What this entity is
The canonical name is Gene Ontology functional annotation resource, with the known alias GO (Gene Ontology). 1 The report does not specify a stable external identifier for this resource. 1
The NMDC context audit refines the provenance description: the KBase Data Lakehouse data atlas labels Gene Ontology and Rhea reference ontologies hosted under kbase.nmdc_arkin as “NMDC integrated,” although the audit identifies this labeling as provenance blur rather than proof that the resources are NMDC-native. 2 This distinction is relevant when interpreting GO annotations used in downstream analyses and supports retaining explicit authority and provenance metadata alongside the resource. 2
Key facts from AMR cofitness analysis
The analysis used GO annotations from interproscan to assess functional enrichment in antimicrobial-resistance cofitness neighborhoods across 28 organisms. 1 InterProScan provided 68% gene coverage, reported as 3.6× better than the old SEED annotations. 1
Among GO terms enriched in at least 3 organisms at FDR (false discovery rate) < 0.05, flagellum-dependent cell motility (GO:0071973) occurred in 5 organisms with mean odds ratio (OR) 4.7, flagellum assembly (GO:0044780) occurred in 5 organisms with mean OR 5.3, bacterial-type flagellum (GO:0009288) occurred in 4 organisms with mean OR 4.9, and flagellum-dependent swarming (GO:0071978) occurred in 4 organisms with mean OR 5.0. 1 Histidine biosynthesis (GO:0000105) occurred in 3 organisms with mean OR 5.3, and tryptophan biosynthesis (GO:0000162) occurred in 3 organisms with mean OR 5.3. 1
The old SEED/KEGG annotation analysis found 0/280 significant enrichment tests at FDR < 0.05, whereas the GO analysis found 35/3,193 significant tests. 1 Mechanism-specific GO analyses produced 212 significant results among 9,244 tests. 1
GO annotations strengthened the interpretation that AMR support-network structure is more organism-specific than mechanism-specific: within-mechanism Jaccard similarity increased from 0.069 with old KEGG annotations to 0.207 with InterProScan GO, while cross-mechanism similarity increased from 0.249 to 0.375. 1 The cross-mechanism-versus-within-mechanism comparison had p = 1.0 with old KEGG annotations and p = 4.3×10⁻¹³ with InterProScan GO. 1
The report cautions that GO enrichment may reflect shared dispensability under laboratory conditions rather than direct co-regulation. 1 Broad GO categories such as transmembrane transport and membrane functions may obscure more specific signals because they appear in nearly all support networks and genomes. 1
Related pages
- AMR Co-Fitness Support Networks — source report describing the GO-based AMR cofitness analysis. 1
- NMDC Context Audit — audit of provenance labeling and resource placement for NMDC-named KBase Data Lakehouse holdings. 2
- pangenome-integration — annotation of pangenome cluster representatives improved functional coverage and enrichment detection. 1
- condition-specific-fitness — GO enrichment requires distinguishing condition-specific shared dispensability from direct co-regulation. 1