Differentially Expressed Genes, miRNAs and Network Models: A Strategy to Shed Light on Molecular Interactions Driving HNSCC Tumorigenesis
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. RNAseq Data, from miRNAs to Differentially Expressed Genes (DEGs)
2.2. Extraction of miRNA Targets and Bipartite Network Reconstruction
2.3. Functional and Topological Analysis of PPI Networks Reconstructed from miRNA Targets and DEGs
2.4. Differentially Expressed miRNAs and Survival Analysis
3. Results
3.1. Differentially Expressed Genes (DEGs) in Head and Neck Cancer
3.2. Differentially Expressed miRNAs in Head and Neck Cancer
3.3. PPI Network Models of Genes Most Targeted by Up- and Downregulated miRNAs: From Modulated Pathways to Hubs
3.4. Survival Analysis Using miRNAs Targeting Key Tumor Suppressors and Oncogenes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
HNSCC | Head and Neck Squamous Cell Carcinoma |
PPI | Protein–Protein Interaction |
FC | Log2(Fold Change) |
DEGs | Differentially Expressed Genes |
STAR | Spliced Transcripts Alignment to a Reference |
RPM | Reads Per Million |
GLN | Generalized Linear Model |
FDR | False Discovery Rate |
ECM | Extracellular Matrix |
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Centrality | Average Value |
---|---|
Betweenness | 1384.6 |
Centroid | −437 |
Bridging | 68.4 |
Degree | 14.2 |
Radiality | 4.8 |
Closeness | 0.000506 |
Stress | 18,601 |
Eccentricity | 0.185 |
Eigenvector | 0.0161 |
Diameter 1 | 7 |
Average Distance 1 | 3.18 |
Centrality | Average Value in PPI Network of Genes Targeted by Upregulated miRNAs | Average Value in PPI Network of Genes Targeted by Downregulated miRNAs |
---|---|---|
Betweenness | 515.4 | 457.5 |
Centroid | −260.8 | −234.5 |
Bridging | 12.8 | 7.5 |
Degree | 28.7 | 44.6 |
Radiality | 3.75 | 2.91 |
Closeness | 0.00109 | 0.00115 |
Stress | 7883 | 9399 |
Eccentricity | 0.274 | 0.309 |
Eigenvector | 0.0353 | 0.0369 |
Diameter 1 | 5 | 4 |
Average Distance 1 | 2.24 | 2.08 |
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Arfin, S.; Kumar, D.; Lomagno, A.; Mauri, P.L.; Di Silvestre, D. Differentially Expressed Genes, miRNAs and Network Models: A Strategy to Shed Light on Molecular Interactions Driving HNSCC Tumorigenesis. Cancers 2023, 15, 4420. https://doi.org/10.3390/cancers15174420
Arfin S, Kumar D, Lomagno A, Mauri PL, Di Silvestre D. Differentially Expressed Genes, miRNAs and Network Models: A Strategy to Shed Light on Molecular Interactions Driving HNSCC Tumorigenesis. Cancers. 2023; 15(17):4420. https://doi.org/10.3390/cancers15174420
Chicago/Turabian StyleArfin, Saniya, Dhruv Kumar, Andrea Lomagno, Pietro Luigi Mauri, and Dario Di Silvestre. 2023. "Differentially Expressed Genes, miRNAs and Network Models: A Strategy to Shed Light on Molecular Interactions Driving HNSCC Tumorigenesis" Cancers 15, no. 17: 4420. https://doi.org/10.3390/cancers15174420