Esophageal squamous cell carcinoma: Integrated bioinformatics analysis for differential gene expression with identification of hub genes and lncRNA.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35479061", "kind": "science-record", "revision": 4, "content_hash": "sha256:38d1d68c0e9bf309f9150b70bd4524fbc208595d846950cc8ea2cf1db8735438", "created_at": "2026-11-01T18:14:20Z", "updated_at": "2026-11-01T22:06:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Esophageal squamous cell carcinoma: Integrated bioinformatics analysis for differential gene expression with identification of hub genes and lncRNA.", "doi": "10.1016/j.bbrep.2022.101262", "pmid": "35479061", "authors": ["F M Yasir Hasib"], "journal": "Biochemistry and biophysics reports", "year": 2022, "abstract": "Background: Esophageal squamous cell carcinoma (ESCC) is a typical Gastro-Intestinal (GI) tract neoplasm. This study was conducted to know the Differential Expressed Genes (DEGs) profile of ESCC along with hub gene screening, lncRNA identification, and drug-genes interactions.\nMethods: GSE161533, GSE20347, GSE45670 microarray datasets were retrieved from the NCBI Gene Expression Omnibus (GEO) database. GEO2R was used for the DEGs identification, whereas GO (Gene Ontology) and KEGG enrichment analysis were performed in DAVID. PPI network constructed using STRING and visualized with Cytoscape app with the help of MCODE. The top ten connectivity genes were selected as hub genes-further survival analysis was performed in the Kaplan-Meier plotter. Moreover, Boxplot, pathological stage plots were constructed using GEPIA (Gene Expression Profiling Interactive Analysis). The methylation heatmap assembled in the DiseaseMeth version 2.0. lncRNA (Long non-coding RNA) was identified comparing the list of genes in HUGO, and Gene-drug interactions were accumulated from the DgiDB platform.\nResults: This experiment showed 16 upregulated, and 59 downregulated DEGs shared among the three datasets. Biological process analysis showed significant terms such as extracellular matrix disassembly and collagen catabolism. The extracellular region was detected as the most crucial cellular compartment. Notably, metalloen dopeptidease and serine-type endopeptidase activity showed significant molecular functions term. In contrast, transcriptional misregulation was a highly substantial KEGG pathway. Kaplan-Meier plotter showed higher expression of CXCL8, SPP1, MMP13, CXCL1, and TOP2A have a significant impact on the overall survival of the patients. Nine out of ten hub genes have significantly different expression levels than normal and cancer tissues. HYMAI was the only lncRNA commonly expressed upregulated among the three datasets. Drug-gene interaction showed multiple genes have no drug options exist till now.", "claims": [{"id": "claim-method", "statement": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) was used for the differential gene expression analysis (J. [16].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35479061", "locator": "sections[2] \"Materials and Method\" paragraph 3", "quote": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) was used for the differential gene expression analysis (J. [16]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "No data was used for the research described in the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35479061", "locator": "sections[7] \"Data availability\" paragraph 2", "quote": "No data was used for the research described in the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The three datasets shared 16 upregulated and 59 downregulated differentially expressed genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35479061", "locator": "sections[3] \"Results\" paragraph 2", "quote": "There were 506, 549, and 1768 significant DEGs for the GSE161533, GSE20347, and GSE45670 datasets with 16 upregulated and 59 downregulated genes in common."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The three datasets shared 16 upregulated and 59 downregulated 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:35479061"], "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:GSE161533"], "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:GSE161533"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35479061", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.bbrep.2022.101262", "sha256": 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