Identification of Keratinocyte Differentiation-Involved Genes for Metastatic Melanoma by Gene Expression Profiles.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35003328", "kind": "science-record", "revision": 5, "content_hash": "sha256:bb4f8c06dd20faa56dc5dea97a963620e208b211ae13d7eb385e94a4f4f62114", "created_at": "2026-11-01T17:36:43Z", "updated_at": "2026-11-01T22:48:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Keratinocyte Differentiation-Involved Genes for Metastatic Melanoma by Gene Expression Profiles.", "doi": "10.1155/2021/9652768", "pmid": "35003328", "authors": ["Kezhu Li", "Shu Guo", "Shuang Tong", "Qiang Sun", "Shifeng Jin", "Bingran Qi", "Yining Shao", "Nan Xu"], "journal": "Computational and mathematical methods in medicine", "year": 2021, "abstract": "BACKGROUND: Melanoma is the deadliest type of skin cancer. Until now, its pathological mechanisms, particularly the mechanism of metastasis, remain largely unknown. Our study on the identification of genes in association with metastasis for melanoma provides a novel understanding of melanoma.\nMETHODS: From the Gene Expression Omnibus (GEO) database, the gene expression microarray datasets GSE46517, GSE7553, and GSE8401 were downloaded. We made use of R aiming at analyzing the differentially expressed genes (DEGs) between metastatic and nonmetastatic melanoma. R was also used in differentially expressed miRNA (DEM) data mining from GSE18509, GSE19387, GSE24996, GSE34460, GSE35579, GSE36236, and GSE54492 datasets referring to Li's study. Based on the DEG and DEM data, we performed functional enrichment analysis through the application of the DAVID database. Furthermore, we constructed the protein-protein interaction (PPI) network and established functional modules by making use of the STRING database. Through making use of Cytoscape, the PPI results were visualized. We predicted the targets of the DEMs through applying TargetScan, miRanda, and PITA databases and identified the overlapping genes between DEGs and predicted targets, followed by the construction of DEM-DEG pair network. The expressions of these keratinocyte differentiation-involved genes in Module 1 were identified based on the data from TCGA.\nRESULTS: 239 DEGs were screened out in all 3 datasets, which were inclusive of 21 positively regulated genes and 218 negatively regulated genes. Based on these 239 DEGs, we finished constructing the PPI network which was formed from 225 nodes and 846 edges. We finished establishing 3 functional modules. And we analyzed 92 overlapping genes and 26 miRNA, including 11 upregulated genes targeted by 11 negatively regulated DEMs and 81 downregulated genes targeted by 15 positively regulated DEMs. As proof of the differential expression of metastasis-associated genes, eleven keratinocyte differentiation-involved genes, including LOR, EVPL, SPRR1A, FLG, SPRR1B, SPRR2B, TGM1, DSP, CSTA, CDSN, and IVL in Module 1, were obviously downregulated in metastatic melanoma tissue in comparison with primary melanoma tissue based on the data from TCGA.\nCONCLUSION: 239 melanoma metastasis-associated genes and 26 differentially expressed miRNA were identified in our study. The keratinocyte differentiation-involved genes may take part in melanoma metastasis, providing a latent molecular mechanism for this disease.", "claims": [{"id": "claim-method", "statement": "We conducted the DEG and DEM analysis through the application of the limma software package in Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/limma.html) [16] in R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35003328", "locator": "sections[4] \"2.2. Screening DEGs and DEMs\" paragraph 2", "quote": "We conducted the DEG and DEM analysis through the application of the limma software package in Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/limma.html) [16] in R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data analyzed during this study are obtained from published article or are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35003328", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "All data analyzed during this study are obtained from published article or are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 239 melanoma metastasis-associated genes and 26 differentially expressed miRNAs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35003328", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "239 melanoma metastasis-associated genes and 26 differentially expressed miRNA were identified in our study."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 239 melanoma metastasis-associated genes and 26 differentially expressed miRNAs.", "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:35003328"], "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:GSE18509"], "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:GSE18509"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35003328", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/9652768", "sha256": 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