Identification and expression of prognostic-related genes in kidney renal clear cell carcinoma and their possible regulatory mechanisms.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39280680", "kind": "science-record", "revision": 4, "content_hash": "sha256:2da3ab0d18a47275e2c5d5551501e7cd7a536fd16401fb8363fa753bdcd97f1f", "created_at": "2026-11-01T20:29:26Z", "updated_at": "2026-11-01T22:55:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and expression of prognostic-related genes in kidney renal clear cell carcinoma and their possible regulatory mechanisms.", "doi": "10.21037/tau-24-299", "pmid": "39280680", "authors": ["Qian Liu", "Jun Ding"], "journal": "Translational andrology and urology", "year": 2024, "abstract": "Background: Many factors affect the prognosis of kidney renal clear cell carcinoma (KIRC). Early diagnosis can significantly improve the prognosis of KIRC patients. Therefore, a method needs to be developed to diagnose KIRC early, predict patient prognosis, and improve personalized treatments. The objective of this study is to utilize bioinformatics tools and public database resources to identify differentially expressed genes (DEGs) between renal cancer tissues and adjacent normal tissues, and to further screen for prognostic-related genes (PRGs) of KIRC.\nMethods: KIRC was studied using R language and FunRich software and several databases, including the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), the University of Alabama at Birmingham cancer data analysis Portal (UALCAN), and Tumor Immune Estimation Resource (TIMER) databases. Moreover, quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the expression of multiple genes in KIRC and adjacent normal tissues.\nResults: There were substantial differences in immune cell infiltration between the KIRC and adjacent normal tissues in the GSE40435 and GSE46699 datasets. In addition, we screened multiple PRGs of KIRC by combining the GEO and TCGA data. The UALCAN database verified that some representative PRGs were differently expressed depending on the lymph node metastasis status, grade, and stage of KIRC. The qRT-PCR results confirmed the expression of the PRGs in KIRC and adjacent normal tissues. Through the GO and KEGG analyses, interaction analysis, and TIMER database, we found that the prognosis of KIRC was closely related to immune microenvironment and vascular endothelial growth factor (VEGF)/VEGF receptor (VEGFR) signaling.\nConclusions: Our findings could contribute to the prognosis prediction of KIRC, the selection of personalized treatments, and the early diagnosis of KIRC.", "claims": [{"id": "claim-method", "statement": "Differential expression between KIRC tissues and adjacent normal tissues was analyzed using the “limma” package, with significant genes identified at a P value <0.05 and an absolute logFC >1. CIBERSORT was used to assess immune cell infiltration. Pearson correlation analysis was applied to explore relationships between PRGs and TFs. Gene Ontology and KEGG pathway analyses were performed using “clusterProfiler”. Survival outcomes based on PRG expression were evaluated using univariate Cox proportional hazards models.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39280680", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "Differential expression between KIRC tissues and adjacent normal tissues was analyzed using the “limma” package, with significant genes identified at a P value <0.05 and an absolute logFC >1. CIBERSORT was used to assess immune cell infiltration. Pearson correlation analysis was applied to explore relationships between PRGs and TFs. Gene Ontology and KEGG pathway analyses were performed using “clusterProfiler”. Survival outcomes based on PRG expression were evaluated using univariate Cox proportional hazards models."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Available at https://tau.amegroups.com/article/view/10.21037/tau-24-299/dss 10.21037/tau-24-299", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39280680", "locator": "sections[24] \"Data Sharing Statement\" paragraph 2", "quote": "Available at https://tau.amegroups.com/article/view/10.21037/tau-24-299/dss 10.21037/tau-24-299"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:39280680"], "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:GSE40435"], "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:GSE40435"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39280680", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tau-24-299", "sha256": 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"Homo sapiens", "title": "Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE46699", "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=GSE46699", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46699", "version": null, "note": "Available at https://tau.amegroups.com/article/view/10.21037/tau-24-299/dss 10.21037/tau-24-299", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Available at https://tau.amegroups.com/article/view/10.21037/tau-24-299/dss 10.21037/tau-24-299", "access_statement_kind": 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"title": "Smoking and Obesity Related Molecular Alterations in Clear Cell Renal Cell Carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE40435 not downloaded", "asset:data:geo:GSE40435 licence not read", "asset:data:geo:GSE46699 not downloaded", "asset:data:geo:GSE46699 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differential expression between KIRC tissues and adjacent normal tissues was analyzed using the “limma” package, with significant genes identified at a P value <0.05 and an absolute logFC >1. CIBERSORT was used to assess immune cell infiltration. Pearson correlation analysis was applied to explore relationships between PRGs and TFs. Gene Ontology and KEGG pathway analyses were performed using “clusterProfiler”. Survival outcomes based on PRG expression were evaluated using univariate Cox proportional hazards models."}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "targets": [], "gaps": []}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:39280680", "data:geo:GSE40435"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE40435"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:31:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10101, "completion_tokens": 2304, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:39280680", "type": "paper", "label": "pmid:39280680"}, {"id": "source:pmid:39280680", "type": "manuscript", "label": "PMID 39280680 full text"}, {"id": "data:geo:GSE40435", "type": "dataset", "label": "GEO GSE40435"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39280680", "type": "paper", "label": "pmid:39280680"}, {"id": "source:pmid:39280680", "type": "manuscript", "label": "PMID 39280680 full text"}, {"id": "data:geo:GSE40435", "type": "dataset", "label": "GEO GSE40435"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39280680", "type": "extraction", "used": ["source:pmid:39280680"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE40435", "type": "accession_resolution", "used": ["data:geo:GSE40435"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:39280680", "parent_hash": "sha256:f80189739be4b2ec721eb3149c3cad1799e8aa1471db8ce42131f1113daa35df", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE40435 licence not read", "asset:data:geo:GSE40435 not downloaded", "asset:data:geo:GSE46699 licence not read", "asset:data:geo:GSE46699 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differential expression between KIRC tissues and adjacent normal tissues was analyzed using the “limma” package, with significant genes identified at a P value <0.05 and an absolute logFC >1. 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