Bioinformatics analysis of C3 and CXCR4 demonstrates their potential as prognostic biomarkers in clear cell renal cell carcinoma (ccRCC).

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34266404", "kind": "science-record", "revision": 7, "content_hash": "sha256:5365908a4a406102bc25e8ae49cd84a267bd51b35e020eac1226e30574937a0b", "created_at": "2026-11-01T15:41:43Z", "updated_at": "2026-11-01T22:04:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of C3 and CXCR4 demonstrates their potential as prognostic biomarkers in clear cell renal cell carcinoma (ccRCC).", "doi": "10.1186/s12885-021-08525-w", "pmid": "34266404", "authors": ["Jing Quan", "Yuchen Bai", "Yunbei Yang", "Er Lei Han", "Hong Bai", "Qi Zhang", "Dahong Zhang"], "journal": "BMC cancer", "year": 2021, "abstract": "BACKGROUND: The molecular prognostic biomarkers of clear cell renal cell carcinoma (ccRCC) are still unknown. We aimed at researching the candidate biomarkers and potential therapeutic targets of ccRCC.\nMETHODS: Three ccRCC expression microarray datasets (include GSE14762, GSE66270 and GSE53757) were downloaded from the gene expression omnibus (GEO) database. The differentially expressed genes (DEGs) between ccRCC and normal tissues were explored. The potential functions of identified DEGs were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). And then the protein - protein interaction network (PPI) was established to screen the hub genes. After that, the expressions of hub genes were identified by the oncomine database. The hub genes' prognostic values of patients with ccRCC were analyzed by GEPIA database.\nRESULTS: A total of 137 DEGs were identified by utilizing the limma package and RRA method, including 63 upregulated genes and 74 downregulated genes. It is found that 137 DEGs were mainly enriched in 82 functional terms and 24 pathways in accordance with the research results. Thirteen highest-scoring genes were screened as hub genes (include 10 upregulated genes and 3 downregulated candidate genes) by utilizing the PPI network and module analysis. Through integrating the oncoming database and GEPIA database, the author found that C3 and CXCR4 are not only overexpressed in ccRCC, but also associated with the prognosis of ccRCC. Further results could reveal that patients with high C3 expression had a poor overall survival (OS), while patients with high CTSS and TLR3 expressions had a good OS; patients with high C3 and CXCR4 expressions had a poor disease-free survival (DFS), while ccRCC patients with high TLR3 expression had a good DFS.\nCONCLUSION: These findings suggested that C3 and CXCR4 were the candidate biomarkers and potential therapeutic targets of ccRCC patients.", "claims": [{"id": "claim-method", "statement": "The Robust Rank Aggreg (RRA) analysis (http://cran.r-project.org/) was used to list the up-regulated and down-regulated genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34266404", "locator": "sections[4] \"Detection of DEGs\" paragraph 2", "quote": "The Robust Rank Aggreg (RRA) analysis (http://cran.r-project.org/) was used to list the up-regulated and down-regulated genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are all included within the thesis. The gene expression data can be accessed on Gene Expression Omnibus (GEO). Oncomine database was used to get the expression profile of hub genes. GEPIA database was used to obtain the overall survival and disease free survival analysis of genes.\nThe datasets analysed during this study are available in the:\n1. GSE14762_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE14762&format=file\n2. GSE15641_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE15641&format=file\n3. GSE53757_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE53757&format=file\n4. GSE53757_series_matrix.txt: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53757/matrix/GSE53757_series_matrix.txt.gz", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34266404", "locator": "sections[21] \"Availability of data and materials\" paragraphs 1-7", "quote": "The data used to support the findings of this study are all included within the thesis. The gene expression data can be accessed on Gene Expression Omnibus (GEO). Oncomine database was used to get the expression profile of hub genes. GEPIA database was used to obtain the overall survival and disease free survival analysis of genes.\nThe datasets analysed during this study are available in the:\n1. GSE14762_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE14762&format=file\n2. GSE15641_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE15641&format=file\n3. GSE53757_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE53757&format=file\n4. GSE53757_series_matrix.txt: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53757/matrix/GSE53757_series_matrix.txt.gz"}], "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:34266404"], "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:GSE14762"], "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:GSE14762"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34266404", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-021-08525-w", "sha256": "sha256:baacdc7732b92991807079037c7fbc6c56c0c6ecc022d59aed5c1f1f03b8fa9d", "bytes": 32433, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-021-08525-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8283915", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14762", "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=GSE14762", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14762", "version": null, "note": "The data used to support the findings of this study are all included within the thesis. The gene expression data can be accessed on Gene Expression Omnibus (GEO). Oncomine database was used to get the expression profile of hub genes. GEPIA database was used to obtain the overall survival and disease free survival analysis of genes.\nThe datasets analysed during this study are available in the:\n1. GSE14762_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE14762&format=file\n2. GSE15641_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE15641&format=file\n3. GSE53757_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE53757&format=file\n4. GSE53757_series_matrix.txt: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53757/matrix/GSE53757_series_matrix.txt.gz", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are all included within the thesis. The gene expression data can be accessed on Gene Expression Omnibus (GEO). Oncomine database was used to get the expression profile of hub genes. GEPIA database was used to obtain the overall survival and disease free survival analysis of genes.\nThe datasets analysed during this study are available in the:\n1. GSE14762_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE14762&format=file\n2. GSE15641_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE15641&format=file\n3. GSE53757_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE53757&format=file\n4. GSE53757_series_matrix.txt: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53757/matrix/GSE53757_series_matrix.txt.gz", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM368639", "GSM368640", "GSM368641", "GSM368642", "GSM368643", "GSM368644", "GSM368645", "GSM368646", "GSM368647", "GSM368648", "GSM368649", "GSM368650", "GSM368651", "GSM368652", "GSM368653", "GSM368654", "GSM368655", "GSM368656", "GSM368657", "GSM368658", "GSM368659", "GSM368660"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "4866", "taxon": "Homo sapiens", "title": "Renal Cell Carcinoma: Hypoxia and Endocytosis", "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 data used to support the findings of this study are all included within the thesis. The gene expression data can be accessed on Gene Expression Omnibus (GEO). Oncomine database was used to get the expression profile of hub genes. GEPIA database was used to obtain the overall survival and disease free survival analysis of genes.\nThe datasets analysed during this study are available in the:\n1. GSE14762_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE14762&format=file\n2. GSE15641_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE15641&format=file\n3. GSE53757_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE53757&format=file\n4. GSE53757_series_matrix.txt: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53757/matrix/GSE53757_series_matrix.txt.gz", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are all included within the thesis. The gene expression data can be accessed on Gene Expression Omnibus (GEO). Oncomine database was used to get the expression profile of hub genes. GEPIA database was used to obtain the overall survival and disease free survival analysis of genes.\nThe datasets analysed during this study are available in the:\n1. GSE14762_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE14762&format=file\n2. GSE15641_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE15641&format=file\n3. GSE53757_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE53757&format=file\n4. GSE53757_series_matrix.txt: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53757/matrix/GSE53757_series_matrix.txt.gz", "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:GSE66270", "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=GSE66270", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66270", "version": null, "note": "The data used to support the findings of this study are all included within the thesis. The gene expression data can be accessed on Gene Expression Omnibus (GEO). Oncomine database was used to get the expression profile of hub genes. GEPIA database was used to obtain the overall survival and disease free survival analysis of genes.\nThe datasets analysed during this study are available in the:\n1. GSE14762_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE14762&format=file\n2. GSE15641_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE15641&format=file\n3. GSE53757_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE53757&format=file\n4. GSE53757_series_matrix.txt: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53757/matrix/GSE53757_series_matrix.txt.gz", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are all included within the thesis. The gene expression data can be accessed on Gene Expression Omnibus (GEO). Oncomine database was used to get the expression profile of hub genes. GEPIA database was used to obtain the overall survival and disease free survival analysis of genes.\nThe datasets analysed during this study are available in the:\n1. GSE14762_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE14762&format=file\n2. GSE15641_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE15641&format=file\n3. GSE53757_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE53757&format=file\n4. GSE53757_series_matrix.txt: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53757/matrix/GSE53757_series_matrix.txt.gz", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1618387", "GSM1618388", "GSM1618389", "GSM1618390", "GSM1618391", "GSM1618392", "GSM1618393", "GSM1618394", "GSM1618395", "GSM1618396", "GSM1618397", "GSM1618398", "GSM1618399", "GSM1618400", "GSM1618401", "GSM1618402", "GSM1618403", "GSM1618404", "GSM1618405", "GSM1618406", "GSM1618407", "GSM1618408", "GSM1618409", "GSM1618410", "GSM1618411", "GSM1618412", "GSM1618413", "GSM1618414"], "sample_count": 28, "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 without 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": "asset:table:pmid:34266404:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4ab16c54a0d4eaeaeea84bca1a036cd66727164e519b2849bd793fd959b34a56", "bytes": 385, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Details for GEO ccRCC data", "structure": {"pmcid": "PMC8283915", "section_index": 3, "section_title": "Access to public resources", "row_count": 5, "column_count": 5}, "table": {"label": "Table 1", "caption": "Details for GEO ccRCC data", "rows": [["Reference", "GEO", "Platform", "Sample"], ["normal", "tumor"], ["Furge K [8]1", "GSE14762", "GPL4866", "11", "11"], ["Jung K [9]2", "GSE66270", "GPL570", "14", "14"], ["Von Roemeling CA [10]3", "GSE53757", "GPL570", "72", "72"]], "row_count": 5, "column_count": 5, "numeric_cells": 15, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:34266404:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e9fba88a09a4d1d0bcd2d41f127ee46c833c21b1ea130e3a0d269b4bdf127adb", "bytes": 1367, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab2", "version": null, "note": "The genes differentially expressed both in GEO database were identified in ccRCC samples", "structure": {"pmcid": "PMC8283915", "section_index": 10, "section_title": "DEGs identification in ccRCC", "row_count": 3, "column_count": 2}, "table": {"label": "Table 2", "caption": "The genes differentially expressed both in GEO database were identified in ccRCC samples", "rows": [["", "Gene names"], ["Upregulated DEGs", "EGLN3, CA9, ANGPTL4, IGFBP3, ENO2, NDUFA4L2, SPAG4, HK2, CXCR4, APOC1, NOL3, LAPTM5, LPCAT1, PSMB9, CTSS, TYROBP, NETO2, RRM2, TMEM45A, CAV2, LOC101928916 /// NNMT, TNFAIP6, PFKP, TLR3, LGALS1, MIR6787 /// SLC16A3, C3, COL23A1, C1QA, CSTA, CAV1, ITGB2, SEMA5B, PLOD2, C1QB, TRIB3, MS4A6A, PDK1, BIRC3, DDB2, ENTPD1, TREM2, EVI2A, P2RX7, HILPDA, LOC56901, FBXO16 /// ZNF395, ST8SIA4, CTHRC1, PRKCDBP, ENPP3, ISG20, MNDA, SLC16A3, ZNF395, FCER1G, PLK2, TNFSF13B, FCGR3A /// FCGR3B, RGS1, TLR2, TGFBI, CASP1"], ["Downregulated DEGs", "KCNJ1, KNG1, CLCNKB, FGF9, DMRT2, CALB1, RHCG, CLDN8, ATP6V0A4, SFRP1, ATP6V1G3, NPHS2, HS6ST2, ABAT, ATP6V1B1, AQP2, ALDH6A1, DIO1, SLC34A1, ATP6V0D2, RHBG, MAN1C1, FGF1, PVALB, UMOD, GPC3, DPEP1, SERPINA5, XPNPEP2, DCXR, TMEM52B, ACOX2, TMEM213, LPPR1, HEPACAM2, GPR110, TFCP2L1, FXYD4, HRG, GGT6, ERP27, SLC12A3, TYRP1, DUSP9, SH3GL2, SMIM5, SUCLG1, UPP2, SLC4A1, SLC22A8, SLC7A8, HSD11B2, ACAA1, SOST, ENPP6, RP11-999E24.3, ALDH4A1TCF21, EFHD1, FBP1, HPD, TMEM30B, SLC13A3, SLC22A7, AFM, ACSF2, PCK2, PLG, FABP1, LOC155006, SUCNR1, LINC01187, CRYAA, CHL1"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:34266404:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:74ccd330e8e741d8ee4b6a7da943e9c058e150e2481e08dacfb7ba3c7a1af1c1", "bytes": 9858, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab3", "version": null, "note": "Significant results of the GO enrichment analysis of DEGs", "structure": {"pmcid": "PMC8283915", "section_index": 11, "section_title": "GO and KEGG analysis of DEG", "row_count": 83, "column_count": 5}, "table": {"label": "Table 3", "caption": "Significant results of the GO enrichment analysis of DEGs", "rows": [["Function", "Term", "Count", "PValue", "Genes"], ["biological processes", "GO:0007588 ~ excretion", "7", "2.64E-07", "NPHS2, CLCNKB, UMOD, ATP6V1B1, ATP6V0A4, KCNJ1, AQP2"], ["GO:0001666 ~ response to hypoxia", "11", "5.42E-07", "CAV1, NOL3, CA9, PLOD2, CXCR4, EGLN3, TLR2, HSD11B2, ABAT, CASP1, ANGPTL4"], ["GO:0090383 ~ phagosome acidification", "4", "9.87E-04", "ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["GO:0033572 ~ transferrin transport", "4", "0.002115", "ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["GO:0008286 ~ insulin receptor signaling pathway", "5", "0.002575", "CAV2, ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["GO:0032755 ~ positive regulation of interleukin-6 production", "4", "0.004349", "P2RX7, TLR2, FCER1G, TLR3"], ["GO:0034220 ~ ion transmembrane transport", "7", "0.004506", "FXYD4, CLCNKB, ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2, AQP2"], ["GO:0015695 ~ organic cation transport", "3", "0.00525", "RHCG, SLC7A8, RHBG"], ["GO:0006885 ~ regulation of pH", "3", "0.005972", "RHCG, ATP6V1B1, ATP6V0A4"], ["GO:0090090 ~ negative regulation of canonical Wnt signaling pathway", "6", "0.006989", "CTHRC1, CAV1, SOST, GPC3, SFRP1, PSMB9"], ["GO:0042493 ~ response to drug", "8", "0.007086", "P2RX7, CA9, SFRP1, LGALS1, SLC34A1, HSD11B2, ABAT, NNMT"], ["GO:0008152 ~ metabolic process", "6", "0.007913", "ENPP6, LPCAT1, SUCLG1, MAN1C1, ACSF2, ACAA1"], ["GO:0032092 ~ positive regulation of protein binding", "4", "0.010136", "CTHRC1, CAV1, PLK2, TRIB3"], ["GO:0055074 ~ calcium ion homeostasis", "3", "0.011171", "CAV1, ATP6V1B1, CALB1"], ["GO:0006508 ~ proteolysis", "10", "0.011293", "C1QA, C1QB, GGT6, SFRP1, C3, CTSS, CASP1, PLG, DPEP1, XPNPEP2"], ["GO:0055114 ~ oxidation-reduction process", "11", "0.011711", "ALDH6A1, TYRP1, PLOD2, NDUFA4L2, RRM2, EGLN3, HSD11B2, ALDH4A1, DIO1, DCXR, HPD"], ["GO:0010951 ~ negative regulation of endopeptidase activity", "5", "0.012067", "KNG1, C3, SERPINA5, HRG, CSTA"], ["GO:0050900 ~ leukocyte migration", "5", "0.012407", "SLC16A3, CAV1, SLC7A8, FCER1G, ITGB2"], ["GO:0045880 ~ positive regulation of smoothened signaling pathway", "3", "0.013221", "GPC3, SFRP1, FGF9"], ["GO:0001798 ~ positive regulation of type IIa hypersensitivity", "2", "0.014597", "C3, FCER1G"], ["GO:2000054 ~ negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification", "2", "0.014597", "SOST, SFRP1"], ["GO:0061621 ~ canonical glycolysis", "3", "0.01542", "ENO2, PFKP, HK2"], ["GO:0001503 ~ ossification", "4", "0.020939", "SOST, SLC34A1, ATP6V1B1, ATP6V0A4"], ["GO:0006954 ~ inflammatory response", "8", "0.021562", "KNG1, TNFAIP6, P2RX7, CXCR4, C3, TLR2, TLR3, ITGB2"], ["GO:0050717 ~ positive regulation of interleukin-1 alpha secretion", "2", "0.021815", "P2RX7, CASP1"], ["GO:2000116 ~ regulation of cysteine-type endopeptidase activity", "2", "0.021815", "BIRC3, PSMB9"], ["GO:0070634 ~ transepithelial ammonium transport", "2", "0.021815", "RHCG, RHBG"], ["GO:0019065 ~ receptor-mediated endocytosis of virus by host cell", "2", "0.021815", "CAV2, CAV1"], ["GO:0015991 ~ ATP hydrolysis coupled proton transport", "3", "0.022874", "ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["GO:0051480 ~ regulation of cytosolic calcium ion concentration", "3", "0.022874", "CAV1, PVALB, CALB1"], ["GO:0001525 ~ angiogenesis", "6", "0.024169", "CAV1, FGF9, TGFBI, HRG, FGF1, ANGPTL4"], ["GO:0002931 ~ response to ischemia", "3", "0.024234", "CAV1, NOL3, HK2"], ["GO:0072221 ~ metanephric distal convoluted tubule development", "2", "0.028982", "UMOD, CALB1"], ["GO:0002283 ~ neutrophil activation involved in immune response", "2", "0.028982", "FCER1G, TYROBP"], ["GO:0007162 ~ negative regulation of cell adhesion", "3", "0.029996", "KNG1, TGFBI, HRG"], ["GO:0006955 ~ immune response", "8", "0.03533", "RGS1, TNFSF13B, C3, ENPP3, TLR2, CTSS, FCGR3A, FCGR3B"], ["GO:0070836 ~ caveola assembly", "2", "0.036096", "CAV2, CAV1"], ["GO:0015696 ~ ammonium transport", "2", "0.036096", "RHCG, RHBG"], ["GO:0006873 ~ cellular ion homeostasis", "2", "0.036096", "RHCG, SLC4A1"], ["GO:0019740 ~ nitrogen utilization", "2", "0.036096", "RHCG, RHBG"], ["GO:0010543 ~ regulation of platelet activation", "2", "0.036096", "FCER1G, HRG"], ["GO:0051005 ~ negative regulation of lipoprotein lipase activity", "2", "0.036096", "APOC1, ANGPTL4"], ["GO:0034123 ~ positive regulation of toll-like receptor signaling pathway", "2", "0.036096", "TLR2, TLR3"], ["GO:0031623 ~ receptor internalization", "3", "0.039536", "CAV1, FCER1G, ITGB2"], ["GO:0006094 ~ gluconeogenesis", "3", "0.041225", "ENO2, FBP1, PCK2"], ["GO:0050776 ~ regulation of immune response", "5", "0.041952", "C3, ITGB2, FCGR3A, TREM2, TYROBP"], ["GO:0030514 ~ negative regulation of BMP signaling pathway", "3", "0.04294", "CAV1, SOST, SFRP1"], ["GO:0000187 ~ activation of MAPK activity", "4", "0.043944", "P2RX7, CXCR4, FGF1, DUSP9"], ["GO:0007596 ~ blood coagulation", "5", "0.046407", "P2RX7, SERPINA5, FCER1G, ENTPD1, PLG"], ["GO:0032760 ~ positive regulation of tumor necrosis factor production", "3", "0.046448", "TLR2, FCER1G, TLR3"], ["cell composition", "GO:0070062 ~ extracellular exosome", "61", "4.70E-17", "FGF9, SLC7A8, CALB1, AQP2, EFHD1, GPC3, PVALB, CXCR4, PLOD2, SERPINA5, TMEM52B, TGFBI, SLC4A1, FCGR3A, ATP6V0D2, FCGR3B, DPEP1, HPD, KNG1, ALDH6A1, CRYAA, SUCLG1, SLC22A8, PFKP, FBP1, C1QA, C1QB, RHCG, MNDA, ABAT, CSTA, CHL1, SH3GL2, ENPP6, C3, ENPP3, APOC1, ITGB2, UMOD, ATP6V1B1, ENO2, HS6ST2, HRG, SUCNR1, ENTPD1, SLC12A3, LGALS1, PCK2, MAN1C1, PLG, PSMB9, XPNPEP2, AFM, GGT6, SFRP1, NPHS2, SLC13A3, FABP1, ATP6V0A4, IGFBP3, DCXR"], ["GO:0016323 ~ basolateral plasma membrane", "12", "6.23E-08", "CLDN8, CAV1, RHCG, CA9, SLC22A7, SLC22A8, SLC7A8, RHBG, UMOD, SLC4A1, ATP6V1B1, AQP2"], ["GO:0005886 ~ plasma membrane", "53", "4.79E-06", "CLDN8, TLR2, SLC7A8, AQP2, GPC3, CXCR4, TGFBI, SLC4A1, FCGR3A, FCGR3B, DPEP1, KNG1, COL23A1, SLC22A7, SUCLG1, SLC22A8, SLC34A1, TNFSF13B, RHCG, CA9, ATP6V1G3, TREM2, SH3GL2, CHL1, ENPP6, CAV2, CAV1, FXYD4, C3, RHBG, TRIB3, CLCNKB, ITGB2, KCNJ1, ENO2, TMEM30B, FCER1G, HRG, SUCNR1, ENTPD1, TYROBP, SLC12A3, PLG, XPNPEP2, SLC16A3, P2RX7, RGS1, SFRP1, NPHS2, SLC13A3, DIO1, ATP6V0A4, DCXR"], ["GO:0005887 ~ integral component of plasma membrane", "25", "5.00E-05", "CAV2, CAV1, FXYD4, SLC12A3, SLC22A7, ENPP3, SLC22A8, TLR2, RHBG, SLC34A1, SLC7A8, TLR3, CLCNKB, AQP2, SLC16A3, P2RX7, LAPTM5, GPC3, RHCG, NPHS2, FCER1G, SLC13A3, SLC4A1, ENTPD1, TYROBP"], ["GO:0016471 ~ vacuolar proton-transporting V-type ATPase complex", "4", "7.28E-05", "ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["GO:0072562 ~ blood microparticle", "8", "1.04E-04", "KNG1, C1QB, AFM, C3, HRG, SLC4A1, PLG, ANGPTL4"], ["GO:0005578 ~ proteinaceous extracellular matrix", "10", "1.24E-04", "CTHRC1, SOST, GPC3, SFRP1, LGALS1, TGFBI, UMOD, FGF1, CHL1, ANGPTL4"], ["GO:0016324 ~ apical plasma membrane", "10", "2.30E-04", "CAV1, RHCG, SLC12A3, SLC34A1, UMOD, ATP6V1B1, ATP6V0A4, ATP6V0D2, DPEP1, AQP2"], ["GO:0005615 ~ extracellular space", "22", "4.94E-04", "KNG1, CTHRC1, C3, FGF9, LGALS1, HILPDA, CTSS, PLG, TNFAIP6, AFM, GPC3, SOST, TNFSF13B, SFRP1, SERPINA5, TGFBI, ENO2, CSTA, FGF1, IGFBP3, DPEP1, ANGPTL4"], ["GO:0031225 ~ anchored component of membrane", "6", "0.001254", "ENPP6, GPC3, UMOD, FCGR3B, DPEP1, XPNPEP2"], ["GO:0016021 ~ integral component of membrane", "53", "0.002201", "CLDN8, TLR2, SLC7A8, TLR3, AQP2, CXCR4, EVI2A, TMEM52B, SMIM5, SLC4A1, FCGR3A, FCGR3B, COL23A1, SLC22A7, SLC22A8, SLC34A1, DMRT2, HEPACAM2, TNFSF13B, CA9, RHCG, SPAG4, HSD11B2, TREM2, CHL1, NETO2, CAV2, TYRP1, CAV1, TMEM213, ENPP3, RHBG, CLCNKB, UMOD, KCNJ1, SEMA5B, LPCAT1, TMEM30B, FCER1G, HS6ST2, SUCNR1, ENTPD1, MS4A6A, TYROBP, TMEM45A, SLC12A3, NDUFA4L2, HILPDA, GGT6, SFRP1, SLC13A3, DIO1, ATP6V0A4"], ["GO:0043234 ~ protein complex", "10", "0.002667", "CAV2, CAV1, SOST, PVALB, SERPINA5, NPHS2, DDB2, FABP1, PRKCDBP, BIRC3"], ["GO:0005576 ~ extracellular region", "22", "0.004463", "KNG1, ENPP6, FGF9, C3, APOC1, UMOD, CTSS, PLG, C1QA, C1QB, AFM, SOST, TNFSF13B, SFRP1, SERPINA5, TGFBI, HRG, FGF1, TREM2, CASP1, IGFBP3, ANGPTL4"], ["GO:0009986 ~ cell surface", "11", "0.005205", "SFRP1, CXCR4, LGALS1, TLR2, SLC34A1, FCER1G, TLR3, HILPDA, ITGB2, PLG, TYROBP"], ["GO:0002080 ~ acrosomal membrane", "3", "0.007858", "CAV2, CAV1, SERPINA5"], ["GO:0005602 ~ complement component C1 complex", "2", "0.014107", "C1QA, C1QB"], ["GO:0045121 ~ membrane raft", "6", "0.015662", "CAV2, CAV1, NPHS2, TLR2, SLC34A1, BIRC3"], ["GO:0000139 ~ Golgi membrane", "10", "0.024687", "CAV2, CAV1, LPCAT1, ST8SIA4, TLR3, HS6ST2, HEPACAM2, MAN1C1, SH3GL2, HPD"], ["GO:0005581 ~ collagen trimer", "4", "0.027574", "C1QA, CTHRC1, C1QB, COL23A1"], ["GO:0005759 ~ mitochondrial matrix", "7", "0.028942", "PDK1, ALDH6A1, SUCLG1, ALDH4A1, ABAT, PCK2, ACSF2"], ["GO:0005782 ~ peroxisomal matrix", "3", "0.042028", "ACOX2, FABP1, ACAA1"], ["molecular function", "GO:0019864 ~ IgG binding", "4", "6.11E-05", "FCER1G, UMOD, FCGR3A, FCGR3B"], ["GO:0008201 ~ heparin binding", "7", "0.001175", "KNG1, SOST, SFRP1, FGF9, SERPINA5, HRG, FGF1"], ["GO:0005102 ~ receptor binding", "10", "0.001189", "KNG1, ACOX2, P2RX7, CAV1, TNFSF13B, C3, HRG, HILPDA, PLG, TYROBP"], ["GO:0030506 ~ ankyrin binding", "3", "0.009327", "RHCG, RHBG, SLC4A1"], ["GO:0001530 ~ lipopolysaccharide binding", "3", "0.011232", "P2RX7, TLR2, TREM2"], ["GO:0043027 ~ cysteine-type endopeptidase inhibitor activity involved in apoptotic process", "3", "0.012243", "NOL3, BIRC3, DPEP1"], ["GO:0015301 ~ anion:anion antiporter activity", "3", "0.012243", "SLC22A7, SLC22A8, SLC4A1"], ["GO:0051117 ~ ATPase binding", "4", "0.017177", "CAV1, FXYD4, ATP6V1G3, ATP6V0A4"], ["GO:0042802 ~ identical protein binding", "12", "0.022021", "CLDN8, CAV1, NOL3, SFRP1, CRYAA, FBP1, ALDH4A1, TLR3, SH3GL2, DCXR, TYROBP, ANGPTL4"], ["GO:0015078 ~ hydrogen ion transmembrane transporter activity", "3", "0.022995", "ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["GO:0004869 ~ cysteine-type endopeptidase inhibitor activity", "3", "0.025762", "KNG1, HRG, CSTA"]], "row_count": 83, "column_count": 5, "numeric_cells": 265, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:34266404:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:36b657994b95a03865c5ed2736f3f44a8eddfe87a6b89878f4e6701e6e7bf546", "bytes": 2670, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#Tab4", "version": null, "note": "KEGG pathway analysis of DEGs associated with ccRCC", "structure": {"pmcid": "PMC8283915", "section_index": 11, "section_title": "GO and KEGG analysis of DEG", "row_count": 25, "column_count": 4}, "table": {"label": "Table 4", "caption": "KEGG pathway analysis of DEGs associated with ccRCC", "rows": [["Term", "Count", "P Value", "Genes"], ["hsa04966:Collecting duct acid secretion", "6", "1.77E-05", "CLCNKB, SLC4A1, ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["hsa05150:Staphylococcus aureus infection", "7", "5.12E-05", "C1QA, C1QB, C3, ITGB2, FCGR3A, FCGR3B, PLG"], ["hsa04145:Phagosome", "10", "9.64E-05", "C3, TLR2, ITGB2, CTSS, ATP6V1G3, FCGR3A, ATP6V1B1, ATP6V0A4, FCGR3B, ATP6V0D2"], ["hsa05323:Rheumatoid arthritis", "7", "7.65E-04", "TNFSF13B, TLR2, ITGB2, ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["hsa05152:Tuberculosis", "9", "0.001573", "C3, TLR2, FCER1G, ITGB2, CTSS, FCGR3A, ATP6V0A4, FCGR3B, ATP6V0D2"], ["hsa04610:Complement and coagulation cascades", "6", "0.001629", "KNG1, C1QA, C1QB, C3, SERPINA5, PLG"], ["hsa01100:Metabolic pathways", "26", "0.006292", "ACOX2, TYRP1, ENPP3, HK2, UPP2, ATP6V1B1, LPCAT1, ENO2, ALDH4A1, ATP6V0D2, HPD, ALDH6A1, NDUFA4L2, SUCLG1, FBP1, PFKP, PCK2, MAN1C1, GGT6, RRM2, ABAT, ATP6V1G3, ATP6V0A4, DCXR, ACAA1, NNMT"], ["hsa03320:PPAR signaling pathway", "5", "0.009598", "ACOX2, FABP1, PCK2, ACAA1, ANGPTL4"], ["hsa00010:Glycolysis / Gluconeogenesis", "5", "0.009598", "ENO2, FBP1, PFKP, HK2, PCK2"], ["hsa05140:Leishmaniasis", "5", "0.011719", "C3, TLR2, ITGB2, FCGR3A, FCGR3B"], ["hsa01200:Carbon metabolism", "6", "0.013278", "ALDH6A1, SUCLG1, ENO2, FBP1, PFKP, HK2"], ["hsa05133:Pertussis", "5", "0.01412", "C1QA, C1QB, C3, ITGB2, CASP1"], ["hsa05110:Vibrio cholerae infection", "4", "0.026859", "ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["hsa05134:Legionellosis", "4", "0.029616", "C3, TLR2, ITGB2, CASP1"], ["hsa04721:Synaptic vesicle cycle", "4", "0.043794", "ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["hsa05230:Central carbon metabolism in cancer", "4", "0.045546", "SLC16A3, PDK1, PFKP, HK2"], ["hsa00640:Propanoate metabolism", "3", "0.047335", "ALDH6A1, SUCLG1, ABAT"], ["hsa01130:Biosynthesis of antibiotics", "7", "0.04889", "SUCLG1, ENO2, FBP1, PFKP, HK2, PCK2, ACAA1"], ["hsa05120:Epithelial cell signaling in Helicobacter pylori infection", "4", "0.051005", "ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["hsa00051:Fructose and mannose metabolism", "3", "0.060164", "FBP1, PFKP, HK2"], ["hsa04650:Natural killer cell mediated cytotoxicity", "5", "0.065949", "FCER1G, ITGB2, FCGR3A, FCGR3B, TYROBP"], ["hsa00190:Oxidative phosphorylation", "5", "0.084557", "NDUFA4L2, ATP6V1G3, ATP6V1B1, ATP6V0A4, ATP6V0D2"], ["hsa04960:Aldosterone-regulated sodium reabsorption", "3", "0.085035", "FXYD4, HSD11B2, KCNJ1"], ["hsa05322:Systemic lupus erythematosus", "5", "0.086365", "C1QA, C1QB, C3, FCGR3A, FCGR3B"]], "row_count": 25, "column_count": 4, "numeric_cells": 75, "header_rows": 1, "locator": "section[11]/table-wrap[2]#Tab4"}}], "gaps": ["asset:data:geo:GSE14762 not downloaded", "asset:data:geo:GSE14762 licence not read", "asset:data:geo:GSE53757 not downloaded", "asset:data:geo:GSE53757 licence not read", "asset:data:geo:GSE66270 not downloaded", "asset:data:geo:GSE66270 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-4", "family": null, "specific": null, "label": "Robust Rank Aggreg (RRA) analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Robust Rank Aggreg (RRA) analysis (http://cran.r-project.org/) was used to list the up-regulated and down-regulated genes."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE14762", "GSE66270", "GSE53757"], "resolved_accessions": ["GSE14762", "GSE66270", "GSE53757"], "statements": ["The data used to support the findings of this study are all included within the thesis. The gene expression data can be accessed on Gene Expression Omnibus (GEO). Oncomine database was used to get the expression profile of hub genes. GEPIA database was used to obtain the overall survival and disease free survival analysis of genes.\nThe datasets analysed during this study are available in the:\n1. GSE14762_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE14762&format=file\n2. GSE15641_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE15641&format=file\n3. GSE53757_RAW: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE53757&format=file\n4. GSE53757_series_matrix.txt: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53757/matrix/GSE53757_series_matrix.txt.gz"], "basis": "The paper names GSE14762, GSE66270, GSE53757 in Gene Expression Omnibus (GEO), National Center for Biotechnology Information (NCBI) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34266404", "data:geo:GSE14762", "asset:table:pmid:34266404:1", "asset:table:pmid:34266404:2", "asset:table:pmid:34266404:3", "asset:table:pmid:34266404:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14762"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 26737, "completion_tokens": 2453, "cached_tokens": 9097}}, "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:34266404", "type": "paper", "label": "pmid:34266404"}, {"id": "source:pmid:34266404", "type": "manuscript", "label": "PMID 34266404 full text"}, {"id": "data:geo:GSE14762", "type": "dataset", "label": "GEO GSE14762"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34266404", "type": "paper", "label": "pmid:34266404"}, {"id": "source:pmid:34266404", "type": "manuscript", "label": "PMID 34266404 full text"}, {"id": "data:geo:GSE14762", "type": "dataset", "label": "GEO GSE14762"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34266404", "type": "extraction", "used": ["source:pmid:34266404"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14762", "type": "accession_resolution", "used": ["data:geo:GSE14762"], "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:34266404", "parent_hash": "sha256:0346b07a9d2a2288f0939858ce5ba83cf69eabfb5b4e50b6a72a45e60d1aedc3", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE14762 licence not read", "asset:data:geo:GSE14762 not downloaded", "asset:data:geo:GSE53757 licence not read", "asset:data:geo:GSE53757 not downloaded", "asset:data:geo:GSE66270 licence not read", "asset:data:geo:GSE66270 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ts of ccRCC. 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