tooluniverse-systems-biology

Submit gene symbols to Enrichr or Reactome pathway enrichment tools, then sort results by adjusted p-value below 0.05. Report the top 10-20 pathways with IDs, p-values, and overlapping genes, and note explicitly if no enrichment is found.

Map the protein's UniProt accession to Reactome pathways using the Reactome mapping tool, then retrieve detailed reactions and subpathways for the most relevant hits. If Reactome returns empty results, verify the UniProt ID or fall back to keyword search with the protein name.

Reactome offers detailed human-curated mechanistic pathways with reactions, KEGG covers metabolic maps and disease pathways, and WikiPathways contains community-curated emerging pathways. Cross-validate key findings across at least two sources since databases disagree on pathway membership.

Enrichment can fail when gene lists are too small, use IDs instead of gene symbols, or when the gene set genuinely lacks pathway overlap. Try alternative Enrichr libraries like Reactome or GO Biological Process, and check that symbols are correctly cased.

Reactome has limited coverage for non-model organisms, KEGG keyword search may miss synonyms, WikiPathways has variable curation quality, and BioModels often returns no results. Broaden keywords and check pathway version dates when results are sparse.