{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30697079", "kind": "science-record", "revision": 8, "content_hash": "sha256:562fb09a51bc641acc364cc7e16ab6ac855f27982069c9028560eb8fd63520a5", "created_at": "2026-11-01T15:40:41Z", "updated_at": "2026-11-01T22:43:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated analysis of lncRNA-associated ceRNA network reveals potential biomarkers for the prognosis of hepatitis B virus-related hepatocellular carcinoma.", "doi": "10.2147/CMAR.S186561", "pmid": "30697079", "authors": ["Hongyan Li", "Xiaonan Zhao", "Chenghua Li", "Chuanlun Sheng", "Zhenzi Bai"], "journal": "Cancer management and research", "year": 2019, "abstract": "BACKGROUND: There is evidence that abnormal expression of lncRNAs is associated with hepatitis B virus (HBV) infection-induced hepatocellular carcinoma (HCC). However, the mechanisms remain not fully elucidated. The study aimed to identify novel lncRNAs and explore their underlying mechanisms based on the ceRNA hypothesis.\nMETHODS: The RNA and miRNA expression profiling in 20 tumor and matched adjacent tissues from HBV-HCC patients were retrieved from the Gene Expression Omnibus database under accession numbers GSE77509 and GSE76903, respectively. Differentially expressed lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs) were identified using the EdgeR package. Protein-protein interaction (PPI) network was constructed for DEGs followed by module analysis. The ceRNA network was constructed based on interaction relationships between miRNAs and mRNAs/lncRNAs. The functions of DEGs were predicted using DAVID and BinGO databases. The prognosis values (overall survival [OS] and recurrence-free survival [RFS]) of ceRNA network genes were determined using The Cancer Genome Atlas (TCGA) data with Cox regression analysis and Kaplan-Meier method.\nRESULTS: The present study screened 643 DELs, 83 DEMs, and 1,187 DEGs. PPI network analysis demonstrated that CDK1 and CCNE1 were hub genes and extracted in functionally related modules. E2F2, CDK1, and CCNE1 were significantly enriched into cell cycle pathway. FAM182B-miR-125b-5p-E2F2 and LINC00346-miR-10a-5p-CDK1/CCNE1 ceRNA axes were obtained by constructing the ceRNA network. Patients with high expressions of DELs and DEGs in the above ceRNA axes had poor OS, while patients with the high expression of DEMs possessed excellent OS. CDK1 was also an RFS-related biomarker, with its high expression predicting poor RFS. The upregulation of LINC00346 and CDK1 but the downregulation of miR-10a-5p in HCC was validated in other microarray datasets and TCGA database.\nCONCLUSION: The LINC00346-miR-10a-5p-CDK1 axis may be an important mechanism for HBV-related HCC, and genes in this ceRNA axis may be potential prognostic biomarkers and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "Univariate Cox regression analysis was performed to screen prognosis-related DELs, DEMs, and DEGs using the survival package (Version 2.40.1; https://cran.r-project. org/package=survival). The Kaplan–Meier (KM) method with the log-rank test was employed to compare the overall survival (OS) and recurrence-free survival (RFS) between the high- and low-expression groups through the GraphPad Prism software (Version 5; GraphPad Software, Inc., La Jolla, CA, USA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30697079", "locator": "sections[8] \"Prognosis values of DELs, DEMs, and DEGs in ceRNA network\" paragraph 2", "quote": "Univariate Cox regression analysis was performed to screen prognosis-related DELs, DEMs, and DEGs using the survival package (Version 2.40.1; https://cran.r-project. org/package=survival)."}, {"asset": "source:pmid:30697079", "locator": "sections[8] \"Prognosis values of DELs, DEMs, and DEGs in ceRNA network\" paragraph 2", "quote": "The Kaplan–Meier (KM) method with the log-rank test was employed to compare the overall survival (OS) and recurrence-free survival (RFS) between the high- and low-expression groups through the GraphPad Prism software (Version 5; GraphPad Software, Inc., La Jolla, CA, USA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30697079", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/)."}], "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:30697079"], "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:GSE121248"], "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:GSE121248"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30697079", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S186561", "sha256": "sha256:e8a61e7a6f1e8cb7fbd37e6520cc9806baba044e911e374dba0db58ed999f7f2", "bytes": 42661, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CMAR.S186561", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6340501", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE121248", "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=GSE121248", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE121248", "version": null, "note": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). 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The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM629246", "GSM629247", "GSM629248", "GSM629249", "GSM629250", "GSM629251", "GSM629252", "GSM629253", "GSM629254", "GSM629255", "GSM629256", "GSM629257", "GSM629258", "GSM629259", "GSM629260", "GSM629261", "GSM629262", "GSM629263", "GSM629264", "GSM629265"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "9052", "taxon": "Homo sapiens", "title": "RNA-seq analysis generated a comprehensive landscape of transcriptomes and revealed complex patterns of transcripts in Chinese HBV-related hepatocellular carcinoma", "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:GSE27462", "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=GSE27462", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27462", "version": null, "note": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM678525", "GSM678526", "GSM678527", "GSM678528", "GSM678529", "GSM678530", "GSM678531", "GSM678532", "GSM678533", "GSM678534"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "11269", "taxon": "Homo sapiens", "title": "Long non-coding RNAs and mRNAs expression analysis of HCC", "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:GSE69580", "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=GSE69580", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE69580", "version": null, "note": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1704144", "GSM1704145", "GSM1704146", "GSM1704147", "GSM1704148", "GSM1704149", "GSM1704150", "GSM1704151", "GSM1704152", "GSM1704153"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "10850", "taxon": "Homo sapiens", "title": "Differential miRNA expression profiles betweenHBV-related  HCC tumor versus non-tumor liver tissue", "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:GSE76903", "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=GSE76903", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76903", "version": null, "note": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2040356", "GSM2040357", "GSM2040358", "GSM2040359", "GSM2040360", "GSM2040361", "GSM2040362", "GSM2040363", "GSM2040364", "GSM2040365", "GSM2040366", "GSM2040367", "GSM2040368", "GSM2040369", "GSM2040370", "GSM2040371", "GSM2040372", "GSM2040373", "GSM2040374", "GSM2040375", "GSM2040376", "GSM2040377", "GSM2040378", "GSM2040379", "GSM2040380", "GSM2040381", "GSM2040382", "GSM2040383", "GSM2040384", "GSM2040385", "GSM2040386", "GSM2040387", "GSM2040388", "GSM2040389", "GSM2040390", "GSM2040391", "GSM2040392", "GSM2040393", "GSM2040394", "GSM2040395", "GSM2040396", "GSM2040397", "GSM2040398", "GSM2040399", "GSM2040400", "GSM2040401", "GSM2040402", "GSM2040403", "GSM2040404", "GSM2040405", "GSM2040406", "GSM2040407", "GSM2040408", "GSM2040409", "GSM2040410", "GSM2040411", "GSM2040412", "GSM2040413", "GSM2040414", "GSM2040415"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "miRNA-seq analysis of hepatocellular carcinoma with portal vein tumor thrombosis", "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:GSE77509", "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=GSE77509", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE77509", "version": null, "note": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). 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"2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30697079:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7695dfbbc220c8418471147485147c10dc1ccd81885192d11d2599b19a1d89ca", "bytes": 1506, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#t8-cmar-11-877", "version": null, "note": "Confirmation of expressions of crucial lncRNAs, miRNAs, and mRNAs using other datasets", "structure": {"pmcid": "PMC6340501", "section_index": 9, "section_title": "Validation of expressions of crucial DELs, DEMs, and DEGs in ceRNA network", "row_count": 22, "column_count": 6}, "table": {"label": "Table 8", "caption": "Confirmation of expressions of crucial lncRNAs, miRNAs, and mRNAs using other datasets", "rows": [["RNA type", "Dataset", "Symbol", "Tumor (mean ± SD)", "Control (mean ± SD)", "P-value"], [""], ["lncRNA", "GSE27462", "FAM182B", "75.834±27.913", "71.793±23.127", "0.8096"], ["LINC00346", "124.665±28.955", "72.848±14.226", "0.01208"], ["TCGA", "FAM182B", "3.403±1.255", "2.539±0.944", "0.081"], ["LINC00346", "14.834±3.436", "12.679±1.403", "0.0397"], ["miRNA", "GSE69580", "miR-125b-5p", "39.384±23.416", "355.428±82.423", "0.000606"], ["miR-10a-5p", "4.229±2.103", "10.111±2.647", "0.00507"], ["TCGA", "miR-125b-5p", "8.962±1.092", "10.203±0.352", "4.09E–08"], ["miR-10a-5p", "13.607±1.198", "14.779±0.472", "4.89E–06"], ["mRNA", "GSE121248", "E2F2", "4.252±0.181", "4.239±0.157", "0.696"], ["CDK1", "7.224±1.105", "5.379±0.799", "2.68793E–16"], ["CCNE1", "7.056±1.032", "6.415±0.216", "0.00000344"], ["GSE94660", "E2F2", "0.83±0.443", "0.0611±0.028", "1.234E–07"], ["CDK1", "2.141±0.769", "0.251±0.121", "2.9E–10"], ["CCNE1", "1.412±0.669", "0.242±0.129", "9.01E–08"], ["GSE25599", "E2F2", "0.769±0.496", "0.302±0.255", "0.01958"], ["CDK1", "5.116±2.925", "1.152±0.923", "0.005978"], ["CCNE1", "2.015±1.820", "0.430±0.242", "0.02254"], ["TCGA", "E2F2", "5.612±1.296", "2.959±1.076", "0.000926"], ["CDK1", "8.018±1.428", "4.579±1.266", "0.00374"], ["CCNE1", "6.322±1.993", "3.162±0.979", "0.00193"]], "row_count": 22, "column_count": 6, "numeric_cells": 73, "header_rows": 1, "locator": "section[16]/table-wrap[1]#t8-cmar-11-877"}}, {"id": "asset:table:pmid:30697079:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3bae17633ae76d5d181c9e11797747e02f2e70b847c9ef8e6c9d8bc0ec662226", "bytes": 2323, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#t1-cmar-11-877", "version": null, "note": "Differentially expressed genes, miRNAs, and lncRNAs", "structure": {"pmcid": "PMC6340501", "section_index": 11, "section_title": "Differential expression analysis", "row_count": 22, "column_count": 9}, "table": {"label": "Table 1", "caption": "Differentially expressed genes, miRNAs, and lncRNAs", "rows": [["Symbol", "LogFC", "FDR", "Symbol", "LogFC", "FDR", "Symbol", "LogFC", "FDR"], [""], ["CDC6", "1.05", "2.01E–03", "hsa-miR-215-3p", "29.41", "3.08E–06", "LINC01662", "4.62", "1.21E–07"], ["CCNE1", "1.02", "1.22E–02", "hsa-miR-301b", "3.80", "8.46E–11", "DSCR8", "4.49", "1.73E–17"], ["CDK1", "1.04", "2.02E–03", "hsa-miR-483-3p", "3.42", "3.40E–09", "LINC01976", "4.30", "7.43E–06"], ["E2F2", "1.03", "7.83E–03", "hsa-miR-410-3p", "3.25", "1.76E–08", "LINC00632", "3.70", "8.51E–13"], ["BUB1", "1.11", "6.22E–04", "hsa-miR-7974", "3.25", "3.05E–08", "DSCR4", "3.63", "2.03E–12"], ["CCNB1", "1.03", "2.17E–03", "hsa-miR-483-5p", "3.22", "2.62E–08", "LINC02089", "3.50", "9.85E–05"], ["SFN", "1.54", "4.46E–06", "hsa-miR-200c-3p", "3.17", "4.31E–08", "MIR2052HG", "3.34", "4.32E–11"], ["GNG4", "1.48", "6.54E–05", "hsa-miR-183-5p", "3.11", "6.10E–08", "PRNT", "2.54", "1.17E–03"], ["UBE2C", "1.23", "2.15E–04", "hsa-miR-1910-5p", "3.09", "4.44E–04", "LINC00346", "2.02", "3.33E–05"], ["GNGT1", "2.04", "1.49E–05", "hsa-miR-493-5p", "3.08", "8.66E–08", "FAM182B", "1.30", "1.04E–02"], ["KIF4A", "1.15", "5.96E–04", "hsa-miR-139-5p", "−2.22", "1.49E–04", "PACRG-AS3", "−1.24", "2.72E–02"], ["GNG13", "1.40", "1.87E–02", "hsa-miR-30c-2-3p", "−1.59", "1.04E–02", "LINC01558", "−1.59", "1.17E–03"], ["PF4", "−1.36", "2.03E–02", "hsa-miR-378i", "−1.54", "1.32E–02", "LINC02312", "−1.60", "1.47E–03"], ["IL-6", "−1.04", "2.94E–02", "hsa-miR-199a-5p", "−1.45", "2.11E–02", "LINC02453", "−1.74", "3.36E–04"], ["CXCR1", "−1.056", "1.64E–02", "hsa-miR-30a-5p", "−1.45", "2.16E–02", "LILRB1-AS1", "−1.87", "0.013104"], ["INS", "−3.6", "9.75E–11", "hsa-miR-125b-5p", "−1.43", "2.29E–02", "LINC01561", "−2.05", "7.28E–05"], ["RD3L", "−3.16", "2.70E–10", "hsa-miR-378d", "−1.43", "2.43E–02", "LINC01550", "−2.09", "1.89E–05"], ["VGLL1", "−2.96", "4.88E–06", "hsa-miR-10a-5p", "−1.41", "2.62E–02", "LINC01620", "−2.16", "2.77E–05"], ["TH", "−2.85", "7.02E–15", "hsa-miR-133a-3p", "−1.38", "3.15E–02", "LINC01554", "−2.19", "5.61E–06"], ["CLDN8", "−2.83", "3.13E–06", "hsa-miR-101-3p", "−1.37", "3.12E–02", "B3GALT5-AS1", "−2.31", "3.83E–06"]], "row_count": 22, "column_count": 9, "numeric_cells": 156, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t1-cmar-11-877"}}, {"id": "asset:table:pmid:30697079:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:afeadb3928f6d00e1afaa3fe361569cfff9d0b6f2fe5c1863b78a1fe60e8318b", "bytes": 6057, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#t2-cmar-11-877", "version": null, "note": "GO enrichment for differentially expressed genes using the DAVID database", "structure": {"pmcid": "PMC6340501", "section_index": 12, "section_title": "Function enrichment for DEGs", "row_count": 22, "column_count": 4}, "table": {"label": "Table 2", "caption": "GO enrichment for differentially expressed genes using the DAVID database", "rows": [["Category", "Term", "FDR", "Genes"], [""], ["Up", "GO:0007049~cell cycle", "4.24E–10", "E2F1, KIF23, E2F2, KIFC1, XRCC2, E2F7, E2F8, MAEL, PKMYT1, TTK, PTTG1, AURKB, GTSE1, KIF2C, CCNE1, CDCA8, CDC45, CDCA2, PIWIL3, CDCA5, CDC6, CDK1, EGFL6, MND1, PBK, HMGA2, UBE2C, PRDM9, BUB1B, ERN2, NEK2, ANLN, CEP55, SPC24, SPC25, NCAPH, DUSP13, HJURP, NCAPG, CENPA, BUB1, FBXO43, SKA3, SKA1, TRIP13, EXO1, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, CDKN3, CDC25C, CDC25A, GSG2, CCNB1, CCNB2, TEX11"], ["GO:0022402~cell cycle process", "1.13E–11", "KIF23, E2F1, KIFC1, XRCC2, MAEL, PKMYT1, TTK, AURKB, PTTG1, GTSE1, CCNE1, KIF2C, CDCA8, CDCA2, PIWIL3, CDCA5, CDC6, CDK1, MND1, PBK, UBE2C, HMGA2, PRDM9, BUB1B, ERN2, NEK2, ANLN, CEP55, SPC24, SPC25, NCAPH, DUSP13, CENPA, NCAPG, FBXO43, BUB1, SKA3, SKA1, TRIP13, EXO1, DLGAP5, KIF18A, NUF2, NDC80, BIRC5, CDC20, CDC25C, CDKN3, CDC25A, CCNB1, CCNB2, TEX11"], ["GO:0022403~cell cycle phase", "1.74E–15", "E2F1, KIF23, KIFC1, XRCC2, NEK2, MAEL, TTK, PKMYT1, ANLN, PTTG1, CEP55, AURKB, GTSE1, SPC24, CCNE1, KIF2C, SPC25, NCAPH, CDCA8, DUSP13, NCAPG, BUB1, FBXO43, CDCA2, SKA3, PIWIL3, SKA1, CDCA5, TRIP13, EXO1, CDK1, CDC6, DLGAP5, NUF2, KIF18A, MND1, CDC20, BIRC5, NDC80, PBK, HMGA2, CDKN3, CDC25C, UBE2C, CDC25A, CCNB1, PRDM9, CCNB2, BUB1B, TEX11"], ["GO:0000279~M phase", "3.28E–16", "KIF23, KIFC1, XRCC2, NEK2, MAEL, TTK, PKMYT1, ANLN, PTTG1, CEP55, AURKB, SPC24, KIF2C, SPC25, NCAPH, CDCA8, DUSP13, NCAPG, BUB1, FBXO43, CDCA2, SKA3, PIWIL3, SKA1, CDCA5, TRIP13, EXO1, CDK1, CDC6, DLGAP5, NUF2, KIF18A, MND1, CDC20, BIRC5, NDC80, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, PRDM9, CCNB2, BUB1B, TEX11"], ["GO:0000278~mitotic cell cycle", "2.13E–11", "E2F1, KIF23, KIFC1, NEK2, TTK, PKMYT1, ANLN, PTTG1, CEP55, AURKB, GTSE1, SPC24, CCNE1, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, CENPA, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, CDC20, BIRC5, NDC80, PBK, HMGA2, CDKN3, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B"], ["GO:0007067~mitosis", "6.55E–14", "KIF23, KIFC1, NEK2, PKMYT1, ANLN, CEP55, AURKB, PTTG1, SPC24, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B"], ["GO:0000280~nuclear division", "6.55E–14", "KIF23, KIFC1, NEK2, PKMYT1, ANLN, CEP55, AURKB, PTTG1, SPC24, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B"], ["GO:0000087~M phase of mitotic cell cycle", "9.83E–14", "KIF23, KIFC1, NEK2, PKMYT1, ANLN, CEP55, AURKB, PTTG1, SPC24, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B"], ["GO:0048285~organelle fission", "1.97E–13", "KIF23, KIFC1, NEK2, PKMYT1, ANLN, CEP55, AURKB, PTTG1, SPC24, KIF2C, SPC25, CDCA8, NCAPH, NCAPG, BUB1, CDCA2, SKA3, SKA1, CDCA5, CDK1, CDC6, DLGAP5, NUF2, KIF18A, BIRC5, NDC80, CDC20, PBK, HMGA2, CDC25C, UBE2C, CDC25A, CCNB1, CCNB2, BUB1B"], ["GO:0051301~cell division", "2.47E–08", "KIF23, KIFC1, NEK2, ANLN, CEP55, AURKB, PTTG1, SPC24, CCNE1, SPC25, CDCA8, NCAPH, NCAPG, CDCA2, BUB1, SKA3, POU3F2, SKA1, CDCA5, CDK1, CDC6, NUF2, BIRC5, NDC80, CDC20, HMGA2, UBE2C, CDC25C, CDC25A, CCNB1, CCNB2, BUB1B"], ["Down", "GO:0007267~cell–cell signaling", "1.82E–07", "EDN3, GABRB3, FCRL2, VIPR1, VIPR2, GDNF, WNT2, KCNQ5, WISP2, SLC1A2, GRIN2B, CHRNA4, EFNB3, NPBWR1, IL26, NRXN1, NTSR1, IL22, SIGLEC6, GRM7, WNT9A, DRD1, GRAP, OXT, DRD5, TH, MME, RIMS1, CCL24, INS, CCL21, PRIMA1, BMP3, IL6, PLP1, NOS1, NTF3, DLGAP2, GABRA5, NPY5R, KCNK3, CCL17, WNT7B, CXCL14, PNOC, GRIA1, NTRK2, ADRA1A, SLC5A7, WNT7A, IL2, HTR2A"], ["GO:0006952~defense response", "2.83E–07", "KLRC4, KLRC2, KLRC3, CXCR1, CFP, GRIN2B, HAMP, RNASE7, IFNG, XCR1, NLRP7, CAMP, PRG2, PSG3, IL22, NCR1, NCR3, CCR9, PROK2, PSG8, PPBP, CD40LG, GRM7, DEFA3, PLA2G2D, CTSG, NGF, KIR3DL2, CLEC1B, C7, DRD1, CCK, CCL24, AZU1, FCN3, INS, CCL21, FCN2, CNR2, SFTPD, IL1RAPL2, SELP, IL6, IL5, IL1RL1, GABRA5, CCL19, CD5L, STAB2, S100A12, CCL17, MPO, SELE"], ["GO:0044057~regulation of system process", "3.67E–05", "BMP10, EDN3, DRD1, CCK, ERBB4, MYL3, EDN2, DRD5, OXT, TH, GDNF, DES, GRIN2B, INS, IFNG, LGI1, ARC, GNAO1, NOS1, NTF3, NPY1R, NPY5R, PROK2, TNNT3, CHRM2, NTRK2, TBXA2R, AVPR1A, IL2, HTR2A, NGF"], ["GO:0007268~synaptic transmission", "1.17E–04", "DRD1, GABRB3, DRD5, OXT, TH, VIPR1, RIMS1, WNT2, KCNQ5, SLC1A2, GRIN2B, CHRNA4, PRIMA1, PLP1, NOS1, NTF3, DLGAP2, NPBWR1, GABRA5, NRXN1, NTSR1, NPY5R, KCNK3, PNOC, GRIA1, GRM7, SLC5A7, WNT7A, HTR2A"], ["GO:0051046~regulation of secretion", "1.79E–03", "EDN3, IL6, EDN2, OXT, FGF23, NPY1R, GDNF, NPY5R, GCK, GRIN2B, CD40LG, INS, GRM7, IFNG, NTRK2, AVPR1A, CHRNA4, TRPV6, IL2, HTR2A, NGF"], ["GO:0006935ĉhemotaxis", "3.12E–03", "EDN3, IL6, EDN2, CXCR1, CCL19, PF4, CCL17, CCR9, AZU1, CCL24, PROK2, PPBP, CXCL14, CCL21, IFNG, SFTPD, XCR1, LECT2"], ["GO:0042742~defense response to bacterium", "8.64E–03", "SELP, IL6, CAMP, PRG2, STAB2, S100A12, AZU1, CFP, PPBP, HAMP, RNASE7, IFNG, DEFA3, CTSG"], ["GO:0050900~leukocyte migration", "9.20E–03", "AZU1, EDN3, SELP, IL6, EDN2, IFNG, ELANE, SFTPD, PF4, SELE"], ["GO:0022610~biological adhesion", "1.39E–02", "CLDN8, CLSTN2, OPCML, DSCAML1, CLDN10, L1CAM, MEGF10, WISP2, SRPX, TNR, DPT, DSCAM, TECTA, SELP, MAG, HAPLN4, RET, CDHR1, PCDH11X, CDHR2, IGFALS, SIGLEC11, AJAP1, STAB2, NRXN1, PCDH19, CTNNA3, CLEC4M, DSG4, LYVE1, FREM3, HEPACAM, SIGLEC6, FREM2, CD40LG, DSG1, CDH19, ITGAD, CNTN3, SELE, COL20A1, IL2"], ["GO:0006954înflammatory response", "2.80E–02", "SELP, C7, IL6, IL5, CXCR1, CCL19, IL22, S100A12, CCL17, NCR3, AZU1, CFP, CCL24, PROK2, FCN3, CD40LG, INS, CCL21, FCN2, CNR2, XCR1, SELE, PLA2G2D, NGF"]], "row_count": 22, "column_count": 4, "numeric_cells": 58, "header_rows": 1, "locator": "section[12]/table-wrap[1]#t2-cmar-11-877"}}, {"id": "asset:table:pmid:30697079:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d2bbe71022ee8409ef83cdc5b8723cfd71624e1e5c40d15583674527b96400ad", "bytes": 2569, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#t3-cmar-11-877", "version": null, "note": "KEGG pathway enrichment for differentially expressed genes using the DAVID database", "structure": {"pmcid": "PMC6340501", "section_index": 12, "section_title": "Function enrichment for DEGs", "row_count": 19, "column_count": 4}, "table": {"label": "Table 3", "caption": "KEGG pathway enrichment for differentially expressed genes using the DAVID database", "rows": [["Category", "Term", "FDR", "Genes"], [""], ["Up", "hsa04110:cell cycle", "2.16E–08", "E2F1, E2F2, CDK1, CDC6, PKMYT1, TTK, CDC20, PTTG1, SFN, CDC25C, CDC25A, CCNB1, CCNE1, CDC45, CCNB2, BUB1, BUB1B"], ["hsa04080:neuroactive ligand–receptor interaction", "2.66E–04", "GABRD, CGA, GABRG2, GABRA2, GABRA3, GLRA2, LEP, GRM4, SSTR5, KISS1R, HTR1B, GABRR1, GRID2, NPFFR2, TAAR1, HTR1D, GLP1R"], ["hsa04115:p53 signaling pathway", "2.08E–02", "CCNB1, CDK1, CCNE1, CCNB2, SFN, GTSE1"], ["hsa04060:cytokine–cytokine receptor interaction", "2.69E–02", "LEP, CCR8, CCL20, GDF5, EGF, BMP7, CCL7, IL11, CCL26"], ["hsa04062:chemokine signaling pathway", "2.73E–02", "CCR8, GNGT1, CCL20, GNG13, GNG4, CCL7, CCL26"], ["hsa00604:glycosphingolipid biosynthesis", "2.99E–02", "ST6GALNAC5, B4GALNT1"], ["hsa04512:ECM–receptor interaction", "3.14E–02", "IBSP, COMP, COL2A1, COL11A1"], ["hsa04350:TGF-beta signaling pathway", "3.33E–02", "COMP, GDF5, BMP7, PITX2"], ["hsa03320:PPAR signaling pathway", "4.83E–02", "LPL, MMP1, FABP6"], ["Down", "hsa00830:retinol metabolism", "8.15E–10", "CYP3A4, CYP1A1, CYP2B6, CYP2C8, ADH1B, CYP26A1, ADH7, CYP1A2, CYP3A43, CYP2A13, CYP4A11, UGT2B17, CYP4A22, LRAT, ADH4, CYP2A6, CYP2A7, RDH16"], ["hsa00982:drug metabolism", "2.89E–05", "CYP3A4, CYP2B6, CYP2C8, ADH1B, ADH7, CYP1A2, CYP2E1, GSTM5, CYP3A43, CYP2A13, UGT2B17, ADH4, CYP2A6, CYP2A7"], ["hsa04080:neuroactive ligand–receptor interaction", "1.79E–04", "GPR83, DRD1, GABRB3, DRD5, PTH1R, PRSS1, VIPR1, VIPR2, GCGR, GRIN2B, CNR2, GLP2R, GABRP, NPBWR1, GABRA5, NPY1R, NTSR1, NPY5R, GRIA1, CHRM2, GRM7, PTGDR, TBXA2R, AVPR1A, ADRA1A, CTSG, HTR2A"], ["hsa04060:cytokine–cytokine receptor interaction", "2.07E–04", "CXCR1, CNTFR, PF4, PF4V1, CCL24, CXCR5, CCL21, IFNG, XCR1, AMHR2, IL6, IL5, FLT3, TNFRSF13B, TNFRSF13C, IL26, CCL19, IL22, CCL17, CCR9, TSLP, CXCL14, PPBP, CD40LG, IL5RA, NGFR, IL2"], ["hsa00980:metabolism of xenobiotics by CYP/CYP450", "3.64E–04", "CYP3A43, CYP3A4, UGT2B17, CYP1A1, CYP2B6, ADH4, CYP2C8, ADH1B, ADH7, CYP2E1, CYP1A2, GSTM5"], ["hsa00232:caffeine metabolism", "1.50E–03", "CYP2A13, NAT2, CYP2A6, CYP2A7, CYP1A2"], ["hsa00983:drug metabolism", "2.10E–02", "CYP3A43, CYP3A4, CYP2A13, UGT2B17, NAT2, UPP2, CYP2A6, CYP2A7"], ["hsa04340:Hedgehog signaling pathway", "2.00E–02", "WNT2, WNT1, WNT10A, WNT7B, WNT9A, HHIP, GAS1, WNT7A, BMP5"]], "row_count": 19, "column_count": 4, "numeric_cells": 46, "header_rows": 1, "locator": "section[12]/table-wrap[2]#t3-cmar-11-877"}}, {"id": "asset:table:pmid:30697079:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:963d37d9ed400dfea629b2cc3f382ca151642bcc83c80e0411aa38862eca765e", "bytes": 2442, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t4-cmar-11-877", "version": null, "note": "Topological features for each protein in PPI network", "structure": {"pmcid": "PMC6340501", "section_index": 13, "section_title": "PPI network construction", "row_count": 32, "column_count": 10}, "table": {"label": "Table 4", "caption": "Topological features for each protein in PPI network", "rows": [["Gene", "Degree", "Gene", "CC", "Gene", "BC", "Gene", "APL", "Overlapped", "Expression"], [""], ["GNGT1", "87", "IL6", "0.3179", "IL6", "0.2515", "IL6", "3.1461", "CCNB1", "Up"], ["GNG13", "85", "CHRM2", "0.2989", "UBE2C", "0.1845", "CHRM2", "3.3455", "CDK1", "Up"], ["GNG4", "64", "SH3GL2", "0.2959", "NGF", "0.1695", "SH3GL2", "3.3792", "GNG4", "Up"], ["CDK1", "56", "EGF", "0.2947", "TH", "0.1586", "EGF", "3.3933", "UBE2C", "Up"], ["CCNB1", "52", "ESR1", "0.2890", "GNGT1", "0.1413", "ESR1", "3.4607", "GNGT1", "Up"], ["CDC20", "48", "CCL20", "0.2848", "FOSB", "0.1406", "CCL20", "3.5112", "KIF4A", "Up"], ["BUB1", "48", "GNGT1", "0.2846", "MMP1", "0.1388", "GNGT1", "3.5140", "PF4", "Down"], ["CCNB2", "47", "GNG13", "0.2823", "CHRM2", "0.1186", "GNG13", "3.5421", "GNG13", "Up"], ["KIF2C", "47", "INS", "0.2821", "SH3GL2", "0.1164", "INS", "3.5449", "", ""], ["PMCH", "45", "UBE2C", "0.2808", "EGF", "0.1106", "UBE2C", "3.5618", "", ""], ["AURKB", "44", "PF4", "0.2803", "E2F1", "0.1043", "PF4", "3.5674", "", ""], ["CENPA", "43", "PTHLH", "0.2786", "ESR1", "0.1013", "PTHLH", "3.5899", "", ""], ["KIF20A", "39", "GNG4", "0.2777", "GNG13", "0.0956", "GNG4", "3.6011", "", ""], ["BUB1B", "39", "NGF", "0.2766", "INS", "0.0904", "NGF", "3.6152", "", ""], ["NCAPG", "38", "GNAO1", "0.2728", "KIF4A", "0.0670", "GNAO1", "3.6657", "", ""], ["CDCA8", "38", "KIF4A", "0.2722", "PTHLH", "0.0669", "KIF4A", "3.6742", "", ""], ["GCGR", "37", "PPBP", "0.2713", "CDK1", "0.0637", "PPBP", "3.6854", "", ""], ["NPSR1", "37", "GNA14", "0.2709", "ACAN", "0.0632", "GNA14", "3.6910", "", ""], ["BIRC5", "37", "LEP", "0.2707", "CCL20", "0.0620", "LEP", "3.6938", "", ""], ["TTK", "37", "TERT", "0.2707", "GNAO1", "0.0593", "TERT", "3.6938", "", ""], ["NDC80", "37", "GNAZ", "0.2669", "CAMK2B", "0.0547", "GNAZ", "3.7472", "", ""], ["DLGAP5", "36", "NGFR", "0.2661", "LPL", "0.0444", "NGFR", "3.7584", "", ""], ["UBE2C", "35", "SYT9", "0.2655", "CYP19A1", "0.0430", "SYT9", "3.7669", "", ""], ["CDC45", "35", "E2F1", "0.2651", "CCNB1", "0.0417", "E2F1", "3.7725", "", ""], ["PF4", "34", "HTR1B", "0.2645", "GNG4", "0.0402", "HTR1B", "3.7809", "", ""], ["KIF4A", "34", "CDK1", "0.2639", "CHRNA1", "0.0394", "CDK1", "3.7893", "", ""], ["PBK", "34", "PMCH", "0.2639", "PF4", "0.0393", "PMCH", "3.7893", "", ""], ["KIF23", "34", "HTR1D", "0.2639", "RHO", "0.0370", "HTR1D", "3.7893", "", ""], ["CXCR1", "33", "CCNB1", "0.2625", "NOS1", "0.0353", "CCNB1", "3.8090", "", ""], ["XCR1", "33", "CXCR1", "0.2597", "NGFR", "0.0348", "CXCR1", "3.8511", "", ""]], "row_count": 32, "column_count": 10, "numeric_cells": 136, "header_rows": 1, "locator": "section[13]/table-wrap[1]#t4-cmar-11-877"}}, {"id": "asset:table:pmid:30697079:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8a7889e10452f86dccc0efd9a4e4eb98a92c04abc596da2893e78b18a9cbfdfd", "bytes": 6713, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#t5-cmar-11-877", "version": null, "note": "BinGO enrichment for genes in modules", "structure": {"pmcid": "PMC6340501", "section_index": 13, "section_title": "PPI network construction", "row_count": 44, "column_count": 4}, "table": {"label": "Table 5", "caption": "BinGO enrichment for genes in modules", "rows": [["Module", "Description", "FDR", "Genes in test set"], [""], ["M1", "Mitotic cell cycle", "9.74E–37", "CDCA5|BUB1B|CDCA8|NCAPG|TTK|CENPA|SKA1|AUR KB|CDC20|CCNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BU B1|CEP55|DLGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18 A|CDK1|BIRC5|KIF2C|SPC24|CDKN3|SPC25"], ["Nuclear division", "9.74E–37", "CDCA5|BUB1B|CDCA8|NCAPG|SKA1|AURKB|CDC20|C CNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP55|D LGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1|BIRC 5|KIF2C|SPC24|SPC25"], ["Mitosis", "9.74E–37", "CDCA5|BUB1B|CDCA8|NCAPG|SKA1|AURKB|CDC20|C CNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP55|D LGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1|BIRC 5|KIF2C|SPC24|SPC25"], ["M phase of mitotic cell cycle", "1.65E–36", "CDCA5|BUB1B|CDCA8|NCAPG|SKA1|AURKB|CDC20|C CNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP55|D LGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1|BIRC 5|KIF2C|SPC24|SPC25"], ["Organelle fission", "1.65E–36", "CDCA5|BUB1B|CDCA8|NCAPG|SKA1|AURKB|CDC20|C CNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP55|D LGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1|BIRC 5|KIF2C|SPC24|SPC25"], ["M phase", "2.75E–36", "CDCA5|BUB1B|CDCA8|NCAPG|TTK|SKA1|AURKB|CDC 20|CCNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP 55|DLGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1 |BIRC5|KIF2C|TRIP13|SPC24|SPC25"], ["Cell cycle phase", "1.03E–35", "CDCA5|BUB1B|CDCA8|NCAPG|TTK|SKA1|AURKB|CDC 20|CCNB2|CCNB1|PTTG1|NUF2|PBK|NEK2|BUB1|CEP 55|DLGAP5|UBE2C|KIF23|NDC80|ANLN|KIF18A|CDK1 |BIRC5|KIF2C|TRIP13|SPC24|CDKN3|SPC25"], ["Cell cycle process", "5.27E–34", "CDCA5|BUB1B|CDCA8|NCAPG|TTK|CENPA|SK A1|AURKB|CDC20|CCNB2|CCNB1|PTTG1|NUF 2|PBK|NEK2|BUB1|CEP55|DLGAP5|UBE2C|KIF 23|NDC80|ANLN|KIF18A|CDK1|BIRC5|KIF2C| TRIP13|SPC24|CDKN3|SPC25"], ["Cell cycle", "7.78E–34", "CDCA5|HJURP|BUB1B|CDCA8|NCAPG|TTK|CENPA|SK A1|AURKB|CDC20|CCNB2|CCNB1|CDC45|PTTG1|NU F2|PBK|NEK2|BUB1|CEP55|DLGAP5|UBE2C|KIF23|ND C80|ANLN|KIF18A|CDK1|BIRC5|KIF2C|TRIP13|SPC24| CDKN3|SPC25"], ["Cell division", "8.53E–28", "UBE2C|CDCA5|BUB1B|CDCA8|NCAPG|KIF23|SKA1|A URKB|NDC80|CDC20|CCNB2|ANLN|CCNB1|PTTG1| NUF2|CDK1|BIRC5|NEK2|KIF2C|BUB1|CEP55|SPC24 |SPC25"], ["M2", "G-protein-coupled receptor protein signaling pathway", "4.81E–36", "NPFFR2|CHRM2|PMCH|CXCR5|HTR2A|ADRA1A|GNGT 1|GNA14|GRM4|CXCR1|CNR2|TBXA2R|NPBWR1|KISS 1R|CCR9|CCR8|PROK2|TAC3|NTSR1|P2RY12|XCR1|ED N2|NPY5R|GCGR|HTR1D|NPY1R|HTR1B|CCK|AVPR1A| SSTR5|GNG13|PPYR1|PNOC"], ["Cell surface receptor-linked signaling pathway", "8.03E–26", "NPFFR2|CHRM2|PMCH|CXCR5|HTR2A|ADRA1A|GNGT 1|GNA14|GRM4|CXCR1|CNR2|TBXA2R|NPBWR1|KISS 1R|CCR9|CCR8|PROK2|TAC3|NTSR1|P2RY12|XCR1|ED N2|NPY5R|EDN3|GCGR|HTR1D|NPY1R|HTR1B|CCK|A VPR1A|SSTR5|GNG13|PPYR1|PNOC|PF4"], ["Signaling", "6.64E–24", "NPFFR2|CHRM2|PMCH|CXCR5|OXT|HTR2A|ADRA1A |GNGT1|GNA14|GRM4|CXCR1|CNR2|GRM7|TBXA2R| GNG4|NPBWR1|KISS1R|CCR9|CCR8|PROK2|TAC3|CCL 19|NTSR1|P2RY12|XCR1|EDN2|NPY5R|CCL21|EDN3| CCL20|GCGR|HTR1D|NPY1R|HTR1B|CCK|AVPR1A|SST R5|GNG13|APLN|PPYR1|PNOC|GNRH2|PF4"], ["Behavior", "1.44E–23", "PMCH|OXT|HTR2A|GRM4|CXCR1|CNR2|KISS1R|CCR 9|CCR8|PROK2|CCL19|NTSR1|XCR1|EDN2|NPY5R|C CL21|EDN3|CCL20|NPY1R|HTR1B|CCK|AVPR1A|PPBP |PPYR1|PF4"], ["Signaling pathway", "3.33E–20", "NPFFR2|CHRM2|PMCH|CXCR5|HTR2A|ADRA1A|GNGT 1|GNA14|GRM4|CXCR1|CNR2|TBXA2R|GNG4|NPBW R1|KISS1R|CCR9|CCR8|PROK2|TAC3|NTSR1|P2RY12|X CR1|EDN2|NPY5R|EDN3|GCGR|HTR1D|NPY1R|HTR1B |CCK|AVPR1A|SSTR5|GNG13|PPYR1|PNOC|PF4"], ["Signaling process", "2.04E–17", "CHRM2|PMCH|OXT|HTR2A|ADRA1A|GNGT1|GNA14| GRM4|CNR2|GRM7|NPBWR1|KISS1R|PROK2|CCL19|N TSR1|P2RY12|XCR1|EDN2|NPY5R|CCL21|EDN3|CCL2 0|GCGR|HTR1D|NPY1R|HTR1B|CCK|AVPR1A|SSTR5|G NG13|APLN|PNOC|GNRH2|PF4"], ["Signal transmission", "2.04E–17", "CHRM2|PMCH|OXT|HTR2A|ADRA1A|GNGT1|GNA14| GRM4|CNR2|GRM7|NPBWR1|KISS1R|PROK2|CCL19|N TSR1|P2RY12|XCR1|EDN2|NPY5R|CCL21|EDN3|CCL2 0|GCGR|HTR1D|NPY1R|HTR1B|CCK|AVPR1A|SSTR5|G NG13|APLN|PNOC|GNRH2|PF4"], ["Signal transduction", "1.43E–14", "CHRM2|PMCH|OXT|HTR2A|ADRA1A|GNGT1|GNA14| GRM4|CNR2|KISS1R|PROK2|CCL19|P2RY12|XCR1|ED N2|CCL21|EDN3|CCL20|GCGR|HTR1D|NPY1R|HTR1B| CCK|AVPR1A|SSTR5|GNG13|APLN|PNOC|GNRH2|PF4"], ["Response to stimulus", "2.05E–12", "NPFFR2|CHRM2|PMCH|OXT|HTR2A|ADRA1A|GNGT1| GRM4|CXCR1|CNR2|GRM7|GNG4|KISS1R|CCR9|CCR8 |PROK2|CCL19|NTSR1|P2RY12|XCR1|EDN2|NPY5R|C CL21|EDN3|CCL20|GCGR|HTR1D|NPY1R|HTR1B|CCK| AVPR1A|PPBP|GNG13|APLN|PPYR1|PF4"], ["Response to chemical stimulus", "2.96E–11", "XCR1|EDN2|CCL21|EDN3|CCL20|GCGR|HTR1D|NP Y1R|HTR1B|OXT|CCK|HTR2A|AVPR1A|PPBP|ADRA1A |GNG13|CXCR1|CNR2|GNG4|CCR9|CCR8|PROK2|CC L19|PF4"], ["M3", "Cyclic-nucleotide-mediated signaling", "6.43E–09", "GLP1R|VIPR1|GLP2R|PTH1R|DRD1|PTHLH|DRD5"], ["G-protein-coupled receptor protein signaling pathway", "2.93E–08", "VIPR1|GPR15|GLP2R|PTH1R|DRD1|TAAR1|PTHLH|DR D5|PTGDR"], ["Second messenger-mediated signaling", "9.78E–08", "GLP1R|VIPR1|GLP2R|PTH1R|DRD1|PTHLH|DRD5"], ["G-protein signaling, coupled to cyclic nucleotide second messenger", "9.78E–08", "VIPR1|GLP2R|PTH1R|DRD1|PTHLH|DRD5"], ["Cell surface receptor-linked signaling pathway", "2.27E–05", "VIPR1|GPR15|GLP2R|PTH1R|DRD1|TAAR1|PTHLH|DR D5|PTGDR"], ["Signaling", "3.01E–05", "GLP1R|VIPR1|GPR15|VIPR2|GLP2R|PTH1R|DRD1|CGA|T AAR1|PTHLH|DRD5|PTGDR"], ["Signaling pathway", "5.37E–05", "GLP1R|VIPR1|GPR15|GLP2R|PTH1R|DRD1|TAAR1|PTH LH|DRD5|PTGDR"], ["Intracellular signal transduction", "8.25E–05", "GLP1R|VIPR1|GLP2R|PTH1R|DRD1|PTHLH|DRD5"], ["Cell–cell signaling", "1.41E–04", "VIPR1|VIPR2|DRD1|CGA|PTHLH|DRD5"], ["Signal transduction", "1.59E–04", "GLP1R|VIPR1|VIPR2|GLP2R|PTH1R|DRD1|CGA|PTHLH |DRD5"], ["Signaling process", "4.51E–04", "GLP1R|VIPR1|VIPR2|GLP2R|PTH1R|DRD1|CGA|PTHLH |DRD5"], ["Cell communication", "7.10E–04", "VIPR1|VIPR2|DRD1|CGA|PTHLH|DRD5"], ["M4", "Drug metabolic process", "3.44E–16", "CYP2A6|CYP2C8|CYP2B6|CYP1A2|CYP1A1|CYP2E1|C YP3A4"], ["Secondary metabolic process", "4.89E–11", "CYP26A1|CYP2A6|CYP1A2|CYP1A1|CYP2E1|CYP3A4"], ["Oxidation reduction", "2.91E–10", "CYP26A1|CYP2A6|CYP2C8|CYP2B6|CYP4A11|CYP1A2|C YP1A1|CYP2E1|CYP3A4"], ["Steroid metabolic process", "4.84E–10", "CYP2A6|CYP2B6|CYP1A2|CYP1A1|UGT2B17|CYP2E1| CYP3A4"], ["Lipid metabolic process", "1.79E–09", "CYP26A1|CYP2A6|CYP2B6|CYP4A11|CYP1A2|CYP1A1| UGT2B17|CYP2E1|CYP3A4"], ["Response to drug", "1.12E–07", "CYP2A6|CYP2C8|CYP2B6|CYP1A2|CYP1A1|CYP3A4"], ["Cellular catabolic process", "2.17E–06", "CYP26A1|CYP2A6|CYP2C8|CYP2B6|CYP1A2|CYP1A1| CYP3A4"], ["Small molecule metabolic process", "3.78E–06", "CYP26A1|CYP2A6|CYP2C8|CYP2B6|CYP4A11|CYP1A2| CYP1A1|CYP3A4"], ["Cellular lipid metabolic process", "6.87E–06", "CYP26A1|CYP4A11|CYP1A2|CYP1A1|CYP2E1|CYP3A4"], ["Catabolic process", "9.30E–06", "CYP26A1|CYP2A6|CYP2C8|CYP2B6|CYP1A2|CYP1A1| CYP3A4"]], "row_count": 44, "column_count": 4, "numeric_cells": 74, "header_rows": 1, "locator": "section[13]/table-wrap[2]#t5-cmar-11-877"}}, {"id": "asset:table:pmid:30697079:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8720a5dad12fc033cbf66457256206fe695ffd3d3f5eb732b4ad205b94d543a3", "bytes": 522, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#t6-cmar-11-877", "version": null, "note": "KEGG pathways for genes in ceRNA network", "structure": {"pmcid": "PMC6340501", "section_index": 14, "section_title": "CeRNA network construction", "row_count": 6, "column_count": 3}, "table": {"label": "Table 6", "caption": "KEGG pathways for genes in ceRNA network", "rows": [["Term", "P-value", "Genes"], [""], ["hsa04110:cell cycle", "2.85E–06", "CCNB1, E2F2, CDK1, CCNE1, CDC6, BUB1, SFN"], ["hsa04115:p53 signaling pathway", "0.001617", "CCNB1, CDK1, CCNE1, SFN"], ["hsa04080:neuroactive ligand–receptor interaction", "0.04606", "GPR83, GABRB3"], ["hsa05200:pathways in cancer", "0.046995", "E2F2, CCNE1"]], "row_count": 6, "column_count": 3, "numeric_cells": 9, "header_rows": 1, "locator": "section[14]/table-wrap[1]#t6-cmar-11-877"}}, {"id": "asset:table:pmid:30697079:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ddb38bf1d20056e74c7a2d16466b887fcf58d0281bb88430e939a9394eb47be6", "bytes": 969, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#t7-cmar-11-877", "version": null, "note": "Cox regression analysis to screen survival-related genes", "structure": {"pmcid": "PMC6340501", "section_index": 15, "section_title": "Prognosis prediction for DELs, DEMs, and DEGs", "row_count": 19, "column_count": 5}, "table": {"label": "Table 7", "caption": "Cox regression analysis to screen survival-related genes", "rows": [["ID", "Overall survival", "Recurrence-free survival"], [""], ["", "HR", "P-value", "HR", "P-value"], [""], ["E2F2", "1.24", "0.049", "1.19", "0.16"], ["CDC6", "1.28", "0.0372", "1.41", "0.0099"], ["CCNE1", "1.05", "0.0456", "1.08", "0.32"], ["CDK1", "1.32", "0.022", "1.48", "0.0036"], ["BUB1", "1.31", "0.013", "1.37", "0.0054"], ["CCNB1", "1.4", "0.014", "1.36", "0.023"], ["SFN", "1.22", "0.0023", "1.19", "0.0055"], ["hsa-miR-10a-5p", "0.882", "0.04", "0.854", "0.27"], ["hsa-miR-125b-5p", "0.835", "0.019", "0.952", "0.74"], ["hsa-miR-133a-3p", "0.11", "0.045", "0.879", "0.39"], ["hsa-miR-199a-5p", "0.986", "0.88", "0.907", "0.28"], ["hsa-miR-30a-5p", "0.911", "0.0452", "0.866", "0.32"], ["LINC00346", "1.67", "0.0051", "0.99", "0.85"], ["DSCR4", "1.03", "0.68", "0.994", "0.95"], ["FAM182B", "1.152", "0.047", "0.84", "0.19"]], "row_count": 19, "column_count": 5, "numeric_cells": 67, "header_rows": 3, "locator": "section[15]/table-wrap[1]#t7-cmar-11-877"}}, {"id": "asset:table:pmid:30697079:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7695dfbbc220c8418471147485147c10dc1ccd81885192d11d2599b19a1d89ca", "bytes": 1506, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#t8-cmar-11-877", "version": null, "note": "Confirmation of expressions of crucial lncRNAs, miRNAs, and mRNAs using other datasets", "structure": {"pmcid": "PMC6340501", "section_index": 16, "section_title": "Validation of expressions of crucial DELs, DEMs, and DEGs in ceRNA network", "row_count": 22, "column_count": 6}, "table": {"label": "Table 8", "caption": "Confirmation of expressions of crucial lncRNAs, miRNAs, and mRNAs using other datasets", "rows": [["RNA type", "Dataset", "Symbol", "Tumor (mean ± SD)", "Control (mean ± SD)", "P-value"], [""], ["lncRNA", "GSE27462", "FAM182B", "75.834±27.913", "71.793±23.127", "0.8096"], ["LINC00346", "124.665±28.955", "72.848±14.226", "0.01208"], ["TCGA", "FAM182B", "3.403±1.255", "2.539±0.944", "0.081"], ["LINC00346", "14.834±3.436", "12.679±1.403", "0.0397"], ["miRNA", "GSE69580", "miR-125b-5p", "39.384±23.416", "355.428±82.423", "0.000606"], ["miR-10a-5p", "4.229±2.103", "10.111±2.647", "0.00507"], ["TCGA", "miR-125b-5p", "8.962±1.092", "10.203±0.352", "4.09E–08"], ["miR-10a-5p", "13.607±1.198", "14.779±0.472", "4.89E–06"], ["mRNA", "GSE121248", "E2F2", "4.252±0.181", "4.239±0.157", "0.696"], ["CDK1", "7.224±1.105", "5.379±0.799", "2.68793E–16"], ["CCNE1", "7.056±1.032", "6.415±0.216", "0.00000344"], ["GSE94660", "E2F2", "0.83±0.443", "0.0611±0.028", "1.234E–07"], ["CDK1", "2.141±0.769", "0.251±0.121", "2.9E–10"], ["CCNE1", "1.412±0.669", "0.242±0.129", "9.01E–08"], ["GSE25599", "E2F2", "0.769±0.496", "0.302±0.255", "0.01958"], ["CDK1", "5.116±2.925", "1.152±0.923", "0.005978"], ["CCNE1", "2.015±1.820", "0.430±0.242", "0.02254"], ["TCGA", "E2F2", "5.612±1.296", "2.959±1.076", "0.000926"], ["CDK1", "8.018±1.428", "4.579±1.266", "0.00374"], ["CCNE1", "6.322±1.993", "3.162±0.979", "0.00193"]], "row_count": 22, "column_count": 6, "numeric_cells": 73, "header_rows": 1, "locator": "section[16]/table-wrap[1]#t8-cmar-11-877"}}], "gaps": ["asset:data:geo:GSE121248 not downloaded", "asset:data:geo:GSE121248 licence not read", "asset:data:geo:GSE25599 not downloaded", "asset:data:geo:GSE25599 licence not read", "asset:data:geo:GSE27462 not downloaded", "asset:data:geo:GSE27462 licence not read", "asset:data:geo:GSE69580 not downloaded", "asset:data:geo:GSE69580 licence not read", "asset:data:geo:GSE76903 not downloaded", "asset:data:geo:GSE76903 licence not read", "asset:data:geo:GSE77509 not downloaded", "asset:data:geo:GSE77509 licence not read", "asset:data:geo:GSE94660 not downloaded", "asset:data:geo:GSE94660 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "reordered", "quote": "Univariate Cox regression analysis was performed to screen prognosis-related DELs, DEMs, and DEGs using the survival package (Version 2.40.1; https://cran.r-project. org/package=survival). The Kaplan–Meier (KM) method with the log-rank test was employed to compare the overall survival (OS) and recurrence-free survival (RFS) between the high- and low-expression groups through the GraphPad Prism software (Version 5; GraphPad Software, Inc., La Jolla, CA, USA)."}}, {"id": "method-2", "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-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "differential_expression", "specific": "edger", "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": "EdgeR"}}, {"id": "method-5", "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"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE77509", "GSE76903", "GSE121248", "GSE94660", "GSE25599", "GSE69580", "GSE27462"], "resolved_accessions": ["GSE77509", "GSE76903", "GSE121248", "GSE94660", "GSE25599", "GSE69580", "GSE27462"], "statements": ["All the microarray data were downloaded from the GEO database in NCBI (http://www.ncbi.nlm.nih.gov/geo/). The mRNA and miRNA Seq-data were obtained from TCGA (https://tcga-data.nci.nih.gov/)."], "basis": "The paper names GSE77509, GSE76903, GSE121248, GSE94660, GSE25599, GSE69580, GSE27462 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": ["cox_ph"], "assets": ["source:pmid:30697079", "data:geo:GSE121248", "asset:table:pmid:30697079:1", "asset:table:pmid:30697079:2", "asset:table:pmid:30697079:3", "asset:table:pmid:30697079:4", "asset:table:pmid:30697079:5", "asset:table:pmid:30697079:6", "asset:table:pmid:30697079:7", "asset:table:pmid:30697079:8", "asset:table:pmid:30697079:9"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE121248"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:46Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 36120, "completion_tokens": 2953, "cached_tokens": 784}}, "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:30697079", "type": "paper", "label": "pmid:30697079"}, {"id": "source:pmid:30697079", "type": "manuscript", "label": "PMID 30697079 full text"}, {"id": "data:geo:GSE121248", "type": "dataset", "label": "GEO GSE121248"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30697079", "type": "paper", "label": "pmid:30697079"}, {"id": "source:pmid:30697079", "type": "manuscript", "label": "PMID 30697079 full text"}, {"id": "data:geo:GSE121248", "type": "dataset", "label": "GEO GSE121248"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30697079", "type": "extraction", "used": ["source:pmid:30697079"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE121248", "type": "accession_resolution", "used": ["data:geo:GSE121248"], "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:30697079", "parent_hash": "sha256:e66ac7b3f17d1b6ac8e35663906402c926b1f482db0800c2431a83f864a0a9be", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE121248 licence not read", "asset:data:geo:GSE121248 not downloaded", "asset:data:geo:GSE25599 licence not read", "asset:data:geo:GSE25599 not downloaded", "asset:data:geo:GSE27462 licence not read", "asset:data:geo:GSE27462 not downloaded", "asset:data:geo:GSE69580 licence not read", "asset:data:geo:GSE69580 not downloaded", "asset:data:geo:GSE76903 licence not read", "asset:data:geo:GSE76903 not downloaded", "asset:data:geo:GSE77509 licence not read", "asset:data:geo:GSE77509 not downloaded", "asset:data:geo:GSE94660 licence not read", "asset:data:geo:GSE94660 not downloaded", "execution.not_run", "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": 0.99, "evidence": ["of miR-10a-5p in HCC was validated in other microarray datasets and TCGA database. CONCLUSION: The", "s Availability of data and materials All the microarray data were downloaded from the GEO database i"], "order_basis": "paper_text_order:1997", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Univariate Cox regression analysis was performed to screen prognosis-related DELs, DEMs, and DEGs using the survival package (Version 2.40.1; https://cran.r-project. org/package=survival). The Kaplan–Meier (KM) method with the log-rank test was employed to compare the overall survival (OS) and recurrence-free survival (RFS) between the high- and low-expression groups through the GraphPad Prism software (Version 5; GraphPad Software, Inc., La Jolla, CA, USA)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:21:31+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}