Microarray studies on the effect of silencing tynA in Escherichia coli K-12.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26981396", "kind": "science-record", "revision": 8, "content_hash": "sha256:c79b3165159efa19f782868dc0d3dad940c5967e7ad640f1144dffd2bbf57370", "created_at": "2026-11-01T15:40:17Z", "updated_at": "2026-11-01T22:42:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Microarray studies on the effect of silencing tynA in Escherichia coli K-12.", "doi": "10.1016/j.gdata.2015.12.018", "pmid": "26981396", "authors": ["Heli Elovaara"], "journal": "Genomics data", "year": 2016, "abstract": "To study the biological role of the tynA gene product of Escherichia coli, a primary amine oxidase (ECAO, E.C. 1.4.3.21), the tynA gene was genetically silenced by conjugation with a kanamycin resistance cassette. We used a microarray method to compare the mRNA expression in the modified strain (ΔtynA) to that in the wild type (wt) strain at the time of induction of ECAO expression (0 h) as well as 1 h and 4 h after the induction. These data in brief describe the different experimental conditions, sample preparation, data collection and analysis of the conducted microarray experiment. The differential expression of genes in the studied strains 1 h after the induction of ECAO expression is described. The microarray data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE65385.", "claims": [{"id": "claim-method", "statement": "The statistical comparison between the samples was carried out using the Limma package [6].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981396", "locator": "sections[8] \"Microarray data analysis\" paragraph 2", "quote": "The statistical comparison between the samples was carried out using the Limma package [6]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE65385.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981396", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The microarray data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE65385."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used gcRMA normalization and Limma for statistical comparison, and the source data are accessible through GEO Series accession GSE65385.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981396", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The microarray data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE65385."}, {"asset": "source:pmid:26981396", "locator": "sections[9] \"Results\" paragraph 3", "quote": "However, the existing data are freely available (see link to the deposited data)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used gcRMA normalization and Limma for statistical comparison, and the source data are accessible through GEO Series accession GSE65385.", "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:26981396"], "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": "complete", "blocked_on": null, "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": ["data:geo:GSE65385"], "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": ["data:geo:GSE65385"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26981396", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.12.018", "sha256": "sha256:f67585a065acf793581a93e41546b09d8ddd0e6a389f61125b42c2ed5ba8348f", "bytes": 12671, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.12.018", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4778652", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE65385", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65385", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65385", "version": null, "note": "The microarray data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE65385.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE65385.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1594176", "GSM1594177", "GSM1594178", "GSM1594179", "GSM1594180", "GSM1594181"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "3154", "taxon": "Escherichia coli", "title": "Comparison of Escherichia coli K-12 tynA- with wild type Escherichia coli K-12", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26981396:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:efcf0c693a4d08ca3cd277f5dcf7e924ee79bca9d2e8143ef39dfafd4e053105", "bytes": 859, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#t0005", "version": null, "note": "Differentially down-regulated (FC < − 2.5) genes in ΔtynA vs. wt E. coli 1 h after tynA induction. According to the David functional annotation analysis the gene list of down-regulated genes at time point 1 h was specifically associated (p-value < 0.05) with pathways of phenylalanine metabolism and biosynthesis of siderophore group nonribosomal peptide.", "structure": {"pmcid": "PMC4778652", "section_index": 9, "section_title": "Results", "row_count": 6, "column_count": 3}, "table": {"label": "Table 1", "caption": "Differentially down-regulated (FC < − 2.5) genes in ΔtynA vs. wt E. coli 1 h after tynA induction. According to the David functional annotation analysis the gene list of down-regulated genes at time point 1 h was specifically associated (p-value < 0.05) with pathways of phenylalanine metabolism and biosynthesis of siderophore group nonribosomal peptide.", "rows": [["Gene symbol", "Gene", "FC"], ["tynA", "Tyramine oxide, copper containing", "− 19.49"], ["feaB", "Phenylacetaldehyde dehydrogenase", "− 4.08"], ["fhuF", "Ferric ion reductase involved in ferric hydroximate transport", "− 2.97"], ["c0651", "Hypothetical protein ybcY precursor", "− 2.68"], ["wcaJ", "Putative UDP-glucose lipid carrier transferase", "− 2.62"]], "row_count": 6, "column_count": 3, "numeric_cells": 6, "header_rows": 1, "locator": "section[9]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26981396:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e05672e451c90222d5b4c8250c23fbbbce118128f99ddb430c508e814bb5ec9b", "bytes": 544, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#t0010", "version": null, "note": "Differentially up-regulated (FC > 2.50) genes in ΔtynA vs. wt E. coli 1 h after the induction of ECAO expression.", "structure": {"pmcid": "PMC4778652", "section_index": 9, "section_title": "Results", "row_count": 6, "column_count": 3}, "table": {"label": "Table 2", "caption": "Differentially up-regulated (FC > 2.50) genes in ΔtynA vs. wt E. coli 1 h after the induction of ECAO expression.", "rows": [["Gene symbol", "Gene", "FC"], ["ydiE", "Hypothetical protein", "3.13"], ["tnaC", "Tryptonase leader peptide", "3.07"], ["metN", "dl-Methionine transporter ATP-binding subunit", "2.88"], ["c2375", "Hypothetical protein", "2.83"], ["yddM", "Predicted DNA-binding transcriptional regulator", "2.57"]], "row_count": 6, "column_count": 3, "numeric_cells": 6, "header_rows": 1, "locator": "section[9]/table-wrap[2]#t0010"}}], "gaps": ["asset:data:geo:GSE65385 not downloaded", "asset:data:geo:GSE65385 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The statistical comparison between the samples was carried out using the Limma package [6]."}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": "R1", "reachable": true, "accessions": ["GSE65385"], "resolved_accessions": ["GSE65385"], "statements": ["The microarray data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE65385."], "basis": "The paper names GSE65385 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:26981396", "data:geo:GSE65385", "asset:table:pmid:26981396:1", "asset:table:pmid:26981396:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE65385"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:47Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 30388, "completion_tokens": 2477, "cached_tokens": 2088}}, "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:26981396", "type": "paper", "label": "pmid:26981396"}, {"id": "source:pmid:26981396", "type": "manuscript", "label": "PMID 26981396 full text"}, {"id": "data:geo:GSE65385", "type": "dataset", "label": "GEO GSE65385"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26981396", "type": "paper", "label": "pmid:26981396"}, {"id": "source:pmid:26981396", "type": "manuscript", "label": "PMID 26981396 full text"}, {"id": "data:geo:GSE65385", "type": "dataset", "label": "GEO GSE65385"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26981396", "type": "extraction", "used": ["source:pmid:26981396"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE65385", "type": "accession_resolution", "used": ["data:geo:GSE65385"], "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:26981396", "parent_hash": "sha256:539db2e23331067978d3062b3565764ca37e537b7758031f50dc4178954cfeda", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE65385 licence not read", "asset:data:geo:GSE65385 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["Microarray studies on the effect of silencing tynA in E", "h a kanamycin resistance cassette. We used a microarray method to compare the mRNA expression in the", "ata collection and analysis of the conducted microarray experiment. The differential expression of g", "duction of ECAO expression is described. The microarray data have been deposited in NCBI's Gene Expr"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": [". Both wild type (wt) and ΔtynA strains were cultured in conditions, which induce the expression of E"], "order_basis": "paper_text_order:1191", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The statistical comparison between the samples was carried out using the Limma package [6]."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}