Identification of Novel Biomarkers Related to Lung Squamous Cell Carcinoma Using Integrated Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34659450", "kind": "science-record", "revision": 4, "content_hash": "sha256:b54527dd6bea1425d49f48f0d763a7a729fd7cc936a5aeba4d0005545db32d23", "created_at": "2026-11-01T17:36:19Z", "updated_at": "2026-11-01T22:04:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Novel Biomarkers Related to Lung Squamous Cell Carcinoma Using Integrated Bioinformatics Analysis.", "doi": "10.1155/2021/9059116", "pmid": "34659450", "authors": ["Haiyan Wang", "Lizhi Huang", "Li Chen", "Jing Ji", "Yuanyuan Zheng", "Zhen Wang"], "journal": "Computational and mathematical methods in medicine", "year": 2021, "abstract": "BACKGROUND: Lung squamous cell carcinoma (LUSC) is one of the most common types of lung carcinoma and has specific clinicopathologic characteristics. In this study, we screened novel molecular biomarkers relevant to the prognosis of LUSC to explore new diagnostic and treatment approaches for this disease.\nMETHODS: We downloaded GSE73402 from the Gene Expression Omnibus (GEO) database. GSE73402 contains 62 samples, which could be classified as four subtypes according to their pathology and stages. Via weighted gene coexpression network analysis (WGCNA), the main module was identified and was further analyzed using differentially expressed genes (DEGs) analysis. Then, by protein-protein interaction (PPI) network and Gene Expression Profiling Interactive Analysis (GEPIA), hub genes were screened for potential biomarkers of LUSC.\nRESULTS: Via WGCNA, the yellow module containing 349 genes was identified, and it is strongly related to the subtype of CIS (carcinoma in situ). DEGs analysis detected 180 genes that expressed differentially between the subtype of CIS and subtype of early-stage carcinoma (Stage I and Stage II). A PPI network of DEGs was constructed, and the top 20 genes with the highest correlations were selected for GEPIA database to explore their effect on LUSC survival prognosis. Finally, ITGA5, TUBB3, SCNN1B, and SERPINE1 were screened as hub genes in LUSC.\nCONCLUSIONS: ITGA5, TUBB3, SCNN1B, and SERPINE1 may have great diagnostic and prognostic significance for LUSC and have great potential to be new treatment targets for LUSC.", "claims": [{"id": "claim-method", "statement": "Via weighted gene coexpression network analysis (WGCNA), the main module was identified and was further analyzed using differentially expressed genes (DEGs) analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34659450", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Via weighted gene coexpression network analysis (WGCNA), the main module was identified and was further analyzed using differentially expressed genes (DEGs) analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding authors upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34659450", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding authors upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ITGA5, TUBB3, SCNN1B, and SERPINE1 were screened as hub genes in LUSC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34659450", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Finally, ITGA5, TUBB3, SCNN1B, and SERPINE1 were screened as hub genes in LUSC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ITGA5, TUBB3, SCNN1B, and SERPINE1 were screened as hub genes in LUSC.", "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:34659450"], "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:GSE73402"], "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:GSE73402"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34659450", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/9059116", "sha256": "sha256:90228101794465f01ea3cb7f8d9c08a508df271ba816d70869c154bebd7a60ec", "bytes": 25489, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/9059116", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8519687", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE73402", "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=GSE73402", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73402", "version": null, "note": "The data used to support the findings of this study are available from the corresponding authors upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding authors upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1892756", "GSM1892757", "GSM1892758", "GSM1892759", "GSM1892760", "GSM1892761", "GSM1892762", "GSM1892763", "GSM1892764", "GSM1892765", "GSM1892766", "GSM1892767", "GSM1892768", "GSM1892769", "GSM1892770", "GSM1892771", "GSM1892772", "GSM1892773", "GSM1892774", "GSM1892775", "GSM1892776", "GSM1892777", "GSM1892778", "GSM1892779", "GSM1892780", "GSM1892781", "GSM1892782", "GSM1892783", "GSM1892784", "GSM1892785", "GSM1892786", "GSM1892787", "GSM1892788", "GSM1892789", "GSM1892790", "GSM1892791", "GSM1892792", "GSM1892793", "GSM1892794", "GSM1892795", "GSM1892796", "GSM1892797", "GSM1892798", "GSM1892799", "GSM1892800", "GSM1892801", "GSM1892802", "GSM1892803", "GSM1892804", "GSM1892805", "GSM1892806", "GSM1892807", "GSM1892808", "GSM1892809", "GSM1892810", "GSM1892811", "GSM1892812", "GSM1892813", "GSM1892814", "GSM1892815", "GSM1892816", "GSM1892817"], "sample_count": 62, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Sixty-two lung squamous precancerous and cancer samples obtained from brochoscopy", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE73402 not downloaded", "asset:data:geo:GSE73402 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "weighted gene coexpression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Via weighted gene coexpression network analysis (WGCNA), the main module was identified and was further analyzed using differentially expressed genes (DEGs) analysis."}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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