Identification of Differentially Expressed Long Noncoding RNAs as Functional Biomarkers and Construction of Function Enrichment Network in Oral Squamous Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35795287", "kind": "science-record", "revision": 3, "content_hash": "sha256:90a2ad2e8cae9c91ca40b1af05e36bbddfa33f31fc8a55a9d81a20397e757d67", "created_at": "2026-11-01T18:14:50Z", "updated_at": "2026-11-01T21:28:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Differentially Expressed Long Noncoding RNAs as Functional Biomarkers and Construction of Function Enrichment Network in Oral Squamous Cell Carcinoma.", "doi": "10.1155/2022/1572249", "pmid": "35795287", "authors": ["Fang Xiao", "Ke Wang", "Yaojun Chen", "Yanzhen Zhang"], "journal": "Evidence-based complementary and alternative medicine : eCAM", "year": 2022, "abstract": "Objective: This study aims to find the novel lncRNAs closely related to the progression of oral squamous cell carcinoma (OSCC) by comprehensively analyzing microarray.\nMethods: Chip dataset GSE84805 was downloaded from the Gene Expression Omnibus (GEO) database, lncRNA expression profiles of OSCC and paracancerous tissue were obtained, probes sequences reannotation was conducted, and differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs) were identified. Finally, these data were analyzed by constructing the lncRNA-function enrichment network.\nResults: We found that 465 lncRNAs are differentially expressed consisting of 193 upregulated lncRNAs and 272 downregulated lncRNAs. Meanwhile, 811 DEGs were identified with 498 upregulated genes and 313 downregulated genes. Analysis of the lncRNA-function enrichment network showed that these aberrant lncRNAs may be related to focal adhesion, inflammatory response pathway, cell cycle, matrix metalloproteinases, and other biological functions. Also, we found that some key lncRNAs such as LINC00152 and HOXA11-AS have been shown to play an important role in tumor proliferation and migration.\nConclusion: The key lncRNAs may serve as potential molecular markers or therapeutic targets in OSCC formation and development. It can also help us to understand the molecular mechanism of occurrence and development in OSCC.", "claims": [{"id": "claim-method", "statement": "We identify DELs and DEGs using a paired T-test with a nominal significance level for the local false discovery rate [19] being less than 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35795287", "locator": "sections[5] \"2.3. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE84805"], "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:GSE84805"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35795287", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/1572249", "sha256": "sha256:2d272e2588684588990ab9bf778d635db424a6d155dbbcbe2392d4f93f8d9230", "bytes": 29931, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/1572249", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9252645", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84805", "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=GSE84805", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84805", "version": null, "note": "The datasets used and analyzed in this study are accessible upon request from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analyzed in this study are accessible upon request from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2251632", "GSM2251633", "GSM2251634", "GSM2251635", "GSM2251636", "GSM2251637", "GSM2251638", "GSM2251639", "GSM2251640", "GSM2251641", "GSM2251642", "GSM2251643"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "16956", "taxon": "Homo sapiens", "title": "Aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE84805 not downloaded", "asset:data:geo:GSE84805 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-2", "family": null, "specific": null, "label": "paired T-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We identify DELs and DEGs using a paired T-test with a nominal significance level for the local false discovery rate [19] being less than 0.05."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["hierarchical_cluster"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: hierarchical."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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