Bioinformatics analysis of immune infiltration in human diabetic retinopathy and identification of immune-related hub genes and their ceRNA networks.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39402134", "kind": "science-record", "revision": 4, "content_hash": "sha256:b7669f0174a2773e5b91ba3292f2b3060efe4da10f7c871d535ae7ddbaf9df48", "created_at": "2026-11-01T20:29:38Z", "updated_at": "2026-11-01T22:55:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of immune infiltration in human diabetic retinopathy and identification of immune-related hub genes and their ceRNA networks.", "doi": "10.1038/s41598-024-75055-3", "pmid": "39402134", "authors": ["Jingru Li", "Chaozhong Li", "Xinyu Wu", "Shuai Yu", "Guihu Sun", "Peng Ding", "Si Lu", "Lijiao Zhang", "Ping Yang", "Yunzhu Peng", "Jingyun Fu", "Luqiao Wang"], "journal": "Scientific reports", "year": 2024, "abstract": "Diabetic retinopathy (DR) is the most common microvascular complication in diabetic patients, and recent studies have shown that immune regulatory mechanisms are closely associated with retinal damage in DR. Therefore, this study focused on exploring immune cells and immune-related genes (IRGs) in DR and gaining insight into the ceRNA mechanisms by which IRGs regulate DR progression. Four datasets from human DR model retinal tissues were obtained from the Gene Expression Omnibus (GEO) database. R software was first used to identify differentially expressed mRNAs (DE-mRNAs) in the dataset GSE160306-mRNAs, then the distribution of immune cells in the gene matrix was analyzed by xCell and ImmuCellAI, ImmPort and InnateDB database were used to obtain immune-related hub genes (IRHGs) in the DR, and finally the STRING online tool and Cytoscape to construct the immune-related ceRNA network. The datasets GSE102485, GSE160308 and GSE160306-lncRNAs were used to validate the results of the ceRNA network further. The results of immune cell infiltration analysis showed that macrophages are important immune cells in DR; immune-related gene screening showed that FCGR2B is an IRHG in DR, and 2 immune-related ceRNA networks of IRHG were obtained: DDN-AS1/miR-10a-5p/FCGR2B and LINC01515/miR-10a-5p/FCGR2B. Our study suggests that infiltration of immune cells, especially the immune role of macrophages, is an important component of DR progression; the immune-related hub gene FCGR2B and its ceRNA network may be a key regulatory network for DR progression. The discovery of key immune cells, IRHG and ceRNA networks in this study may provide new prospects for early intervention and targeted treatment of DR.", "claims": [{"id": "claim-method", "statement": "The datasets GSE160306 and GSE160308 were of high-throughput sequencing count data, so the R package DESeq2 (version 1.32.0) was used for the difference analysis of the 2 datasets to obtain the DE-mRNAs, DE-miRNAs, and DE-lncRNAs between the DR group and the control group33. For the dataset GSE102485, the GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) platform was used in this study to identify differentially expressed mRNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39402134", "locator": "sections[11] \"Statistical analysis of gene expression matrix\" paragraph 2", "quote": "The datasets GSE160306 and GSE160308 were of high-throughput sequencing count data, so the R package DESeq2 (version 1.32.0) was used for the difference analysis of the 2 datasets to obtain the DE-mRNAs, DE-miRNAs, and DE-lncRNAs between the DR group and the control group33."}, {"asset": "source:pmid:39402134", "locator": "sections[11] \"Statistical analysis of gene expression matrix\" paragraph 3", "quote": "For the dataset GSE102485, the GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) platform was used in this study to identify differentially expressed mRNAs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analysed during the current study are available in the National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)-Gene Expression Omnibus (GEO) databases (https:/www.ncbi.nlm.nih.gov/gds/) with accession numbers GSE160306, GSE160308 and GSE102485, xCell (xCell, http://xCell.ucsf.edu/), ImmuCellAI (ImmuCellAI, http://bioinfo.life.hust.edu.cn/ImmuCellAI), Metascape (Metascape, a gene annotation & analysis resource, http://metascape.org, version 3.5), STRING database (STRING, https://string-db.org/), Cytoscape software (Cytoscape, https://cytoscape.org/), GSEA (http://software.broadinstitute.org/gsea/index.jsp), Molecular Signatures Database (http://www.gsea-msigdb.org/gsea/downloads.jsp), ImmPort database (https://www.immport.org/), InnateDB database (https://www.innatedb.com), miRcode (http://www.mircode.org/) and DIANA-LncBase (https://diana.e-ce.uth.gr/lncbasev3, version 3.0) databases. All data generated and analyzed in this study can be found in these databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39402134", "locator": "sections[29] \"notes\" paragraph 1", "quote": "The datasets generated during and/or analysed during the current study are available in the National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)-Gene Expression Omnibus (GEO) databases (https:/www.ncbi.nlm.nih.gov/gds/) with accession numbers GSE160306, GSE160308 and GSE102485, xCell (xCell, http://xCell.ucsf.edu/), ImmuCellAI (ImmuCellAI, http://bioinfo.life.hust.edu.cn/ImmuCellAI), Metascape (Metascape, a gene annotation & analysis resource, http://metascape.org, version 3.5), STRING database (STRING, https://string-db.org/), Cytoscape software (Cytoscape, https://cytoscape.org/), GSEA (http://software.broadinstitute.org/gsea/index.jsp), Molecular Signatures Database (http://www.gsea-msigdb.org/gsea/downloads.jsp), ImmPort database (https://www.immport.org/), InnateDB database (https://www.innatedb.com), miRcode (http://www.mircode.org/) and DIANA-LncBase (https://diana.e-ce.uth.gr/lncbasev3, version 3.0) databases. All data generated and analyzed in this study can be found in these databases."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The results of immune cell infiltration analysis showed that macrophages are important immune cells in DR; immune-related gene screening showed that FCGR2B is an IRHG in DR, and 2 immune-related ceRNA networks of IRHG were obtained: DDN-AS1/miR-10a-5p/FCGR2B and LINC01515/miR-10a-5p/FCGR2B.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39402134", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The results of immune cell infiltration analysis showed that macrophages are important immune cells in DR; immune-related gene screening showed that FCGR2B is an IRHG in DR, and 2 immune-related ceRNA networks of IRHG were obtained: DDN-AS1/miR-10a-5p/FCGR2B and LINC01515/miR-10a-5p/FCGR2B."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The results of immune cell infiltration analysis showed that macrophages are important immune cells in DR; immune-related gene screening showed that FCGR2B is an IRHG in DR, and 2 immune-related ceRNA networks of IRHG were obtained: DDN-AS1/miR-10a-5p/FCGR2B and LINC01515/miR-10a-5p/FCGR2B.", "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:39402134"], "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:GSE102485"], "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:GSE102485"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39402134", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-75055-3", "sha256": "sha256:b51f63d59ccf04a2d06d2608f7802561e54c970a1d90370fd81b57913ebe32df", "bytes": 45305, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-75055-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11473686", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102485", "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=GSE102485", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102485", "version": null, "note": "The datasets generated during and/or analysed during the current study are available in the National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)-Gene Expression Omnibus (GEO) databases (https:/www.ncbi.nlm.nih.gov/gds/) with accession numbers GSE160306, GSE160308 and GSE102485, xCell (xCell, http://xCell.ucsf.edu/), ImmuCellAI (ImmuCellAI, http://bioinfo.life.hust.edu.cn/ImmuCellAI), Metascape (Metascape, a gene annotation & analysis resource, http://metascape.org, version 3.5), STRING database (STRING, https://string-db.org/), Cytoscape software (Cytoscape, https://cytoscape.org/), GSEA (http://software.broadinstitute.org/gsea/index.jsp), Molecular Signatures Database (http://www.gsea-msigdb.org/gsea/downloads.jsp), ImmPort database (https://www.immport.org/), InnateDB database (https://www.innatedb.com), miRcode (http://www.mircode.org/) and DIANA-LncBase (https://diana.e-ce.uth.gr/lncbasev3, version 3.0) databases. All data generated and analyzed in this study can be found in these databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analysed during the current study are available in the National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)-Gene Expression Omnibus (GEO) databases (https:/www.ncbi.nlm.nih.gov/gds/) with accession numbers GSE160306, GSE160308 and GSE102485, xCell (xCell, http://xCell.ucsf.edu/), ImmuCellAI (ImmuCellAI, http://bioinfo.life.hust.edu.cn/ImmuCellAI), Metascape (Metascape, a gene annotation & analysis resource, http://metascape.org, version 3.5), STRING database (STRING, https://string-db.org/), Cytoscape software (Cytoscape, https://cytoscape.org/), GSEA (http://software.broadinstitute.org/gsea/index.jsp), Molecular Signatures Database (http://www.gsea-msigdb.org/gsea/downloads.jsp), ImmPort database (https://www.immport.org/), InnateDB database (https://www.innatedb.com), miRcode (http://www.mircode.org/) and DIANA-LncBase (https://diana.e-ce.uth.gr/lncbasev3, version 3.0) databases. All data generated and analyzed in this study can be found in these databases.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2739339", "GSM2739340", "GSM2739341", "GSM2739342", "GSM2739343", "GSM2739344", "GSM2739345", "GSM2739346", "GSM2739347", "GSM2739348", "GSM2739349", "GSM2739350", "GSM2739351", "GSM2739352", "GSM2739353", "GSM2739354", "GSM2739355", "GSM2739356", "GSM2739357", "GSM2739358", "GSM2739359", "GSM2739360", "GSM2739361", "GSM2739362", "GSM2739363", "GSM2739364", "GSM2739365", "GSM2739366", "GSM2739367", "GSM2739368"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Induced Expression of VEGFC, ANGPT, and EFNB2 and Their Receptors Characterizes Neovascularization in Proliferative Diabetic Retinopathy", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE160306", "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=GSE160306", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE160306", "version": null, "note": "The datasets generated during and/or analysed during the current study are available in the National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)-Gene Expression Omnibus (GEO) databases (https:/www.ncbi.nlm.nih.gov/gds/) with accession numbers GSE160306, GSE160308 and GSE102485, xCell (xCell, http://xCell.ucsf.edu/), ImmuCellAI (ImmuCellAI, http://bioinfo.life.hust.edu.cn/ImmuCellAI), Metascape (Metascape, a gene annotation & analysis resource, http://metascape.org, version 3.5), STRING database (STRING, https://string-db.org/), Cytoscape software (Cytoscape, https://cytoscape.org/), GSEA (http://software.broadinstitute.org/gsea/index.jsp), Molecular Signatures Database (http://www.gsea-msigdb.org/gsea/downloads.jsp), ImmPort database (https://www.immport.org/), InnateDB database (https://www.innatedb.com), miRcode (http://www.mircode.org/) and DIANA-LncBase (https://diana.e-ce.uth.gr/lncbasev3, version 3.0) databases. All data generated and analyzed in this study can be found in these databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analysed during the current study are available in the National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)-Gene Expression Omnibus (GEO) databases (https:/www.ncbi.nlm.nih.gov/gds/) with accession numbers GSE160306, GSE160308 and GSE102485, xCell (xCell, http://xCell.ucsf.edu/), ImmuCellAI (ImmuCellAI, http://bioinfo.life.hust.edu.cn/ImmuCellAI), Metascape (Metascape, a gene annotation & analysis resource, http://metascape.org, version 3.5), STRING database (STRING, https://string-db.org/), Cytoscape software (Cytoscape, https://cytoscape.org/), GSEA (http://software.broadinstitute.org/gsea/index.jsp), Molecular Signatures Database (http://www.gsea-msigdb.org/gsea/downloads.jsp), ImmPort database (https://www.immport.org/), InnateDB database (https://www.innatedb.com), miRcode (http://www.mircode.org/) and DIANA-LncBase (https://diana.e-ce.uth.gr/lncbasev3, version 3.0) databases. All data generated and analyzed in this study can be found in these databases.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4871112", "GSM4871113", "GSM4871114", "GSM4871115", "GSM4871116", "GSM4871117", "GSM4871118", "GSM4871119", "GSM4871120", "GSM4871121", "GSM4871122", "GSM4871123", "GSM4871124", "GSM4871125", "GSM4871126", "GSM4871127", "GSM4871128", "GSM4871129", "GSM4871130", "GSM4871131", "GSM4871132", "GSM4871133", "GSM4871134", "GSM4871135", "GSM4871136", "GSM4871137", "GSM4871138", "GSM4871139", "GSM4871140", "GSM4871141", "GSM4871142", "GSM4871143", "GSM4871144", "GSM4871145", "GSM4871146", "GSM4871147", "GSM4871148", "GSM4871149", "GSM4871150", "GSM4871151", "GSM4871152", "GSM4871153", "GSM4871154", "GSM4871155", "GSM4871156", "GSM4871157", "GSM4871158", "GSM4871159", "GSM4871160", "GSM4871161", "GSM4871162", "GSM4871163", "GSM4871164", "GSM4871165", "GSM4871166", "GSM4871167", "GSM4871168", "GSM4871169", "GSM4871170", "GSM4871171", "GSM4871172", "GSM4871173", "GSM4871174", "GSM4871175", "GSM4871176", "GSM4871177", "GSM4871178", "GSM4871179", "GSM4871180", "GSM4871181", "GSM4871182", "GSM4871183", "GSM4871184", "GSM4871185", "GSM4871186", "GSM4871187", "GSM4871188", "GSM4871189", "GSM4871190"], "sample_count": 79, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "In-depth transcriptomic analyses investigating molecular mechanisms underlying diabetic retinopathy (totalRNA)", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE160308", "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=GSE160308", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE160308", "version": null, "note": "The datasets generated during and/or analysed during the current study are available in the National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)-Gene Expression Omnibus (GEO) databases (https:/www.ncbi.nlm.nih.gov/gds/) with accession numbers GSE160306, GSE160308 and GSE102485, xCell (xCell, http://xCell.ucsf.edu/), ImmuCellAI (ImmuCellAI, http://bioinfo.life.hust.edu.cn/ImmuCellAI), Metascape (Metascape, a gene annotation & analysis resource, http://metascape.org, version 3.5), STRING database (STRING, https://string-db.org/), Cytoscape software (Cytoscape, https://cytoscape.org/), GSEA (http://software.broadinstitute.org/gsea/index.jsp), Molecular Signatures Database (http://www.gsea-msigdb.org/gsea/downloads.jsp), ImmPort database (https://www.immport.org/), InnateDB database (https://www.innatedb.com), miRcode (http://www.mircode.org/) and DIANA-LncBase (https://diana.e-ce.uth.gr/lncbasev3, version 3.0) databases. All data generated and analyzed in this study can be found in these databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analysed during the current study are available in the National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)-Gene Expression Omnibus (GEO) databases (https:/www.ncbi.nlm.nih.gov/gds/) with accession numbers GSE160306, GSE160308 and GSE102485, xCell (xCell, http://xCell.ucsf.edu/), ImmuCellAI (ImmuCellAI, http://bioinfo.life.hust.edu.cn/ImmuCellAI), Metascape (Metascape, a gene annotation & analysis resource, http://metascape.org, version 3.5), STRING database (STRING, https://string-db.org/), Cytoscape software (Cytoscape, https://cytoscape.org/), GSEA (http://software.broadinstitute.org/gsea/index.jsp), Molecular Signatures Database (http://www.gsea-msigdb.org/gsea/downloads.jsp), ImmPort database (https://www.immport.org/), InnateDB database (https://www.innatedb.com), miRcode (http://www.mircode.org/) and DIANA-LncBase (https://diana.e-ce.uth.gr/lncbasev3, version 3.0) databases. 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For the dataset GSE102485, the GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) platform was used in this study to identify differentially expressed mRNAs."}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "ble (including P-value, fold change, gene annotation, etc"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}], "targets": [], "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: deseq2."}, "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": ["GSE160306", "GSE160308", "GSE102485"], "resolved_accessions": ["GSE160306", "GSE160308", "GSE102485"], "statements": ["The datasets generated during and/or analysed during the current study are available in the National Institutes of Health (NIH)-National Center for Biotechnology Information (NCBI)-Gene Expression Omnibus (GEO) databases (https:/www.ncbi.nlm.nih.gov/gds/) with accession numbers GSE160306, GSE160308 and GSE102485, xCell (xCell, http://xCell.ucsf.edu/), ImmuCellAI (ImmuCellAI, http://bioinfo.life.hust.edu.cn/ImmuCellAI), Metascape (Metascape, a gene annotation & analysis resource, http://metascape.org, version 3.5), STRING database (STRING, https://string-db.org/), Cytoscape software (Cytoscape, https://cytoscape.org/), GSEA (http://software.broadinstitute.org/gsea/index.jsp), Molecular Signatures Database (http://www.gsea-msigdb.org/gsea/downloads.jsp), ImmPort database (https://www.immport.org/), InnateDB database (https://www.innatedb.com), miRcode (http://www.mircode.org/) and DIANA-LncBase (https://diana.e-ce.uth.gr/lncbasev3, version 3.0) databases. All data generated and analyzed in this study can be found in these databases."], "basis": "The paper names GSE160306, GSE160308, GSE102485 in Gene Expression Omnibus (GEO) 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:39402134", "data:geo:GSE102485"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102485"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:35:02Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12335, "completion_tokens": 2521, "cached_tokens": 264}}, "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:39402134", "type": "paper", "label": "pmid:39402134"}, {"id": "source:pmid:39402134", "type": "manuscript", "label": "PMID 39402134 full text"}, {"id": "data:geo:GSE102485", "type": "dataset", "label": "GEO GSE102485"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39402134", "type": "paper", "label": "pmid:39402134"}, {"id": "source:pmid:39402134", "type": "manuscript", "label": "PMID 39402134 full text"}, {"id": "data:geo:GSE102485", "type": "dataset", "label": "GEO GSE102485"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39402134", "type": "extraction", "used": ["source:pmid:39402134"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102485", "type": "accession_resolution", "used": ["data:geo:GSE102485"], "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:39402134", "parent_hash": "sha256:e1149bb524b83d59d11d835d7c5002cbb6d0d36afea348fe19db8d7e6b5445b2", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE102485 licence not read", "asset:data:geo:GSE102485 not downloaded", "asset:data:geo:GSE160306 licence not read", "asset:data:geo:GSE160306 not downloaded", "asset:data:geo:GSE160308 licence not read", "asset:data:geo:GSE160308 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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 datasets GSE160306 and GSE160308 were of high-throughput sequencing count data, so the R package DESeq2 (version 1.32.0) was used for the difference analysis of the 2 datasets to obtain the DE-mRNAs, DE-miRNAs, and DE-lncRNAs between the DR group and the control group33. 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