Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph
Abstract
:1. Introduction
2. Materials and Methods
2.1. Construction of the Molecular Association Network
2.2. NcRNA and Protein Sequence
2.3. Disease MeSH Descriptors and Directed Acyclic Graph
2.4. Drug Molecular Fingerprint
2.5. Stacked Autoencoder
2.6. Node Representation
3. Results and Discussion
3.1. Evaluate the Five-Fold Cross Validation Performance of Our Method
3.2. Comparison of Different Feature Extraction Methods
3.3. Comparison of Different Classifiers
3.4. Additional Comparison Experiment for lncRNA-Disease Association Prediction
3.5. Analysis Based on a Specific miRNA, lncRNA, and Protein
4. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Relationship Type | Database | Number of Associations |
---|---|---|
miRNA–lncRNA | lncRNASNP2 [23] | 8374 |
miRNA–disease | HMDD [10] | 16,427 |
miRNA–protein | miRTarBase [24] | 4944 |
lncRNA–disease | LncRNADisease [9] lncRNASNP2 [23] | 1264 |
lncRNA–protein Protein–disease Drug–protein Drug–disease Protein–protein | LncRNA2Target [25] DisGeNET [26] DrugBank [27] CTD [28] STRING [11] | 690 25,087 11,107 18,416 19,237 |
Total | N/A | 105,546 |
Node | Number of Nodes |
---|---|
Disease | 2062 |
LncRNA | 769 |
MiRNA | 1023 |
Protein | 1649 |
Drug | 1025 |
Total | 6528 |
Fold | Acc. (%) | Sen. (%) | Spec. (%) | Prec. (%) | MCC (%) | AUC (%) |
---|---|---|---|---|---|---|
0 | 92.25 | 92.68 | 91.82 | 91.89 | 84.51 | 97.35 |
1 | 92.43 | 92.52 | 92.35 | 92.36 | 84.87 | 97.34 |
2 | 92.49 | 92.84 | 92.13 | 92.19 | 84.98 | 97.39 |
3 | 92.58 | 92.75 | 92.42 | 92.44 | 85.16 | 97.39 |
4 | 92.13 | 92.28 | 91.98 | 92.01 | 84.26 | 97.29 |
Average | 92.38± 0.18 | 92.61± 0.22 | 92.14± 0.25 | 92.18± 0.23 | 84.76± 0.37 | 97.35± 0.04 |
Feature | Acc. (%) | Sen. (%) | Spec. (%) | Prec. (%) | MCC (%) | AUC (%) |
---|---|---|---|---|---|---|
Attribute | 88.62 ± 0.14 | 91.48 ± 0.13 | 85.76 ± 0.2 | 86.53 ± 0.17 | 77.37 ± 0.28 | 94.47 ± 0.11 |
Behavior | 90.7 ± 0.14 | 88.84 ± 0.15 | 92.56 ± 0.19 | 92.27 ± 0.19 | 81.45 ± 0.29 | 96.26 ± 0.05 |
Both | 92.38± 0.18 | 92.61± 0.22 | 92.14± 0.25 | 92.18± 0.23 | 84.76± 0.37 | 97.35± 0.04 |
Classifier | Acc. (%) | Sen. (%) | Spec. (%) | Prec. (%) | MCC (%) | AUC (%) |
---|---|---|---|---|---|---|
Adaboost | 80.03 ± 0.29 | 80.91 ± 0.3 | 79.14 ± 0.43 | 79.51 ± 0.36 | 60.07 ± 0.58 | 87.99 ± 0.28 |
Logistic | 79.92 ± 0.29 | 82.78 ± 0.29 | 77.06 ± 0.49 | 78.3 ± 0.37 | 59.94 ± 0.57 | 87.47 ± 0.26 |
Naive Bayes | 55.93 ± 0.15 | 24.83 ± 0.24 | 87.04 ± 0.32 | 65.7 ± 0.5 | 15.15 ± 0.41 | 72.13 ± 0.34 |
XGBoost | 84.37 ± 1.3 | 82.89 ± 2.96 | 85.85 ± 0.56 | 85.42 ± 0.37 | 68.8 ± 2.58 | 92.7 ± 0.66 |
Random Forest | 92.38± 0.18 | 92.61± 0.22 | 92.14± 0.25 | 92.18± 0.23 | 84.76± 0.37 | 97.35± 0.04 |
Number | Disease Name | Probability | Evidence |
---|---|---|---|
1 | Melanoma | 0.85 | LncRNADisease |
2 | Cervical cancer | 0.85 | LncRNADisease |
3 | Rheumatoid arthritis | 0.85 | MNDR 2.0 |
4 | Hepatocellular carcinoma | 0.85 | MNDR 2.0, LncRNADisease |
5 | Myelodysplastic syndrome | 0.846551724 | Unconfirmed |
6 | Schizophrenia | 0.842857143 | Unconfirmed |
7 | Chronic lymphocytic leukemia | 0.840909091 | Unconfirmed |
8 | Diffuse large b-cell lymphoma | 0.837460815 | Unconfirmed |
9 | Cardiac hypertrophy | 0.833766234 | Unconfirmed |
10 | Digeorge syndrome | 0.8 | Unconfirmed |
11 | Multiple sclerosis | 0.8 | Unconfirmed |
12 | Acute promyelocytic leukemia | 0.786551724 | Unconfirmed |
13 | Autism spectrum disorder | 0.75 | Unconfirmed |
14 | Colorectal cancer | 0.75 | MNDR 2.0, LncRNADisease |
15 | Osteosarcoma | 0.75 | MNDR 2.0, LncRNADisease |
16 | Squamous cell carcinoma | 0.75 | MNDR 2.0, LncRNADisease |
17 | Atherosclerosis | 0.75 | LncRNADisease |
18 | Glioblastoma | 0.75 | LncRNADisease |
19 | Pituitary adenoma | 0.75 | LncRNADisease |
20 | Pre-eclampsia | 0.75 | LncRNADisease |
LncRNA–miRNA Pairs | Associated Proteins Respectively | PPI Network Edges |
---|---|---|
NONHSAT007662.2/hsa-miR-205-5p | 70/27 | 1066 |
NONHSAT017460.2/hsa-miR-148a-3p | 74/28 | 877 |
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Guo, Z.-H.; Yi, H.-C.; You, Z.-H. Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph. Cells 2019, 8, 866. https://doi.org/10.3390/cells8080866
Guo Z-H, Yi H-C, You Z-H. Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph. Cells. 2019; 8(8):866. https://doi.org/10.3390/cells8080866
Chicago/Turabian StyleGuo, Zhen-Hao, Hai-Cheng Yi, and Zhu-Hong You. 2019. "Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA–miRNA–Disease–Drug–Protein Graph" Cells 8, no. 8: 866. https://doi.org/10.3390/cells8080866