Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Zao-Jiao-Ci in the Treatment of LSCC.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34257654", "kind": "science-record", "revision": 5, "content_hash": "sha256:98e0adbe75ce42ff2e05bd471cf185f8da8ef24438ece83e466a261717b2a20c", "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": "Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Zao-Jiao-Ci in the Treatment of LSCC.", "doi": "10.1155/2021/8862821", "pmid": "34257654", "authors": ["Feng Xiang", "Linman Li", "Jieling Lin", "Shasha Li", "Guiyuan Peng"], "journal": "Journal of oncology", "year": 2021, "abstract": "OBJECTIVE: Zao-Jiao-Ci (ZJC), a traditional Chinese medicine, is considered as a promising candidate to treat laryngeal squamous cell carcinoma (LSCC). However, the underlying molecular mechanism remains unclear.\nMETHODS: Gene expression profiles of GSE36668 were available from the GEO database, and differentially expressed genes (DEGs) of LSCC were obtained by R package; subsequently, enrichment analysis on KEGG and GO of DEGs was performed. The active ingredients of ZJC were screened from the TCMSP database, and the matched candidate targets were obtained by PharmMapper. Furthermore, we constructed protein-protein interaction (PPI) networks of DEGs and candidate targets, respectively, and we screened the core network from the merged network through combining the two PPI networks using Cytoscape 3.7.2. The key targets derived from the core network were analyzed to find out the associated KEGG signal enrichment pathway. By the GEPIA online website, Kaplan-Meier analysis was used to complete the overall survival and disease-free survival of the selected genes in the core module.\nRESULTS: We identified 96 candidate targets of ZJC and 86 DEGs of LSCC, the latter including 50 upregulated genes and 36 downregulated genes. DEGs were obviously enriched in the following biological functions: extracellular structure organization, the extracellular matrix organization, and endodermal cell differentiation. The 60 key targets from the core network were enriched in the signal pathways including transcriptional misregulation cancer, cell cycle, and so on. We found that LSCC patients with high expression of HIST1H3J, HIST1H3F, and ITGA4 had worse overall survival, while higher expression of NTRK1, COPS5, HIST1H3A, and HIST1H3G had significantly worse disease-free survival.\nCONCLUSION: It suggested that the interaction between ZJC and LSCC was related to the signal pathways of transcriptional misregulation cancer and cell cycle, revealing that it may be the mechanism of ZJC in the treatment of LSCC.", "claims": [{"id": "claim-method", "statement": "By the GEPIA online website, Kaplan–Meier analysis was used to complete the overall survival and disease-free survival of the selected genes in the core module.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34257654", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "By the GEPIA online website, Kaplan–Meier analysis was used to complete the overall survival and disease-free survival of the selected genes in the core module."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original data series GSE84957 used to support the findings of this study is downloaded from the Gene Expression Omnibus (GEO) microarray dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34257654", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "The original data series GSE84957 used to support the findings of this study is downloaded from the Gene Expression Omnibus (GEO) microarray dataset."}], "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:34257654"], "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:GSE84957"], "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:GSE84957"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34257654", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/8862821", "sha256": "sha256:5d76e1a40ca10468910eab4a1c2043d25e51e5e6bfb2221b94b19c8d76db8710", "bytes": 26393, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/8862821", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8257394", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84957", "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=GSE84957", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84957", "version": null, "note": "The original data series GSE84957 used to support the findings of this study is downloaded from the Gene Expression Omnibus (GEO) microarray dataset.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original data series GSE84957 used to support the findings of this study is downloaded from the Gene Expression Omnibus (GEO) microarray dataset.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2254690", "GSM2254691", "GSM2254692", "GSM2254693", "GSM2254694", "GSM2254695", "GSM2254696", "GSM2254697", "GSM2254698", "GSM2254699", "GSM2254700", "GSM2254701", "GSM2254702", "GSM2254703", "GSM2254704", "GSM2254705", "GSM2254706", "GSM2254707"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "17843", "taxon": "Homo sapiens", "title": "Long Noncoding RNA and mRNA Expression Profile in Laryngeal Squamous Cell Carcinoma", "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:34257654:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:976c45274fd3e05a69bfd2dfc6aef9a7debfd9664d4bfe0be021ec0faa721683", "bytes": 611, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#tab1", "version": null, "note": "The active ingredients in ZJC.", "structure": {"pmcid": "PMC8257394", "section_index": 10, "section_title": "3.1. Active Ingredients and Targets of ZJC", "row_count": 12, "column_count": 4}, "table": {"label": "Table 1", "caption": "The active ingredients in ZJC.", "rows": [["No.", "Component", "OB (%)", "DL"], ["1", "Fisetin", "52.60", "0.24"], ["2", "Fustin", "50.91", "0.24"], ["3", "(-)-Taxifolin", "60.51", "0.27"], ["4", "Flavanone", "41.35", "0.24"], ["5", "Beta-sitosterol", "36.91", "0.75"], ["6", "Sitosterol", "36.91", "0.75"], ["7", "Kaempferol", "41.88", "0.24"], ["8", "Stigmasterol", "43.83", "0.76"], ["9", "Stigmast-4-ene-3,6-dione", "39.12", "0.79"], ["10", "Ent-epicatechin", "48.96", "0.24"], ["11", "Quercetin", "46.43", "0.28"]], "row_count": 12, "column_count": 4, "numeric_cells": 34, "header_rows": 1, "locator": "section[10]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:34257654:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f58b90217028c102800c3a5c009d693a8d709ca2f4b99d7a92fae611f703cdaa", "bytes": 8154, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tab2", "version": null, "note": "Differently expressed genes from GSE84957.", "structure": {"pmcid": "PMC8257394", "section_index": 12, "section_title": "3.3. LSCC Differentially Expressed Genes (DEGs)", "row_count": 82, "column_count": 7}, "table": {"label": "Table 2", "caption": "Differently expressed genes from GSE84957.", "rows": [["GeneSample", "logFC", "AveExpr", "t", "P value", "Adj. P value", "B"], ["CST1", "4.255518022", "7.417759878", "14.09776157", "1.49E − 11", "3.71E − 07", "15.51198443"], ["XLOC_004426", "3.044228211", "3.370726783", "11.59258332", "4.32E − 10", "3.61E − 06", "12.75595229"], ["MMP11", "3.903325333", "6.986877144", "11.58573097", "4.36E − 10", "3.61E − 06", "12.74750381"], ["GPRIN1", "3.857745044", "5.653573411", "11.29565743", "6.67E − 10", "4.15E − 06", "12.38486185"], ["COL7A1", "3.191737644", "9.258242733", "10.78042002", "1.45E − 09", "7.22E − 06", "11.71597451"], ["FAM3D", "−5.792545067", "7.2950313", "−10.09792", "4.24E − 09", "1.51E − 05", "10.77877059"], ["LRP12", "3.580821556", "4.005304867", "9.316160682", "1.54E − 08", "4.26E − 05", "9.629111691"], ["CTHRC1", "4.740806433", "7.128087172", "9.196467428", "1.89E − 08", "4.30E − 05", "9.445581444"], ["LOC100506027", "4.143287578", "4.568671189", "8.999347488", "2.66E − 08", "4.97E − 05", "9.138857621"], ["TJP3", "−3.364634633", "7.834813517", "−8.904023211", "3.14E − 08", "4.97E − 05", "8.9885142"], ["IGFBP3", "3.604138167", "10.55244692", "8.893742313", "3.20E − 08", "4.97E − 05", "8.972220302"], ["ARSI", "3.152646867", "3.986923189", "8.298478812", "9.26E − 08", "0.000121313", "8.002153147"], ["TMEM158", "3.718106033", "4.697089117", "8.222894187", "1.06E − 07", "0.000132353", "7.875178695"], ["PLAUR", "3.027472033", "7.824632761", "8.051498015", "1.46E − 07", "0.000165132", "7.584034636"], ["MSR1", "3.918547922", "4.497970906", "7.705672", "2.80E − 07", "0.000248682", "6.98290287"], ["TGFBI", "3.415596633", "9.235072794", "7.534242043", "3.89E − 07", "0.000311941", "6.678084284"], ["SPP1", "4.853097222", "7.318721011", "7.296283387", "6.17E − 07", "0.000415016", "6.247440183"], ["CYP4B1", "−3.938406289", "5.174530178", "−7.145413133", "8.31E − 07", "0.000492716", "5.96986977"], ["SH3BGRL2", "−4.071528089", "6.438326422", "−7.12999436", "8.57E − 07", "0.000495582", "5.941304558"], ["LOC100653149", "3.268119356", "5.443807811", "7.078046014", "9.50E − 07", "0.000525005", "5.844794163"], ["MMP1", "4.862459922", "6.783056994", "7.002232691", "1.10E − 06", "0.000590601", "5.70320204"], ["TM4SF19", "4.052795678", "5.81647465", "6.87435807", "1.43E − 06", "0.000696569", "5.462380919"], ["COL5A2", "3.504323078", "7.584409283", "6.759032897", "1.80E − 06", "0.000815742", "5.243053839"], ["HOXD11", "3.550990856", "5.087563172", "6.54672159", "2.78E − 06", "0.001117349", "4.834020589"], ["CXCL11", "4.762321211", "4.652769394", "6.519758265", "2.94E − 06", "0.00115171", "4.781590785"], ["LOC100652832", "3.253860656", "6.465006439", "6.502526246", "3.05E − 06", "0.00115171", "4.748026804"], ["CXCL10", "4.519192844", "5.640273644", "6.498769364", "3.07E − 06", "0.00115171", "4.740703422"], ["XLOC_006053", "−3.635899633", "9.156396294", "−6.475756406", "3.22E − 06", "0.00115171", "4.69579809"], ["KRT17", "4.404712111", "11.51599561", "6.464235069", "3.30E − 06", "0.00115171", "4.673287016"], ["PTHLH", "4.098820033", "7.949679894", "6.341212465", "4.26E − 06", "0.001315184", "4.431701824"], ["CXCL12", "−3.476515767", "8.330393117", "−6.24092991", "5.26E − 06", "0.001422596", "4.233143024"], ["XLOC_l2_006021", "4.372459256", "11.50269782", "6.229963809", "5.38E − 06", "0.001424781", "4.211342414"], ["COL8A1", "3.211121667", "6.060922078", "6.177430972", "6.01E − 06", "0.001526438", "4.106669064"], ["CLCA4", "−5.919341656", "8.217143061", "−6.126082361", "6.70E − 06", "0.001661254", "4.003977039"], ["HMGA2", "3.706329122", "3.703429261", "6.117033971", "6.83E − 06", "0.00166615", "3.985842669"], ["WISP1", "3.021981556", "5.595450789", "6.039266244", "8.06E − 06", "0.001838778", "3.829512486"], ["NRG1", "3.430506311", "6.615773067", "6.013403137", "8.51E − 06", "0.001907796", "3.777336092"], ["ANKRD20A9P", "−3.027104311", "6.964110233", "−5.991259577", "8.92E − 06", "0.001947336", "3.732590438"], ["GCNT3", "−3.483360222", "5.808183467", "−5.968076797", "9.38E − 06", "0.001965485", "3.685672938"], ["MYOC", "−3.290936644", "3.378123278", "−5.964261662", "9.45E − 06", "0.001965485", "3.677944815"], ["ODZ2", "3.030850211", "7.342800339", "5.955698768", "9.63E − 06", "0.001965485", "3.660592194"], ["DNAPTP3", "4.162512589", "8.355008817", "5.948057503", "9.79E − 06", "0.001979224", "3.645098841"], ["FUT3", "−3.452809133", "7.136305", "−5.832221646", "1.25E − 05", "0.00221345", "3.409270286"], ["CRNN", "−6.524733278", "9.72241585", "−5.821941297", "1.28E − 05", "0.002227034", "3.388254529"], ["CFD", "−3.520037456", "9.369048272", "−5.800510125", "1.34E − 05", "0.002286888", "3.344398953"], ["COL1A2", "3.096446333", "11.78684306", "5.800402532", "1.34E − 05", "0.002286888", "3.34417863"], ["CXCL9", "3.067348622", "6.615663178", "5.759709415", "1.47E − 05", "0.002369549", "3.260741185"], ["PDPN", "3.170275733", "10.0438188", "5.709284988", "1.64E − 05", "0.00252911", "3.157054467"], ["INHBA", "3.099887078", "5.809753317", "5.656043661", "1.84E − 05", "0.002640463", "3.04722486"], ["MMP12", "4.162521167", "3.736549417", "5.638864584", "1.91E − 05", "0.002687547", "3.011710913"], ["SCARA5", "−3.861003467", "7.106386856", "−5.634806253", "1.92E − 05", "0.002687547", "3.003315853"], ["COL4A1", "3.293993722", "11.03886292", "5.623430739", "1.97E − 05", "0.002709232", "2.979773593"], ["COL5A1", "3.205179622", "8.674301744", "5.604407653", "2.05E − 05", "0.00279295", "2.940368581"], ["ANKRD20A5P", "−3.118826611", "5.357065783", "−5.574210889", "2.19E − 05", "0.002873117", "2.877727019"], ["TNXB", "−3.390147544", "8.386793894", "−5.46437267", "2.79E − 05", "0.003345526", "2.648949986"], ["CCDC25", "−3.340572133", "7.218539933", "−5.461095079", "2.81E − 05", "0.003345526", "2.6421014"], ["FN1", "3.580535444", "11.63254756", "5.427958008", "3.02E − 05", "0.003525959", "2.572791248"], ["MAL", "−6.360331133", "8.9132381", "−5.380498508", "3.36E − 05", "0.003726774", "2.473306046"], ["FBN2", "3.702098767", "4.647001128", "5.317540391", "3.86E − 05", "0.003963698", "2.340945176"], ["KRT4", "−5.783585056", "12.44990214", "−5.27501498", "4.24E − 05", "0.004304541", "2.251297748"], ["MSC", "3.021481811", "5.778950494", "5.273063535", "4.25E − 05", "0.004304541", "2.247179302"], ["MYZAP", "−3.966621", "6.975986556", "−5.218924365", "4.80E − 05", "0.00453758", "2.132761995"], ["CHI3L1", "3.447755856", "8.454925183", "5.212706409", "4.86E − 05", "0.004565936", "2.119601631"], ["XLOC_008370", "−4.086801056", "5.071876417", "−5.195774385", "5.05E − 05", "0.004618685", "2.083744902"], ["AMY1C", "−3.066162922", "4.171807861", "−5.181124682", "5.22E − 05", "0.004702673", "2.052698071"], ["FAM107 A", "−3.366929044", "6.613174211", "−5.153177492", "5.55E − 05", "0.004829406", "1.993410827"], ["CA9", "4.004719489", "4.832498267", "5.105740988", "6.17E − 05", "0.005199505", "1.89260426"], ["SFI1", "−3.172654489", "7.898643289", "−5.038975245", "7.16E − 05", "0.005657681", "1.75036129"], ["KRT24", "−4.307497756", "6.663276378", "−4.903497209", "9.71E − 05", "0.006802832", "1.460515802"], ["FAM3B", "−3.002864178", "7.472917967", "−4.851035631", "0.000109236", "0.007385034", "1.347873623"], ["PSCA", "−4.424161267", "6.177034822", "−4.836697273", "0.000112824", "0.007525305", "1.317050516"], ["TREM1", "3.132156567", "5.329140306", "4.802412753", "0.000121894", "0.007755997", "1.243287728"], ["MMP7", "4.0077695", "8.433879583", "4.797447382", "0.000123267", "0.007808567", "1.232597743"], ["XLOC_l2_007931", "−3.335940244", "10.48608082", "−4.789159173", "0.000125595", "0.007875182", "1.214750103"], ["KRT6B", "4.076616322", "9.703940506", "4.773184049", "0.000130209", "0.007978995", "1.180336064"], ["SERPINE1", "3.5038576", "7.4466057", "4.752919626", "0.00013631", "0.008152053", "1.136656679"], ["ABCA8", "−3.2918408", "5.542601178", "−4.749840302", "0.000137262", "0.008169717", "1.130016856"], ["SNX31", "−3.294362333", "3.714450967", "−4.727065435", "0.000144517", "0.008363625", "1.080888859"], ["KRT16", "3.956891967", "10.74006252", "4.71119429", "0.000149801", "0.008567571", "1.046633089"], ["RSAD2", "3.410952911", "5.3110705", "4.667343136", "0.000165442", "0.009086152", "0.951904596"], ["CEACAM5", "−3.982757711", "9.060092478", "−4.649201732", "0.000172387", "0.009343839", "0.912681384"]], "row_count": 82, "column_count": 7, "numeric_cells": 511, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tab2"}}, {"id": "asset:table:pmid:34257654:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9a7c9efe77e9b02e0c1cdea0e9891fe9f32c67ad34934aff9950b2325013fefe", "bytes": 5284, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tab3", "version": null, "note": "The topological properties of the 60 key nodes.", "structure": {"pmcid": "PMC8257394", "section_index": 14, "section_title": "3.5. PPI Network Construction and Key Targets Screening", "row_count": 61, "column_count": 7}, "table": {"label": "Table 3", "caption": "The topological properties of the 60 key nodes.", "rows": [["Name (the key targets)", "Degree", "Betweenness", "Betweenness centrality", "Closeness", "Closeness centrality", "Topological coefficient"], ["YWHAZ", "155", "3001.377571", "0.01183919", "0.585365854", "0.58536585", "0.14373835"], ["YWHAG", "87", "816.3912445", "0.00322033", "0.537313433", "0.53731343", "0.16424877"], ["MCM5", "101", "1080.133008", "0.00426068", "0.542518837", "0.54251884", "0.14457089"], ["STAU1", "114", "1407.485881", "0.00555195", "0.550218341", "0.55021834", "0.13468492"], ["ITGA4", "208", "7021.25165", "0.02769593", "0.616891065", "0.61689106", "0.10712371"], ["APP", "125", "5666.777349", "0.02235309", "0.557522124", "0.55752212", "0.10929128"], ["CUL3", "211", "7900.538977", "0.03116436", "0.626865672", "0.62686567", "0.1083315"], ["CUL2", "121", "2193.490854", "0.00865241", "0.556906077", "0.55690608", "0.1311238"], ["CUL4A", "84", "1104.388869", "0.00435636", "0.519052523", "0.51905252", "0.14961657"], ["CUL1", "158", "2737.270054", "0.0107974", "0.579976985", "0.57997699", "0.12774443"], ["COPS5", "173", "4596.081368", "0.01812964", "0.592941176", "0.59294118", "0.11812865"], ["YWHAQ", "116", "2340.92677", "0.00923399", "0.5532382", "0.5532382", "0.13955671"], ["EEF1A1", "111", "2303.865101", "0.0090878", "0.553846154", "0.55384615", "0.15726594"], ["OBSL1", "151", "2614.051749", "0.01031135", "0.572077185", "0.57207719", "0.11367624"], ["TARDBP", "99", "902.4212542", "0.00355968", "0.540192926", "0.54019293", "0.14812918"], ["HSPA8", "102", "1110.484051", "0.0043804", "0.549019608", "0.54901961", "0.1617004"], ["HSPA5", "124", "2786.82878", "0.01099289", "0.56187291", "0.56187291", "0.15308876"], ["HSP90AA1", "115", "3058.241745", "0.0120635", "0.558139535", "0.55813953", "0.13921995"], ["EIF4A3", "94", "923.5252369", "0.00364293", "0.535031847", "0.53503185", "0.14405585"], ["HSP90AB1", "111", "2024.466508", "0.00798568", "0.555066079", "0.55506608", "0.14751182"], ["MYC", "88", "1227.898615", "0.00484355", "0.536741214", "0.53674121", "0.11599255"], ["CCDC8", "145", "2628.810161", "0.01036957", "0.568848758", "0.56884876", "0.11392955"], ["HDAC1", "84", "1756.679856", "0.00692938", "0.525547445", "0.52554745", "0.11154264"], ["RPA1", "106", "1443.910092", "0.00569563", "0.544864865", "0.54486486", "0.13668578"], ["RPA2", "98", "1508.905701", "0.00595201", "0.541353383", "0.54135338", "0.13008096"], ["HNRNPA1", "130", "1803.567503", "0.00711433", "0.565656566", "0.56565657", "0.14709052"], ["EGFR", "143", "4724.066642", "0.01863449", "0.572727273", "0.57272727", "0.1103327"], ["HIST1H3F", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["UBC", "133", "3538.655204", "0.01395853", "0.566929134", "0.56692913", "0.12972445"], ["CUL7", "174", "4304.231567", "0.01697841", "0.594339623", "0.59433962", "0.10695547"], ["HNRNPK", "90", "914.3729176", "0.00360682", "0.535600425", "0.53560043", "0.17748918"], ["TUBB", "85", "1017.885462", "0.00401514", "0.537886873", "0.53788687", "0.16372149"], ["HNRNPU", "106", "2391.698718", "0.00943426", "0.547826087", "0.54782609", "0.15722622"], ["CDK2", "172", "5391.386868", "0.02126679", "0.592941176", "0.59294118", "0.11382953"], ["EWSR1", "85", "1514.316862", "0.00597335", "0.532206969", "0.53220697", "0.15183716"], ["CDC5L", "113", "2162.954989", "0.00853196", "0.550819672", "0.55081967", "0.13024984"], ["NEDD8", "86", "533.4516789", "0.00210425", "0.528301887", "0.52830189", "0.14769424"], ["HIST1H3A", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["HIST1H3D", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["TRAF6", "100", "2757.045931", "0.01087541", "0.538461538", "0.53846154", "0.09652163"], ["HIST1H3C", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["NPM1", "156", "3506.462925", "0.01383155", "0.58400927", "0.58400927", "0.14115178"], ["HIST1H3E", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["HIST1H3I", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["HIST1H3G", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["FUS", "109", "1065.023899", "0.00420108", "0.551422319", "0.55142232", "0.157963"], ["HIST1H3J", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["HIST1H3H", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["HIST1H3B", "86", "437.5273205", "0.00172586", "0.529411765", "0.52941176", "0.14705882"], ["NTRK1", "270", "16394.02825", "0.06466766", "0.673796791", "0.67379679", "0.09989618"], ["FLNA", "89", "1820.058448", "0.00717938", "0.537313433", "0.53731343", "0.15216314"], ["FN1", "307", "27515.32665", "0.10853658", "0.708860759", "0.70886076", "0.09048518"], ["SIRT7", "128", "2444.801055", "0.00964373", "0.5532382", "0.5532382", "0.11177503"], ["GRB2", "136", "4533.847683", "0.01788415", "0.570135747", "0.57013575", "0.12538522"], ["FBXO6", "129", "2240.28371", "0.00883699", "0.558139535", "0.55813953", "0.11844315"], ["VCP", "103", "1651.524516", "0.00651458", "0.544864865", "0.54486486", "0.14998166"], ["CAND1", "152", "2355.429527", "0.0092912", "0.578645235", "0.57864524", "0.12845528"], ["XPO1", "106", "2782.081388", "0.01097416", "0.543103448", "0.54310345", "0.12465874"], ["MCM2", "207", "6633.522707", "0.0261665", "0.621454994", "0.62145499", "0.11887293"], ["YWHAE", "93", "1174.476977", "0.00463283", "0.537313433", "0.53731343", "0.16260551"]], "row_count": 61, "column_count": 7, "numeric_cells": 362, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tab3"}}], "gaps": ["asset:data:geo:GSE84957 not downloaded", "asset:data:geo:GSE84957 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"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": "protein-protein interaction"}}, {"id": "method-3", "family": null, "specific": null, "label": "Kaplan–Meier analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "By the GEPIA online website, Kaplan–Meier analysis was used to complete the overall survival and disease-free survival of the selected genes in the core module."}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE84957"], "resolved_accessions": ["GSE84957"], "statements": ["The original data series GSE84957 used to support the findings of this study is downloaded from the Gene Expression Omnibus (GEO) microarray dataset."], "basis": "The paper names GSE84957 in Gene Expression Omnibus (GEO) microarray dataset and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:34257654", "data:geo:GSE84957", "asset:table:pmid:34257654:1", "asset:table:pmid:34257654:2", "asset:table:pmid:34257654:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE84957"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:16Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22137, "completion_tokens": 1222, "cached_tokens": 792}}, "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:34257654", "type": "paper", "label": "pmid:34257654"}, {"id": "source:pmid:34257654", "type": "manuscript", "label": "PMID 34257654 full text"}, {"id": "data:geo:GSE84957", "type": "dataset", "label": "GEO GSE84957"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34257654", "type": "paper", "label": "pmid:34257654"}, {"id": "source:pmid:34257654", "type": "manuscript", "label": "PMID 34257654 full text"}, {"id": "data:geo:GSE84957", "type": "dataset", "label": "GEO GSE84957"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34257654", "type": "extraction", "used": ["source:pmid:34257654"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE84957", "type": "accession_resolution", "used": ["data:geo:GSE84957"], "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:34257654", "parent_hash": "sha256:f7f7ac42697edeb92fc148bef0acca53c96899ebc3af94201575ca2cad783fd8", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE84957 licence not read", "asset:data:geo:GSE84957 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "analysis_only", "id": "assay:1"}]}