Altered Expression of a Unique Set of Genes Reveals Complex Etiology of Schizophrenia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31920755", "kind": "science-record", "revision": 7, "content_hash": "sha256:89022fe610e25a1802bbd1e2cd4b9a1d74b7672c6a27763ad8be97796bc6e15f", "created_at": "2026-11-01T15:40:54Z", "updated_at": "2026-11-01T22:01:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Altered Expression of a Unique Set of Genes Reveals Complex Etiology of Schizophrenia.", "doi": "10.3389/fpsyt.2019.00906", "pmid": "31920755", "authors": ["Ashutosh Kumar", "Vikas Pareek", "Himanshu N Singh", "Muneeb A Faiq", "Ravi K Narayan", "Khursheed Raza", "Pavan Kumar"], "journal": "Frontiers in psychiatry", "year": 2019, "abstract": "Background: The etiology of schizophrenia is extensively debated, and multiple factors have been contended to be involved. A panoramic view of the contributing factors in a genome-wide study can be an effective strategy to provide a comprehensive understanding of its causality. Materials and Methods: GSE53987 dataset downloaded from GEO-database, which comprised mRNA expression data of post-mortem brain tissue across three regions from control (C) and age-matched subjects (T) of schizophrenia (N = Hippocampus [HIP]: C-15, T-18, Prefrontal cortex [PFC]: C-15, T-19, Associative striatum [STR]: C-18, T-18). Bio-conductor-affy-package used to compute mRNA expression, and further t-test applied to investigate differential gene expression. The analysis of the derived genes performed using the PANTHER Classification System and NCBI database. Further, a protein interactome analysis of the derived gene set was performed using STRING v10 database (https://string-db.org/) Results: A set of 40 genes showed significantly altered (p < 0.01) expression across all three brain regions. The analyses unraveled genes implicated in biological processes and events, and molecular pathways relating basic neuronal functions. Conclusions: The aberrant expression of genes maintaining basic cell machinery explains compromised neuronal processing in SCZ.", "claims": [{"id": "claim-method", "statement": "After calculation of mRNA expression intensity, a simple unpaired two tailed t-test (significance set at p ≤ 0.01) was applied to the data to filter out the set of genes expressed significantly in all three brain regions.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31920755", "locator": "sections[4] \"Data Retrieval and Analysis\" paragraph 2", "quote": "After calculation of mRNA expression intensity, a simple unpaired two tailed t-test (significance set at p ≤ 0.01) was applied to the data to filter out the set of genes expressed significantly in all three brain regions."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset used for this study can be found in the NCBI Genome Expression Omnibus, GEO accession: GSE53987 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53987).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31920755", "locator": "sections[14] \"Data Availability Statement\" paragraph 2", "quote": "The dataset used for this study can be found in the NCBI Genome Expression Omnibus, GEO accession: GSE53987 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53987)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31920755"], "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:GSE53987"], "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:GSE53987"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31920755", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fpsyt.2019.00906", "sha256": "sha256:e8ca486dc0de1b84914dd7272bd2e2977e7b52bcb0c61079478a65b1aa1a0946", "bytes": 35574, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fpsyt.2019.00906", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6920214", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE53987", "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=GSE53987", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53987", "version": null, "note": "The dataset used for this study can be found in the NCBI Genome Expression Omnibus, GEO accession: GSE53987 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53987).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset used for this study can be found in the NCBI Genome Expression Omnibus, GEO accession: GSE53987 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53987).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1304852", "GSM1304853", "GSM1304854", "GSM1304855", "GSM1304856", "GSM1304857", "GSM1304858", "GSM1304859", "GSM1304860", "GSM1304861", "GSM1304862", "GSM1304863", "GSM1304864", "GSM1304865", "GSM1304866", "GSM1304867", "GSM1304868", "GSM1304869", "GSM1304870", "GSM1304871", "GSM1304872", "GSM1304873", "GSM1304874", "GSM1304875", "GSM1304876", "GSM1304877", "GSM1304878", "GSM1304879", "GSM1304880", "GSM1304881", "GSM1304882", "GSM1304883", "GSM1304884", "GSM1304885", "GSM1304886", "GSM1304887", "GSM1304888", "GSM1304889", "GSM1304890", "GSM1304891", "GSM1304892", "GSM1304893", "GSM1304894", "GSM1304895", "GSM1304896", "GSM1304897", "GSM1304898", "GSM1304899", "GSM1304900", "GSM1304901", "GSM1304902", "GSM1304903", "GSM1304904", "GSM1304905", "GSM1304906", "GSM1304907", "GSM1304908", "GSM1304909", "GSM1304910", "GSM1304911", "GSM1304912", "GSM1304913", "GSM1304914", "GSM1304915", "GSM1304916", "GSM1304917", "GSM1304918", "GSM1304919", "GSM1304920", "GSM1304921", "GSM1304922", "GSM1304923", "GSM1304924", "GSM1304925", "GSM1304926", "GSM1304927", "GSM1304928", "GSM1304929", "GSM1304930", "GSM1304931", "GSM1304932", "GSM1304933", "GSM1304934", "GSM1304935", "GSM1304936", "GSM1304937", "GSM1304938", "GSM1304939", "GSM1304940", "GSM1304941", "GSM1304942", "GSM1304943", "GSM1304944", "GSM1304945", "GSM1304946", "GSM1304947", "GSM1304948", "GSM1304949", "GSM1304950", "GSM1304951", "GSM1304952", "GSM1304953", "GSM1304954", "GSM1304955", "GSM1304956", "GSM1304957", "GSM1304958", "GSM1304959", "GSM1304960", "GSM1304961", "GSM1304962", "GSM1304963", "GSM1304964", "GSM1304965", "GSM1304966", "GSM1304967", "GSM1304968", "GSM1304969", "GSM1304970", "GSM1304971", "GSM1304972", "GSM1304973", "GSM1304974", "GSM1304975", "GSM1304976", "GSM1304977", "GSM1304978", "GSM1304979", "GSM1304980", "GSM1304981", "GSM1304982", "GSM1304983", "GSM1304984", "GSM1304985", "GSM1304986", "GSM1304987", "GSM1304988", "GSM1304989", "GSM1304990", "GSM1304991", "GSM1304992", "GSM1304993", "GSM1304994", "GSM1304995", "GSM1304996", "GSM1304997", "GSM1304998", "GSM1304999", "GSM1305000", "GSM1305001", "GSM1305002", "GSM1305003", "GSM1305004", "GSM1305005", "GSM1305006", "GSM1305007", "GSM1305008", "GSM1305009", "GSM1305010", "GSM1305011", "GSM1305012", "GSM1305013", "GSM1305014", "GSM1305015", "GSM1305016", "GSM1305017", "GSM1305018", "GSM1305019", "GSM1305020", "GSM1305021", "GSM1305022", "GSM1305023", "GSM1305024", "GSM1305025", "GSM1305026", "GSM1305027", "GSM1305028", "GSM1305029", "GSM1305030", "GSM1305031", "GSM1305032", "GSM1305033", "GSM1305034", "GSM1305035", "GSM1305036", "GSM1305037", "GSM1305038", "GSM1305039", "GSM1305040", "GSM1305041", "GSM1305042", "GSM1305043", "GSM1305044", "GSM1305045", "GSM1305046", "GSM1305047", "GSM1305048", "GSM1305049", "GSM1305050", "GSM1305051", "GSM1305052", "GSM1305053", "GSM1305054", "GSM1305055", "GSM1305056"], "sample_count": 205, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Microarray profiling of PFC, HPC and STR from subjects with schizophrenia, bipolar, MDD or control", "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:31920755:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:28e53fdabde807d6aa7add369e28b62346cfa350788acb9c1885ed8b723837a3", "bytes": 4618, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T1", "version": null, "note": "Genome wide m-RNA expression (statistical significance set at p ≤ 0.01) in three brain regions of schizophrenic patients and healthy controls (data represented as mean).", "structure": {"pmcid": "PMC6920214", "section_index": 5, "section_title": "Results", "row_count": 43, "column_count": 13}, "table": {"label": "Table 1", "caption": "Genome wide m-RNA expression (statistical significance set at p ≤ 0.01) in three brain regions of schizophrenic patients and healthy controls (data represented as mean).", "rows": [["", "", "Hippocampus", "", "Prefrontal cortex", "", "Associative striatum"], ["Gene symbol", "Control", "SCZ", "Fold change", "p-value", "Control", "SCZ", "Fold change", "p-value", "Control", "SCZ", "Fold change", "p-value"], ["(n = 15)", "(n = 18)", "(Control/SCZ)", "(n=15)", "(n = 19)", "(Control/SCZ)", "(n = 18)", "(n = 18)", "(Control/SCZ)"], ["MSANTD3", "8.33", "8.03", "0.96", "0.001", "8.71", "8.71", "0.98", "0.003", "8.15", "8.03", "0.99", "0.006"], ["CXADR", "5.52", "5", "0.9", "0.001", "5.46", "5.46", "0.93", "0.003", "5.83", "5.44", "0.93", "0.004"], ["ZNF385B", "6.27", "5.47", "0.87", "<0.001", "8.3", "8.3", "0.97", "0.005", "8.44", "7.61", "0.9", "0.008"], ["SAFB2", "7.12", "7.46", "1.05", "0.005", "6.88", "6.88", "1.04", "0.002", "7.49", "7.74", "1.03", "0.006"], ["FBXO9 1559094_at", "9.49", "8.71", "0.91", "<0.001", "10.19", "10.19", "0.95", "0.002", "8.78", "8.28", "0.94", "0.002"], ["FBXO9 1559096_x_at", "10.68", "10.07", "0.94", "<0.001", "11.25", "11.25", "0.97", "0.004", "10.27", "9.95", "0.97", "0.003"], ["MCL1", "9.74", "10.23", "1.05", "0.002", "9.76", "9.76", "1.03", "0.002", "9.83", "10.25", "1.04", "0.002"], ["PITPNA", "10.74", "10.39", "0.96", "<0.001", "11.18", "11.18", "0.99", "0.006", "10.31", "10.16", "0.99", "0.008"], ["PSMC3", "9.64", "9.17", "0.95", "<0.001", "9.92", "9.92", "0.98", "0.008", "10.15", "9.8", "0.97", "0.008"], ["IFITM2", "9.77", "10.46", "1.07", "0.001", "9.29", "9.29", "1.06", "0.003", "10.04", "10.47", "1.04", "0.008"], ["ICMT", "8.09", "7.93", "0.98", "0.008", "8.22", "8.22", "0.97", "0.001", "8.83", "8.43", "0.95", "<0.001"], ["UQCRC1", "10.7", "10.29", "0.96", "<0.001", "11.06", "11.06", "0.99", "0.003", "10.69", "10.46", "0.98", "0.008"], ["ASNA1", "9.3", "8.99", "0.96", "<0.001", "9.42", "9.42", "0.99", "0.006", "9.19", "8.99", "0.98", "0.008"], ["TIAL1", "7.97", "7.7", "0.96", "<0.001", "7.94", "7.94", "0.98", "0.003", "7.89", "7.67", "0.97", "0.003"], ["GTF2H1", "7.59", "7.02", "0.92", "<0.001", "8.04", "8.04", "0.97", "0.002", "7.38", "6.96", "0.94", "0.003"], ["ANPEP", "9.22", "10.26", "1.11", "< 0.001", "8.81", "8.81", "1.09", "0.004", "9.36", "10.11", "1.08", "0.005"], ["SOX9", "9.39", "9.7", "1.03", "0.008", "9.07", "9.07", "1.05", "0.001", "9.41", "9.7", "1.03", "0.002"], ["CHSY1", "8.18", "8.64", "1.05", "0.001", "8.29", "8.29", "1.04", "0.002", "8.2", "8.49", "1.03", "0.007"], ["BCL6", "9.78", "10.48", "1.07", "<0.001", "10.18", "10.18", "1.03", "0.002", "9.52", "10", "1.05", "0.009"], ["PDCD6", "10.11", "9.65", "0.95", "<0.001", "10.29", "10.29", "0.98", "0.004", "10.01", "9.73", "0.97", "0.005"], ["ERCC1", "9.13", "8.84", "0.97", "<0.001", "9.09", "9.09", "0.98", "0.008", "8.85", "8.65", "0.98", "<0.001"], ["MYO5A", "8.7", "8.3", "0.95", "0.003", "9.24", "9.24", "0.96", "0.004", "7.69", "7.35", "0.95", "0.002"], ["KCNK1", "10.73", "10.4", "0.97", "0.003", "10.9", "10.9", "0.98", "0.003", "10.08", "9.78", "0.97", "0.008"], ["GNAO1", "10.58", "10.23", "0.96", "0.006", "10.61", "10.61", "0.97", "0.001", "10.37", "10.03", "0.97", "0.005"], ["HAPLN1", "5.84", "5.14", "0.88", "0.002", "5.88", "5.88", "0.94", "0.002", "4.77", "4.49", "0.94", "0.007"], ["PPM1E", "9.12.", "8.26", "0.9", "0.007", "7.62", "7.62", "0.96", "0.008", "6.37", "6.08", "0.95", "0.001"], ["KAT5.", "8.46", "8.29", "0.97", "0.001", "8.7", "8.7", "0.99", "0.008", "8.68", "8.56", "0.99", "0.008"], ["MAPK9", "8.13", "7.5", "0.92", "<0.001", "8.74", "8.74", "0.96", "0.001", "8.03", "7.63", "0.95", "0.003"], ["SPAG7", "9.9", "9.65", "0.97", "<0.001", "9.92", "9.92", "0.99", "0.001", "9.52", "9.37", "0.98", "0.001"], ["ANAPC5", "11.02", "10.84", "0.98", "<0.001", "10.95", "10.95", "0.99", "0.001", "11.02", "10.8", "0.98", "0.009"], ["ATP5D", "10.71", "10.4", "0.97", "<0.001", "10.76", "10.76", "0.98", "0.005", "10.66", "10.46", "0.98", "0.008"], ["UBE4B", "7.76", "7.5", "0.96", "0.006", "8.03", "8.03", "0.98", "0.01", "7.71", "7.45", "0.97", "0.004"], ["SCRN3", "8.12", "7.65", "0.94", "0.001", "8.18", "8.18", "0.98", "0.008", "7.64", "7.27", "0.95", "0.002"], ["SMIM7", "9.13", "8.77", "0.96", "0.001", "9.35", "9.35", "0.98", "0.005", "9.38", "9.05", "0.96", "0.002"], ["PDK4", "8.24", "9.15", "1.11", "0.001", "7.98", "7.98", "1.11", "<0.001", "8.6", "9.27", "1.07", "0.003"], ["RBM18", "9.31", "8.99", "0.96", "0.001", "9.6", "9.6", "0.99", "0.006", "9.18", "8.96", "0.98", "0.003"], ["SAMD5", "6.76", "6.38", "0.94", "0.006", "6.85", "6.85", "0.96", "0.001", "7.47", "6.85", "0.92", "<0.001"], ["CADPS", "6.43", "6.2", "0.96", "0.004", "6.4", "6.4", "0.96", "0.005", "6.1", "5.89", "0.97", "0.004"], ["LOC100506538///NDUFAF6", "8.13", "7.57", "0.94", "0.001", "8.5", "8.5", "0.97", "0.004", "8.11", "7.69", "0.95", "0.008"], ["LOC100507534", "6.38", "5.28", "0.83", "0.002", "6.29", "6.29", "0.88", "< 0.001", "4.42", "4.19", "0.95", "0.007"]], "row_count": 43, "column_count": 13, "numeric_cells": 492, "header_rows": 3, "locator": "section[5]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:31920755:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b0aec16342c0a0c0240088ec7a2a1231d032f9c68a123048e00118a97e4aff9d", "bytes": 972, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#T2", "version": null, "note": "Involvement of the gene set in biological processes and events.", "structure": {"pmcid": "PMC6920214", "section_index": 5, "section_title": "Results", "row_count": 14, "column_count": 3}, "table": {"label": "Table 2", "caption": "Involvement of the gene set in biological processes and events.", "rows": [["a", "Ubiquitination", "FBXO9, ANAPC5, UBE4, SMIM7"], ["b", "Enzyme activity", "PPM1E, MAPK9, ATP5D, ICMT, PDK4, PSMC3"], ["c", "Energy production mechanisms", "UQCRC1, ASNA1, ATP5D, PDK4"], ["d", "Cell growth", "MAPK9, ANAPC5, CHSY1"], ["e", "Programmed cell death", "IFITM2a, TIAL1a, PDCD6a, MCL-1b"], ["f", "Cytoplasmic vesicular transport and exocytosis", "MYO5A, PITPNA, ASNA1, CADPS, SCRN3"], ["g", "Dynamic regulation of cytoskeleton", "MYO5A"], ["h", "Ion channel homeostasis", "KCNK1, PDCD6"], ["i", "Lipid binding and synthesis", "PITPNA, CAPDS"], ["j", "DNA repair", "ERCC1, KAT5"], ["k", "m-RNA transcription", "MSANTD3, GTF2H1, GNAO1, MAPK9"], ["l", "Post transcriptional gene modifications", "KAT5"], ["m", "Protein translation", "TIAL1"], ["n", "Cell cycle regulation", "ANAPC5, MAPK9"]], "row_count": 14, "column_count": 3, "numeric_cells": 1, "header_rows": 0, "locator": "section[5]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:GSE53987 not downloaded", "asset:data:geo:GSE53987 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "simple unpaired two-tailed t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "After calculation of mRNA expression intensity, a simple unpaired two tailed t-test (significance set at p ≤ 0.01) was applied to the data to filter out the set of genes expressed significantly in all three brain regions."}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE53987"], "resolved_accessions": ["GSE53987"], "statements": ["The dataset used for this study can be found in the NCBI Genome Expression Omnibus, GEO accession: GSE53987 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53987)."], "basis": "The paper names GSE53987 in NCBI Genome Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:31920755", "data:geo:GSE53987", "asset:table:pmid:31920755:1", "asset:table:pmid:31920755:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE53987"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28630, "completion_tokens": 1251, "cached_tokens": 648}}, "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:31920755", "type": "paper", "label": "pmid:31920755"}, {"id": "source:pmid:31920755", "type": "manuscript", "label": "PMID 31920755 full text"}, {"id": "data:geo:GSE53987", "type": "dataset", "label": "GEO GSE53987"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31920755", "type": "paper", "label": "pmid:31920755"}, {"id": "source:pmid:31920755", "type": "manuscript", "label": "PMID 31920755 full text"}, {"id": "data:geo:GSE53987", "type": "dataset", "label": "GEO GSE53987"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31920755", "type": "extraction", "used": ["source:pmid:31920755"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE53987", "type": "accession_resolution", "used": ["data:geo:GSE53987"], "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:31920755", "parent_hash": "sha256:a2967d9269195f6ac7acbb8df091fd5f86dfb5edcf5a9831d95d5909116e7c12", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE53987 licence not read", "asset:data:geo:GSE53987 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}