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pmid:24398116
Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues.
Jia-Shing Chen · Shang-Chi Lin · Chia-Ying Chen · Yen-Ting Hsieh · Ping-Hui Pai · Long-Kung Chen · Shengwan Lee
BMC research notes · 2014 doi:10.1186/1756-0500-7-15
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24398116", "kind": "science-record", "revision": 4, "content_hash": "sha256:b748e8ec1f03bb69f5eaf9cc9f1444866698f6c8998daddb22b760716f30f38d", "created_at": "2026-11-01T15:40:04Z", "updated_at": "2026-11-01T21:19:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues.", "doi": "10.1186/1756-0500-7-15", "pmid": "24398116", "authors": ["Jia-Shing Chen", "Shang-Chi Lin", "Chia-Ying Chen", "Yen-Ting Hsieh", "Ping-Hui Pai", "Long-Kung Chen", "Shengwan Lee"], "journal": "BMC research notes", "year": 2014, "abstract": "BACKGROUND: Rice is one of the major crop species in the world helping to sustain approximately half of the global population's diet especially in Asia. However, due to the impact of extreme climate change and global warming, rice crop production and yields may be adversely affected resulting in a world food crisis. Researchers have been keen to understand the effects of drought, temperature and other environmental stress factors on rice plant growth and development. Gene expression microarray technology represents a key strategy for the identification of genes and their associated expression patterns in response to stress. Here, we report on the development of the rice OneArray® microarray platform which is suitable for two major rice subspecies, japonica and indica.\nRESULTS: The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. The results were submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE50844 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50844). A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. GO enrichment analysis demonstrates these results are in agreement with the known physiological processes of the different organs/tissues. Furthermore, qRT-PCR validation was performed on 66 genes, and found to significantly correlate with the microarray results (R = 0.95, p < 0.001***).\nCONCLUSION: The rice OneArray® 22 K microarray, the first rice microarray, covering both japonica and indica subspecies was designed and validated in a comprehensive study of gene expression in rice tissues. The rice OneArray® microarray platform revealed high specificity and sensitivity. Additional information for the rice OneArray® microarray can be found at http://www.phalanx.com.tw/index.php.", "claims": [{"id": "claim-method", "statement": "Gene set analysis was performed using Gene Ontology terms with functional annotation, as described in DAVID Bioinformatics Resources 6.7 (http://david.abcc.ncifcrf.gov/) [9,10].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24398116", "locator": "sections[6] \"Comparison of gene expression in rice root and shoot using gene ontology analysis\" paragraph 2", "quote": "Gene set analysis was performed using Gene Ontology terms with functional annotation, as described in DAVID Bioinformatics Resources 6.7 (http://david.abcc.ncifcrf.gov/) [9,10]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All normalized and raw data were submitted to NCBI’s Gene Expression Omnibus (GEO) for others to examine. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE50844"], "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:GSE50844"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:24398116", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/1756-0500-7-15", "sha256": "sha256:1f6a5f72a12a98a0f6110552c179eca0f62646a3786f69cb98a9c4c867729e77", "bytes": 26340, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/1756-0500-7-15", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3891988", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE50844", "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=GSE50844", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE50844", "version": null, "note": "All normalized and raw data were submitted to NCBI’s Gene Expression Omnibus (GEO) for others to examine. 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"Percentage", "P-value"], ["Down-regulated genes: 3845 (shoot vs. root)", "Regulation of transcription", "110", "2.86%", "6.28E-13"], ["", "Regulation of transcription, NA-dependent", "71", "1.85%", "1.20E-10"], ["", "Regulation of RNA metabolic process", "71", "1.85%", "1.48E-10"], ["", "Transcription", "65", "1.69%", "8.87E-10"], ["", "Response to oxidative stress", "27", "0.70%", "1.93E-08"], ["", "Oxidation reduction", "81", "2.11%", "1.21E-05"], ["", "Cell wall polysaccharide metabolic process", "5", "0.13%", "0.008210995"], ["", "Oxylipin metabolic process", "5", "0.13%", "0.008210995"], ["", "Xylan metabolic process", "5", "0.13%", "0.008210995"], ["", "Xylan catabolic process", "5", "0.13%", "0.008210995"], ["", "Oxylipin biosynthetic process", "5", "0.13%", "0.008210995"], ["Shoot-specific genes: 438", "Response to oxidative stress", "11", "2.51%", "4.30E-05"], ["", "Oxidation reduction", "27", "6.16%", "1.30E-03"], ["", "Cell wall polysaccharide metabolic process", "4", "0.91%", "1.50E-03"], ["", "Xylan metabolic process", "4", "0.91%", "1.50E-03"], ["", "Hemicellulose metabolic process", "4", "0.91%", "1.50E-03"], ["", "Xylan catabolic process", "4", "0.91%", "1.50E-03"], ["", "Regulation of transcription", "27", "6.16%", "5.30E-03"], ["", "Polysaccharide metabolic process", "8", "1.83%", "6.90E-03"]], "row_count": 20, "column_count": 5, "numeric_cells": 59, "header_rows": 1, "locator": "section[6]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:24398116:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:45e2844883a66fb0f5819a5a41c72cbfc2b1649c63a02eb329f22486360720bd", "bytes": 6011, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T4", "version": null, "note": "Comparison of expression levels (log2 ration) from qRT-PCR and microarray for selected target genes", "structure": {"pmcid": "PMC3891988", "section_index": 7, "section_title": "qRT-PCR validation", "row_count": 68, "column_count": 4}, "table": {"label": "Table 4", "caption": "Comparison of expression levels (log2 ration) from qRT-PCR and microarray for selected target genes", "rows": [["Target gene", "MSU Gene ID", "Microarray value", "qRT-PCR value"], ["", "", "(log2ratio)", "(log2ratio)"], ["Zinc finger, C3HC4 type, domain containing protein, expressed", "Os07g29600", "0.73", "0.14"], ["bZIP transcription factor domain containing protein, expressed", "Os07g48180", "−0.04", "−0.7"], ["Ankyrin repeat-rich protein, putative, expressed", "Os08g15840", "−0.99", "−0.66"], ["bZIP transcription factor domain containing protein, expressed", "Os08g26880", "1.42", "1.19"], ["Zinc finger family protein, putative, expressed", "Os08g03310", "4.58", "4.99"], ["MYB family transcription factor, putative, expressed", "Os08g33660", "3.93", "2.8"], ["B-box zinc finger family protein, putative, expressed", "Os09g35880", "0.93", "0.97"], ["Zinc finger, C3HC4 type domain containing protein, expressed", "Os09g33670", "−0.13", "−0.12"], ["MYB family transcription factor, putative, expressed", "Os09g36250", "0.75", "0.2"], ["OsWRKY80 - Superfamily of TFs having WRKY and zinc finger domains, expressed", "Os09g30400", "−0.17", "−0.48"], ["BHLH transcription factor, putative, expressed", "Os09g32510", "2.66", "1.73"], ["Zinc finger, C3HC4 type domain containing protein, expressed", "Os09g26400", "−0.17", "−0.53"], ["Dof zinc finger domain containing protein, putative, expressed", "Os09g29960", "2.57", "2.71"], ["Auxin response factor 18, putative, expressed", "Os10g33940", "−1.11", "−0.32"], ["Transcription factor, putative, expressed", "Os12g13170", "−0.08", "0.66"], ["ZOS12-05 - C2H2 zinc finger protein, expressed", "Os12g31840", "−0.45", "−0.38"], ["OsRR4 type-A response regulator, expressed", "Os01g72330", "2.53", "2.42"], ["Inducer of CBF expression 2, putative, expressed", "Os01g70310", "4.86", "4.05"], ["PHD finger protein, putative, expressed", "Os01g66420", "0.02", "−0.28"], ["SNF2 family N-terminal domain containing protein, expressed", "Os02g02290", "0.14", "0.11"], ["MYB family transcription factor, putative, expressed", "Os01g59660", "−1.41", "−0.76"], ["No apical meristem protein, putative, expressed", "Os01g48130", "0.31", "−0.02"], ["GATA transcription factor 25, putative, expressed", "Os02g05510", "−0.53", "−0.09"], ["PHD finger protein, putative, expressed", "Os02g35600", "2.08", "0.74"], ["AP2 domain containing protein, expressed", "Os02g29550", "0.42", "1.23"], ["Two-component response regulator, putative, expressed", "Os02g55320", "0.84", "0.46"], ["OsMADS22 - MADS-box family gene with MIKCc type-box, expressed", "Os02g52340", "2.78", "2.13"], ["Histidine kinase, putative, expressed", "Os02g50480", "0.12", "0.49"], ["DIRP family protein, putative, expressed", "Os03g43800", "−0.18", "0.21"], ["OsWRKY55 - Superfamily of TFs having WRKY and zinc finger domains, expressed", "Os03g20550", "−2.11", "−2.45"], ["ZOS3-23 - C2H2 zinc finger protein, expressed", "Os03g61640", "−0.64", "0.3"], ["NAC domain-containing protein 67, putative, expressed", "Os03g60080", "−4.04", "−4.17"], ["MYB family transcription factor, putative, expressed", "Os04g49450", "−2.27", "−2.01"], ["Auxin response factor, putative, expressed", "Os04g57610", "1.17", "1.13"], ["MYB_Al protein, putative, expressed", "Os04g58020", "0.1", "−0.12"], ["Zinc RING finger protein, putative, expressed", "Os06g03580", "−2.82", "−2.41"], ["bHelix-loop-helix transcription factor, putative, expressed", "Os05g46370", "−0.55", "−0.81"], ["Transcription factor, putative, expressed", "Os05g37170", "−2.58", "−1.44"], ["myb-like DNA-binding domain containing protein, expressed", "Os06g24070", "4.09", "4.63"], ["Zinc finger protein, putative, expressed", "Os06g33810", "0.27", "−0.25"], ["N-terminal asparagine amidohydrolase, putative, expressed", "Os06g41390", "−0.6", "−0.02"], ["TIP41, putative, expressed", "Os03g55270", "−0.73", "−0.5"], ["B3 DNA binding domain containing protein, expressed", "Os01g04800", "−3.02", "−2.99"], ["ZOS1-03 - C2H2 zinc finger protein, expressed", "Os01g04120", "−3.41", "−4.35"], ["TCP family transcription factor, putative, expressed", "Os01g11550", "2.09", "3"], ["RNA-binding zinc finger protein, putative, expressed", "Os07g48410", "0.68", "0.85"], ["GRAS family transcription factor domain containing protein, expressed", "Os07g38030", "1.77", "1.44"], ["Response regulator receiver domain containing protein, expressed", "Os07g49460", "−1.54", "−0.69"], ["Auxin response factor, putative, expressed", "Os08g40900", "−0.82", "0.55"], ["Homeobox associated leucine zipper, putative, expressed", "Os09g21180", "1.06", "0.23"], ["No apical meristem protein, putative, expressed", "Os10g42130", "−0.03", "−0.19"], ["MYB family transcription factor, putative, expressed", "Os01g74410", "−4.45", "−3.84"], ["bZIP transcription factor domain containing protein, expressed", "Os01g55150", "0.18", "0.15"], ["OsWRKY71 - Superfamily of TFs having WRKY and zinc finger domains, expressed", "Os02g08440", "−5.14", "−2.75"], ["Ethylene-responsive transcription factor, putative, expressed", "Os02g43790", "−4.02", "−1.47"], ["TCP family transcription factor, putative, expressed", "Os02g42380", "4.84", "4.24"], ["RING-H2 finger protein, putative, expressed", "Os02g54830", "0.35", "−0.04"], ["Dof zinc finger domain containing protein, putative, expressed", "Os02g47810", "2.99", "1.97"], ["Ethylene-responsive transcription factor, putative, expressed", "Os03g09170", "−5.3", "−3.76"], ["Homeobox associated leucine zipper, putative, expressed", "Os03g08960", "3.17", "2.13"], ["TCP-domain protein, putative, expressed", "Os02g51280", "0.05", "0.4"], ["Response regulator receiver domain containing protein, expressed", "Os03g17570", "−1.86", "−1.42"], ["ZOS3-21 - C2H2 zinc finger protein, expressed", "Os03g60560", "−5.18", "−6.27"], ["MYB family transcription factor, putative, expressed", "Os05g04820", "0.68", "0.7"], ["Actin, putative, expressed", "Os05g36290", "−0.97", "0"], ["TCP-domain protein, putative, expressed", "Os06g12230", "0.89", "0.29"]], "row_count": 68, "column_count": 4, "numeric_cells": 211, "header_rows": 2, "locator": "section[7]/table-wrap[1]#T4"}}], "gaps": ["asset:data:geo:GSE50844 not downloaded", "asset:data:geo:GSE50844 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "GO enrichment"}}, {"id": "method-2", "family": null, "specific": null, "label": "Gene Ontology enrichment analysis using DAVID Bioinformatics Resources 6.7", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Gene set analysis was performed using Gene Ontology terms with functional annotation, as described in DAVID Bioinformatics Resources 6.7 (http://david.abcc.ncifcrf.gov/) [9,10]."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE50844"], "resolved_accessions": ["GSE50844"], "statements": ["All normalized and raw data were submitted to NCBI’s Gene Expression Omnibus (GEO) for others to examine. The data are accessible via GEO Series accession number GSE50844 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50844."], "basis": "The paper names GSE50844 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": ["pathway_enrich"], "assets": ["source:pmid:24398116", "data:geo:GSE50844", "asset:table:pmid:24398116:1", "asset:table:pmid:24398116:2", "asset:table:pmid:24398116:3", "asset:table:pmid:24398116:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE50844"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:24398116", "type": "paper", "label": "pmid:24398116"}, {"id": "source:pmid:24398116", "type": "manuscript", "label": "PMID 24398116 full text"}, {"id": "data:geo:GSE50844", "type": "dataset", "label": "GEO GSE50844"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:24398116", "type": "paper", "label": "pmid:24398116"}, {"id": "source:pmid:24398116", "type": "manuscript", "label": "PMID 24398116 full text"}, {"id": "data:geo:GSE50844", "type": "dataset", "label": "GEO GSE50844"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-24398116", "type": "extraction", "used": ["source:pmid:24398116"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE50844", "type": "accession_resolution", "used": ["data:geo:GSE50844"], "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:24398116", "parent_hash": "sha256:5c21a8a4a3be4f965d8d2bd871a37e2585960b9fafb6c078035c5fd9488ad9da", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE50844 licence not read", "asset:data:geo:GSE50844 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["Development of a microarray for two rice subspecies: characterization an", "lant growth and development. 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