Skip to main content

featureMSEA Tutorial: Feature-based Metabolite Set Enrichment Analysis

5 Analysis Results

After Step 2 completes, results appear in the Analysis Results panel on the right. The panel is driven by row selection in the significant modules table — clicking a row updates the enrichment plot, annotation table, and LLM evaluation panel below.

5.1 Significant Modules Table

The significant modules table lists all enriched metabolite sets that pass the FDR threshold. Each row contains:

Column Description
Pathway Metabolite set name
NES Normalized Enrichment Score — positive indicates enrichment among top-ranked features, negative among bottom-ranked features
p-value Nominal p-value from permutation testing
FDR Benjamini–Hochberg adjusted p-value

Clicking a row triggers the panels below. The full table can be exported via Download Table (CSV).

Selecting a significant module renders the enrichment plot below the table

Figure 5.1: Selecting a significant module renders the enrichment plot below the table

The enrichment plot shows the running enrichment score across the ranked feature list for the selected metabolite set. The peak of the curve marks the leading edge — the subset of annotated features most responsible for the enrichment signal. Export the plot via Download Plot (PNG or PDF).

5.2 Annotation Table and LLM Evaluation

Annotation table and Pathway LLM Evaluation panel

Figure 5.2: Annotation table and Pathway LLM Evaluation panel

Annotation Table — lists the leading edge features for the selected metabolite set, showing feature-level annotation details for the compounds driving the enrichment. Export via Download Table (CSV).

Pathway LLM Evaluation — populated only after Step 3 completes. Displays the following fields for the selected metabolite set:

Field Description
Pathway Name Metabolite set name
Matrix Source Biological sample matrix provided in Step 3
Matrix Confidence Score LLM-assigned score (0–100) reflecting biological plausibility within the specified matrix
Matrix Confidence Reason Reasoning behind the matrix confidence score
Research Topic Research context provided in Step 3
Literature PMIDs (Exact) PubMed IDs from exact-match literature search — click to open in PubMed
Literature PMIDs (Fuzzy) PubMed IDs from fuzzy-match literature search — click to open in PubMed
Topic Confidence Score LLM-assigned score reflecting literature support for the metabolite set in the given research context

If Step 3 has not been run, the LLM Evaluation panel does not appear.