Identification of differentially expressed genes between developing seeds of different soybean cultivars.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697344", "kind": "science-record", "revision": 8, "content_hash": "sha256:87401ace55b6a511a2cafb3ff45c5ff67b90f8ca07952f0c0ac6f78f217b4a47", "created_at": "2026-11-01T15:40:14Z", "updated_at": "2026-11-01T22:42:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of differentially expressed genes between developing seeds of different soybean cultivars.", "doi": "10.1016/j.gdata.2015.08.005", "pmid": "26697344", "authors": ["Rongshuang Lin", "Jane Glazebrook", "Fumiaki Katagiri", "James H Orf", "Susan I Gibson"], "journal": "Genomics data", "year": 2015, "abstract": "Soybean is a major source of protein and oil and a primary feedstock for biodiesel production. Research on soybean seed composition and yield has revealed that protein, oil and yield are controlled quantitatively and quantitative trait loci (QTL) have been identified for each of these traits. However, very limited information is available regarding the genetic mechanisms controlling seed composition and yield. To help address this deficiency, we used Affymetrix Soybean GeneChips® to identify genes that are differentially expressed between developing seeds of the Minsoy and Archer soybean cultivars, which differ in seed weight, yield, protein content and oil content. A total of 700 probe sets were found to be expressed at significantly different (defined as having an adjusted p-value below or equal to 0.05 and an at least 2-fold difference) levels between the two cultivars at one or more of the three developmental stages and in at least one of the two years assayed. Comparison of data from soybeans collected in two different years revealed that 97 probe sets were expressed at significantly different levels in both years. Functional annotations were assigned to 78% of these 97 probe sets based on the SoyBase Affymetrix™ GeneChip® Soybean Genome Array Annotation. Genes involved in receptor binding/activity and protein binding are overrepresented among the group of 97 probe sets that were differentially expressed in both years assayed. Probe sets involved in growth/development, signal transduction, transcription, defense/stress response and protein and lipid metabolism were also identified among the 97 probe sets and their possible implications in the regulation of agronomic traits are discussed. As the Minsoy and Archer soybean cultivars differ with respect to seed size, yield, protein content and lipid content, some of the differentially expressed probe sets identified in this study may thus play important roles in controlling these traits. Others of these probe sets may be involved in regulation of general seed development or metabolism. All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598.", "claims": [{"id": "claim-method", "statement": "The lmFit function (limma package) [35] was used to fit a linear model to identify differentially expressed genes between the two parental lines and the two RILs at each stage. The empirical Bayes (eBayes) method was used to adjust variances, and Benjamini-Hochberg's False Discovery Rate (FDR) was calculated for multiple test correction [36].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697344", "locator": "sections[12] \"Analysis of microarray data\" paragraph 4", "quote": "The lmFit function (limma package) [35] was used to fit a linear model to identify differentially expressed genes between the two parental lines and the two RILs at each stage. The empirical Bayes (eBayes) method was used to adjust variances, and Benjamini-Hochberg's False Discovery Rate (FDR) was calculated for multiple test correction [36]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697344", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using an adjusted p-value ≤0.05 and ≥2-fold expression difference, the study identified 700 differentially expressed probe sets, and the microarray data are available through GEO under accession GSE21598.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "A total of 700 probe sets were found to be expressed at significantly different (defined as having an adjusted p-value below or equal to 0.05 and an at least 2-fold difference) levels between the two cultivars at one or more of the three developmental stages and in at least one of the two years assayed. All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598."}, "evidence": [{"asset": "source:pmid:26697344", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 700 probe sets were found to be expressed at significantly different (defined as having an adjusted p-value below or equal to 0.05 and an at least 2-fold difference) levels between the two cultivars at one or more of the three developmental stages and in at least one of the two years assayed."}, {"asset": "source:pmid:26697344", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using an adjusted p-value ≤0.05 and ≥2-fold expression difference, the study identified 700 differentially expressed probe sets, and the microarray data are available through GEO under accession GSE21598.", "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:26697344"], "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:GSE21598"], "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": {"fdr_threshold": "and Benjamini-Hochberg false discovery rate correction"}, "inputs": ["data:geo:GSE21598"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26697344", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.08.005", "sha256": "sha256:57ed167abb2d85e26d4ac99e87bbae8b46e3b87dae4de9d0e028c42783698440", "bytes": 45704, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.08.005", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4664686", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21598", "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=GSE21598", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21598", "version": null, "note": "All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM539211", "GSM539212", "GSM539213", "GSM539214", "GSM539215", "GSM539216", "GSM539217", "GSM539218", "GSM539219", "GSM539220", "GSM539221", "GSM539222", "GSM539223", "GSM539224", "GSM539225", "GSM539226", "GSM539227", "GSM539228", "GSM539229", "GSM539230", "GSM539231", "GSM539232", "GSM539233", "GSM539234", "GSM539235", "GSM539236", "GSM539237", "GSM539238", "GSM539239", "GSM539240", "GSM539241", "GSM539242", "GSM539243", "GSM539244", "GSM539245", "GSM539246", "GSM539247", "GSM539248", "GSM539249", "GSM539250", "GSM539251", "GSM539252", "GSM539253", "GSM539254", "GSM539255", "GSM539256", "GSM539257", "GSM539258", "GSM539259", "GSM539260", "GSM539261", "GSM539262", "GSM539263", "GSM539264"], "sample_count": 54, "group_sizes": null, "group_sizes_basis": null, "platform": "4592", "taxon": "Glycine max", "title": "Identification of differentially expressed genes between developing seeds of different soybean cultivars", "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:26697344:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6f1d945f6ef3e93d2e2aa77d39e0ab4782a63aa33232c9d5e625cb7a1378b9b0", "bytes": 747, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#t0005", "version": null, "note": "Comparison of seed composition, weight and yield between the Minsoy and Archer cultivars and two recombinant inbred lines (RILs). Data for the two parental lines were taken from published sources [7], [9], [18] and data for the two RILs are based on combined data collected from plants grown during 2000 in Becker, MN and during 2001 in Waseca, MN (unpublished data).", "structure": {"pmcid": "PMC4664686", "section_index": 4, "section_title": "Introduction", "row_count": 5, "column_count": 5}, "table": {"label": "Table 1", "caption": "Comparison of seed composition, weight and yield between the Minsoy and Archer cultivars and two recombinant inbred lines (RILs). Data for the two parental lines were taken from published sources [7], [9], [18] and data for the two RILs are based on combined data collected from plants grown during 2000 in Becker, MN and during 2001 in Waseca, MN (unpublished data).", "rows": [["Trait", "RIL 6049-273", "RIL 6049-32", "Archer", "Minsoy"], ["Yield (bu/a)", "66.1", "33.5", "49", "29"], ["Oil (g/kg)", "166", "162", "187", "178"], ["Protein (g/kg)", "344", "366", "340", "353"], ["Seed weight (mg/seed)", "188", "142", "161", "123"]], "row_count": 5, "column_count": 5, "numeric_cells": 18, "header_rows": 1, "locator": "section[4]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26697344:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:58032ebf86ead7834cc6def65af0b9ca16051bbf67954cd75cd6815bcb767485", "bytes": 1068, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#t0010", "version": null, "note": "Comparison of number of differentially expressed transcripts between Minsoy and Archer and two recombinant inbred lines (RILs). The significant cutoff value is q-value = 0.05 and 2-fold change in expression values. The two RILs are LY (lower yield) line 6049–32 and HY (higher yield) line 6049-273.", "structure": {"pmcid": "PMC4664686", "section_index": 6, "section_title": "Identification of differentially expressed probe sets", "row_count": 10, "column_count": 5}, "table": {"label": "Table 2", "caption": "Comparison of number of differentially expressed transcripts between Minsoy and Archer and two recombinant inbred lines (RILs). The significant cutoff value is q-value = 0.05 and 2-fold change in expression values. The two RILs are LY (lower yield) line 6049–32 and HY (higher yield) line 6049-273.", "rows": [["Affymetrix probe sets", "Stage 1", "Stage 2", "Stage 3", "Total in all stages combineda"], ["Higher in Minsoy in 2007", "117", "120", "167", "273"], ["Higher in Archer in 2007", "172", "140", "135", "301"], ["Total different between Minsoy and Archer in 2007", "289", "260", "302", "574"], ["Higher in Minsoy in 2008", "62", "67", "73", "104"], ["Higher in Archer in 2008", "89", "76", "97", "128"], ["Total different between Minsoy and Archer in 2008", "151", "143", "170", "232"], ["Higher in LY RIL in 2007", "74", "6", "0", "78"], ["Higher in HY RIL in 2007", "55", "14", "0", "66"], ["Total different between LY and HY RILs in 2007", "129", "20", "0", "144"]], "row_count": 10, "column_count": 5, "numeric_cells": 48, "header_rows": 1, "locator": "section[6]/table-wrap[1]#t0010"}}, {"id": "asset:table:pmid:26697344:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d86bcac6397cf6281b40d7a41e829854ee48a7aea800667faa0ee9e6b5cee82a", "bytes": 2069, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#t0015", "version": null, "note": "Probe sets potentially involved in seed growth/development and signal transduction. Probe sets that were found to be expressed at significantly different levels between Minsoy and Archer in one or more developmental stages during 2007 and 2008 were searched for those predicted by their GO assignments to be involved in seed growth/development/signal transduction. Significant differences in transcript levels are defined as having a q-value ≤ 0.05 and fold difference ≥ 2. The developmental stage(s) and year(s) in which significant differences in transcript levels were detected for a particular gene are indicated. The cultivar that has higher expression values is also indicated. S1, S2, S3 represent developmental stage 1 (2 mm seeds), stage 2 (3.5 mm seeds) and stage 3 (5–6 mm seeds), respectively. (07) and (08) refer to 2007 and 2008, respectively.", "structure": {"pmcid": "PMC4664686", "section_index": 7, "section_title": "Functional categories of differentially expressed probe sets", "row_count": 12, "column_count": 4}, "table": {"label": "Table 3", "caption": "Probe sets potentially involved in seed growth/development and signal transduction. Probe sets that were found to be expressed at significantly different levels between Minsoy and Archer in one or more developmental stages during 2007 and 2008 were searched for those predicted by their GO assignments to be involved in seed growth/development/signal transduction. Significant differences in transcript levels are defined as having a q-value ≤ 0.05 and fold difference ≥ 2. The developmental stage(s) and year(s) in which significant differences in transcript levels were detected for a particular gene are indicated. The cultivar that has higher expression values is also indicated. S1, S2, S3 represent developmental stage 1 (2 mm seeds), stage 2 (3.5 mm seeds) and stage 3 (5–6 mm seeds), respectively. (07) and (08) refer to 2007 and 2008, respectively.", "rows": [["Affymetrix probe set ID", "Gene description", "Stage (year)", "Higher expression"], ["Gma.1471.2.S1_at", "Suppressor of PHYA-105 1 (SPA1)", "S1,2 (07);S1,2,3 (08)", "Archer"], ["Gma.12643.1.A1_at", "Light repressible receptor protein kinase", "S1 (07);S1,2,3 (08)", "Minsoy"], ["GmaAffx.88161.1.S1_at", "Phytochrome (PHYA)", "S1 (07);S1,2,3 (08)", "Archer"], ["Gma.7387.1.A1_at", "Pseudo-response regulator 7 (PRR7)", "S1,2,3 (07,08)", "Minsoy"], ["GmaAffx.77896.1.S1_at", "Suppressor of auxin resistance 3 (SAR3)", "S1,2,3 (07,08)", "Archer"], ["GmaAffx.90343.1.S1_at", "GAST1 protein homolog 4 (GASA4)", "S1,2 (07);S2,3 (08)", "Minsoy"], ["GmaAffx.90343.1.S1_s_at", "GAST1 protein homolog 4 (GASA4)", "S1,2 (07);S2,3 (08)", "Minsoy"], ["Gma.473.1.A1_at", "Retinoblastoma-related 1 (RBR1)", "S1 (07);S1,2,3 (08)", "Archer"], ["GmaAffx.21668.1.A1_at", "COBRA (COB)", "S1,2,3 (07,08)", "Archer"], ["GmaAffx.28349.1.S1_at", "Ankyrin repeat_containing 2B (AKR2B)", "S1,2 (07);S1,2,3 (08)", "Archer"], ["GmaAffx.7290.1.A1_at", "alpha-N-acetylglucosaminidase family/NAGLU family", "S3 (07,08)", "Archer"]], "row_count": 12, "column_count": 4, "numeric_cells": 29, "header_rows": 1, "locator": "section[7]/table-wrap[1]#t0015"}}, {"id": "asset:table:pmid:26697344:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e270d2cb687a3b32d697ca0523a3565715308bba8e146cf131f6a35fa285beaf", "bytes": 2409, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[2]#t0020", "version": null, "note": "Probe sets potentially involved in defense and stress responses. Probe sets predicted to be involved in defense and/or stress response and that exhibit significant differences in transcript levels between Minsoy and Archer were identified. See Table 3 legend for additional information.", "structure": {"pmcid": "PMC4664686", "section_index": 7, "section_title": "Functional categories of differentially expressed probe sets", "row_count": 21, "column_count": 4}, "table": {"label": "Table 4", "caption": "Probe sets potentially involved in defense and stress responses. Probe sets predicted to be involved in defense and/or stress response and that exhibit significant differences in transcript levels between Minsoy and Archer were identified. See Table 3 legend for additional information.", "rows": [["Affymetrix probe set ID", "Gene description", "Stage (year)", "Higher expression"], ["Gma.1034.4.S1_s_atb", "Caffeoyl-CoA 3-O-methyltransferase, putative", "S3 (07);S1,3 (08)", "Minsoy"], ["Gma.11082.2.A1_s_atb", "Caffeoyl-CoA 3-O-methyltransferase, putative", "S3 (07);S1,3 (08)", "Minsoy"], ["Gma.11344.1.S1_at", "Disease resistance gene (R gene)", "S1,2,3 (07,08)", "Archer"], ["Gma.13012.1.A1_at", "Disease resistance protein (TIR-NBS-LRR class), putative", "S1,2,3 (07,08)", "Archer"], ["Gma.17871.1.S1_at", "Disease resistance protein (TIR-NBS-LRR class), putative", "S1 (07);S1,2,3 (08)", "Archer"], ["Gma.13036.1.S1_at", "Inducer of CBF expression 1 (ICE1)", "S1,2,3 (07,08)", "Minsoy"], ["Gma.1464.1.S1_at", "Rotamase FKBP 1 (ROF1)", "S1,2 (07);S1,2,3 (08)", "Archer"], ["Gma.1571.1.S1_at", "ALDH10A8, 3-chloroallyl aldehyde dehydrogenase/oxidoreductase", "S1,2 (07);S2,3 (08)", "Minsoy"], ["Gma.16586.1.S1_at", "Harpin-induced 1", "S1,2,3 (07);S3 (08)", "Minsoy"], ["Gma.2628.1.A1_at", "Arabidopsis thaliana peptide-N-glycanase 1 (AtPNG1)", "S1,2 (07,08)", "Archer"], ["Gma.4155.1.S1_ata", "RAP2.12,ERF/AP2 transcription factor family", "S1,2,3 (07,08)", "Minsoy"], ["Gma.4155.2.S1_s_ata", "RAP2.12,ERF/AP2 transcription factor family", "S1,2,3 (07,08)", "Minsoy"], ["GmaAffx.14960.1.S1_s_ata", "RAP2.12,ERF/AP2 transcription factor family", "S1 (07);S1,2,3 (08)", "Minsoy"], ["Gma.7716.1.A1_at", "Zinc induced facilitator 1 (ZIF1)", "S2 (07);S1,2,3 (08)", "Minsoy"], ["Gma.8522.1.S1_at", "Major latex protein-related/MLP-related", "S1,2 (07);S1,2,3 (08)", "Archer"], ["GmaAffx.21668.1.A1_at", "COBRA (COB)", "S1,2,3 (07,08)", "Archer"], ["GmaAffx.59014.1.S1_s_at", "Dehydrin family protein", "S1,2 (07);S1 (08)", "Archer"], ["GmaAffx.66290.1.S1_at", "Disease resistance protein (CC-NBS class), putative", "S1,2 (07);S1,2,3 (08)", "Archer"], ["GmaAffx.77896.1.S1_at", "Suppressor of auxin resistance 3 (SAR3), nucleoporin", "S1,2,3 (07,08)", "Archer"], ["GmaAffx.93642.1.S1_s_at", "Secretory protein, putative", "S2 (07);S1,2 (08)", "Archer"]], "row_count": 21, "column_count": 4, "numeric_cells": 52, "header_rows": 1, "locator": "section[7]/table-wrap[2]#t0020"}}, {"id": "asset:table:pmid:26697344:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:60d0f3dbf82d5991c0765e3346955883912746f12ef3b8f964ad2d84472c3499", "bytes": 1037, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[3]#t0025", "version": null, "note": "Probe sets potentially related to protein metabolism. Probe sets predicted to be involved in protein metabolism and that exhibit significant differences in transcript levels between Minsoy and Archer were identified. See Table 3 legend for additional information.", "structure": {"pmcid": "PMC4664686", "section_index": 7, "section_title": "Functional categories of differentially expressed probe sets", "row_count": 7, "column_count": 4}, "table": {"label": "Table 5", "caption": "Probe sets potentially related to protein metabolism. Probe sets predicted to be involved in protein metabolism and that exhibit significant differences in transcript levels between Minsoy and Archer were identified. See Table 3 legend for additional information.", "rows": [["Affymetrix probe set ID", "Gene description", "Stage (year)", "Higher expression"], ["Gma.13070.2.A1_at", "Ribosomal protein L25", "S1,2,3 (07,08)", "Minsoy"], ["Gma.2628.1.A1_at", "Arabidopsis thaliana peptide-N-glycanase 1 (AtPNG1)", "S1,2 (07)", "Archer"], ["Gma.7719.1.A1_at", "TIF3H1, translation initiation factor", "S1 (07);S1,2,3 (08)", "Archer"], ["GmaAffx.16360.1.S1_at", "Glyoxylate/hydroxypyruvate reductase", "S2 (07);S1,2,3 (08)", "Archer"], ["GmaAffx.20624.1.S1_at", "PUB14, ubiquitin-protein ligase", "S1 (07,08)", "Archer"], ["GmaAffx.93183.1.S1_at", "S-adenosylmethionine decarboxylase (SAMDC)", "S1,2 (07);S1,2,3 (08)", "Archer"]], "row_count": 7, "column_count": 4, "numeric_cells": 15, "header_rows": 1, "locator": "section[7]/table-wrap[3]#t0025"}}, {"id": "asset:table:pmid:26697344:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bb47d081b337d8a23471031b0e0f5dfd0e455b75c269b76651cd3aca3184bf83", "bytes": 1300, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[4]#t0030", "version": null, "note": "Probe sets potentially involved in lipid metabolism. Probe sets predicted to be involved in lipid metabolism and that exhibit significant differences in transcript levels between Minsoy and Archer were identified. Gene function was predicted both on the basis of SoyBase Affymetrix ™ GeneChip® Soybean Genome Array Annotation and the Arabidopsis lipid gene database [14] (http://www.plantbiology.msu.edu/lipids/genesurvey/index.htm). See Table 3 legend for additional information.", "structure": {"pmcid": "PMC4664686", "section_index": 7, "section_title": "Functional categories of differentially expressed probe sets", "row_count": 8, "column_count": 4}, "table": {"label": "Table 6", "caption": "Probe sets potentially involved in lipid metabolism. Probe sets predicted to be involved in lipid metabolism and that exhibit significant differences in transcript levels between Minsoy and Archer were identified. Gene function was predicted both on the basis of SoyBase Affymetrix ™ GeneChip® Soybean Genome Array Annotation and the Arabidopsis lipid gene database [14] (http://www.plantbiology.msu.edu/lipids/genesurvey/index.htm). See Table 3 legend for additional information.", "rows": [["AffyID", "Gene description", "Stage (year)", "Higher expression"], ["Gma.13043.1.S1_at", "Arabidopsis thaliana carboxyesterase 20 (AtCXE20)", "S1,2,3 (07);S3 (08)", "Minsoy"], ["Gma.13216.2.S1_ata", "Ceramidase family protein", "S1,2,3 (07,08)", "Archer"], ["Gma.4488.1.A1_s_ata", "Ceramidase family protein", "S1,2,3 (07,08)", "Archer"], ["Gma.6802.1.A1_at", "GLIP5, carboxylesterase/lipase", "S1,3 (07);S1,2,3 (08)", "Minsoy"], ["GmaAffx.18905.1.S1_at", "Esterase/lipase/thioesterase", "S1,2 (07,08)", "Minsoy"], ["GmaAffx.37987.1.S1_at", "Diacylglycerol acyltransferase family", "S1 (07,08)", "Archer"], ["GmaAffx.6790.1.S1_at", "Epoxide hydrolase, putative", "S1,2,3 (07);S1 (08)", "Minsoy"]], "row_count": 8, "column_count": 4, "numeric_cells": 15, "header_rows": 1, "locator": "section[7]/table-wrap[4]#t0030"}}], "gaps": ["asset:data:geo:GSE21598 not downloaded", "asset:data:geo:GSE21598 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": {"fdr_threshold": "and Benjamini-Hochberg false discovery rate correction"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The lmFit function (limma package) [35] was used to fit a linear model to identify differentially expressed genes between the two parental lines and the two RILs at each stage. The empirical Bayes (eBayes) method was used to adjust variances, and Benjamini-Hochberg's False Discovery Rate (FDR) was calculated for multiple test correction [36]."}}, {"id": "method-2", "family": "genetic_association", "specific": "linkage", "label": "Genetic association (GWAS / linkage / MR)", "dsl_operations": ["gwas_locus_scan", "mr_estimate", "linkage_scan"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["genotype_phenotype_table"], "evidence": {"score": 0.7, "band": "medium", "quote": "QTL"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 2.0, "unit": "fold change", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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": ["GSE21598"], "resolved_accessions": ["GSE21598"], "statements": ["All microarray data and expression values after GCRMA are available at the Gene Expression Omnibus (GEO) at NCBI (http://www.ncbi.nlm.nih.gov/geo), under accession number GSE21598."], "basis": "The paper names GSE21598 in Gene Expression Omnibus (GEO) at NCBI 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:26697344", "data:geo:GSE21598", "asset:table:pmid:26697344:1", "asset:table:pmid:26697344:2", "asset:table:pmid:26697344:3", "asset:table:pmid:26697344:4", "asset:table:pmid:26697344:5", "asset:table:pmid:26697344:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21598"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:39Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 86943, "completion_tokens": 2874, "cached_tokens": 11776}}, "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:26697344", "type": "paper", "label": "pmid:26697344"}, {"id": "source:pmid:26697344", "type": "manuscript", "label": "PMID 26697344 full text"}, {"id": "data:geo:GSE21598", "type": "dataset", "label": "GEO GSE21598"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26697344", "type": "paper", "label": "pmid:26697344"}, {"id": "source:pmid:26697344", "type": "manuscript", "label": "PMID 26697344 full text"}, {"id": "data:geo:GSE21598", "type": "dataset", "label": "GEO GSE21598"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26697344", "type": "extraction", "used": ["source:pmid:26697344"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21598", "type": "accession_resolution", "used": ["data:geo:GSE21598"], "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:26697344", "parent_hash": "sha256:37a9e93a4e4795a2029126fdb166e2ca73721cf3b76659e05e6188ffe2f7037b", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE21598 licence not read", "asset:data:geo:GSE21598 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": ["general seed development or metabolism. All microarray data and expression values after GCRMA are a", "ld. To help address this deficiency, we used Affymetrix Soybean GeneChips® to identify genes that ar", "of these 97 probe sets based on the SoyBase Affymetrix™ GeneChip® Soybean Genome Array Annotation.", "to − 80 °C until RNA extraction. Analysis of microarray data The Affymetrix Soybean GeneChip® contai"], "order_basis": "paper_text_order:516", "id": "assay:1"}, {"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 lmFit function (limma package) [35] was used to fit a linear model to identify differentially expressed genes between the two parental lines and the two RILs at each stage. The empirical Bayes (eBayes) method was used to adjust variances, and Benjamini-Hochberg's False Discovery Rate (FDR) was calculated for multiple test correction [36]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}