EchoGO validation bundle: frozen materials for cross-species consensus enrichment in transcriptomic interpretation

Zenodo (CERN European Organization for Nuclear Research)

Abstract

This record contains the frozen validation materials accompanying EchoGO v0.1.3 and the MethodsX manuscript “EchoGO: cross-species consensus enrichment for transcriptomic interpretation.” It preserves the evidence underlying the manuscript validation exercises, Table 3, Figure 3, the Supplementary Validation Report, and the complete native EchoGO outputs used for inspection and reproducibility assessment. The bundle includes three validation exercises representing different reference and annotation settings: a reference-rich zebrafish embryo chemical-exposure contrast, a Gammarus pulex contrast with native-dominant recovery, and a second G. pulex contrast with additional invertebrate-panel recovery. For each exercise, the archive provides the original and resolved foreground and background vectors, mapping provenance, query contracts, primary- and broader-panel outputs, cached g:Profiler responses, consensus tables, RRvGO summaries, network files, diagnostic outputs, and run manifests. The manuscript-facing materials include the final Figure 3 exports and source data, Table 3 source data, Gammarus panel-overlap and term-provenance tables, and the complete Supplementary Validation Report. Bundle-level metadata, file manifests, software-environment information, and SHA-256 checksums are also included. The record distinguishes two interpretation tiers: a background-aware tier combining native GOseq with g:Profiler analyses using the experiment-specific tested-gene background, and an exploratory tier based on g:Profiler analyses without that background. These streams are preserved separately. Cached g:Profiler responses are retained as the frozen validation record because online annotation resources can change over time. This archive is a manuscript-validation record. It is not a copy of the EchoGO software repository and does not redistribute the upstream raw RNA-seq datasets.

Authors 4

1. Camilo Escobar-Sierra Aachen

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

2. Felix Langschied

   Goethe University Frankfurt

   Affiliation as printed

   Goethe University Frankfurt

3. Angelina Miller Aachen

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

4. Pedro A. Inostroza Aachen

   University of Gothenburg · RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

   University of Gothenburg