The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:22553952", "kind": "science-record", "revision": 7, "content_hash": "sha256:44e1317ab2634a0620ade7ae1ebadefba50f2acab099679fd42b7a3e0e303666", "created_at": "2026-11-01T15:40:02Z", "updated_at": "2026-11-01T21:58:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation.", "doi": "10.1186/1471-2229-12-62", "pmid": "22553952", "authors": ["Jongchan Woo", "Cameron Ross MacPherson", "Jun Liu", "Huan Wang", "Takatoshi Kiba", "Matthew A Hannah", "Xiu-Jie Wang", "Vladimir B Bajic", "Nam-Hai Chua"], "journal": "BMC plant biology", "year": 2012, "abstract": "BACKGROUND: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes a genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation.\nRESULTS: Genome-wide profiling by micro- and tiling-arrays (accessible from GEO: GSE34004) revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of specific versus generic members of closely related gene families with respect to phosphate-starvation. Thus, among others, we showed that PHR1-regulated members of closely related phosphate-responsive families (PHT1;1, PHT1;7-9, SPX1-3, and PHO1;H1) display greater specificity to phosphate-starvation than their more generic counterparts.\nCONCLUSION: Our results uncover much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the most complete genome-wide data on plant nutrient stress to-date.", "claims": [{"id": "claim-method", "statement": "We defined interaction as a gene differentially regulated in at least 2 treatments. With differential regulation being determined by statistical significance (α = 0.001, using Bonferroni correction for multiplicity).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:22553952", "locator": "sections[12] \"Interaction between Pi-responsive genes and those responsive to various AtGenExpress treatments\" paragraph 2", "quote": "We defined interaction as a gene differentially regulated in at least 2 treatments. With differential regulation being determined by statistical significance (α = 0.001, using Bonferroni correction for multiplicity)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The accession code, GSE34004, may be used to access the micro- and tiling-array data from the Gene Expression Omnibus (GEO).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:22553952", "locator": "sections[1] \"Background\" paragraph 6", "quote": "The accession code, GSE34004, may be used to access the micro- and tiling-array data from the Gene Expression Omnibus (GEO)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper found substantially larger, staged phosphate-starvation responses than previously described; it assessed differential expression with eBayes in the Limma R package and Bonferroni correction (α = 0.001), and its micro- and tiling-array source data are available from GEO under accession GSE34004.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:22553952", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Our results uncover much larger, staged responses to phosphate-starvation than previously described."}, {"asset": "source:pmid:22553952", "locator": "sections[32] \"Supplementary Material\" paragraph 3", "quote": "contains statistical data generated from the ebayes function in the Limma package (R, statistical environment) for the response and recovery in both roots and shoots."}, {"asset": "source:pmid:22553952", "locator": "sections[12] \"Interaction between Pi-responsive genes and those responsive to various AtGenExpress treatments\" paragraph 2", "quote": "We defined interaction as a gene differentially regulated in at least 2 treatments. With differential regulation being determined by statistical significance (α = 0.001, using Bonferroni correction for multiplicity)."}, {"asset": "source:pmid:22553952", "locator": "sections[1] \"Background\" paragraph 6", "quote": "The accession code, GSE34004, may be used to access the micro- and tiling-array data from the Gene Expression Omnibus (GEO)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper found substantially larger, staged phosphate-starvation responses than previously described; it assessed differential expression with eBayes in the Limma R package and Bonferroni correction (α = 0.001), and its micro- and tiling-array source data are available from GEO under accession GSE34004.", "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:22553952"], "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. 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