Identification of Colon Cancer-Related RNAs Based on Heterogeneous Networks and Random Walk
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. RNA Expression Data
2.2. The Relationship of RNAs
2.3. Classification of RNA
2.4. Data Preprocessing
2.5. Differential Expression Analysis
2.6. Construct Heterogeneous Network
2.7. RW-DIR
Algorithm 1 Random Walk with Dynamic Incentive Restart (RW-DIR) |
3. Results
3.1. The Heterogeneous Network
3.2. The Result of RW-DIR
3.2.1. Colon Cancer Related mRNAs
3.2.2. Colon Cancer Related miRNAs
3.2.3. Colon Cancer Related lncRNAs
3.3. Performance of RW-DIR
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Types of RNA Associations | Database |
---|---|
mRNA-miRNA | multiMiR [16] |
mRNA-lncRNA | starbase V3.0 [17] |
miRNA-lncRNA | LncBase V2.0 [18] |
mRNA-mRNA | STRING [19] |
Types of RNA | Database |
---|---|
mRNA | Comparative Toxicogenomics Database [20] |
miRNA | miR2disease [21] |
lncRNA | LncRNADisease [22] |
Type of RNA | Number of RNA | Number of Normal Samples | Number of Tumor Samples |
---|---|---|---|
mRNA | 116591 | 41 | 443 |
miRNA | 302 | 8 | 444 |
lncRNA | 1526 | 41 | 443 |
Type of Edge | Number of Node | Number of Edge |
---|---|---|
mRNA-mRNA | 1300 (mRNA) | 7408 |
miRNA- miRNA | 81 (miRNA) | 389 |
lncRNA-lncRNA | 389 (lncRNA) | 604 |
mRNA-miRNA | 56 (mRNA) - 326(miRNA) | 569 |
mRNA-lncRNA | 33 (mRNA) - 70(lncRNA) | 94 |
miRNA-lncRNA | 99 (miRNA) - 57(lncRNA) | 587 |
Top 10 RNAs | Number of RNA | Related Diseases |
---|---|---|
hsa-miR-2682-5p | miRNA | Oral squamous cell carcinoma |
hsa-miR-1277-3p | miRNA | / |
ANGPTL1 | mRNA | Lung cancer, breast cancer, colorectal cancer |
SLC22A18AS | mRNA | Lung adenocarcinoma |
FENDRR | lncRNA | Gastric cancer, lung cancer, hepatocellular carcinoma (HCC), gastric cancer |
PHLPP2 | mRNA | Diabetes, hepatic steatosis, and cancer |
hsa-miR-302a-5p | miRNA | Endometrial carcinoma, glioma and breast cancer |
APCDD1 | mRNA | Breast cancer |
MEX3A | mRNA | Glioma |
hsa-miR-509-3-5p | miRNA | Gastric cancer |
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Chen, B.; Wang, T.; Zhang, J.; Zhang, S.; Shang, X. Identification of Colon Cancer-Related RNAs Based on Heterogeneous Networks and Random Walk. Biology 2022, 11, 1003. https://doi.org/10.3390/biology11071003
Chen B, Wang T, Zhang J, Zhang S, Shang X. Identification of Colon Cancer-Related RNAs Based on Heterogeneous Networks and Random Walk. Biology. 2022; 11(7):1003. https://doi.org/10.3390/biology11071003
Chicago/Turabian StyleChen, Bolin, Teng Wang, Jinlei Zhang, Shengli Zhang, and Xuequn Shang. 2022. "Identification of Colon Cancer-Related RNAs Based on Heterogeneous Networks and Random Walk" Biology 11, no. 7: 1003. https://doi.org/10.3390/biology11071003
APA StyleChen, B., Wang, T., Zhang, J., Zhang, S., & Shang, X. (2022). Identification of Colon Cancer-Related RNAs Based on Heterogeneous Networks and Random Walk. Biology, 11(7), 1003. https://doi.org/10.3390/biology11071003