The potential mechanisms of neuroblastoma in children based on bioinformatics big data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36643678", "kind": "science-record", "revision": 4, "content_hash": "sha256:016a636a5f76cede01b34d4d9fcaf917a2b20b937bc69a8f2ccc36eab152c3d9", "created_at": "2026-11-01T19:01:12Z", "updated_at": "2026-11-01T22:51:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The potential mechanisms of neuroblastoma in children based on bioinformatics big data.", "doi": "10.21037/tp-22-504", "pmid": "36643678", "authors": ["Ze-Fu Chen", "Li-Zhen Wu", "Ze-Ting Chen", "Liang-Ju Su", "Ce-Jun Fu"], "journal": "Translational pediatrics", "year": 2022, "abstract": "Background: In recent years, miRNAs have become a research hotspot, which is related to the occurrence and development of a variety of malignant tumors, but there are few studies in neuroblastoma. In this study, the differentially expressed microRNAs (miRNAs) in neuroblastoma were identified and analyzed using bioinformatics, and their biological functions and related signaling pathways were examined.\nMethods: The neuroblastoma miRNA chip GSE121513 was obtained from the Gene Expression Omnibus (GEO) database and the data of 95 neuroblastoma samples and normal fetal adrenal neuroblastoma samples were analyzed to screen the differential miRNAs. The target genes of the differentially expressed miRNAs were predicted using |log fold change (FC)| ≥4. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were performed to construct a protein-protein interaction network and identify the core target genes.\nResults: A total of 91 differentially expressed miRNAs were identified (P<0.05, |logFC| ≥1), including 52 upregulated and 39 downregulated miRNAs. The target genes of the differential miRNAs (P<0.05, |logFC| ≥4) were pretested, and 602 target genes were obtained. Functional analysis showed that these genes were mainly located in the extracellular matrix region of proteins, and were involved in the negative regulation of cytoplasmic translation, mRNA 3'-untranslated region (UTR) binding, and binding to nucleic acid to inhibit the activity of translation factors. They were also involved in RNA degradation, adhesion pathways, and the phosphatidylinositol-3-kinase (PI3K)-Akt signaling pathway. Ten key target genes were identified via protein interaction network screening.\nConclusions: The differential miRNAs may be related to the occurrence of neuroblastoma were screened.", "claims": [{"id": "claim-method", "statement": "The Model.matrix function in the LimmA program package was used to define groups, the lmFit function was used to establish linear models, and the eBayes function was used to conduct Bayes test for multiple test correction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36643678", "locator": "sections[5] \"Data set arrangement and differential expression analysis\" paragraph 2", "quote": "The Model.matrix function in the LimmA program package was used to define groups, the lmFit function was used to establish linear models, and the eBayes function was used to conduct Bayes test for multiple test correction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene chip numbered GSE121513 was downloaded from the GEO database, including 117 samples in the dataset. The miRNA expression in 8 embryonic stem cell lines, 7 normal fetal adrenal NB samples, 7 normal fetal adrenal cortical samples, and 95 NB samples were included.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36643678", "locator": "sections[4] \"Data sources and methods\" paragraph 2", "quote": "The gene chip numbered GSE121513 was downloaded from the GEO database, including 117 samples in the dataset. The miRNA expression in 8 embryonic stem cell lines, 7 normal fetal adrenal NB samples, 7 normal fetal adrenal cortical samples, and 95 NB samples were included."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 91 differentially expressed miRNAs were identified (P<0.05, |logFC| ≥1), including 52 upregulated and 39 downregulated miRNAs.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "A total of 91 differentially expressed miRNAs were identified (P<0.05, |logFC| ≥1), including 52 upregulated and 39 downregulated miRNAs."}, "evidence": [{"asset": "source:pmid:36643678", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 91 differentially expressed miRNAs were identified (P<0.05, |logFC| ≥1), including 52 upregulated and 39 downregulated miRNAs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 91 differentially expressed miRNAs were identified (P<0.05, |logFC| ≥1), including 52 upregulated and 39 downregulated miRNAs.", "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:36643678"], "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:36643678", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tp-22-504", "sha256": "sha256:972ae50d324594fc1ae27d9c9c0dfcabc232878b61e1d3f18d2be8cca89cfa1c", "bytes": 20035, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tp-22-504", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9834953", "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 gene chip numbered GSE121513 was downloaded from the GEO database, including 117 samples in the dataset. The miRNA expression in 8 embryonic stem cell lines, 7 normal fetal adrenal NB samples, 7 normal fetal adrenal cortical samples, and 95 NB samples were included.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene chip numbered GSE121513 was downloaded from the GEO database, including 117 samples in the dataset. 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