Bioinformatics Analysis Identifies MicroRNAs and Target Genes Associated with Prognosis in Patients with Melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31621692", "kind": "science-record", "revision": 8, "content_hash": "sha256:f8a0f1179309c769f07369bfe7ad848966782ee8dbde56e10c29ebe70cfcb21a", "created_at": "2026-11-01T15:40:50Z", "updated_at": "2026-11-01T22:00:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis Identifies MicroRNAs and Target Genes Associated with Prognosis in Patients with Melanoma.", "doi": "10.12659/MSM.917082", "pmid": "31621692", "authors": ["Qiao Li", "Li-Yu Zhang", "Shuang Wu", "Chen Huang", "Juan Liu", "Ping Wang", "Yuan Cao"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2019, "abstract": "BACKGROUND Melanoma of the skin can be associated with early metastases and poor prognosis. This study aimed to identify microRNAs (miRNAs) and target genes associated with prognosis in melanoma using bioinformatics analysis. MATERIAL AND METHODS The Gene Expression Omnibus (GEO) database identified the microarray dataset GSE20994. Differentially expressed miRNAs (DE-miRNAs) were first identified using R language software and validated by GEO2R. Potential target genes of DE-miRNAs were screened, and their targets and prognostic role were evaluated in the miRTarBase database. Pathway enrichment and functional annotation analysis for target genes were established using the DAVID database. miRNA-hub gene networks and protein-protein interaction (PPI) networks were constructed and visualized using the STRING database and Cytoscape. Kaplan-Meier survival curves were constructed using transcriptome and survival data from the UALCAN web tool. RESULTS There were 132 upregulated and 134 down-regulated DE-miRNAs identified from human melanoma samples. From the top three upregulated miRNAs, there were 580 potential predicted target genes, and from the top three down-regulated miRNAs, there 543 potential predicted target genes. miR-300 was upregulated, and miR-629 was down-regulated in melanoma. Two pivotal bub genes, TP53 and GAPDH, were identified in the PPI network. Five out of ten hub genes were modulated by upregulated miR-580, and five by miR-629. Increased mRNA expression of DAPK2 was associated with increased OS, and increased mRNA expression of SKCM, TECPR2, and ZNF781 were associated with reduced OS. CONCLUSIONS Bioinformatics analysis identified miRNAs and target genes associated with melanoma that may represent potential prognostic and therapeutic biomarkers.", "claims": [{"id": "claim-method", "statement": "Kaplan-Meier survival curves were calculated for the distinct effect of target gene expression on patient survival.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31621692", "locator": "sections[8] \"Kaplan-Meier survival analysis associated with target genes for patients with melanoma\" paragraph 2", "quote": "Kaplan-Meier survival curves were calculated for the distinct effect of target gene expression on patient survival."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray dataset GSE20994 was identified based on the GPL9040 platform (febit Homo sapiens miRBase 13.0), which included samples from 35 patients with melanoma and 22 normal controls, was downloaded and used for this study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31621692", "locator": "sections[3] \"Microarray data in cases of melanoma\" paragraph 2", "quote": "The microarray dataset GSE20994 was identified based on the GPL9040 platform (febit Homo sapiens miRBase 13.0), which included samples from 35 patients with melanoma and 22 normal controls, was downloaded and used for this study."}], "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:31621692"], "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:GSE20994"], "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:GSE20994"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31621692", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.917082", "sha256": "sha256:62bd4cf85fb38eee73bca210df073955670e71a56d70ed1f7910c059e12947a2", "bytes": 29861, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.917082", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6820336", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20994", "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=GSE20994", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20994", "version": null, "note": "The microarray dataset GSE20994 was identified based on the GPL9040 platform (febit Homo sapiens miRBase 13.0), which included samples from 35 patients with melanoma and 22 normal controls, was downloaded and used for this study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray dataset GSE20994 was identified based on the GPL9040 platform (febit Homo sapiens miRBase 13.0), which included samples from 35 patients with melanoma and 22 normal controls, was downloaded and used for this study.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM524757", "GSM524758", "GSM524759", "GSM524760", "GSM524761", "GSM524762", "GSM524763", "GSM524764", "GSM524765", "GSM524766", "GSM524767", "GSM524768", "GSM524769", "GSM524770", "GSM524771", "GSM524772", "GSM524773", "GSM524774", "GSM524775", "GSM524776", "GSM524777", "GSM524778", "GSM524779", "GSM524780", "GSM524781", "GSM524782", "GSM524783", "GSM524784", "GSM524785", "GSM524786", "GSM524787", "GSM524788", "GSM524789", "GSM524790", "GSM524791", "GSM524792", "GSM524793", "GSM524794", "GSM524795", "GSM524796", "GSM524797", "GSM524798", "GSM524799", "GSM524800", "GSM524801", "GSM524802", "GSM524803", "GSM524804", "GSM524805", "GSM524806", "GSM524807", "GSM524808", "GSM524809", "GSM524810", "GSM524811", "GSM524812", "GSM524813"], "sample_count": 57, "group_sizes": null, "group_sizes_basis": null, "platform": "9040", "taxon": "Homo sapiens", "title": "Melanoma Cancer miRNA Blood Profiles", "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:31621692:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c78a6270fb1f2e3126cb72bf42c423d284f194e40661dbe993a0f09a84ee1c01", "bytes": 2368, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t1-medscimonit-25-7784", "version": null, "note": "Top ten up-regulated and down-regulated differentially expressed miRNAs between melanoma and normal control.", "structure": {"pmcid": "PMC6820336", "section_index": 10, "section_title": "Identification of differentially expressed microRNAs (DE-miRNAs) and the prognostic value of target genes in melanoma", "row_count": 21, "column_count": 8}, "table": {"label": "Table 1", "caption": "Top ten up-regulated and down-regulated differentially expressed miRNAs between melanoma and normal control.", "rows": [["miRNAs", "Log2FC", "Average expression", "t", "P value", "adj. 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