The roles of ferroptosis regulatory gene SLC7A11 in renal cell carcinoma: A multi-omics study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34761566", "kind": "science-record", "revision": 3, "content_hash": "sha256:245395c5cf23089fe98a41225e2403e8f2e574078149905fe8fab2737e8a96e7", "created_at": "2026-11-01T17:36:27Z", "updated_at": "2026-11-01T21:26:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The roles of ferroptosis regulatory gene SLC7A11 in renal cell carcinoma: A multi-omics study.", "doi": "10.1002/cam4.4395", "pmid": "34761566", "authors": ["Fangshi Xu", "Yibing Guan", "Li Xue", "Peng Zhang", "Mingrui Li", "Mei Gao", "Tie Chong"], "journal": "Cancer medicine", "year": 2021, "abstract": "BACKGROUND: The ferroptosis inhibitory gene Solute carrier family 7 member 11 (SLC7A11) provides a new strategy for anticancer treatment. However, its function in renal cell carcinoma (RCC) remains elusive.\nMETHODS: The expression and somatic mutation information of SLC7A11 in RCC samples were determined using The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), Gene Expression Omnibus (GEO), Oncomine, and cBioPortal databases. The prognostic value of SLC7A11 was assessed through survival analysis, Receiver operating characteristic curve (ROC) analysis, independent prognostic analysis, clinical subgroup analysis, and nomogram. Its prognostic value was also validated in the ICGC and GSE29607 cohorts. Gene set enrichment analysis (GSEA) was employed to investigate the effects of SLC7A11 on multiple metabolic pathways. The CIBERSORT algorithm and single-sample gene set enrichment analysis (ssGSEA) method were applied to evaluate the effects of SLC7A11 on the tumor immune microenvironment (TIM). SLC7A11's therapeutic correlations were analyzed using the GSE87121, GSE67501, and GSDC datasets. Finally, the biofunctions of SLC7A11 in renal cancer cells and ferroptosis were ascertained by MTT, wound healing, transwell, and western blot assays.\nRESULTS: Through multiple datasets, SLC7A11 was found to be markedly upregulated in RCC. In terms of prognosis, SLC7A11 overexpression conferred a worse prognosis and was identified as an independent prognostic factor. Its prognostic value was validated in ICGC cohort. Moreover, high SL7CA11 expression could stimulate nucleotides, fatty acids, and amino acid metabolism to meet the proliferative consumption of tumor cells. As for the immune effect, SLC7A11 suppressed antitumor immunity by reducing the abundances of CD8+ T and NK cells. Regarding the therapeutic response, SLC7A11 expression was not correlated with the sensitivities of most chemotherapy and targeted drugs. Finally, SLC7A11 promoted the proliferation, migration, and invasion of renal cancer cells by enhancing GPX4 output, which in turn inhibits ferroptosis.\nCONCLUSIONS: SLC7A11 not only deeply influences RCC prognosis and TIM, but also promotes RCC progression by inhibiting ferroptosis and inducing metabolic reprogramming. In addition, SLC7A11 weakly affects the therapeutic effect and sensitivities of multiple chemotherapy and targeted drugs.", "claims": [{"id": "claim-method", "statement": "Cox univariate and multivariate analyses were successively conducted to identify the independent prognostic factors of RCC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34761566", "locator": "sections[5] \"Prognostic analyses\" paragraph 2", "quote": "Cox univariate and multivariate analyses were successively conducted to identify the independent prognostic factors of RCC."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34761566", "locator": "sections[32] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High SLC7A11 expression conferred a poor prognosis, leading to a 3-year survival rate of 62.9%, whereas that of low SLC7A11 expression was 76.2%.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34761566", "locator": "sections[19] \"SLC7A11 provides valuable information for RCC prognostic assessment\" paragraph 2", "quote": "High SLC7A11 expression conferred a poor prognosis, leading to a 3‐year survival rate of 62.9%, whereas that of low SLC7A11 expression was 76.2% (Figure 3A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High SLC7A11 expression conferred a poor prognosis, leading to a 3-year survival rate of 62.9%, whereas that of low SLC7A11 expression was 76.2%.", "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:34761566"], "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:GSE105261"], "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:GSE105261"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34761566", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/cam4.4395", "sha256": "sha256:a20db9140b89b087708ac4b88bb04b9b6edffdf7c6eccb453651ea2046b50f2f", "bytes": 43647, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/cam4.4395", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8683539", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE105261", "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=GSE105261", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE105261", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2825239", "GSM2825240", "GSM2825241", "GSM2825242", "GSM2825243", "GSM2825244", "GSM2825245", "GSM2825246", "GSM2825247", "GSM2825248", "GSM2825249", "GSM2825250", "GSM2825251", "GSM2825252", "GSM2825253", "GSM2825254", "GSM2825255", "GSM2825256", "GSM2825257", "GSM2825258", "GSM2825259", "GSM2825260", "GSM2825261", "GSM2825262", "GSM2825263", "GSM2825264", "GSM2825265", "GSM2825266", "GSM2825267", "GSM2825268", "GSM2825269", "GSM2825270", "GSM2825271", "GSM2825272", "GSM2825273", "GSM2825274", "GSM2825275", "GSM2825276", "GSM2825277", "GSM2825278", "GSM2825279", "GSM2825280", "GSM2825281", "GSM2825282"], "sample_count": 44, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Transcriptome analysis of normal kidney, primary and metastasis ccRCC", "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:GSE150404", "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=GSE150404", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE150404", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4548605", "GSM4548606", "GSM4548607", "GSM4548608", "GSM4548609", "GSM4548610", "GSM4548611", "GSM4548612", "GSM4548613", "GSM4548614", "GSM4548615", "GSM4548616", "GSM4548617", "GSM4548618", "GSM4548619", "GSM4548620", "GSM4548621", "GSM4548622", "GSM4548623", "GSM4548624", "GSM4548625", "GSM4548626", "GSM4548627", "GSM4548628", "GSM4548629", "GSM4548630", "GSM4548631", "GSM4548632", "GSM4548633", "GSM4548634", "GSM4548635", "GSM4548636", "GSM4548637", "GSM4548638", "GSM4548639", "GSM4548640", "GSM4548641", "GSM4548642", "GSM4548643", "GSM4548644", "GSM4548645", "GSM4548646", "GSM4548647", "GSM4548648", "GSM4548649", "GSM4548650", "GSM4548651", "GSM4548652", "GSM4548653", "GSM4548654", "GSM4548655", "GSM4548656", "GSM4548657", "GSM4548658", "GSM4548659", "GSM4548660", "GSM4548661", "GSM4548662", "GSM4548663", "GSM4548664"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "17692", "taxon": "Homo sapiens", "title": "Expression data from patients with different stages of clear cell renal cell carcinoma", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"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": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM391107", "GSM391108", "GSM391109", "GSM391110", "GSM391111", "GSM391112", "GSM391113", "GSM391114", "GSM391115", "GSM391116", "GSM391117", "GSM391118", "GSM391119", "GSM391120", "GSM391121", "GSM391122", "GSM391123", "GSM391124", "GSM391125", "GSM391126", "GSM391127", "GSM391128", "GSM391129", "GSM391130", "GSM391131", "GSM391132", "GSM391133", "GSM391134", "GSM391135", "GSM391136", "GSM391137", "GSM391138", "GSM391139", "GSM391140", "GSM391141", "GSM391142", "GSM391143", "GSM391144", "GSM391145", "GSM391146", "GSM391147", "GSM391148", "GSM391149", "GSM391150", "GSM391151", "GSM391152", "GSM391153", "GSM391154", "GSM391155", "GSM391156", "GSM391157", "GSM391158", "GSM391159", "GSM391160", "GSM391161", "GSM391162", "GSM391163", "GSM391164", "GSM391165", "GSM391166", "GSM391167", "GSM391168", "GSM391169", "GSM391170", "GSM391171", "GSM391172", "GSM391173", "GSM391174", "GSM391175", "GSM391176", "GSM391177", "GSM391178", "GSM391179", "GSM391180", "GSM391181", "GSM391182", "GSM391183", "GSM391184", "GSM391185", "GSM391186", "GSM391187", "GSM391188", "GSM391189", "GSM391190", "GSM391191", "GSM391192", "GSM391193", "GSM391194", "GSM391195", "GSM391196", "GSM391197", "GSM391198"], "sample_count": 92, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Gene signatures of progression and metastasis in renal cell cancer", "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:GSE168845", "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=GSE168845", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE168845", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5171251", "GSM5171252", "GSM5171253", "GSM5171254", "GSM5171255", "GSM5171256", "GSM5171257", "GSM5171258"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "21185", "taxon": "Homo sapiens", "title": "Gene expression profile of cancerous and non-cancerous renal tissues", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE29609", "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=GSE29609", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29609", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM733579", "GSM733580", "GSM733581", "GSM733582", "GSM733583", "GSM733584", "GSM733585", "GSM733586", "GSM733587", "GSM733588", "GSM733589", "GSM733590", "GSM733591", "GSM733592", "GSM733593", "GSM733594", "GSM733595", "GSM733596", "GSM733597", "GSM733598", "GSM733599", "GSM733600", "GSM733601", "GSM733602", "GSM733603", "GSM733604", "GSM733605", "GSM733606", "GSM733607", "GSM733608", "GSM733609", "GSM733610", "GSM733611", "GSM733612", "GSM733613", "GSM733614", "GSM733615", "GSM733616", "GSM733617"], "sample_count": 39, "group_sizes": null, "group_sizes_basis": null, "platform": "1708", "taxon": "Homo sapiens", "title": "Clear-cell renal cell carcinomas tumors", "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:GSE53757", "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=GSE53757", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53757", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1300062", "GSM1300063", "GSM1300064", "GSM1300065", "GSM1300066", "GSM1300067", "GSM1300068", "GSM1300069", "GSM1300070", "GSM1300071", "GSM1300072", "GSM1300073", "GSM1300074", "GSM1300075", "GSM1300076", "GSM1300077", "GSM1300078", "GSM1300079", "GSM1300080", "GSM1300081", "GSM1300082", "GSM1300083", "GSM1300084", "GSM1300085", "GSM1300086", "GSM1300087", "GSM1300088", "GSM1300089", "GSM1300090", "GSM1300091", "GSM1300092", "GSM1300093", "GSM1300094", "GSM1300095", "GSM1300096", "GSM1300097", "GSM1300098", "GSM1300099", "GSM1300100", "GSM1300101", "GSM1300102", "GSM1300103", "GSM1300104", "GSM1300105", "GSM1300106", "GSM1300107", "GSM1300108", "GSM1300109", "GSM1300110", "GSM1300111", "GSM1300112", "GSM1300113", "GSM1300114", "GSM1300115", "GSM1300116", "GSM1300117", "GSM1300118", "GSM1300119", "GSM1300120", "GSM1300121", "GSM1300122", "GSM1300123", "GSM1300124", "GSM1300125", "GSM1300126", "GSM1300127", "GSM1300128", "GSM1300129", "GSM1300130", "GSM1300131", "GSM1300132", "GSM1300133", "GSM1300134", "GSM1300135", "GSM1300136", "GSM1300137", "GSM1300138", "GSM1300139", "GSM1300140", "GSM1300141", "GSM1300142", "GSM1300143", "GSM1300144", "GSM1300145", "GSM1300146", "GSM1300147", "GSM1300148", "GSM1300149", "GSM1300150", "GSM1300151", "GSM1300152", "GSM1300153", "GSM1300154", "GSM1300155", "GSM1300156", "GSM1300157", "GSM1300158", "GSM1300159", "GSM1300160", "GSM1300161", "GSM1300162", "GSM1300163", "GSM1300164", "GSM1300165", "GSM1300166", "GSM1300167", "GSM1300168", "GSM1300169", "GSM1300170", "GSM1300171", "GSM1300172", "GSM1300173", "GSM1300174", "GSM1300175", "GSM1300176", "GSM1300177", "GSM1300178", "GSM1300179", "GSM1300180", "GSM1300181", "GSM1300182", "GSM1300183", "GSM1300184", "GSM1300185", "GSM1300186", "GSM1300187", "GSM1300188", "GSM1300189", "GSM1300190", "GSM1300191", "GSM1300192", "GSM1300193", "GSM1300194", "GSM1300195", "GSM1300196", "GSM1300197", "GSM1300198", "GSM1300199", "GSM1300200", "GSM1300201", "GSM1300202", "GSM1300203", "GSM1300204", "GSM1300205"], "sample_count": 144, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene array analysis of clear cell renal cell carcinoma tissue versus matched normal kidney tissue", "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:GSE66271", "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=GSE66271", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66271", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1618415", "GSM1618416", "GSM1618417", "GSM1618418", "GSM1618419", "GSM1618420", "GSM1618421", "GSM1618422", "GSM1618423", "GSM1618424", "GSM1618425", "GSM1618426", "GSM1618427", "GSM1618428", "GSM1618429", "GSM1618430", "GSM1618431", "GSM1618432", "GSM1618433", "GSM1618434", "GSM1618435", "GSM1618436", "GSM1618437", "GSM1618438", "GSM1618439", "GSM1618440"], "sample_count": 26, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Genome-wide analysis of gene expression patterns in human kidney cancer [patients with metastasis]", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE67501", "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=GSE67501", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE67501", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1648114", "GSM1648115", "GSM1648116", "GSM1648117", "GSM1648118", "GSM1648119", "GSM1648120", "GSM1648121", "GSM1648122", "GSM1648123", "GSM1648124"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "Expression data in human renal cell carcinoma samples from patients who did or did not respond to anti-PD-1 (Nivolumab) immunotherapy", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE87121", "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=GSE87121", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87121", "version": null, "note": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2322632", "GSM2322633", "GSM2322634", "GSM2322635", "GSM2322636", "GSM2322637", "GSM2322638", "GSM2322639", "GSM2322640", "GSM2322641"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Sorafenib resistance associated gene expression in renal cell carcinoma", "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:GSE105261 not downloaded", "asset:data:geo:GSE105261 licence not read", "asset:data:geo:GSE150404 not downloaded", "asset:data:geo:GSE150404 licence not read", "asset:data:geo:GSE15641 not downloaded", "asset:data:geo:GSE15641 licence not read", "asset:data:geo:GSE168845 not downloaded", "asset:data:geo:GSE168845 licence not read", "asset:data:geo:GSE29609 not downloaded", "asset:data:geo:GSE29609 licence not read", "asset:data:geo:GSE53757 not downloaded", "asset:data:geo:GSE53757 licence not read", "asset:data:geo:GSE66271 not downloaded", "asset:data:geo:GSE66271 licence not read", "asset:data:geo:GSE67501 not downloaded", "asset:data:geo:GSE67501 licence not read", "asset:data:geo:GSE87121 not downloaded", "asset:data:geo:GSE87121 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Cox univariate and multivariate analyses", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Cox univariate and multivariate analyses were successively conducted to identify the independent prognostic factors of RCC."}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Cox univariate and multivariate analyses), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE29609", "GSE53757", "GSE66271", "GSE168845", "GSE15641", "GSE105261", "GSE150404", "GSE87121", "GSE67501"], "resolved_accessions": ["GSE29609", "GSE53757", "GSE66271", "GSE168845", "GSE15641", "GSE105261", "GSE150404", "GSE87121", "GSE67501"], "statements": ["The datasets used and/or analyzed in the current study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE29609, GSE53757, GSE66271, GSE168845, GSE15641, GSE105261, GSE150404, GSE87121, GSE67501 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:34761566", "data:geo:GSE105261"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE105261"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:06:59Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12425, "completion_tokens": 3430, "cached_tokens": 188}}, "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:34761566", "type": "paper", "label": "pmid:34761566"}, {"id": "source:pmid:34761566", "type": "manuscript", "label": "PMID 34761566 full text"}, {"id": "data:geo:GSE105261", "type": "dataset", "label": "GEO GSE105261"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34761566", "type": "paper", "label": "pmid:34761566"}, {"id": "source:pmid:34761566", "type": "manuscript", "label": "PMID 34761566 full text"}, {"id": "data:geo:GSE105261", "type": "dataset", "label": "GEO GSE105261"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34761566", "type": "extraction", "used": ["source:pmid:34761566"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE105261", "type": "accession_resolution", "used": ["data:geo:GSE105261"], "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:34761566", "parent_hash": "sha256:a218b97e9a95a1f00cce9a70a558be6bd2e77b7076ef06e46ca71bd62b297649", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE105261 licence not read", "asset:data:geo:GSE105261 not downloaded", "asset:data:geo:GSE150404 licence not read", "asset:data:geo:GSE150404 not downloaded", "asset:data:geo:GSE15641 licence not read", "asset:data:geo:GSE15641 not downloaded", "asset:data:geo:GSE168845 licence not read", "asset:data:geo:GSE168845 not downloaded", "asset:data:geo:GSE29609 licence not read", "asset:data:geo:GSE29609 not downloaded", "asset:data:geo:GSE53757 licence not read", "asset:data:geo:GSE53757 not downloaded", "asset:data:geo:GSE66271 licence not read", "asset:data:geo:GSE66271 not downloaded", "asset:data:geo:GSE67501 licence not read", "asset:data:geo:GSE67501 not downloaded", "asset:data:geo:GSE87121 licence not read", "asset:data:geo:GSE87121 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["er cells and ferroptosis were ascertained by MTT, wound healing, transwell, and western blot"], "order_basis": "paper_text_order:1276", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["tained by MTT, wound healing, transwell, and western blot assays. RESULTS: Through multiple datasets,"], "order_basis": "paper_text_order:1311", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["MATERIALS AND METHODS Cell culture and transfection The normal kidney tubular epithelial cell li", "gy Company. Lipofectamine™ 2000 was used for transfection (Thermo Fisher Scientific). Statistical anal", "O2, and 95% humidity. Small interfering RNA (siRNA) for SLC7A11 silencing was designed and synt"], "order_basis": "paper_text_order:2500", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ence and Technology Company. HK‐2 cells were cultured in minimum essential medium containing 10% feta", "llin/streptomycin. 786‐O and A498 cells were cultured in RPMI‐1640 medium (Roswell Park Memorial Inst"], "order_basis": "paper_text_order:2683", "id": "assay:4"}]}