EchoGO: annotation-context-aware functional interpretation of transcriptomic data

Functional enrichment of transcriptomic datasets can be constrained by incomplete annotation, uneven identifier recognition, and uncertainty about which organism annotation resource provides the most informative functional context. EchoGO is a reproducible downstream framework that retains target GOseq enrichment as the primary functional evidence while evaluating the same transcriptomic response across researcher-selected organism annotation contexts using experiment-specific backgrounds. Evidence is assembled at the GO-term level with its analytical and organism provenance, allowing researchers to distinguish functions supported by the target analysis, functions also recovered through alternative annotation contexts, and additional context-derived hypotheses. Semantic reduction, gene-sharing networks, visualisation, and reporting organise this evidence into interpretable biological summaries. Validation across a reference-rich zebrafish dataset and two annotation-limited Gammarus pulex comparisons revealed contrasting patterns of annotation-context dependence. In zebrafish, 42 of 44 target GO terms were also recovered through alternative fish contexts, while additional contexts expanded the range of functional hypotheses. In G. pulex, limited identifier representation restricted contextual analysis; recovered functions were predominantly translation-related in one comparison and also included contractile biology in the other. EchoGO provides a traceable framework for examining how annotation availability and organism context shape functional interpretation while preserving the target analysis as the experimental anchor.