Transcriptome profiling of TDC cluster deletion mutant of Enterococcus faecalis V583.

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(2012) [1]. The TDC cluster comprises four genes: tyrS, an aminoacyl-tRNA synthetase-like gene; tdcA, which encodes the tyrosine decarboxylase; tyrP, a tyrosine/tyramine exchanger gene and nhaC-2, which encodes an Na(+)/H(+) antiporter and whose role in the tyramine biosynthesis remains unknown [2]. In E. faecalis V583 the last three genes are co-transcribed as a single polycistronic mRNA forming the catabolic operon, while tyrS is transcribed independently of the catabolic genes as a monocistronic mRNA [2]. The catabolic operon is transcriptionally induced by tyrosine and acidic pH. On the opposite, the tyrS expression is repressed by tyrosine concentrations [2]. In this work we report the transcriptional profiling of the TDC cluster deletion mutant (E. faecalis V583 ΔTDC) [2] compared to the wild-type strain, both grown in M17 medium supplemented with tyrosine. The transcriptional profile data of TDC cluster-regulated genes were deposited in the Gene Expression Omnibus (GEO) database under accession no. GSE77864.", "claims": [{"id": "claim-data-access", "statement": "Microarray data are accessible in the link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77864", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27408815", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Microarray data are accessible in the link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77864"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential expression was determined using a p-value threshold of <0.05 and an expression fold-change threshold of >|2|, and the underlying microarray data were deposited in GEO under accession GSE77864.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27408815", "locator": "sections[10] \"Microarray data analysis\" paragraph 2", "quote": "A gene was considered differentially expressed when a p value of at least < 0.05 was obtained and the expression fold-change was at least >|2 |."}, {"asset": "source:pmid:27408815", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The transcriptional profile data of TDC cluster-regulated genes were deposited in the Gene Expression Omnibus (GEO) database under accession no. 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Enterococcus faecalis V583", "title": "Transcriptome profiling of tdc cluster delection mutant of Enterococcus faecalis V583", "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:27408815:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3b5c90da70d80f85b5f05d3c32cf0ce25c687e477dab752ebc712ba1943275ad", "bytes": 724, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4932888", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications", ""], ["Organism/cell line/tissue", "E. faecalis V583"], ["Sex", "N/A"], ["Sequencer or array type", "Oligo-based DNA microarray"], ["Data format", "Raw and normalized"], ["Experimental factors", "E. faecalis V583 ΔTDC (test) versus E. faecalis V583 (reference)"], ["Experimental features", "Microarray comparison was preformed to identify genes differentially expressed in E. faecalis V583 ΔTDC compared to E. faecalis V583 grown in M17 medium supplemented with 0.5% glucose (w/v) and 15 mM tyrosine."], ["Consent", "N/A"], ["Sample source location", "Villaviciosa, Spain"]], "row_count": 9, "column_count": 2, "numeric_cells": 3, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE77864 not downloaded", "asset:data:geo:GSE77864 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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