Bioinformatics Analysis of Neuroblastoma miRNA Based on GEO Data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34285553", "kind": "science-record", "revision": 8, "content_hash": "sha256:be42dc0cb1c4a05b6596131a69518957263b014746b1521250028be5e35bbfc3", "created_at": "2026-11-01T15:41:44Z", "updated_at": "2026-11-01T22:04:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis of Neuroblastoma miRNA Based on GEO Data.", "doi": "10.2147/PGPM.S312171", "pmid": "34285553", "authors": ["Jiandong Shi", "Piaoyan Zhang", "Huarong Su", "Lingyi Cai", "Liang Zhao", "Haixia Zhou"], "journal": "Pharmacogenomics and personalized medicine", "year": 2021, "abstract": "OBJECTIVE: To analyze the changes in downstream genes, signaling pathways, and proteins based on the difference of microRNA (miRNA) expression in neuroblastoma (NB).\nMETHODS: GSE128004 second-generation sequencing expression data were downloaded from GEO, and Limma package of R language was used to analyze differential expression, and a volcano map and heat map were drawn; the target genes corresponding to the differential miRNA were found using the miWalk web tool, and GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) were performed. The key genes were identified and verified in the TCGA database.\nRESULTS: A total of 34 differentially expressed miRNAs were screened out. Among them, 22 up-regulated miRNAs predicted 1163 target genes and 12 down-regulated miRNAs predicted 1474 target genes. Target genes were enriched and analyzed by KEGG to find the FOXO signal pathway, mTOR signal pathway, AMPK signal pathway, and other signal pathways. After GO analysis, axon formation, regulation of chemical synaptic transmitters, regulation of nerve synapses, regulation of cross-synaptic signals, and other physiological processes were assessed. A total of 16 key genes were obtained by PPI analysis, and the survival analysis of TP53 and ATM genes verified in the TCGA database showed statistical significance.\nCONCLUSION: The 34 differential miRNAs may be related to the occurrence and development of NB. TP53 and ATM are related to the prognosis of NB. The role and mechanism of TP53 and ATM in NB need to be further verified.", "claims": [{"id": "claim-data-access", "statement": "The original data of microRNA second-generation sequencing were collected from the GEO database (https://www.ncbi.nlm.nih.gov/gds). The ID number of the second-generation sequencing data is GSE128004, and the sequencing platform was GPL23227 BGISEQ-500 (Homo sapiens). The sequencing samples were collected from the peripheral blood of 15 children with NB and 3 healthy controls, including 15 NB samples (GSM3660254-GSM3660268) and 3 control samples (GSM3660269-GSM3660271).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34285553", "locator": "sections[3] \"Data Collection\" paragraph 2", "quote": "The original data of microRNA second-generation sequencing were collected from the GEO database (https://www.ncbi.nlm.nih.gov/gds). The ID number of the second-generation sequencing data is GSE128004, and the sequencing platform was GPL23227 BGISEQ-500 (Homo sapiens). The sequencing samples were collected from the peripheral blood of 15 children with NB and 3 healthy controls, including 15 NB samples (GSM3660254-GSM3660268) and 3 control samples (GSM3660269-GSM3660271)."}], "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:34285553"], "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:GSE128004"], "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:GSE128004"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34285553", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/PGPM.S312171", "sha256": "sha256:5d3c8eaf2797f2c06dca81a1a5beb26feff6ebfa75b2c1773ca8f76cda57acfb", "bytes": 16089, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/PGPM.S312171", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8286151", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE128004", "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=GSE128004", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE128004", "version": null, "note": "The original data of microRNA second-generation sequencing were collected from the GEO database (https://www.ncbi.nlm.nih.gov/gds). 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The sequencing samples were collected from the peripheral blood of 15 children with NB and 3 healthy controls, including 15 NB samples (GSM3660254-GSM3660268) and 3 control samples (GSM3660269-GSM3660271).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3660254", "GSM3660255", "GSM3660256", "GSM3660257", "GSM3660258", "GSM3660259", "GSM3660260", "GSM3660261", "GSM3660262", "GSM3660263", "GSM3660264", "GSM3660265", "GSM3660266", "GSM3660267", "GSM3660268", "GSM3660269", "GSM3660270", "GSM3660271"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "23227", "taxon": "Homo sapiens", "title": "Exosomal hsa-miR199a-3p promotes  proliferation and metastasis in  neuroblastoma", "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:34285553:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8969d86f84f3e8fc3f86e3e8284d86072fefd98281d71bbd6e944941e0200f98", "bytes": 1820, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t0001", "version": null, "note": "Differentially Expressed miRNAs", "structure": {"pmcid": "PMC8286151", "section_index": 10, "section_title": "Analysis of Differentially Expressed Genes", "row_count": 35, "column_count": 4}, "table": {"label": "Table 1", "caption": "Differentially Expressed miRNAs", "rows": [["", "LogFC", "P.Value", "Change"], ["hsa-miR-877-5p", "6.035876", "4.22E-05", "UP"], ["hsa-miR-7704", "5.846523", "0.000203", "UP"], ["hsa-miR-127-3p", "3.32826", "0.000308", "UP"], ["hsa-miR-369-5p", "3.068657", "0.00172", "UP"], ["hsa-miR-654-5p", "3.769141", "0.004878", "UP"], ["hsa-miR-1468-5p", "3.233108", "0.00564", "UP"], ["hsa-miR-132-5p", "3.147397", "0.006992", "UP"], 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