Bioinformatics analysis of lncRNA‑associated ceRNA network in melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33854593", "kind": "science-record", "revision": 9, "content_hash": "sha256:997a36fa3bcd2a91efc841909245340692c9e588cda668bf7cfe5641258b5d6f", "created_at": "2026-11-01T15:41:32Z", "updated_at": "2026-11-01T22:46:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of lncRNA‑associated ceRNA network in melanoma.", "doi": "10.7150/jca.51851", "pmid": "33854593", "authors": ["Yi Ding", "Min Li", "Tuersong Tayier", "MeiLin Zhang", "Long Chen", "ShuMei Feng"], "journal": "Journal of Cancer", "year": 2021, "abstract": "Melanoma is an extremely malignant tumor with early metastasis and high mortality. Little is known about the process of by which melanoma occurs, as its mechanism is very complex and only limited data are available on its long non-coding RNA (lncRNA)-associated competing endogenous RNAs (ceRNAs). The purpose of this study was to screen out potential prognostic molecules and identify a ceRNA network related to the occurrence of melanoma. We screened 169 differentially expressed mRNAs (DEmRNAs) from E-MTAB-1862 and GSE3189; gene ontology (GO) enrichment analysis showed that these genes were closely related to the development of skin. In the protein-protein interaction network, we screened out a total of 19 hub genes. Furthermore, we predicted the microRNAs (miRNAs) that regulate hub genes using the miRWalk database and then intersected these with GSE35579, resulting in nine DEmiRNAs. We also predicted the lncRNAs that regulate the miRNAs using the LncBasev.2 database. According to the ceRNA hypothesis, and based on the intersection of the DElncRNAs with merged GTEx and TCGA data, we obtained 20 DElncRNAs. A total of four DEmRNAs, nine DEmiRNAs, and 20 DElncRNAs were included in the ceRNA network. Based on Cox stepwise regression and survival analysis, we identified five biomarkers, ZSCAN16-AS1, LINC00520, XIST, DTL, and let-7a-5p, and obtained risk scores. The results showed that most of the differentially expressed genes were related to epithelial-mesenchymal transition (EMT) in melanoma. Finally, we obtained a LINC00520/let-7a-5p/DTL molecular regulatory network. These results suggest that ceRNA networks have an important role in evaluating the prognosis of patients with melanoma and provide a new experimental basis for exploring the EMT process in the development of melanoma.", "claims": [{"id": "claim-data-access", "statement": "We downloaded two expression profile datasets, E-MTAB-1862 and GSE3189, from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) and the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database, respectively. The E-MTAB-1862 dataset consisted of 11 nevus samples and 21 melanoma samples 8, based on the A-AFFY-44-Affymetrix GeneChip Human Genome U133 Plus 2.0 array.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33854593", "locator": "sections[3] \"Data preparation\" paragraph 2", "quote": "We downloaded two expression profile datasets, E-MTAB-1862 and GSE3189, from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) and the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database, respectively. The E-MTAB-1862 dataset consisted of 11 nevus samples and 21 melanoma samples 8, based on the A-AFFY-44-Affymetrix GeneChip Human Genome U133 Plus 2.0 array."}], "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:33854593"], "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:E-MTAB-1862"], "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:E-MTAB-1862"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33854593", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.51851", "sha256": "sha256:231fbc10e0df12484be7d222c18b16456ef85cdd25cf1a418de90bf0a1484216", "bytes": 26575, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/jca.51851", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8040875", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:E-MTAB-1862", "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=E-MTAB-1862", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "E-MTAB-1862", "version": null, "note": "We downloaded two expression profile datasets, E-MTAB-1862 and GSE3189, from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) and the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database, respectively. The E-MTAB-1862 dataset consisted of 11 nevus samples and 21 melanoma samples 8, based on the A-AFFY-44-Affymetrix GeneChip Human Genome U133 Plus 2.0 array.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded two expression profile datasets, E-MTAB-1862 and GSE3189, from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) and the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database, respectively. The E-MTAB-1862 dataset consisted of 11 nevus samples and 21 melanoma samples 8, based on the A-AFFY-44-Affymetrix GeneChip Human Genome U133 Plus 2.0 array.", "access_statement_kind": "repository_route_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:28:57Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE3189", "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=GSE3189", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE3189", "version": null, "note": "We downloaded two expression profile datasets, E-MTAB-1862 and GSE3189, from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) and the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database, respectively. The E-MTAB-1862 dataset consisted of 11 nevus samples and 21 melanoma samples 8, based on the A-AFFY-44-Affymetrix GeneChip Human Genome U133 Plus 2.0 array.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded two expression profile datasets, E-MTAB-1862 and GSE3189, from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) and the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database, respectively. 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The E-MTAB-1862 dataset consisted of 11 nevus samples and 21 melanoma samples 8, based on the A-AFFY-44-Affymetrix GeneChip Human Genome U133 Plus 2.0 array.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded two expression profile datasets, E-MTAB-1862 and GSE3189, from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) and the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database, respectively. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["E-MTAB-1862", "GSE3189", "GSE35579"], "resolved_accessions": ["E-MTAB-1862", "GSE3189", "GSE35579"], "statements": ["We downloaded two expression profile datasets, E-MTAB-1862 and GSE3189, from the European Bioinformatics Institute ArrayExpress database (http://www.ebi.ac.uk/arrayexpress) and the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) database, respectively. The E-MTAB-1862 dataset consisted of 11 nevus samples and 21 melanoma samples 8, based on the A-AFFY-44-Affymetrix GeneChip Human Genome U133 Plus 2.0 array."], "basis": "The paper names E-MTAB-1862, GSE3189, GSE35579 in European Bioinformatics Institute ArrayExpress database and the accession resolves in the repository. 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