TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT) enables automated assessment of global gene regulation linked to disparate expression in user defined genes and gene sets.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40225790", "kind": "science-record", "revision": 4, "content_hash": "sha256:9ea14f843c6f989c21ccaa20aefbd58a7c149bbb156b8745efe3f9c5fb08655e", "created_at": "2026-11-01T20:30:23Z", "updated_at": "2026-11-01T22:56:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT) enables automated assessment of global gene regulation linked to disparate expression in user defined genes and gene sets.", "doi": "10.1093/nargab/lqaf041", "pmid": "40225790", "authors": ["John Toubia", "Yasir Kusay", "Muneeza Maqsood", "Nicholas I Warnock", "David M Lawrence", "Cameron P Bracken", "Philip A Gregory", "Winnie L Kan", "Luke A Selth", "Simon J Conn", "Angel F Lopez", "Susan Branford", "Hamish S Scott", "Chung Hoow Kok", "Gregory J Goodall", "Andreas W Schreiber"], "journal": "NAR genomics and bioinformatics", "year": 2025, "abstract": "Publicly accessible expression data produced by large consortium projects like TCGA and GTEx are increasing in number and size at an unprecedented rate. Their utility cannot be underestimated given the diversity of valuable tools widely used to interrogate these data and the many discoveries of biological and clinical significance already garnered from these datasets. However, there remain undiscovered ways to mine these rich resources and a continuing need to provide researchers with easily accessible and user-friendly applications for complex or bespoke analyses. We introduce TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT), a bioinformatics application automating the stratification and subsequent differential expression analysis of cohort data to provide further insights into gene regulation. TRANSECT works by defining two groups within a cohort based on disparate expression of a gene or a gene set and subsequently compares the groups for differences in global expression. Akin to reverse genetics minus the inherent requirement of in vitro or in vivo perturbations, cell lines or model organisms and all the while working within natural physiological limits of expression, TRANSECT compiles information about global transcriptomic change and functional outcomes. TRANSECT is freely available as a command line application or online at https://transect.au.", "claims": [{"id": "claim-method", "statement": "Differential expression, graphical representation, and the subsequent functional annotation operations of TRANSECT are implemented through edgeR [36], Glimma [37], GSEA [38, 39], and WebGestalt [40].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40225790", "locator": "sections[4] \"Command line application\" paragraph 2", "quote": "Differential expression, graphical representation, and the subsequent functional annotation operations of TRANSECT are implemented through edgeR [36], Glimma [37], GSEA [38, 39], and WebGestalt [40]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in this article were derived from sources in the public domain:\nRECOUNT3, https://rna.recount.bio/GTEx, https://gtexportal.org/home/GDC Data Portal, https://portal.gdc.cancer.gov/", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40225790", "locator": "sections[25] \"Data availability\" paragraphs 1-3", "quote": "The datasets used in this article were derived from sources in the public domain:\nRECOUNT3, https://rna.recount.bio/GTEx, https://gtexportal.org/home/GDC Data Portal, https://portal.gdc.cancer.gov/"}], "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:40225790"], "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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