Characterization of long noncoding RNA and messenger RNA signatures in melanoma tumorigenesis and metastasis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28225791", "kind": "science-record", "revision": 9, "content_hash": "sha256:88fab72a74e8b08b9f70d1ba250fe0731c67caab874e82b0e088c9da827334c4", "created_at": "2026-11-01T15:40:22Z", "updated_at": "2026-11-01T22:42:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterization of long noncoding RNA and messenger RNA signatures in melanoma tumorigenesis and metastasis.", "doi": "10.1371/journal.pone.0172498", "pmid": "28225791", "authors": ["Siqi Wang", "Wenliang Fan", "Bing Wan", "Mengqi Tu", "Feng Jin", "Fang Liu", "Haibo Xu", "Ping Han"], "journal": "PloS one", "year": 2017, "abstract": "The incidence of melanoma, the most aggressive and life-threatening form of skin cancer, has significantly risen over recent decades. Therefore, it is essential to identify the mechanisms that underlie melanoma tumorigenesis and metastasis and to explore novel and effective melanoma treatment strategies. Accumulating evidence s uggests that aberrantly expressed long noncoding RNAs (lncRNAs) have vital functions in multiple cancers. However, lncRNA functions in melanoma tumorigenesis and metastasis remain unclear. In this study, we investigated lncRNA and messenger RNA (mRNA) expression profiles in primary melanomas, metastatic melanomas and normal skin samples from the Gene Expression Omnibus database. We used GSE15605 as the training set (n = 74) and GSE7553 as the validation set (n = 58). In three comparisons (primary melanoma versus normal skin, metastatic melanoma versus normal skin, and metastatic melanoma versus primary melanoma), 178, 295 and 48 lncRNAs and 847, 1758, and 295 mRNAs were aberrantly expressed, respectively. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses to examine the differentially expressed mRNAs, and potential core lncRNAs were predicted by lncRNA-mRNA co-expression networks. Based on our results, 15 lncRNAs and 144 mRNAs were significantly associated with melanoma tumorigenesis and metastasis. A subsequent analysis suggested a critical role for a five-lncRNA signature during melanoma tumorigenesis and metastasis. Low expression of U47924.27 was significantly associated with decreased survival of patients with melanoma. To the best of our knowledge, this study is the first to explore the expression patterns of lncRNAs and mRNAs during melanoma tumorigenesis and metastasis by re-annotating microarray data from the Gene Expression Omnibus (GEO) microarray dataset. These findings reveal potential roles for lncRNAs during melanoma tumorigenesis and metastasis and provide a rich candidate reservoir for future studies.", "claims": [{"id": "claim-method", "statement": "Differentially expressed lncRNAs and mRNAs that were involved in three comparisons were identified by the limma package [26] in the R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28225791", "locator": "sections[5] \"Microarray data processing and differential expression analysis\" paragraph 2", "quote": "Differentially expressed lncRNAs and mRNAs that were involved in three comparisons were identified by the limma package [26] in the R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "PM and metastatic melanoma (MM) gene expression data were obtained from publicly available GEO databases (GSE15605 and GSE7553).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28225791", "locator": "sections[3] \"GEO gene expression data\" paragraph 2", "quote": "PM and metastatic melanoma (MM) gene expression data were obtained from publicly available GEO databases (GSE15605 and GSE7553)."}], "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:28225791"], "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. 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