Hello,
I am trying to perform a Joint Pathway Analysis integrating metabolomics and proteomics data using the Daphnia pulex pathway library in MetaboAnalyst 6.0. However, I consistently receive a “No gene hits!” error when I provide my protein list, regardless of whether I use UniProt IDs or KEGG IDs specific to D. pulex.
However, if I replace the D. pulex UniProt IDs with the UniProt IDs of their Homo sapiens orthologs and switch the pathway library to Homo sapiens, the analysis runs without any issue. I think that problem is specific to the D. pulex pathway library not recognizing the protein identifiers.
Steps performed (leading to the error):
1. Opened Pathway Analysis in MetaboAnalyst 6.0.
2. Selected Joint Pathway Analysis
3. For metabolomics, I first attempted Untargeted metabolomics input; after encountering the error, I switched to Targeted analysis using compound names as identifiers.
4. Uploaded the protein list using:
- D. pulex-specific UniProt IDs (first attempt), then
- D. pulex KEGG IDs (second attempt).
5. Selected Daphnia pulex as the pathway library.
6. Clicked to proceed — error message received: “No gene hits!”
**Working with Homo sapiens orthologs:**
- Same workflow as above, but using Homo sapiens orthologs UniProt IDs and selecting the Homo sapiens pathway library → analysis completes successfully.
- I am attaching screenshots of both analyses (targeted and untargeted)
- Two showing the successful run with the **Homo sapiens** pathway library.
- Two documenting the **“No gene hits!”** error with the **Daphnia pulex** pathway library.
Thank you for your help!