Signatures and prognostic values of related immune targets in tongue cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36684241", "kind": "science-record", "revision": 4, "content_hash": "sha256:982aca9bde7a5dbb5cdcbb240170cad7ede9639962bad3e79abb56b08c55a15a", "created_at": "2026-11-01T19:01:13Z", "updated_at": "2026-11-01T22:51:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Signatures and prognostic values of related immune targets in tongue cancer.", "doi": "10.3389/fsurg.2022.952389", "pmid": "36684241", "authors": ["Xiaofei Lv", "Xi Yu"], "journal": "Frontiers in surgery", "year": 2022, "abstract": "Background: Tongue cancer, as one of the most malignant oral cancers, is highly invasive and has a high risk of recurrence. At present, tongue cancer is not obvious and easy to miss the opportunity for early diagnosis when in the advanced stage. It is important to find markers that can predict the occurrence and progression of tongue cancer.\nMethods: Bioinformatics analysis plays an important role in the acquisition of marker genes. GEO and TCGA data are very important public databases. In addition to expression data, the TCGA database also contains corresponding clinical data. In this study, we screened three GEO data sets that met the standard, which included GSE13601, GSE34105, and GSE34106. These data sets were combined using the SVA package to prepare the data for differential expression analysis, and then the limma package was used to set the standard to p < 0.05 and |log2 (FC)| ≥ 1.5.\nResults: A total of 170 differentially expressed genes (DEGs) were identified. In addition, the DEseq package was used for differential expression analysis using the same criteria for samples in the TCGA database. It ended up with 1,589 DEGs (644 upregulated, 945 downregulated). By merging these two sets of DEGs, 5 common upregulated DEGs (CCL20, SCG5, SPP1, KRT75, and FOLR3) and 15 common downregulated DEGs were obtained.\nConclusions: Further functional analysis of the DEGs showed that CCL20, SCG5, and SPP1 are closely related to prognosis and may be a therapeutic target of TSCC.", "claims": [{"id": "claim-method", "statement": "The limma package and DESeq package in R language were used for differential expression analysis, and the standard cutoff was set to false discovery rate (FDR) < 0.05 and |log2 (FC)| ≥ 1.5 for both GEO and TCGA, respectively (8, 9).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36684241", "locator": "sections[4] \"Screening and analysis of differentially expressed genes\" paragraph 2", "quote": "The limma package and DESeq package in R language were used for differential expression analysis, and the standard cutoff was set to false discovery rate (FDR) < 0.05 and |log2 (FC)| ≥ 1.5 for both GEO and TCGA, respectively (8, 9)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author/s.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36684241", "locator": "sections[17] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author/s."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Functional analysis indicated that CCL20, SCG5, and SPP1 are closely related to prognosis and may be therapeutic targets of TSCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36684241", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Further functional analysis of the DEGs showed that CCL20, SCG5, and SPP1 are closely related to prognosis and may be a therapeutic target of TSCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Functional analysis indicated that CCL20, SCG5, and SPP1 are closely related to prognosis and may be therapeutic targets of TSCC.", "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:36684241"], "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:GSE13601"], "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:GSE13601"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36684241", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fsurg.2022.952389", "sha256": "sha256:8099b7774de7c29849c775a0c30ed8e6ef3df6a885309d1b9c2d898f44bef6fd", "bytes": 19280, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fsurg.2022.952389", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9848309", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13601", "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=GSE13601", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13601", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author/s.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author/s.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM342530", "GSM342531", "GSM342532", "GSM342533", "GSM342534", "GSM342535", "GSM342536", "GSM342537", "GSM342538", "GSM342539", "GSM342540", "GSM342541", "GSM342542", "GSM342543", "GSM342544", "GSM342545", "GSM342546", "GSM342547", "GSM342548", "GSM342549", "GSM342550", "GSM342551", "GSM342552", "GSM342553", "GSM342554", "GSM342555", "GSM342556", "GSM342557", "GSM342558", "GSM342559", "GSM342560", "GSM342561", "GSM342562", "GSM342563", "GSM342564", "GSM342565", "GSM342566", "GSM342567", "GSM342568", "GSM342569", "GSM342570", "GSM342571", "GSM342572", "GSM342573", "GSM342574", 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