HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40796362", "kind": "science-record", "revision": 2, "content_hash": "sha256:0fad8d550da9e4525d575f770445b2aa4f4df49af938fcfba55e1f0a1d0f1769", "created_at": "2026-11-01T20:30:53Z", "updated_at": "2026-11-01T21:35:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures.", "doi": "10.1093/bioinformatics/btaf448", "pmid": "40796362", "authors": ["Louis Paré", "Philippe Bordron", "Laurent David", "Maxime Mahé", "Audrey Bihouée", "Damien Eveillard"], "journal": "Bioinformatics (Oxford, England)", "year": 2025, "abstract": "SUMMARY: Transcriptomic analysis is a key tool for exploring gene expression, but the complexity of biological systems often limits its insights. In particular, the lack of intermodal or multi-layered analysis hinders the ability to fully capture key cellular functions such as metabolism from transcriptomic data alone. Here, we introduce a novel approach that informs transcriptomic data analysis with metabolic network modeling to address this. Unlike traditional methods, HUman MEtabolism Specific Signature (HUMESS) uses genome-scale metabolic modeling and flux analysis to highlight reactions and involved genes based on their metabolic significance, offering a deeper understanding of transcriptomic data. Our computational pipeline, supported by a user-friendly Rshiny application, enhances gene expression analysis by uncovering metabolic phenotypic signatures.\nAVAILABILITY AND IMPLEMENTATION: HUMESS is open source and available under GitLab https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess with the complete documentation available at https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess/-/wikis/Home. A zenodo archive is also available at the following DOI: https://doi.org/10.5281/zenodo.15487717. An RShiny application has been developed to facilitate the exploration and analysis of HUMESS's results. The app is available online at the following address: https://shiny-bird.univ-nantes.fr/app/shinymess but can also be installed locally, available under GitLab https://gitlab.univ-nantes.fr/pare-l/shinymess.", "claims": [{"id": "claim-method", "statement": "Using the sampling results, pairwise correlation is computed for each metabolic reaction against every other reactions, resulting in a symmetric correlation matrix.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40796362", "locator": "sections[5] \"2.3 Identification of essential reactions and associated genes\" paragraph 2", "quote": "Using the sampling results, pairwise correlation is computed for each metabolic reaction against every other reactions, resulting in a symmetric correlation matrix."}], "state": "complete"}, {"id": "claim-data-access", "statement": "No new data were generated in support of this research. The software is available through gitlab at the following address: https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess and the shiny interface is available at the following address: https://gitlab.univ-nantes.fr/pare-l/shinymess", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40796362", "locator": "sections[10] \"Data availability\" paragraph 2", "quote": "No new data were generated in support of this research. The software is available through gitlab at the following address: https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess and the shiny interface is available at the following address: https://gitlab.univ-nantes.fr/pare-l/shinymess"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40796362"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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