Bioinformatics Analysis of mRNAs and miRNAs for Identifying Potential Biomarkers in Lung Adenosquamous Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35281953", "kind": "science-record", "revision": 4, "content_hash": "sha256:f8f76871b7159907e17d24f816cd5ed6bc2aa7a1f7c1d31ef049a947b90eda4a", "created_at": "2026-11-01T18:14:03Z", "updated_at": "2026-11-01T22:06:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis of mRNAs and miRNAs for Identifying Potential Biomarkers in Lung Adenosquamous Carcinoma.", "doi": "10.1155/2022/5851269", "pmid": "35281953", "authors": ["Jin Nie", "Ling Gong", "Zhu Li", "Dong Ou", "Ling Zhang", "Yi Liu", "Jianyong Zhang", "Daishun Liu"], "journal": "Computational and mathematical methods in medicine", "year": 2022, "abstract": "Background: Lung adenosquamous carcinoma (LASC) is a special type of lung cancer. LASC is a malignant tumor with strong aggressiveness and a poor prognosis. Previous studies have revealed that microRNAs (miRNAs) are widely involved in the development of tumors by targeting mRNA. This study is aimed at identifying the key mRNAs and miRNAs of LASC and constructing miRNA-mRNA networks for deeply comprehending the latent molecular mechanisms.\nMethods: mRNA dataset (GSE51852) and miRNA dataset (GSE51853) were extracted and downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were picked out by the GEO2R web tool. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses were conducted in the DAVID database. The protein-protein interaction (PPI) network was performed and analyzed by using the STRING database and Cytoscape software, respectively. TransmiR v2.0 was applied to predict potential transcription factors of miRNAs. The target genes of DEMs were predicted in the miRWalk database.\nResults: In comparison to normal tissues, a total of 1458 DEGs (511 upregulated and 947 downregulated) and 13 DEMs (5 upregulated and 8 downregulated) were screened out in LASC tissues. The PPI network of the DEGs displayed five key modules and seventeen hub genes. Six target genes of the DEMs were predicted, and five essential miRNA-mRNA regulatory pairs were established. Ensuingly, CENPF, one of the target genes, was also the hub genes of GSE51852, which was obtained from MCODE and cytoHubba and regulated by hsa-miR-205.\nConclusions: We constructed the miRNA-mRNA regulatory pairs, which are helpful to study the potential regulatory mechanisms and find out promising diagnosis biomarkers and therapeutic targets for LASC.", "claims": [{"id": "claim-method", "statement": "DEMs and DEGs were selected by GEO2R which is an interactive web tool that can identify differentially expressed genes across experimental conditions, with the same criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35281953", "locator": "sections[4] \"2.2. Identification of DEGs and DEMs\" paragraph 2", "quote": "DEMs and DEGs were selected by GEO2R which is an interactive web tool that can identify differentially expressed genes across experimental conditions, with the same criteria."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in this study are available in the article materials and methods.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35281953", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The data presented in this study are available in the article materials and methods."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 1458 DEGs (511 upregulated and 947 downregulated) and 13 DEMs (5 upregulated and 8 downregulated) were screened out in LASC tissues.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35281953", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In comparison to normal tissues, a total of 1458 DEGs (511 upregulated and 947 downregulated) and 13 DEMs (5 upregulated and 8 downregulated) were screened out in LASC tissues."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 1458 DEGs (511 upregulated and 947 downregulated) and 13 DEMs (5 upregulated and 8 downregulated) were screened out in LASC tissues.", "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:35281953"], "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:GSE51852"], "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:GSE51852"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35281953", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/5851269", "sha256": "sha256:d9d1574c98829eee9163ed2eb951e90772a4492c873382edb534c23fc8ed2ad7", "bytes": 31765, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/5851269", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8906974", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE51852", "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=GSE51852", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51852", "version": null, "note": "The data presented in this study are available in the article materials and methods.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available in the article materials and methods.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1253891", "GSM1253892", "GSM1253893", "GSM1253894", "GSM1253895", "GSM1253896", "GSM1253897", "GSM1253898", "GSM1253899", "GSM1253900", "GSM1253901", "GSM1253902", "GSM1253903", "GSM1253904", "GSM1253905", "GSM1253906", "GSM1253907", "GSM1253908", "GSM1253909", "GSM1253910", "GSM1253911", "GSM1253912", "GSM1253913", "GSM1253914", "GSM1253915", "GSM1253916", "GSM1253917", "GSM1253918", "GSM1253919", "GSM1253920", "GSM1253921", "GSM1253922", "GSM1253923", "GSM1253924", "GSM1253925", "GSM1253926", "GSM1253927", "GSM1253928", "GSM1253929", "GSM1253930", "GSM1253931", "GSM1253932", "GSM1253933", "GSM1253934", "GSM1253935", "GSM1253936", "GSM1253937", "GSM1253938", "GSM1253939", "GSM1253940", "GSM1253941", "GSM1253942", "GSM1253943"], "sample_count": 53, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features [mRNA analysis - 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