RVAgene: generative modeling of gene expression time series data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33974008", "kind": "science-record", "revision": 6, "content_hash": "sha256:b503df6ca2bb85957b0e5603e1cca0a0ad54fcc880603e92b0e5bc0328fd1e60", "created_at": "2026-11-01T15:41:35Z", "updated_at": "2026-11-01T21:25:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RVAgene: generative modeling of gene expression time series data.", "doi": "10.1093/bioinformatics/btab260", "pmid": "33974008", "authors": ["Raktim Mitra", "Adam L MacLean"], "journal": "Bioinformatics (Oxford, England)", "year": 2021, "abstract": "MOTIVATION: Methods to model dynamic changes in gene expression at a genome-wide level are not currently sufficient for large (temporally rich or single-cell) datasets. Variational autoencoders offer means to characterize large datasets and have been used effectively to characterize features of single-cell datasets. Here, we extend these methods for use with gene expression time series data.\nRESULTS: We present RVAgene: a recurrent variational autoencoder to model gene expression dynamics. RVAgene learns to accurately and efficiently reconstruct temporal gene profiles. It also learns a low dimensional representation of the data via a recurrent encoder network that can be used for biological feature discovery, and from which we can generate new gene expression data by sampling the latent space. We test RVAgene on simulated and real biological datasets, including embryonic stem cell differentiation and kidney injury response dynamics. In all cases, RVAgene accurately reconstructed complex gene expression temporal profiles. Via cross validation, we show that a low-error latent space representation can be learnt using only a fraction of the data. Through clustering and gene ontology term enrichment analysis on the latent space, we demonstrate the potential of RVAgene for unsupervised discovery. In particular, RVAgene identifies new programs of shared gene regulation of Lox family genes in response to kidney injury.\nAVAILABILITY AND IMPLEMENTATION: All datasets analyzed in this manuscript are publicly available and have been published previously. RVAgene is available in Python, at GitHub: https://github.com/maclean-lab/RVAgene; Zenodo archive: http://doi.org/10.5281/zenodo.4271097.\nSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.", "claims": [{"id": "claim-method", "statement": "We also performed hierarchical clustering on the pseudotemporally ordered and smoothed data using three standard hierarchical clustering methods: the Nearest Point Algorithm, the Farthest Point Algorithm and UPGMA (the Unweighted Pair Group Method with Arithmetic mean).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33974008", "locator": "sections[9] \"3.3 Comparison of RVAgene with alternative approaches for gene clustering\" paragraph 5", "quote": "We also performed hierarchical clustering on the pseudotemporally ordered and smoothed data using three standard hierarchical clustering methods: the Nearest Point Algorithm, the Farthest Point Algorithm and UPGMA (the Unweighted Pair Group Method with Arithmetic mean)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets analyzed in this manuscript are publicly available and have been published previously.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33974008", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "All datasets analyzed in this manuscript are publicly available and have been published previously."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:33974008"], "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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