Study on differentially expressed genes between stage M and stage MS neuroblastoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36713522", "kind": "science-record", "revision": 4, "content_hash": "sha256:8f9241463abc9ec15562c2de181b60729a0017e68a57f215ca18b93dcc1297a7", "created_at": "2026-11-01T19:01:16Z", "updated_at": "2026-11-01T22:51:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Study on differentially expressed genes between stage M and stage MS neuroblastoma.", "doi": "10.3389/fonc.2022.1083570", "pmid": "36713522", "authors": ["Yuying Wu", "Jun Zhang"], "journal": "Frontiers in oncology", "year": 2022, "abstract": "Objective: To search for the DEGs between stage MS NB and stage M NB and speculate the possible mechanism of spontaneous regression of stage MS NB.\nMaterials and methods: The NB datasets GSE49710 and GSE45547 in the GEO database were selected to screen the DEGs between children with NB stage MS vs. stage M, < 18 months. GO enrichment and KEGG pathway analysis of DEGs was performed using DAVID. The intersecting genes among DEGs and RCD-related genes were selected, and their survival roles and functions were assessed. We then used the collected clinical samples to validate the expression of these genes at the protein level using IHC methods and further analysis to explore their role.\nResults: BIRC5, SLCO4A1, POPDC3, and HK2 were found to be downregulated in stage MS NB and related to apoptosis. BIRC5 and HK2 also participate in autophagy. The TF gene is upregulated in stage MS NB and related to ferroptosis. The above five genes are closely related to the survival of children with NB. And the expression levels of all five genes at the protein level were verified by IHC to be consistent with the results of the preliminary screening described above.\nConclusion: BIRC5, SLCO4A1, POPDC3, HK2 and TF are expected to become new important indicators to predict the prognosis of NB and can be used as the basis for further explored the benign prognosis and spontaneous regression mechanism of stage MS NB.", "claims": [{"id": "claim-method", "statement": "Using the limma package in R software (version 4.1.2), DEGs between stage MS and stage M (<18 months) were screened in two datasets, and the parameters for judging the difference were set as adj. P < 0.05 and | log2FC | > 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36713522", "locator": "sections[4] \"Identification of shared differentially expressed genes (DEGs)\" paragraph 4", "quote": "Using the limma package in R software (version 4.1.2), DEGs between stage MS and stage M (<18 months) were screened in two datasets, and the parameters for judging the difference were set as adj. P < 0.05 and | log2FC | > 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36713522", "locator": "sections[16] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "BIRC5, SLCO4A1, POPDC3, and HK2 were found to be downregulated in stage MS NB and related to apoptosis, while TF was upregulated in stage MS NB and related to ferroptosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36713522", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "BIRC5, SLCO4A1, POPDC3, and HK2 were found to be downregulated in stage MS NB and related to apoptosis. BIRC5 and HK2 also participate in autophagy. The TF gene is upregulated in stage MS NB and related to ferroptosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "BIRC5, SLCO4A1, POPDC3, and HK2 were found to be downregulated in stage MS NB and related to apoptosis, while TF was upregulated in stage MS NB and related to ferroptosis.", "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:36713522"], "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:GSE45547"], "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:GSE45547"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36713522", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2022.1083570", "sha256": "sha256:9099cbd8e88c611f5f19085f5b2af38a2d467ad8c8dc0baf31ba0bb271c6add0", "bytes": 23581, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2022.1083570", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9880530", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE45547", "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=GSE45547", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45547", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. 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P < 0.05 and | log2FC | > 1."}}, {"id": "method-2", "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-3", "family": "image_quantification", "specific": "densitometry", "label": "Image analysis / quantification", "dsl_operations": ["segment_objects", "quantify_intensity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["image_stack"], "evidence": {"score": 0.8, "band": "high", "quote": "Optical Density"}}], "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: 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": ["GSE49710", "GSE45547"], "resolved_accessions": ["GSE49710", "GSE45547"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."], "basis": "The paper names GSE49710, GSE45547 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:36713522", "data:geo:GSE45547"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE45547"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:25:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 7483, "completion_tokens": 2638, "cached_tokens": 128}}, "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:36713522", "type": "paper", "label": "pmid:36713522"}, {"id": "source:pmid:36713522", "type": "manuscript", "label": "PMID 36713522 full text"}, {"id": "data:geo:GSE45547", "type": "dataset", "label": "GEO GSE45547"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36713522", "type": "paper", "label": "pmid:36713522"}, {"id": "source:pmid:36713522", "type": "manuscript", "label": "PMID 36713522 full text"}, {"id": "data:geo:GSE45547", "type": "dataset", "label": "GEO GSE45547"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36713522", "type": "extraction", "used": ["source:pmid:36713522"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE45547", "type": "accession_resolution", "used": ["data:geo:GSE45547"], "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:36713522", "parent_hash": "sha256:b0e66d4df3932cb02a2ffa924c397f325e2608ea476f1c1323f8caca304aef20", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE45547 licence not read", "asset:data:geo:GSE45547 not downloaded", "asset:data:geo:GSE49710 licence not read", "asset:data:geo:GSE49710 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on of these genes at the protein level using IHC methods and further analysis to explore thei", "genes at the protein level were verified by IHC to be consistent with the results of the pre", "sults are visualized. Clinical materials and immunohistochemistry (IHC) To determine DEGs expression in NB, we", "Clinical materials and immunohistochemistry (IHC) To determine DEGs expression in NB, we perf"], "order_basis": "paper_text_order:674", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["downregulated in stage MS NB and related to apoptosis. BIRC5 and HK2 also participate in autophagy"], "order_basis": "paper_text_order:833", "id": "assay:2"}, {"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": ["Using the limma package in R software (version 4.1.2), DEGs between stage MS and stage M (<18 months) were screened in two datasets, and the parameters for judging the difference were set as adj. P < 0.05 and | log2FC | > 1."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}