Comprehensive analysis and identification of key genes and signaling pathways in the occurrence and metastasis of cutaneous melanoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33240619", "kind": "science-record", "revision": 7, "content_hash": "sha256:316f33555c4f0fbc0799ca977ac92d0f50ee08361a70f975724c6dc0eadef87d", "created_at": "2026-11-01T15:41:17Z", "updated_at": "2026-11-01T22:02:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis and identification of key genes and signaling pathways in the occurrence and metastasis of cutaneous melanoma.", "doi": "10.7717/peerj.10265", "pmid": "33240619", "authors": ["Hanying Dai", "Lihuang Guo", "Mingyue Lin", "Zhenbo Cheng", "Jiancheng Li", "Jinxia Tang", "Xisha Huan", "Yue Huang", "Keqian Xu"], "journal": "PeerJ", "year": 2020, "abstract": "BACKGROUND: Melanoma is a malignant tumor of melanocytes, and the incidence has increased faster than any other cancer over the past half century. Most primary melanoma can be cured by local excision, but metastatic melanoma has a poor prognosis. Cutaneous melanoma (CM) is prone to metastasis, so the research on the mechanism of melanoma occurrence and metastasis will be beneficial to diagnose early, improve treatment, and prolong life survival. In this study, we compared the gene expression of normal skin (N), primary cutaneous melanoma (PM) and metastatic cutaneous melanoma (MM) in the Gene Expression Omnibus (GEO) database. Then we identified the key genes and molecular pathways that may be involved in the development and metastasis of cutaneous melanoma, thus to discover potential markers or therapeutic targets.\nMETHODS: Three gene expression profiles (GSE7553, GSE15605 and GSE46517) were downloaded from the GEO database, which contained 225 tissue samples. R software identified the differentially expressed genes (DEGs) between pairs of N, PM and MM samples in the three sets of data. Subsequently, we analyzed the gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of the DEGs, and constructed a protein-protein interaction (PPI) network. MCODE was used to seek the most important modules in PPI network, and then the GO function and KEGG pathway of them were analyzed. Finally, the hub genes were calculated by the cytoHubba in Cytoscape software. The Cancer Genome Atlas (TCGA) data were analyzed using UALCAN and GEPIA to validate the hub genes and analyze the prognosis of patients.\nRESULTS: A total of 134, 317 and 147 DEGs were identified between N, PM and MM in pair. GO functions and KEGG pathways analysis results showed that the upregulated DEGs mainly concentrated in cell division, spindle microtubule, protein kinase activity and the pathway of transcriptional misregulation in cancer. The downregulated DEGs occurred in epidermis development, extracellular exosome, structural molecule activity, metabolic pathways and p53 signaling pathway. The PPI network obtained the most important module, whose GO function and KEGG pathway were enriched in oxidoreductase activity, cell division, cell exosomes, protein binding, structural molecule activity, and metabolic pathways. 14, 18 and 18 DEGs were identified respectively as the hub genes between N, PM and MM, and TCGA data confirmed the expression differences of hub genes. In addition, the overall survival curve of hub genes showed that the differences in these genes may lead to a significant decrease in overall survival of melanoma patients.\nCONCLUSIONS: In this study, several hub genes were found from normal skin, primary melanoma and metastatic melanoma samples. These hub genes may play an important role in the production, invasion, recurrence or death of CM, and may provide new ideas and potential targets for its diagnosis or treatment.", "claims": [{"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nRaw data are available at figshare: Dai, Hanying (2020): Supplemental files. figshare. Online resource. https://doi.org/10.6084/m9.figshare.13019600.v1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33240619", "locator": "sections[25] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nRaw data are available at figshare: Dai, Hanying (2020): Supplemental files. figshare. 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the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7680623", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:33240619:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b5371cafefa83f4531324eb68ea6de2c27eb2305c87369332ca92149d2818fae", "bytes": 546, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#table-1", "version": null, "note": "The information of GEO dataset and DEGs.", "structure": {"pmcid": "PMC7680623", "section_index": 9, "section_title": "Identification of DEGs", "row_count": 5, "column_count": 8}, "table": {"label": "Table 1", "caption": "The information of GEO dataset and DEGs.", "rows": [["GEO datasets", "Platform", "Normal skin (N)", "Primary melanoma (PM)", "Metastatic melanoma (MM)", "Differentially expressed genes (DEGs)"], ["", "", "", "", "", "PM and N", "MM and N", "MM and PM"], ["GSE7553", "GPL570", "4", "16", "40", "843", "1129", "929"], ["GSE15605", "GPL570", "16", "46", "12", "2605", "2829", "1560"], ["GSE46517", "GPL96", "8", "31", "52", "668", "813", "2466"]], "row_count": 5, "column_count": 8, "numeric_cells": 24, "header_rows": 2, "locator": "section[9]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:33240619:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:82a04cdcca37b70ebe735bb947a037d608b23cbf61aaa376ca3b8410d6e72a3b", "bytes": 650, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#table-2", "version": null, "note": "The hub genes among normal skin, primary cutaneous melanoma and metastatic cutaneous melanoma samples.", "structure": {"pmcid": "PMC7680623", "section_index": 12, "section_title": "Hub gene selection and analysis", "row_count": 3, "column_count": 4}, "table": {"label": "Table 2", "caption": "The hub genes among normal skin, primary cutaneous melanoma and metastatic cutaneous melanoma samples.", "rows": [["", "PM and N", "MM and N", "MM and PM"], ["Upregulated", "MMP9, MMP1", "AURKA, CCNB1, TPX2", ""], ["Downregulated", "KRT19, BMP2, HMGCS2, KLF4, EPHB3, EFNA3, PIP, ADH1B, FGFR3, SDC1, CEBPA, EPHB6", "LOR, FLG, JUP, DSC1, SPRR1B, DSG1, DSP, SPRR1A, BUB1B, KRT5, KRT14, CDSN, IVL, DSG3, TGM1", "LOR, IVL, FLG, SPRR1B, DSG3, KRT5, CDSN, TGM1, DSG1, KRT16, SPRR1A, PKP1, KRT14, DSC3, DSP, CSTA, S100A7, DSC1"]], "row_count": 3, "column_count": 4, "numeric_cells": 3, "header_rows": 1, "locator": "section[12]/table-wrap[1]#table-2"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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