Genome-wide transcriptional profiling of wheat infected with Fusarium graminearum.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484265", "kind": "science-record", "revision": 3, "content_hash": "sha256:4e6d498d0db14c6c3a69beef5d1d8d6cbc757e9940616e8e2c07fd111bb3b7cd", "created_at": "2026-11-01T15:40:13Z", "updated_at": "2026-11-01T18:47:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome-wide transcriptional profiling of wheat infected with Fusarium graminearum.", "doi": "10.1016/j.gdata.2015.06.020", "pmid": "26484265", "authors": ["Ayumi Kosaka", "Tomohiro Ban", "Alagu Manickavelu"], "journal": "Genomics data", "year": 2015, "abstract": "Fusarium head blight (FHB) is a destructive disease in wheat caused by Fusarium graminearum (F. g). It infects during the flowering stage favored by warm and highly humid climates. In order to understand possible wheat defense mechanism, gene expression analysis in response to F. g was undertaken in three genotypes of wheat, Japanese landrace cultivar Nobeokabouzu (highly resistant), Chinese cv. Sumai 3 (resistant) and Australian cv. Gamenya (susceptible). For microarray analysis, 3 and 7 days after inoculation (dai) samples were used in Agilent wheat custom array 4x38k. At 3 dai, the highest number of genes was up-regulated in Nobeokabouzu followed by Sumai 3 and minimum expression in Gamenya. Whereas at 7 dai, Sumai 3 expressed more genes compared to others. Further narrowing down by excluding commonly expressed genes in three genotypes and grouping according to the gene function has identified differentially high expression of genes involved in detoxification process such as multidrug resistant protein, multidrug resistance-associated protein, UDP-glycosyltransferase and ABC transporters in Nobeokabouzu at 3 dai. However in Sumai 3 many defense-related genes such as peroxidase, proteases and genes involved in plant cell wall defense at 7 dai were identified. These findings showed the difference of molecular defense mechanism among the cultivars in response to the pathogen. The complete data was accessed in NCBI GEO database with accession number GSE59721.", "claims": [{"id": "claim-data-access", "statement": "The complete data was accessed in NCBI GEO database with accession number GSE59721.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484265", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The complete data was accessed in NCBI GEO database with accession number GSE59721."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper does not specify a named statistical method beyond normalization and statistical analysis, and reports that the complete source data are accessible through NCBI GEO under accession number GSE59721.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484265", "locator": "sections[6] \"Data analyses\" paragraph 2", "quote": "After normalization and statistical analysis, the data were grouped by Venn diagram to categorize the up-regulated genes."}, {"asset": "source:pmid:26484265", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The complete data was accessed in NCBI GEO database with accession number GSE59721."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper does not specify a named statistical method beyond normalization and statistical analysis, and reports that the complete source data are accessible through NCBI GEO under accession number GSE59721.", "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:26484265"], "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:GSE59721"], "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:GSE59721"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484265", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.06.020", "sha256": "sha256:e4f5e8bf4fd40d38f7a8d5699e5638a6dac11f095353795ea62f1738bc07e2a9", "bytes": 9149, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.06.020", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4584024", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE59721", "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=GSE59721", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59721", "version": null, "note": "The complete data was accessed in NCBI GEO database with accession number GSE59721.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The complete data was accessed in NCBI GEO database with accession number GSE59721.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1444278", "GSM1444279", "GSM1444280", "GSM1444281", "GSM1444282", "GSM1444283", "GSM1444284", "GSM1444285", "GSM1444286", "GSM1444287", "GSM1444288", "GSM1444289", "GSM1444290", "GSM1444291", "GSM1444292", "GSM1444293", "GSM1444294", "GSM1444295", "GSM1444296", "GSM1444297", "GSM1444298", "GSM1444299", "GSM1444300", "GSM1444301", "GSM1444302", "GSM1444303", "GSM1444304", "GSM1444305", "GSM1444306", "GSM1444307", "GSM1444308", "GSM1444309", "GSM1444310", "GSM1444311", "GSM1444312", "GSM1444313"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "9805", "taxon": "Triticum aestivum", "title": "Altered Gene Expression Profiles of Wheat Genotypes against Fusarium Head Blight", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26484265:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:287beb3d733037f27b219e04989c5ed1088bd86a984e383a8733ba85e25ccb6a", "bytes": 458, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#t0005", "version": null, "note": "Number of differentially expressed genes in F.g-inoculated wheat at 3 and 7 days after inoculation (dai) in three genotypes.", "structure": {"pmcid": "PMC4584024", "section_index": 6, "section_title": "Data analyses", "row_count": 6, "column_count": 5}, "table": {"label": "Table 1", "caption": "Number of differentially expressed genes in F.g-inoculated wheat at 3 and 7 days after inoculation (dai) in three genotypes.", "rows": [["Genotype", "Number of genes"], ["3 dai", "7 dai"], ["Up", "Down", "Up", "Down"], ["Nobeokabouzu", "1228", "241", "107", "662"], ["Sumai 3", "347", "36", "593", "45"], ["Gamenya", "41", "23", "37", "107"]], "row_count": 6, "column_count": 5, "numeric_cells": 15, "header_rows": 3, "locator": "section[6]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE59721 not downloaded", "asset:data:geo:GSE59721 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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE59721"], "resolved_accessions": ["GSE59721"], "statements": ["The complete data was accessed in NCBI GEO database with accession number GSE59721."], "basis": "The paper names GSE59721 in NCBI GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26484265", "data:geo:GSE59721", "asset:table:pmid:26484265:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE59721"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:56Z", "independence": "same_provider"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 22265, "completion_tokens": 2055, "cached_tokens": 1809}}, "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:26484265", "type": "paper", "label": "pmid:26484265"}, {"id": "source:pmid:26484265", "type": "manuscript", "label": "PMID 26484265 full text"}, {"id": "data:geo:GSE59721", "type": "dataset", "label": "GEO GSE59721"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484265", "type": "paper", "label": "pmid:26484265"}, {"id": "source:pmid:26484265", "type": "manuscript", "label": "PMID 26484265 full text"}, {"id": "data:geo:GSE59721", "type": "dataset", "label": "GEO GSE59721"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484265", "type": "extraction", "used": ["source:pmid:26484265"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE59721", "type": "accession_resolution", "used": ["data:geo:GSE59721"], "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:26484265", "parent_hash": "sha256:7ad5a6e2191be003c28bec600bc8f0f0297a2393556b52af69ed117d9b9e7a2d", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE59721 licence not read", "asset:data:geo:GSE59721 not downloaded", "execution.not_run", "method", "operations", "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": 0.93, "evidence": ["nd Australian cv. Gamenya (susceptible). For microarray analysis, 3 and 7 days after inoculation (da"], "order_basis": "paper_text_order:503", "id": "assay:1"}]}