I am conducting a master's research project where I have incorporated a terpene into a polysaccharide-based hydrogel and aim to evaluate its osteoinductive activity in mesenchymal stem cells using molecular biology techniques. To complement this, I am performing a network pharmacology analysis to explore potential targets of the terpene that may be involved in osteogenesis.
Here is the workflow I have followed so far:
Now, I am exploring the most robust approach for further analysis and would appreciate insights on the following options:
I would greatly value your suggestions on which approach would yield the most meaningful biological insights or if there are alternative methods I should consider. Thank you in advance for your guidance!
Start with GO/KEGG enrichment on all targets. Then, focus on hub genes using Cytoscape metrics or CytoHubba. Perform clustering (MCODE for tight clusters) and analyze GO/KEGG for each cluster. Integrate results by comparing hub genes and clusters to identify key targets in osteogenesis.
Dr Amit Kumar Tiwari , If I understood correctly, you are suggesting that I integrate the enrichment results of the hub genes by comparing them with the clusters to identify the main clusters. Is that correct? Do you recommend any specific package for this analysis?
Best regards!
Yes, that’s correct Wanderson Gabriel Gomes de Melo. By comparing the hub genes with the clusters, you can identify key biological pathways and targets. For this analysis, I recommend using Cytoscape along with its enrichment analysis plugins (e.g., ClueGO or EnrichmentMap) to streamline the interpretation of results.
- Badges
- Science topic