EchoGO: A Cross-Species Consensus Framework for Functional Enrichment in Non-Model Organisms

Zenodo (CERN European Organization for Nuclear Research)

Abstract

EchoGO v0.1.2 — Reference-based RNA-seq inputs (native support) EchoGO now supports both: De novo transcriptomes (Trinity → Trinotate → GOseq), and Reference-based RNA-seq workflows (e.g., HISAT2/STAR + featureCounts + DESeq2), as long as you provide the expected EchoGO input bundle. This update expands EchoGO beyond de novo-only projects and enables the same cross-species consensus enrichment approach for organisms with published genomes. If your differential expression analysis is reference-based, you can now use EchoGO to standardize your downstream enrichment, generate curated reports/plots, and transfer functional signals across species by integrating orthology-based enrichment from model organisms (or any organisms relevant to your study design). ✨ New Native support for reference-based RNA-seq experiment layouts where DESeq2 and GOseq are already computed. Recognized input files: allcounts_table.txt dge_ .csv .GOseq.enriched.tsv Trinotate_for_EchoGO.tsv and/or _eggNOG_for_EchoGO.tsv 🧠 Behavior / compatibility In reference-based mode, GOseq gene_ids may already be gene symbols/names rather than transcript IDs. If GOseq gene_ids do not match annotation transcript_id, EchoGO treats them as already-usable names (intended behavior for reference-based pipelines). 📚 Documentation (updated) echogo_scaffold("my_project") now documents both supported input layouts and expected filenames in input/_README.txt. Updated vignettes: EchoGO_workflow EchoGO_interpretation reference-based-inputs (reference-based input bundle + expected filenames)

Authors 3

1. Camilo Escobar-Sierra Aachen Institute for Environmental Research

   RWTH Aachen University

   Affiliation as printed

   Institute for Environmental Research, RWTH Aachen University, Aachen, Germany;

2. Felix Langschied

   Goethe University Frankfurt

   Affiliation as printed

   Institute of Cell Biology and Neuroscience, Applied Bioinformatics Group, Goethe University Frankfurt, Frankfurt am Main, Germany

3. Pedro A. Inostroza Aachen Institute for Environmental Research

   RWTH Aachen University · University of Gothenburg

   Affiliation as printed

   Institute for Environmental Research, RWTH Aachen University, Aachen, Germany; Department of Biological and Environmental Science, University of Gothenburg, Gothenburg, Sweden