Dear ExpressAnalyst team,
I’ve been using ExpressAnalyst for transcriptomic data analysis and have successfully run several differential expression and enrichment analyses in the past using both my own microarray datasets (rat hippocampus) and your provided examples.
However, I am now encountering a persistent issue with the Enrichment Network module. Specifically, I keep getting the error message:
“No such nodes were found!”
This happens under the following conditions:
- When analyzing my own dataset, which previously worked perfectly and generated a network graph a year ago.
- When analyzing your own demo dataset(“Basic Protocol 1 – 4”, mouse_counts.txt and mouse_meta.txt), following all the steps outlined in the tutorial.
- Regardless of the database used for enrichment (GO Biological Process, KEGG, Reactome, etc.).
- Regardless of the gene filtering thresholds applied (e.g., adjusted p < 0.05, log2FC > 1).
The DE analysis and enrichment tables work fine (e.g., volcano plots still display enriched pathways), but the network module fails to generate nodes or connections under any tested configuration.
This suggests that the issue is not related to input format, ID type, species mismatch, or pathway database selection, but could be a platform-side bug or mapping issue.
Has there been any recent change affecting how gene IDs are mapped to enrichment terms for visualization in the network? Or could there be a backend issue affecting the Enrichment Network module?
Thank you in advance for your support and for providing such a useful platform.
Best regards,
Carmen García Ruano