The screening of pivotal gene expression signatures and biomarkers in renal carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31772671", "kind": "science-record", "revision": 8, "content_hash": "sha256:d780c8778217230c8768cbd93e4c3b20e5a38e4574628a9b9fc4dd385ed50d58", "created_at": "2026-11-01T15:40:52Z", "updated_at": "2026-11-01T22:01:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The screening of pivotal gene expression signatures and biomarkers in renal carcinoma.", "doi": "10.7150/jca.30656", "pmid": "31772671", "authors": ["Hailong Ruan", "Sen Li", "Junwei Tong", "Qi Cao", "Zhengshuai Song", "Keshan Wang", "Yu Huang", "Lin Bao", "Xuanyu Chen", "Hongmei Yang", "Ke Chen", "Xiaoping Zhang"], "journal": "Journal of Cancer", "year": 2019, "abstract": "Renal cell carcinoma (RCC) is one of the most common malignancies in the urinary system, among which the proportion of clear cell RCC (ccRCC) is over 80%. This study aims to explore potential signaling pathways and key biomarkers that drive RCC progression. The RCC GEO Datasets GSE15641 was featured to screen differentially expressed genes (DEGs). The pathway enrichment and functional annotation of differentially expressed genes were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO). We screened Hub genes from DEGs using protein-protein interaction (PPI) networks and Cytoscape software. The survival and diagnostic analysis of these hub genes was performed to evaluate their potential prognostic and diagnostic value for ccRCC. In GSE15641 dataset, 598 DEGs were captured according to screening criteria (406 up-regulated genes and 192 down-regulated genes). Meanwhile, 15 hub genes were screened out from DEGs using PPI and Cytoscape. Kaplan Meier and ROC curve analysis identified three potential prognostic and diagnostic biomarkers (TGFB1, TIMP1 and VIM) for ccRCC from 15 hub genes. Gene set enrichment analysis (GSEA) revealed that these three dysregulated genes are mainly enriched in primary immunodeficiency, ECM receptor interaction, cytokine receptor interaction and natural killer cell-mediated cytotoxicity pathway. In summary, our findings discovered pivotal gene expression signatures and signaling pathways in the progression of ccRCC. TGFB1, TIMP1 and VIM might contribute to the progression of ccRCC, which could have potential as biomarkers or therapeutic targets for ccRCC.", "claims": [{"id": "claim-method", "statement": "The comparison of the expression levels of the paired tumor tissues was analyzed by a paired t test. The comparison of expression levels of unpaired tumor tissues was analyzed by unpaired t test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31772671", "locator": "sections[11] \"Statistical Analysis\" paragraph 2", "quote": "The comparison of the expression levels of the paired tumor tissues was analyzed by a paired t test. The comparison of expression levels of unpaired tumor tissues was analyzed by unpaired t test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded the GSE15641 dataset from the GEO database, which is a publicly available cancer database. 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The microarray data of GSE15641 dataset include 23 normal kidney tissues and 32 ccRCC tissues, which was based on GPL96 platform ([HG-U133A] Affymetrix Human Genome U133A Array) by Jones et al 12."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31772671"], "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:GSE15641"], "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:GSE15641"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31772671", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.30656", "sha256": "sha256:c631b06ca6931b51fbfac474ab919e644c4227a7b2a42b2bf3dd251349b9eb01", "bytes": 21544, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/jca.30656", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6856756", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15641", "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=GSE15641", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15641", "version": null, "note": "We downloaded the GSE15641 dataset from the GEO database, which is a publicly available cancer database. 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