Identification of Potential Core Genes Between Primary and Metastatic Malignant Melanoma and Analysis of Their Immune Correlation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35046701", "kind": "science-record", "revision": 4, "content_hash": "sha256:094adc248efc9ef24f85a74d2c4c29d9576098ad771153b56932fc47c0097e77", "created_at": "2026-11-01T17:36:46Z", "updated_at": "2026-11-01T22:05:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Potential Core Genes Between Primary and Metastatic Malignant Melanoma and Analysis of Their Immune Correlation.", "doi": "10.2147/IJGM.S338890", "pmid": "35046701", "authors": ["Cong-Li Jia", "Fu Yang", "Rui-Ning Li"], "journal": "International journal of general medicine", "year": 2022, "abstract": "PURPOSE: To identify the potential differential genes between primary and metastatic melanoma, screen out immune-related genes in core genes and analyze their immune correlation, thus searching for the early diagnostic biomarkers of cutaneous malignant melanoma (CMM) and the targets of curbing metastasis.\nMATERIALS AND METHODS: We analyzed two microarray datasets (GSE8401 and GSE46517) derived from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between primary and metastatic melanoma were screened out using the GEO2R tool. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to identify the functions and pathways of DEGs. We analyzed protein-protein interaction of these DEGs based on the Search Tool for the Retrieval of Interacting Genes database and showed by Cytoscape software. In addition, the online Gene Expression Profiling Interactive Analysis tool (GEPIA) was used to analyze the prognostic value of hub genes expressed in metastatic melanoma patients. Immune-related genes in hub genes were screened and further analyzed.\nRESULTS: A total of 178 upregulated DEGs and 4 downregulated DEGs were identified. 23 terms and 4 pathways were confirmed related to metastatic melanoma. Ten hub genes with a high degree of connectivity were found. Overexpression of three hub genes (DSG1, FLG, PKP1) (P<0.01) was associated with metastasis and poor prognosis of CMM. Among them, the patients with overexpression of PKP1 suffered shorter survival. In addition, 2 immune-related genes (EGFR and CDH1) in hub genes were screened out and both of them were related to anti-tumor immunity, although their expression level did not affect the overall survival of CMM patients significantly.\nCONCLUSION: Our study suggests that DSG1, FLG and PKP1 were overexpressed in metastatic melanoma compared with primary melanoma, and overexpression of these three genes was an unfavorable prognostic factor ifor CMM patients, which may indicate that they are associated with promoting metastasis of malignant melanoma. EGFR and CDH1 play a crucial role in anti-tumor immunity for CMM. Further research is needed to explore the value of these genes in the inhibition of metastasis and treatment of CMM.", "claims": [{"id": "claim-method", "statement": "We used GEO2R online analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) to screen the DEGs between metastatic malignant melanoma and primary tumor samples. Genes that matched the cutoff criteria, adjusted P<0.05 and |logFC|≥1.5, were viewed as DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35046701", "locator": "sections[4] \"Differential Genes Screening\" paragraph 2", "quote": "We used GEO2R online analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) to screen the DEGs between metastatic malignant melanoma and primary tumor samples. Genes that matched the cutoff criteria, adjusted P<0.05 and |logFC|≥1.5, were viewed as DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data in this study came from the GEO public database, and the original data had passed the ethical review and obtained the written informed consent of the patients when provided.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35046701", "locator": "sections[17] \"Ethics and Consent Statements\" paragraph 2", "quote": "The data in this study came from the GEO public database, and the original data had passed the ethical review and obtained the written informed consent of the patients when provided."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 178 upregulated DEGs and 4 downregulated DEGs were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35046701", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 178 upregulated DEGs and 4 downregulated DEGs were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 178 upregulated DEGs and 4 downregulated DEGs were identified.", "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:35046701"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The data in this study came from the GEO public database, and the original data had passed the ethical review and obtained the written informed consent of the patients when provided."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:35046701"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:15:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 7596, "completion_tokens": 1195, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35046701", "type": "paper", "label": "pmid:35046701"}, {"id": "source:pmid:35046701", "type": "manuscript", "label": "PMID 35046701 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35046701", "type": "paper", "label": "pmid:35046701"}, {"id": "source:pmid:35046701", "type": "manuscript", "label": "PMID 35046701 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35046701", "type": "extraction", "used": ["source:pmid:35046701"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35046701", "parent_hash": "sha256:f69b506854b53e294f67eb34ef0edc7a691145223f3ab3cb91bb935cea83202c", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["asis. 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