GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33758032", "kind": "science-record", "revision": 7, "content_hash": "sha256:27f134df596821282b855bddecc43e188ab93c73969a36353d7d0a5965a2c819", "created_at": "2026-11-01T15:41:30Z", "updated_at": "2026-11-01T22:03:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.", "doi": "10.1128/mSystems.01305-20", "pmid": "33758032", "authors": ["Zhongyou Li", "Katja Koeppen", "Victoria I Holden", "Samuel L Neff", "Liviu Cengher", "Elora G Demers", "Dallas L Mould", "Bruce A Stanton", "Thomas H Hampton"], "journal": "mSystems", "year": 2021, "abstract": "The NCBI Gene Expression Omnibus (GEO) provides tools to query and download transcriptomic data. However, less than 4% of microbial experiments include the sample group annotations required to assess differential gene expression for high-throughput reanalysis, and data deposited after 2014 universally lack these annotations. Our algorithm GAUGE (general annotation using text/data group ensembles) automatically annotates GEO microbial data sets, including microarray and RNA sequencing studies, increasing the percentage of data sets amenable to analysis from 4% to 33%. Eighty-nine percent of GAUGE-annotated studies matched group assignments generated by human curators. To demonstrate how GAUGE annotation can lead to scientific insight, we created GAPE (GAUGE-annotated Pseudomonas aeruginosa and Escherichia coli transcriptomic compendia for reanalysis), a Shiny Web interface to analyze 73 GAUGE-annotated P. aeruginosa studies, three times more than previously available. GAPE analysis revealed that PA3923, a gene of unknown function, was frequently differentially expressed in more than 50% of studies and significantly coregulated with genes involved in biofilm formation. Follow-up wet-bench experiments demonstrate that PA3923 mutants are indeed defective in biofilm formation, consistent with predictions facilitated by GAUGE and GAPE. We anticipate that GAUGE and GAPE, which we have made freely available, will make publicly available microbial transcriptomic data easier to reuse and lead to new data-driven hypotheses.IMPORTANCE GEO archives transcriptomic data from over 5,800 microbial experiments and allows researchers to answer questions not directly addressed in published papers. However, less than 4% of the microbial data sets include the sample group annotations required for high-throughput reanalysis. This limitation blocks a considerable amount of microbial transcriptomic data from being reused easily. Here, we demonstrate that the GAUGE algorithm could make 33% of microbial data accessible to parallel mining and reanalysis. GAUGE annotations increase statistical power and, thereby, make consistent patterns of differential gene expression easier to identify. In addition, we developed GAPE (GAUGE-annotated Pseudomonas aeruginosa and Escherichia coli transcriptomic compendia for reanalysis), a Shiny Web interface that performs parallel analyses on P. aeruginosa and E. coli compendia. Source code for GAUGE and GAPE is freely available and can be repurposed to create compendia for other bacterial species.", "claims": [{"id": "claim-method", "statement": "The Mantel test assesses the correlation between the string distance matrix of sample titles and the Euclidean distance matrix of gene expression data (Fig. 1C).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33758032", "locator": "sections[3] \"GAUGE accurately selects and annotates sample groups, extending the number of studies that can be systematically analyzed.\" paragraph 2", "quote": "The Mantel test assesses the correlation between the string distance matrix of sample titles and the Euclidean distance matrix of gene expression data (Fig. 1C)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The source code of GAUGE and the P. aeruginosa and E. coli ANOVA compendia created in this study can be found at https://github.com/DartmouthStantonLab/GAUGE.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33758032", "locator": "sections[17] \"GAUGE and Shiny app availability.\" paragraph 2", "quote": "The source code of GAUGE and the P. aeruginosa and E. coli ANOVA compendia created in this study can be found at https://github.com/DartmouthStantonLab/GAUGE."}], "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:33758032"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33758032", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1128/mSystems.01305-20", "sha256": "sha256:2aa6f3e81e50792818ee0604297deafcc9a00f034cc3fde2d83ebae11ad4e40f", "bytes": 51168, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1128/mSystems.01305-20", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8547006", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:33758032:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6808fd62653bf4a31bd022fd5f03d759180fbebdfbb0ffcbcb7aecc9641dd03b", "bytes": 1000, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#tab1", "version": null, "note": "Top 10 most frequently differentially expressed genes in 73 GAUGE-annotated P. aeruginosa studies", "structure": {"pmcid": "PMC8547006", "section_index": 5, "section_title": "GAUGE-annotated ANOVA compendium reveals frequently differentially expressed genes with undefined functions.", "row_count": 11, "column_count": 5}, "table": {"label": "TABLE 1", "caption": "Top 10 most frequently differentially expressed genes in 73 GAUGE-annotated P. aeruginosa studies", "rows": [["Standing", "Locus tag", "Gene product description", "No. of studiesa", "Median log2 FCb"], ["1", "PA0105", "Cytochrome c oxidase, subunit II", "43", "2.882226"], ["2", "PA1041", "Probable outer membrane protein precursorc", "41", "2.765857"], ["3", "PA3723", "Probable FMN oxidoreductasec", "41", "2.654894"], ["4", "PA2851", "Translation elongation factor P", "41", "1.929715"], ["5", "PA2445", "Glycine cleavage system protein P2", "40", "3.101212"], ["6", "PA4296", "Two-component response regulator, PprB", "40", "3.019888"], ["7", "PA3418", "Leucine dehydrogenase", "40", "2.789049"], ["8", "PA5172", "Ornithine carbamoyltransferase, catabolic", "40", "2.625181"], ["9", "PA1984", "NAD+-dependent aldehyde dehydrogenase", "39", "3.385404"], ["10", "PA3923", "Hypothetical protein", "39", "2.942898"]], "row_count": 11, "column_count": 5, "numeric_cells": 40, "header_rows": 1, "locator": "section[5]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:33758032:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:40cda766f0a7b4cf73cca345a2f1fa8c3cd56e0512d4e3299176508746043555", "bytes": 1252, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#tab2", "version": null, "note": "GAPE identifies studies in which the biofilm formation pathway is enriched", "structure": {"pmcid": "PMC8547006", "section_index": 6, "section_title": "Correlation and pathway enrichment analysis suggest that hypothetical protein PA3923 plays a role in biofilm formation, a clinically relevant phenotype.", "row_count": 8, "column_count": 5}, "table": {"label": "TABLE 2", "caption": "GAPE identifies studies in which the biofilm formation pathway is enriched", "rows": [["GSE no.", "Titlea", "PA3923 DEb", "Biofilm formation pathway reportedc", "Reference"], ["GSE21966", "Transcriptional profiling of P. aeruginosa isolated from 3 individuals with cystic fibrosis over time", "", "✓", "32"], ["GSE62970", "Expression data of clinical P. aeruginosa isolates grown in vitro in minimal glucose medium", "✓", "", "NA"], ["GSE67006", "Expression data from P. aeruginosa wild type and Δanr grown as biofilms on ΔF508 cystic fibrosis bronchial epithelial cells (CFBEs)", "", "✓", "33"], ["GSE28719", "Gene expression of P. aeruginosa ΔPA1006/nbvF mutant in the absence and presence of nitrate", "✓", "✓", "34"], ["GSE39044", "Regulon of transcriptional regulator PA2449 in P. aeruginosa PAO1", "✓", "", "35"], ["GSE8408", "Transcriptomic analysis of the sulfate starvation response in P. aeruginosa", "✓", "", "36"], ["GSE78255", "Gene expression data from P. aeruginosa PAO1 and mutator (ΔmutS) evolved for 940 generations in LB with and without subinhibitory concentrations of ciprofloxacin (0.05 μg/ml)", "✓", "", "37"]], "row_count": 8, "column_count": 5, "numeric_cells": 19, "header_rows": 1, "locator": "section[6]/table-wrap[1]#tab2"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-2", "family": "machine_learning", "specific": "decision_tree", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "decision tree"}}, {"id": "method-3", "family": null, "specific": null, "label": "Two-tailed Mantel test with 999 permutations, using GEO series matrix data retrieved through Entrez Direct and GEOquery for microarray studies and uniformly processed gene-level count tables downloaded from refine.bio for RNA-seq studies.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Mantel test assesses the correlation between the string distance matrix of sample titles and the Euclidean distance matrix of gene expression data (Fig. 1C)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The source code of GAUGE and the P. aeruginosa and E. coli ANOVA compendia created in this study can be found at https://github.com/DartmouthStantonLab/GAUGE."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:33758032", "asset:table:pmid:33758032:1", "asset:table:pmid:33758032:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 37578, "completion_tokens": 2393, "cached_tokens": 785}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33758032", "type": "paper", "label": "pmid:33758032"}, {"id": "source:pmid:33758032", "type": "manuscript", "label": "PMID 33758032 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33758032", "type": "paper", "label": "pmid:33758032"}, {"id": "source:pmid:33758032", "type": "manuscript", "label": "PMID 33758032 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33758032", "type": "extraction", "used": ["source:pmid:33758032"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33758032", "parent_hash": "sha256:17adee62694ce320f5847dc13e04b17e8e108b8fb5aca35af2d0dae58a892242", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["annotates GEO microbial data sets, including microarray and RNA sequencing studies, increasing the p", "ically analyzed. To establish GAUGE, we used microarray studies because they have a standardized mat", "me is applied to Fig. 3 and 4. GAUGE selects microarray studies and detects sample groups with high", "P value distribution of 368 Mantel tests of microarray studies. (B and C) Annotation rate (B) and e"], "order_basis": "paper_text_order:550", "id": "assay:1"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d 96-well enzyme-linked immunosorbent assay (ELISA) plates or on bovine serum albumin (BSA)-coa", "on bovine serum albumin (BSA)-coated 96-well ELISA plates as a control (22). Biofilm formation", "the wild-type PA14 strain on laminin-coated ELISA plates and BSA-coated ELISA plates. Each dat", "n laminin-coated ELISA plates and BSA-coated ELISA plates. Each data point indicates the averag"], "order_basis": "paper_text_order:7233", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["ANOVA"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}