Pathway Search — Help

Clinical associations in MCA are annotated with KEGG Disease IDs (H numbers) where applicable. Each disease entry in the KEGG flat file carries a PATHWAY field listing the molecular pathways implicated in that disease (e.g., Clostridioides difficile infection → hsa05111 Biofilm formation). Additionally, KEGG BRITE (br08402) organises diseases into broader network pathway categories (nt-pathways such as nt06160 Hepatitis C).

Specificity: high. This link is curated — the disease ID was deliberately assigned to a clinical association by the MCA curation pipeline, and the disease-to-pathway annotation is maintained by KEGG. A taxon appearing "via disease" in a pathway result has a direct, evidence-graded clinical association that implicates that pathway.

Metabolites in MCA passports are annotated with KEGG Compound IDs (C numbers). Each compound entry in the KEGG flat file lists the metabolic pathways it participates in (e.g., butyrate C00246 → Butanoate metabolism, Microbial metabolism in diverse environments). A taxon appears "via compound" in a pathway result when one of its metabolites biochemically participates in that pathway.

Specificity: moderate to low. Many metabolites — particularly short-chain fatty acids, bile acids, and cofactors — participate in a large number of pathways. A taxon producing acetate or pyruvate will appear under Glycolysis, TCA cycle, Butanoate metabolism, and others simultaneously, even if the clinical relevance to a specific pathway is incidental. Interpret compound-based links as biochemical participation, not as disease-pathway causal evidence. Use the compound name shown in the chip to judge whether the connection is meaningful for your context.

Bloom triggers in MCA passports are annotated with KEGG Drug IDs (D numbers) where a specific drug is named (e.g., vancomycin → D08679). KEGG Drug entries do not carry a PATHWAY field. Instead, KEGG BRITE (br08310) classifies drugs by their molecular target class — the receptor family, enzyme class, or transporter family the drug acts on (e.g., G Protein-coupled receptors › Beta-adrenergic).

Note: Drug target classes are not KEGG pathway map IDs and do not appear in pathway search results. They are shown separately on the taxon panel (By Taxon mode) as a mechanistic annotation of which drug families can trigger blooms in that taxon. A taxon's presence under a drug target class means a drug in that class is a documented bloom trigger — not that the taxon is directly involved in the target pathway.

Given a taxon, retrieve all KEGG pathways it is linked to — via its clinical association disease IDs, bloom trigger drug target classes, and metabolite compound IDs.

For a given taxon and pathway combination, show only the clinical associations that are linked to that pathway — useful for narrowing a passport to a specific biological context.

The primary search direction: given a KEGG pathway, retrieve all MCA taxa linked to it, and see which KEGG IDs (diseases, compounds) create the connection.

Given a disease condition (by name or KEGG Disease ID), find which MCA taxa are associated with it and which KEGG pathways that disease annotates.

A browseable index of all KEGG pathways that have at least one linked MCA taxon, sorted by the number of taxa linked to each pathway. Useful for identifying which biological processes are most represented in MCA.

Given a taxon, find other MCA taxa that share at least one KEGG pathway — surfacing functional or disease-context overlap between taxa that may not be taxonomically related.