19.1 | 76.36% | 1.30% |
chemical homeostasis | 27.6 | 41.82% | 4.50% | cell death | 19 | 46.36% | 2.46% |
regulation of biological quality | 27.2 | 68.18% | 1.99% | positive regulation of cell communication | 19 | 42.73% | 2.75% |
positive regulation of biological process | 27 | 82.73% | 1.46% | cellular response to peptide | 18.9 | 23.64% | 7.45% |
regulation of cell communication | 26.7 | 64.55% | 2.13% | positive regulation of signaling | 18.9 | 42.73% | 2.74% |
cellular response to organic substance | 26.5 | 56.36% | 2.59% | regulation of cell differentiation | 18.9 | 40.91% | 2.90% |
cellular response to oxygen-containing compound | 26.2 | 42.73% | 4.03% | programmed cell death | 18.7 | 44.55% | 2.55% |
positive regulation of cellular process | 24.1 | 77.27% | 1.49% | hormone secretion | 18.4 | 21.82% | 8.39% |
response to peptide hormone | 24 | 28.18% | 7.79% | negative regulation of cellular process | 18.2 | 66.36% | 1.50% |
glucose homeostasis | 23.2 | 23.64% | 10.83% | hormone transport | 18.1 | 21.82% | 8.14% |
regulation of developmental process | 23.2 | 53.64% | 2.43% | small molecule metabolic process | 18.1 | 42.73% | 2.62% |
carbohydrate homeostasis | 23.1 | 23.64% | 10.79% | regulation of molecular function | 18 | 53.64% | 1.93% |
multicellular organismal process | 23 | 84.55% | 1.26% | Late onset | 17.9 | 23.38% | 41.86% |
positive regulation of metabolic process | 22.4 | 63.64% | 1.85% | positive regulation of biosynthetic process | 17.9 | 44.55% | 2.45% |
regulation of response to stimulus | 22.4 | 64.55% | 1.82% | regulation of phosphate metabolic process | 17.9 | 38.18% | 3.03% |
Abnormal waist to hip ratio | 22 | 24.68% | 54.29% | regulation of phosphorus metabolic process | 17.9 | 38.18% | 3.03% |
Increased waist to hip ratio | 22 | 24.68% | 54.29% | regulation of response to stress | 17.8 | 37.27% | 3.13% |
response to insulin | 21.1 | 22.73% | 9.88% | regulation of hormone secretion | 17.6 | 20.00% | 9.32% |
response to external stimulus | 20.9 | 54.55% | 2.15% | macromolecule localization | 17.4 | 53.64% | 1.89% |
developmental process | 20.6 | 77.27% | 1.35% | regulation of intracellular signal transduction | 17.3 | 40.91% | 2.66% |
cellular developmental process | 20.5 | 64.55% | 1.70% | cell surface receptor signaling pathway | 17.2 | 50.91% | 1.99% |
regulation of cell population proliferation | 20.5 | 43.64% | 2.90% | positive regulation of cellular metabolic process | 17.2 | 54.55% | 1.83% |
regulation of signal transduction | 20.5 | 55.45% | 2.07% | negative regulation of multicellular organismal process | 17 | 32.73% | 3.60% |
regulation of apoptotic process | 20.4 | 40.91% | 3.17% | intracellular signal transduction | 16.9 | 49.09% | 2.05% |
cellular response to nitrogen compound | 20.3 | 30.91% | 4.98% | cellular response to endogenous stimulus | 16.8 | 36.36% | 3.04% |
cellular response to organonitrogen compound | 20.3 | 30.00% | 5.27% | anatomical structure development | 16.7 | 70.00% | 1.34% |
regulation of cell death | 20.3 | 42.73% | 2.95% | organic substance transport | 16.7 | 49.09% | 2.03% |
cell population proliferation | 20.2 | 46.36% | 2.60% | protein secretion | 16.7 | 21.82% | 7.08% |
regulation of programmed cell death | 20.1 | 40.91% | 3.11% | establishment of protein localization to extracellular region | 16.6 | 21.82% | 7.06% |
Insulin resistance | 20 | 29.87% | 29.87% | multicellular organismal homeostasis | 16.5 | 25.45% | 5.23% |
cellular response to stimulus | 19.9 | 81.82% | 1.22% | positive regulation of cellular biosynthetic process | 16.5 | 42.73% | 2.39% |
animal organ development | 19.8 | 59.09% | 1.85% | protein localization to extracellular region | 16.4 | 21.82% | 6.92% |
cell differentiation | 19.8 | 63.64% | 1.68% | regulation of small molecule metabolic process | 16.4 | 21.82% | 6.92% |
regulation of transport | 19.8 | 43.64% | 2.78% | regulation of protein localization | 16.3 | 30.00% | 3.91% |
cell communication | 19.7 | 77.27% | 1.31% | multicellular organism development | 16.2 | 63.64% | 1.47% |
response to hormone | 19.6 | 32.73% | 4.29% | negative regulation of biological process | 16.1 | 70.00% | 1.31% |
ML Algorithm | Data | Marker Code | Marker Name | Importantance | Gene |
---|---|---|---|---|---|
DecisionTree | A | M313 | 209480_at | 8.54 | HLA-DQB1 |
M399 | 212999_x_at | 6.83 | HLA-DQB1 | ||
M398 | 212998_x_at | 5.98 | HLA-DQB1 | ||
M710 | 238996_x_at | 5.98 | ALDOA | ||
M370 | 211654_x_at | 5.12 | HLA-DQB1 | ||
M417 | 214631_at | 5.12 | ZBTB33 | ||
B | M148 | ILMN_1720311 | 13.07 | SLC25A46 | |
M302 | ILMN_1790797 | 9.44 | VPS28 | ||
M61 | ILMN_1672899 | 9.44 | POMC | ||
M161 | ILMN_1726470 | 7.99 | OTUD5 | ||
M41 | ILMN_1666192 | 7.99 | DCTN5 | ||
M88 | ILMN_1684802 | 7.99 | TAF5 | ||
RandomForest | A | M667 | 233510_s_at | 0.53 | PARVG |
M710 | 238996_x_at | 0.41 | ALDOA | ||
M313 | 209480_at | 0.40 | HLA-DQB1 | ||
M546 | 223016_x_at | 0.25 | ZRANB2 | ||
M203 | 205025_at | 0.19 | ZBTB48 | ||
M141 | 202462_s_at | 0.18 | DDX46 | ||
M399 | 212999_x_at | 0.16 | HLA-DQB1 | ||
M636 | 230031_at | 0.15 | HSPA5 | ||
M140 | 202455_at | 0.15 | HDAC5 | ||
M80 | 1569150_x_at | 0.15 | PDLIM7 | ||
B | M51 | ILMN_1670576 | 2.08 | IRF5 | |
M41 | ILMN_1666192 | 1.97 | DCTN5 | ||
M148 | ILMN_1720311 | 1.68 | SLC25A46 | ||
M345 | ILMN_1813746 | 1.19 | CORO2A | ||
M333 | ILMN_1806408 | 1.00 | ACADVL | ||
M61 | ILMN_1672899 | 0.86 | POMC | ||
M146 | ILMN_1718822 | 0.82 | STYXL1 | ||
M239 | ILMN_1762095 | 0.81 | TMTC4 | ||
M136 | ILMN_1709800 | 0.64 | POMZP3 | ||
M265 | ILMN_1771697 | 0.52 | VRK3 |
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Elsherbini, A.M.; Alsamman, A.M.; Elsherbiny, N.M.; El-Sherbiny, M.; Ahmed, R.; Ebrahim, H.A.; Bakkach, J. Decoding Diabetes Biomarkers and Related Molecular Mechanisms by Using Machine Learning, Text Mining, and Gene Expression Analysis. Int. J. Environ. Res. Public Health 2022, 19, 13890. https://doi.org/10.3390/ijerph192113890
Elsherbini AM, Alsamman AM, Elsherbiny NM, El-Sherbiny M, Ahmed R, Ebrahim HA, Bakkach J. Decoding Diabetes Biomarkers and Related Molecular Mechanisms by Using Machine Learning, Text Mining, and Gene Expression Analysis. International Journal of Environmental Research and Public Health. 2022; 19(21):13890. https://doi.org/10.3390/ijerph192113890
Chicago/Turabian StyleElsherbini, Amira M., Alsamman M. Alsamman, Nehal M. Elsherbiny, Mohamed El-Sherbiny, Rehab Ahmed, Hasnaa Ali Ebrahim, and Joaira Bakkach. 2022. "Decoding Diabetes Biomarkers and Related Molecular Mechanisms by Using Machine Learning, Text Mining, and Gene Expression Analysis" International Journal of Environmental Research and Public Health 19, no. 21: 13890. https://doi.org/10.3390/ijerph192113890
APA StyleElsherbini, A. M., Alsamman, A. M., Elsherbiny, N. M., El-Sherbiny, M., Ahmed, R., Ebrahim, H. A., & Bakkach, J. (2022). Decoding Diabetes Biomarkers and Related Molecular Mechanisms by Using Machine Learning, Text Mining, and Gene Expression Analysis. International Journal of Environmental Research and Public Health, 19(21), 13890. https://doi.org/10.3390/ijerph192113890