A 16-miRNA Prognostic Model to Predict Overall Survival in Neuroblastoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35846139", "kind": "science-record", "revision": 3, "content_hash": "sha256:f1b5743ba5f88c555fd5fb7a92ebaeddfaa1edbda9956c8f24112501661bb1e9", "created_at": "2026-11-01T18:14:55Z", "updated_at": "2026-11-01T21:28:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A 16-miRNA Prognostic Model to Predict Overall Survival in Neuroblastoma.", "doi": "10.3389/fgene.2022.827842", "pmid": "35846139", "authors": ["Jiepin Wang", "Dong Xiao", "Junxiang Wang"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Neuroblastoma is the most malignant childhood tumor. The outcome of neuroblastoma is hard to predict due to the limitation of prognostic markers. In our study, we constructed a 16-miRNA prognostic model to predict the overall survival of neuroblastoma patients for early diagnosis. A total of 205 DE miRNAs were screened using RNA sequencing data from GSE121513. Lasso Cox regression analysis generated a 16-miRNA signature consisting of hsa-let-7c, hsa-miR-135a, hsa-miR-137, hsa-miR-146a, hsa-miR-149, hsa-miR-15a, hsa-miR-195, hsa-miR-197, hsa-miR-200c, hsa-miR-204, hsa-miR-302a, hsa-miR-331, hsa-miR-345, hsa-miR-383, hsa-miR-93, and hsa-miR-9star. The concordance index of multivariate Cox regression analysis was 0.9, and the area under the curve (AUC) values of 3-year and 5-year survival were 0.92 and 0.943, respectively. The mechanism was further investigated using the TCGA and GSE90689 datasets. Two miRNA-gene interaction networks were constructed among DEGs from two datasets. Functional analysis revealed that immune-related processes were involved in the initiation and metastasis of neuroblastoma. CIBERSORT and survival analysis suggested that lower CD8 T-cell proportion and higher SPTA1 expressions were related to a better prognosis. Our study demonstrated that the miRNA signature may be useful in prognosis prediction and management improvement.", "claims": [{"id": "claim-method", "statement": "The glmnet package and survival package installed in R were used to construct the Lasso Cox model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35846139", "locator": "sections[5] \"miRNA-Related Prognostic Model Establishment\" paragraph 2", "quote": "The glmnet package and survival package installed in R were used to construct the Lasso Cox model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material; further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35846139", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/supplementary material; further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The concordance index of multivariate Cox regression analysis was 0.9, and the area under the curve (AUC) values of 3-year and 5-year survival were 0.92 and 0.943, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35846139", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 205 DE miRNAs were screened using RNA sequencing data from GSE121513."}, {"asset": "source:pmid:35846139", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Lasso Cox regression analysis generated a 16-miRNA signature consisting of hsa-let-7c, hsa-miR-135a, hsa-miR-137, hsa-miR-146a, hsa-miR-149, hsa-miR-15a, hsa-miR-195, hsa-miR-197, hsa-miR-200c, hsa-miR-204, hsa-miR-302a, hsa-miR-331, hsa-miR-345, hsa-miR-383, hsa-miR-93, and hsa-miR-9star."}, {"asset": "source:pmid:35846139", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The concordance index of multivariate Cox regression analysis was 0.9, and the area under the curve (AUC) values of 3-year and 5-year survival were 0.92 and 0.943, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The concordance index of multivariate Cox regression analysis was 0.9, and the area under the curve (AUC) values of 3-year and 5-year survival were 0.92 and 0.943, respectively.", "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:35846139"], "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:GSE121513"], "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:GSE121513"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35846139", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2022.827842", "sha256": "sha256:1d872963a4b6be4f7cde69c53b0bef1ba9d900ba13174a47a037041b63b58fdf", "bytes": 31261, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2022.827842", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9278893", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE121513", "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=GSE121513", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE121513", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material; further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material; further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3438489", "GSM3438490", "GSM3438491", "GSM3438492", "GSM3438493", "GSM3438494", "GSM3438495", "GSM3438496", "GSM3438497", "GSM3438498", "GSM3438499", "GSM3438500", "GSM3438501", "GSM3438502", "GSM3438503", "GSM3438504", "GSM3438505", "GSM3438506", "GSM3438507", "GSM3438508", "GSM3438509", "GSM3438510", "GSM3438511", "GSM3438512", "GSM3438513", "GSM3438514", "GSM3438515", "GSM3438516", "GSM3438517", "GSM3438518", "GSM3438519", "GSM3438520", "GSM3438521", "GSM3438522", "GSM3438523", "GSM3438524", "GSM3438525", "GSM3438526", "GSM3438527", "GSM3438528", "GSM3438529", "GSM3438530", "GSM3438531", "GSM3438532", "GSM3438533", "GSM3438534", "GSM3438535", "GSM3438536", "GSM3438537", "GSM3438538", "GSM3438539", "GSM3438540", "GSM3438541", "GSM3438542", "GSM3438543", "GSM3438544", "GSM3438545", "GSM3438546", "GSM3438547", "GSM3438548", "GSM3438549", "GSM3438550", "GSM3438551", "GSM3438552", "GSM3438553", "GSM3438554", "GSM3438555", "GSM3438556", "GSM3438557", "GSM3438558", "GSM3438559", "GSM3438560", "GSM3438561", "GSM3438562", "GSM3438563", "GSM3438564", "GSM3438565", "GSM3438566", "GSM3438567", "GSM3438568", "GSM3438569", "GSM3438570", "GSM3438571", "GSM3438572", "GSM3438573", "GSM3438574", "GSM3438575", "GSM3438576", "GSM3438577", "GSM3438578", "GSM3438579", "GSM3438580", "GSM3438581", "GSM3438582", "GSM3438583", "GSM3438584", "GSM3438585", "GSM3438586", "GSM3438587", "GSM3438588", "GSM3438589", "GSM3438590", "GSM3438591", "GSM3438592", "GSM3438593", "GSM3438594", "GSM3438595", "GSM3438596", "GSM3438597", "GSM3438598", "GSM3438599", "GSM3438600", "GSM3438601", "GSM3438602", "GSM3438603", "GSM3438604", "GSM3438605"], "sample_count": 117, "group_sizes": null, "group_sizes_basis": null, "platform": "25696", "taxon": "Homo sapiens", "title": "Real-time quantitative PCR miRNA expression data of normal foetal adrenal neuroblasts and cortex cells, neuroblastoma tumors and embryonic stem cells", "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:GSE86889", "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=GSE86889", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE86889", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material; further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material; further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2252099", "GSM2252100", "GSM2252101", "GSM2252102", "GSM2252103", "GSM2252104", "GSM2252105", "GSM2252106", "GSM2252107", "GSM2252108", "GSM2252109", "GSM2252110", "GSM2252111", "GSM2252112", "GSM2252113", "GSM2308356", "GSM2308357", "GSM2308358", "GSM2308359", "GSM2308360", "GSM2308361", "GSM2308362", "GSM2308363", "GSM2308364", "GSM2308365", "GSM2308366", "GSM2308367", "GSM2308368", "GSM2308369", "GSM2308370", "GSM2308371", "GSM2308372", "GSM2308373", "GSM2308374", "GSM2308375"], "sample_count": 35, "group_sizes": null, "group_sizes_basis": null, "platform": "14943", "taxon": "Homo sapiens", "title": "A genome-wide microRNA profiling indicates miR-424-5p and miR-503-5p as regulators of ALK expression in neuroblastoma", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE90689", "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=GSE90689", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE90689", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material; further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material; further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2410432", "GSM2410433", "GSM2410434", "GSM2410435", "GSM2410436", "GSM2410437", "GSM2410438", "GSM2410439", "GSM2410440", "GSM2410441", "GSM2410442", "GSM2410443", "GSM2410444", "GSM2410445", "GSM2410446", "GSM2410447", "GSM2410448", "GSM2410449", "GSM2410450", "GSM2410451", "GSM2410452", "GSM2410453", "GSM2410454", "GSM2410455", "GSM2410456", "GSM2410457", "GSM2410458", "GSM2410459", "GSM2410460", "GSM2410461", "GSM2410462", "GSM2410463", "GSM2410464", "GSM2410465", "GSM2410466", "GSM2410467", "GSM2410468", "GSM2410469", "GSM2410470", "GSM2410471", "GSM2410472", "GSM2410473", "GSM2410474", "GSM2410475", "GSM2410476", "GSM2410477", "GSM2410478", "GSM2410479", "GSM2410480", "GSM2410481", "GSM2410482", "GSM2410483", "GSM2410484", "GSM2410485", "GSM2410486", "GSM2410487", "GSM2410488"], "sample_count": 57, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Children with neuroblastoma show altered erythrocyte’s maturation in bone marrow and decreased number of erythrocytes in peripheral blood", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE121513 not downloaded", "asset:data:geo:GSE121513 licence not read", "asset:data:geo:GSE86889 not downloaded", "asset:data:geo:GSE86889 licence not read", "asset:data:geo:GSE90689 not downloaded", "asset:data:geo:GSE90689 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The glmnet package and survival package installed in R were used to construct the Lasso Cox model."}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE121513", "GSE90689", "GSE86889"], "resolved_accessions": ["GSE121513", "GSE90689", "GSE86889"], "statements": ["The original contributions presented in the study are included in the article/supplementary material; further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE121513, GSE90689, GSE86889 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": ["cox_ph"], "assets": ["source:pmid:35846139", "data:geo:GSE121513"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE121513"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:56:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9428, "completion_tokens": 2368, "cached_tokens": 256}}, "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:35846139", "type": "paper", "label": "pmid:35846139"}, {"id": "source:pmid:35846139", "type": "manuscript", "label": "PMID 35846139 full text"}, {"id": "data:geo:GSE121513", "type": "dataset", "label": "GEO GSE121513"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35846139", "type": "paper", "label": "pmid:35846139"}, {"id": "source:pmid:35846139", "type": "manuscript", "label": "PMID 35846139 full text"}, {"id": "data:geo:GSE121513", "type": "dataset", "label": "GEO GSE121513"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35846139", "type": "extraction", "used": ["source:pmid:35846139"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE121513", "type": "accession_resolution", "used": ["data:geo:GSE121513"], "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:35846139", "parent_hash": "sha256:2e84384e90d2926778fad2f259602409d591a375f26e910f813279a228482f9e", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE121513 licence not read", "asset:data:geo:GSE121513 not downloaded", "asset:data:geo:GSE86889 licence not read", "asset:data:geo:GSE86889 not downloaded", "asset:data:geo:GSE90689 licence not read", "asset:data:geo:GSE90689 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["A total of 205 DE miRNAs were screened using RNA sequencing data from GSE121513. Lasso Cox regression an"], "order_basis": "paper_text_order:356", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The glmnet package and survival package installed in R were used to construct the Lasso Cox model."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}