Dear MetaboAnalyst Support Team,
I am reaching out to kindly request your assistance regarding a pathway analysis I conducted in MetaboAnalyst 6.0. I uploaded the metabolites from the file “KEGG ID identified amino acids” into the compound list and used the following settings:
- Visualization method: Scatter plot (testing significant features)
- Enrichment method: Hypergeometric Test
- Topology measure: Relative-betweeness Centrality
- Reference metabolome: Use all compounds in the selected pathway library
- Pathway library: Mammals [20] Homo sapiens (KEGG)
The analysis yielded the following significant results after FDR correction:
- Arginine biosynthesis: Match Status: 3/14; p: 6.4776E-5; FDR: 0.0051821
- Taurine and hypotaurine metabolism: Match Status: 2/8; p: 9.9601E-4; FDR: 0.03984
Other pathways did not remain significant after FDR correction.
On your platform, it is mentioned that the enriched functions reflect both platform/protocol-specific effects and biological perturbations, and it is highly recommended to upload a reference metabolome containing all measurable metabolites from the platform to eliminate the former effects. Following this recommendation, I provided all measured metabolites (found in the second document, “KEGG ID all measured amino acids”) as the reference metabolome. Unfortunately, with this reference metabolome, no significant results remained.
Could you kindly advise whether it is necessary to provide a reference metabolome when working with such a small number of metabolites to exclude platform/protocol-specific effects? Are there other adjustments or settings you would recommend to further refine the analysis? Given your extensive experience and expertise, I would greatly appreciate your insights and suggestions.
Thank you very much for your time and assistance.
Best regards,
Martin Oestreich
KEGG ID all meaured amino acids.csv (211 Bytes)
KEGG ID identified amino acids .csv (83 Bytes)