LDAI-ISPS: LncRNA–Disease Associations Inference Based on Integrated Space Projection Scores
Abstract
:1. Introduction
- Provide guidance with less cost and time for the subsequent biological experimental verification related to complex diseases;
- Speed up our understanding on the pathogenesis of complex diseases;
- Give new ideas for disease prevention, diagnosis, treatment, and prognosis;
- Have a profound implication on drug development and medical improvement.
- Most of the off-the-shelf computational models cannot be used for inferring isolated diseases and new lncRNAs directly;
- Supervised learning of machine learning needs a negative sample to train the class classifier, but such negative sample cannot be obtained;
- Those that only rely on the known network topology will produce biased prediction results.
2. Results
2.1. Influence of Parameter Selection on Performance
2.2. Comparison with Other Methods
2.2.1. Evaluation Metrics of Performance
2.2.2. Comparison Results on Performance
2.3. Prediction for New lncRNAs and Isolated Diseases
2.4. Case Study
2.4.1. Case Study for Potential Associations
2.4.2. Case Study for Isolated Diseases
3. Discussion
4. Materials and Methods
4.1. Materials
4.1.1. LncRNA–Disease Association Network
4.1.2. Disease Semantic Similarity
4.1.3. LncRNA Functional Similarity
4.2. Disease (LncRNA) Gaussian Interaction Profile Central Similarity
4.3. Disease (LncRNA) Integrated Similarities
4.4. LDAI-ISPS Workflow Model
4.4.1. Construction of lncRNA-Disease Weighted Network
4.4.2. Space Projection Scores of lncRNA–Disease Associations
4.4.3. Prediction Score Based on Space Projection Scores
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
LOOCV | leave-one-out cross validation |
ROC | receiver operating characteristic |
AUC | area under the ROC curve |
FPR | false positive rate |
TPR | true positive rate |
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Disease | lncRNA Name | Evidence | Rank |
---|---|---|---|
Cervical cancer | LSINCT5 | Ref. [60] | 1 |
Cervical cancer | HOTAIR | LncRNADisease | 2 |
Cervical cancer | MEG3 | LncRNADisease | 3 |
Cervical cancer | EPB41L4A-AS1 | Ref. [61] | 4 |
Cervical cancer | PANDAR | Ref. [3] | 5 |
Type 2 diabetes | IGF2-AS | Ref. [62] | 1 |
Type 2 diabetes | MEG3 | LncRNADisease | 2 |
Type 2 diabetes | PINK1-AS | Ref. [63] | 3 |
Type 2 diabetes | Gas5 | LncRNADisease | 4 |
Type 2 diabetes | PCAT-1 | Unconfirmed | 5 |
Disease | lncRNA Name | Evidence | Rank |
---|---|---|---|
Prostate cancer | PCAT-1 | LncRNADisease | 1 |
Prostate cancer | C1QTNF9B-AS1 | LncRNADisease | 2 |
Prostate cancer | CBR3-AS1 | LncRNADisease | 3 |
Prostate cancer | PCA3 | LncRNADisease | 4 |
Prostate cancer | PCAT1 | LncRNADisease | 5 |
Alzheimer’s disease | BACE1-AS | LncRNADisease | 1 |
Alzheimer’s disease | GDNFOS | LncRNADisease | 2 |
Alzheimer’s disease | SNHG3 | LncRNADisease | 3 |
Alzheimer’s disease | SOX2-OT | LncRNADisease | 4 |
Alzheimer’s disease | CDKN2B-AS10 | Ref. [64] | 5 |
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Zhang, Y.; Chen, M.; Li, A.; Cheng, X.; Jin, H.; Liu, Y. LDAI-ISPS: LncRNA–Disease Associations Inference Based on Integrated Space Projection Scores. Int. J. Mol. Sci. 2020, 21, 1508. https://doi.org/10.3390/ijms21041508
Zhang Y, Chen M, Li A, Cheng X, Jin H, Liu Y. LDAI-ISPS: LncRNA–Disease Associations Inference Based on Integrated Space Projection Scores. International Journal of Molecular Sciences. 2020; 21(4):1508. https://doi.org/10.3390/ijms21041508
Chicago/Turabian StyleZhang, Yi, Min Chen, Ang Li, Xiaohui Cheng, Hong Jin, and Yarong Liu. 2020. "LDAI-ISPS: LncRNA–Disease Associations Inference Based on Integrated Space Projection Scores" International Journal of Molecular Sciences 21, no. 4: 1508. https://doi.org/10.3390/ijms21041508