I have datasets of lncRNA, mRNA, miRNA, and the proteome of a virus's host-pathogen interaction, does anybody know how to establish a ceRNA network or identify hub genes? How can we get the hub genes that are dysregulated by lncRNA, mRNA, miRNA,and the proteome?
Here is the general protocol. You’ll find lots of related pipelines for each step(s) in github.
1. Data Preprocessing: Clean and preprocess your datasets, ensuring data quality and consistency.
2. Identify Differentially Expressed Genes: Use appropriate tools to identify differentially expressed genes (DEGs) for each dataset (lncRNA, mRNA, miRNA, and proteome) between different conditions (e.g., infected vs. uninfected).
3. miRNA-lncRNA-mRNA Interactions: Predict miRNA-lncRNA and miRNA-mRNA interactions using bioinformatics tools or databases. This helps establish the ceRNA interactions.
4. Construct ceRNA Network: Combine the interactions from step 3 to construct the ceRNA network, where lncRNAs, mRNAs, and miRNAs form nodes, and their interactions form edges.
5. Network Analysis: Perform network analysis to identify hub genes or central nodes. You can use centrality measures like degree, betweenness, closeness, or eigenvector centrality to identify these hubs.
6. Integration with Proteome Data: Integrate proteome data with the ceRNA network by mapping DEGs to proteins. This can help you identify hub genes that are regulated at both the RNA and protein levels.
7. Functional Analysis: Perform functional enrichment analysis on hub genes to understand their potential roles and pathways in the host-pathogen interaction.
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