Expression profiling analysis of autophagy-related genes in perineural invasion of cutaneous squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29552123", "kind": "science-record", "revision": 8, "content_hash": "sha256:d3e352dd38cce007db2c636c09eaa899533ba3fbda8e15edc041425b407ae708", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T21:59:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Expression profiling analysis of autophagy-related genes in perineural invasion of cutaneous squamous cell carcinoma.", "doi": "10.3892/ol.2018.7971", "pmid": "29552123", "authors": ["Li-Qiang Zheng", "Shan-Yi Li", "Cheng-Xin Li"], "journal": "Oncology letters", "year": 2018, "abstract": "The aim of the present study was to identify the potential autophagy-related genes and to explore the underlying molecular mechanisms involved in cutaneous squamous cell carcinoma of head and neck (cSCCHN) by bioinformatics analysis. The Gene Expression Omnibus (GEO) series GSE86544 was downloaded from the GEO database. The primary data was generated from cSCCHN with clinical perineural invasion (PNI) and cSCCHN without PNI, and was further analyzed in order to identify differentially expressed genes (DEGs). The results revealed 239 autophagy-related DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed and intersected to investigate the predicted functions of the key DEGs, including hypoxia-inducible factor 1α (HIF1A), mitogen-activated protein kinase 8 (MAPK8), mammalian target of rapamycin (mTOR) and B-cell lymphoma 2 like 1 (BCL2L1). Up and downregulated genes shared one pathway, namely 'pathways in cancer'. Next, the protein-protein interaction (PPI) network of the autophagy-related DEGs was constructed using Cytoscape 3.30 software. HIF1A, MAPK8, mTOR and BCL2L1 were key nodes in the PPI network. Additionally, RAB23 gene expression was positively correlated with HIF1A, MAPK8 and ADP ribosylation factor GTPase activating protein 1 (ARFGAP1), but negatively correlated with mTOR and BCL2L1. The present results suggested that the genes HIF1A, MAPK8, mTOR, BCL2L1 and RAB23 may be associated with and serve as potential therapeutic targets in cSCCHN with clinical PNI.", "claims": [{"id": "claim-method", "statement": "To obtain the P-value, multiple testing corrections were applied with the Benjamini-Hochberg method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29552123", "locator": "sections[5] \"Data preprocessing and analysis of DEGs\" paragraph 2", "quote": "To obtain the P-value, multiple testing corrections were applied with the Benjamini-Hochberg method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray expression profile dataset GSE86544, submitted by Warren et al (22) and based on the GEO Platform10588 Illumina HumanHT-12 V4.0 expression beadchip (Illumina, Inc., San Diego, CA, USA), was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The dataset contained 24 samples, including 9 cSCCHN, 7 cSCCHN with incidental PNI and 8 cSCCHN with clinical PNI. In the present study, the cSCCHN with clinical PNI or without PNI samples were analyzed by bioinformatics. The dataset was downloaded from the GEO database on February 2, 2017.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29552123", "locator": "sections[4] \"Microarray data\" paragraph 2", "quote": "The microarray expression profile dataset GSE86544, submitted by Warren et al (22) and based on the GEO Platform10588 Illumina HumanHT-12 V4.0 expression beadchip (Illumina, Inc., San Diego, CA, USA), was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The dataset contained 24 samples, including 9 cSCCHN, 7 cSCCHN with incidental PNI and 8 cSCCHN with clinical PNI. In the present study, the cSCCHN with clinical PNI or without PNI samples were analyzed by bioinformatics. The dataset was downloaded from the GEO database on February 2, 2017."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Bioinformatics analysis of the GSE86544 microarray dataset downloaded from the Gene Expression Omnibus database revealed 239 autophagy-related differentially expressed genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29552123", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The Gene Expression Omnibus (GEO) series GSE86544 was downloaded from the GEO database."}, {"asset": "source:pmid:29552123", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The results revealed 239 autophagy-related DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Bioinformatics analysis of the GSE86544 microarray dataset downloaded from the Gene Expression Omnibus database revealed 239 autophagy-related differentially expressed genes.", "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:29552123"], "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:GSE86544"], "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:GSE86544"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29552123", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ol.2018.7971", "sha256": "sha256:e87f0afc2de7de5e50583c530812b5c3dd24be0c6753d71ec90d0d7c5729ffa9", "bytes": 42898, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/ol.2018.7971", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5840673", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE86544", "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=GSE86544", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE86544", "version": null, "note": "The microarray expression profile dataset GSE86544, submitted by Warren et al (22) and based on the GEO Platform10588 Illumina HumanHT-12 V4.0 expression beadchip (Illumina, Inc., San Diego, CA, USA), was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The dataset contained 24 samples, including 9 cSCCHN, 7 cSCCHN with incidental PNI and 8 cSCCHN with clinical PNI. In the present study, the cSCCHN with clinical PNI or without PNI samples were analyzed by bioinformatics. The dataset was downloaded from the GEO database on February 2, 2017.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray expression profile dataset GSE86544, submitted by Warren et al (22) and based on the GEO Platform10588 Illumina HumanHT-12 V4.0 expression beadchip (Illumina, Inc., San Diego, CA, USA), was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The dataset contained 24 samples, including 9 cSCCHN, 7 cSCCHN with incidental PNI and 8 cSCCHN with clinical PNI. In the present study, the cSCCHN with clinical PNI or without PNI samples were analyzed by bioinformatics. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE86544"], "resolved_accessions": ["GSE86544"], "statements": ["The microarray expression profile dataset GSE86544, submitted by Warren et al (22) and based on the GEO Platform10588 Illumina HumanHT-12 V4.0 expression beadchip (Illumina, Inc., San Diego, CA, USA), was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The dataset contained 24 samples, including 9 cSCCHN, 7 cSCCHN with incidental PNI and 8 cSCCHN with clinical PNI. In the present study, the cSCCHN with clinical PNI or without PNI samples were analyzed by bioinformatics. The dataset was downloaded from the GEO database on February 2, 2017."], "basis": "The paper names GSE86544 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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