Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction
Abstract
:1. Introduction
2. Results and Discussion
2.1. Hepatocellular Carcinoma (HCC)
2.2. Non-Small Cell Lung Cancer (NSCLC)
2.3. Esophageal Squamous Cell Cancer (ESCC)
2.4. Prostate Cancer
2.5. Colorectal/Colon Cancer
2.6. Breast Cancer
2.7. Confirmation of Significance of the FDR Criterion
2.8. Discrimination Performance between Patients and Healthy Controls
2.9. Confident Candidate Selection by PCA-Based Unsupervised FE
2.10. Usefulness of Unmatched Data and Number of False Negatives
3. Materials and Methods
3.1. Gene Expression Profiles
3.1.1. HCC
3.1.2. NSCLC
3.1.3. ESCC
3.1.4. Prostate Cancer
3.1.5. Colorectal/Colon Cancer
3.1.6. Breast Tumors
3.2. PCA-Based Unsupervised FE
3.3. Identification of Significant miRNA–mRNA Pairs
3.4. Validation Using Starbase
3.5. Discrimination between Patients and Healthy Controls
3.6. Validation Using FDR
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Number of Samples | Number of Probes | ||||
---|---|---|---|---|---|
Cancers | GEO ID | Tumors | Controls | Selected | Non-Selected |
HCC | |||||
mRNA | GSE45114 | 24 | 25 | 269 | 22,963 |
miRNA | GSE36915 | 68 | 21 | 58 | 1087 |
NSCLC | |||||
mRNA | GSE18842 | 46 | 45 | 1098 | 53,504 |
miRNA | GSE15008 | 187 | 174 | 268 | 3428 |
ESCC | |||||
mRNA | GSE38129 | 30 | 30 | 189 | 22,088 |
miRNA | GSE19337 | 76 | 76 | 37 | 1217 |
Prostate cancer | |||||
mRNA | GSE21032 | 150 | 29 | 399 | 43,020 |
miRNA | GSE84318 | 27 | 27 | 23 | 700 |
Colon/colorectal cancer | |||||
mRNA | GSE41258 | 186 | 54 | 309 | 21,974 |
miRNA | GSE48267 | 30 | 30 | 12 | 839 |
Breast cancer | |||||
mRNA | GSE29174 | 110 | 11 | 980 | 33,600 |
miRNA | GSE28884 | 173 | 16 | 18 | 2258 |
HCC | NSCLC | ESCC | ||||
---|---|---|---|---|---|---|
mRNA | miRNA | mRNA | miRNA | mRNA | miRNA | |
FDR | 262 | 38 | 978 | 0 | 189 | 0 |
BH | 269 | 58 | 1091 | 268 | 189 | 37 |
Prostate Cancer | Colon/Colorectal Cancer | Breast Cancer | ||||
mRNA | miRNA | mRNA | miRNA | mRNA | miRNA | |
FDR | 399 | 7 | 305 | 12 | 861 | 0 |
BH | 399 | 23 | 309 | 12 | 908 | 18 |
mRNA | miRNA | |||
---|---|---|---|---|
HCC | hc | HCC | hc | |
HCC | 20 | 0 | 64 | 0 |
hc | 4 | 25 | 4 | 21 |
(L, p-value, odds ratio) | (4, , ∞) | (10, *, ∞) | ||
NSCLC | hc | NSCLC | hc | |
NSCLC | 46 | 0 | 171 | 12 |
hc | 0 | 45 | 16 | 162 |
(L, p-value, odds ratio) | (2,*, ∞) | (5, *, ) | ||
ESCC | hc | ESCC | hc | |
ESCC | 28 | 2 | 63 | 11 |
hc | 2 | 28 | 13 | 65 |
(L, p-value, odds ratio) | (2, , ) | (6, *, ) | ||
Pancreatic cancer | hc | Pancreatic cancer | hc | |
Pancreatic cancer | 139 | 4 | 22 | 3 |
hc | 11 | 25 | 5 | 24 |
(L, p-value, odds ratio) | (8, *, ) | (4, , ) | ||
Colorectal cancer | hc | Colon cancer | hc | |
Colon/Colorectal cancer | 178 | 5 | 27 | 3 |
hc | 8 | 49 | 3 | 27 |
(L, p-value, odds ratio) | (8, *, ) | (4, , ) | ||
Breast cancer | hc | Breast cancer | hc | |
Breast cancer | 110 | 0 | 169 | 5 |
hc | 0 | 11 | 4 | 11 |
(L, p-value, odds ratio) | (3, , ∞) | (18, , ) |
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Taguchi, Y.-h. Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction. Int. J. Mol. Sci. 2016, 17, 696. https://doi.org/10.3390/ijms17050696
Taguchi Y-h. Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction. International Journal of Molecular Sciences. 2016; 17(5):696. https://doi.org/10.3390/ijms17050696
Chicago/Turabian StyleTaguchi, Y-h. 2016. "Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction" International Journal of Molecular Sciences 17, no. 5: 696. https://doi.org/10.3390/ijms17050696