Signature microRNAs and long noncoding RNAs in laryngeal cancer recurrence identified using a competing endogenous RNA network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31059106", "kind": "science-record", "revision": 8, "content_hash": "sha256:d23ebfd372c3956e28cb7ba44b6ed7650f89995703fde1d7d2157df8d5352cd3", "created_at": "2026-11-01T15:40:44Z", "updated_at": "2026-11-01T22:43:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Signature microRNAs and long noncoding RNAs in laryngeal cancer recurrence identified using a competing endogenous RNA network.", "doi": "10.3892/mmr.2019.10143", "pmid": "31059106", "authors": ["Zhengyi Tang", "Ganguan Wei", "Longcheng Zhang", "Zhiwen Xu"], "journal": "Molecular medicine reports", "year": 2019, "abstract": "The aim of the present study was to identify novel microRNA (miRNA) or long noncoding RNA (lncRNA) signatures of laryngeal cancer recurrence and to investigate the regulatory mechanisms associated with this malignancy. Datasets of recurrent and nonrecurrent laryngeal cancer samples were downloaded from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus database (GSE27020 and GSE25727) to examine differentially expressed miRNAs (DE‑miRs), lncRNAs (DE‑lncRs) and mRNAs (DEGs). miRNA‑mRNA and lncRNA‑miRNA networks were constructed by investigating the associations among these RNAs in various databases. Subsequently, the interactions identified were combined into a competing endogenous RNA (ceRNA) regulatory network. Feature genes in the miRNA‑mRNA network were identified via topological analysis and a recursive feature elimination algorithm. A support vector machine (SVM) classifier was established using the betweenness centrality values in the miRNA‑mRNA network, consisting of 32 optimal feature‑coding genes. The classification effect was tested using two validation datasets. Furthermore, coding genes in the ceRNA network were examined via pathway enrichment analyses. In total, 21 DE‑lncRs, 507 DEGs and 55 DE‑miRs were selected. The SVM classifier exhibited an accuracy of 94.05% (79/84) for sample classification prediction in the TCGA dataset, and 92.66 and 91.07% in the two validation datasets. The ceRNA regulatory network comprised 203 nodes, corresponding to mRNAs, miRNAs and lncRNAs, and 346 lines, corresponding to the interactions among RNAs. In particular, the interactions with the highest scores were HLA complex group 4 (HCG4)‑miR‑33b, HOX transcript antisense RNA (HOTAIR)‑miR‑1‑MAGE family member A2 (MAGEA2), EMX2 opposite strand/antisense RNA (EMX2OS)‑miR‑124‑calcitonin related polypeptide α (CALCA) and EMX2OS‑miR‑124‑γ‑aminobutyric acid type A receptor γ2 subunit (GABRG2). Gene enrichment analysis of the genes in the ceRNA network identified that 11 pathway terms and 16 molecular function terms were significantly enriched. The SVM classifier based on 32 feature coding genes exhibited high accuracy in the classification of laryngeal cancer samples. miR‑1, miR‑33b, miR‑124, HOTAIR, HCG4 and EMX2OS may be novel biomarkers of recurrent laryngeal cancer, and HCG4‑miR‑33b, HOTAIR‑miR‑1‑MAGEA2 and EMX2OS‑miR‑124‑CALCA/GABRG2 may be associated with the molecular mechanisms regulating recurrent laryngeal cancer.", "claims": [{"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31059106", "locator": "sections[23] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "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:31059106"], "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:GSE25727"], "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:GSE25727"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31059106", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/mmr.2019.10143", "sha256": "sha256:a87cd6fbcdbca7bbfc96c3f1d49be201b1aef9ff769465383450316db3e07bc1", "bytes": 47642, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/mmr.2019.10143", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6522811", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25727", "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=GSE25727", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25727", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM631941", "GSM631942", "GSM631943", "GSM631944", "GSM631945", "GSM631946", "GSM631947", "GSM631948", "GSM631949", "GSM631950", "GSM631951", "GSM631952", "GSM631953", "GSM631954", "GSM631955", "GSM631956", "GSM631957", "GSM631958", "GSM631959", "GSM631960", "GSM631961", "GSM631962", "GSM631963", "GSM631964", "GSM631965", "GSM631966", "GSM631967", "GSM631968", "GSM631969", "GSM631970", "GSM631971", "GSM631972", "GSM631973", "GSM631974", "GSM631975", "GSM631976", "GSM631977", "GSM631978", "GSM631979", "GSM631980", "GSM631981", "GSM631982", "GSM631983", "GSM631984", "GSM631985", "GSM631986", "GSM631987", "GSM631988", "GSM631989", "GSM631990", "GSM631991", "GSM631992", "GSM631993", "GSM631994", "GSM631995", "GSM631996"], "sample_count": 56, "group_sizes": null, "group_sizes_basis": null, "platform": "8432", "taxon": "Homo sapiens", "title": "Identification and validation of gene expression models that predict clinical outcome in patients with early stage laryngeal cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE27020", "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=GSE27020", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27020", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM665544", "GSM665545", "GSM665546", "GSM665547", "GSM665548", "GSM665549", "GSM665550", "GSM665551", "GSM665552", "GSM665553", "GSM665554", "GSM665555", "GSM665556", "GSM665557", "GSM665558", "GSM665559", "GSM665560", "GSM665561", "GSM665562", "GSM665563", "GSM665564", "GSM665565", "GSM665566", "GSM665567", "GSM665568", "GSM665569", "GSM665570", "GSM665571", "GSM665572", "GSM665573", "GSM665574", "GSM665575", "GSM665576", "GSM665577", "GSM665578", "GSM665579", "GSM665580", "GSM665581", "GSM665582", "GSM665583", "GSM665584", "GSM665585", "GSM665586", "GSM665587", "GSM665588", "GSM665589", "GSM665590", "GSM665591", "GSM665592", "GSM665593", "GSM665594", "GSM665595", "GSM665596", "GSM665597", "GSM665598", "GSM665599", "GSM665600", "GSM665601", "GSM665602", "GSM665603", "GSM665604", "GSM665605", "GSM665606", "GSM665607", "GSM665608", "GSM665609", "GSM665610", "GSM665611", "GSM665612", "GSM665613", "GSM665614", "GSM665615", "GSM665616", "GSM665617", "GSM665618", "GSM665619", "GSM665620", "GSM665621", "GSM665622", "GSM665623", "GSM665624", "GSM665625", "GSM665626", "GSM665627", "GSM665628", "GSM665629", "GSM665630", "GSM665631", "GSM665632", "GSM665633", "GSM665634", "GSM665635", "GSM665636", "GSM665637", "GSM665638", "GSM665639", "GSM665640", "GSM665641", "GSM665642", "GSM665643", "GSM665644", "GSM665645", "GSM665646", "GSM665647", "GSM665648", "GSM665649", "GSM665650", "GSM665651", "GSM665652"], "sample_count": 109, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Identification and validation of a multigene predictor of recurrence in primary laryngeal cancer.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31059106:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a745b59a26bbb2d9807a265a8ce64efd9ff197b00c16e681b799431bab7d5ca1", "bytes": 1238, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#tIII-mmr-19-06-4806", "version": null, "note": "Significantly enriched pathways in the competing endogenous RNA regulatory network.", "structure": {"pmcid": "PMC6522811", "section_index": 10, "section_title": "Molecular function and pathway enrichment analysis", "row_count": 12, "column_count": 5}, "table": {"label": "Table III.", "caption": "Significantly enriched pathways in the competing endogenous RNA regulatory network.", "rows": [["KEGG pathway ID", "KEGG pathway name", "Gene count", "P-value", "Differentially expressed genes"], ["hsa04530", "Tight junction", "5", "0.001", "MYH1, CLDN6, MYH4, CTNNA2, CLDN10"], ["hsa04970", "Salivary secretion", "4", "0.001", "HTN3, ATP1B4, ATP1A2, STATH"], ["hsa04080", "Neuroactive ligand-receptor interaction", "6", "0.004", "GABRA2, GABRG2, PTH2R, OPRK1, CHRNA1, GRIK2"], ["hsa04918", "Thyroid hormone synthesis", "3", "0.007", "6528, ATP1B4, ATP1A2"], ["hsa04964", "Proximal tubule bicarbonate reclamation", "2", "0.008", "ATP1B4, ATP1A2"], ["hsa04960", "Aldosterone-regulated sodium reabsorption", "2", "0.020", "ATP1B4, ATP1A2"], ["hsa05033", "Nicotine addiction", "2", "0.020", "GABRA2, GABRG2"], ["hsa04973", "Carbohydrate digestion and absorption", "2", "0.025", "ATP1B4, ATP1A2"], ["hsa04670", "Leukocyte transendothelial migration", "3", "0.026", "CLDN6, CTNNA2, CLDN10"], ["hsa04978", "Mineral absorption", "2", "0.032", "ATP1B4, ATP1A2"], ["hsa04514", "Cell adhesion molecules (CAMs)", "3", "0.041", "CLDN6, NCAM2, CLDN10"]], "row_count": 12, "column_count": 5, "numeric_cells": 37, "header_rows": 1, "locator": "section[18]/table-wrap[1]#tIII-mmr-19-06-4806"}}, {"id": "asset:table:pmid:31059106:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2df3e319f66e1ea49df05d1e0275a1306a3c496d0fda80412c2746cd42e2d9b9", "bytes": 2665, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[2]#tIV-mmr-19-06-4806", "version": null, "note": "Significantly enriched molecular functions in the competing endogenous RNA regulatory network.", "structure": {"pmcid": "PMC6522811", "section_index": 10, "section_title": "Molecular function and pathway enrichment analysis", "row_count": 17, "column_count": 5}, "table": {"label": "Table IV.", "caption": "Significantly enriched molecular functions in the competing endogenous RNA regulatory network.", "rows": [["GO term ID", "GO term name", "Gene count", "P-value", "Genes"], ["GO:0006936", "Muscle contraction", "11", "4.17×10−7", "TRDN, ACTC1, MYH1, MYL1, MYLK2, MYH4, SMPX, TTN, CHRNA1, SCN5A, CASQ2"], ["GO:0003012", "Muscle system process", "11", "9.88×10−7", "TRDN, ACTC1, MYH1, MYL1, MYLK2, MYH4, SMPX, TTN, CHRNA1, SCN5A, CASQ2"], ["GO:0008015", "Blood circulation", "10", "1.89×10−5", "CALCA, CALCB, ACTC1, MYL1, MYLK2, CARTPT, ATP1A2, TAC4, SCN5A, EPO"], ["GO:0003013", "Circulatory system process", "10", "1.89×10−5", "CALCA, CALCB, ACTC1, MYL1, MYLK2, CARTPT, ATP1A2, TAC4, SCN5A, EPO"], ["GO:0007267", "Cell-cell signaling", "16", "9.03×10−5", "FGF5, GABRG2, GABRA2, GRIK2, OPRK1, MYLK2, ATP1A2, CXCL6, IL22, CTNNA2, CALCA, PNOC, SLC1A6, CARTPT, SLC30A8, CHRNA1"], ["GO:0006811", "Ion transport", "18", "1.32×10−4", "GABRG2, SLC5A5, GABRA2, GRIK2, ATP1B4, KCNA6, ATP1A2, TCN1, BEST3, SLC1A6, SLC5A8, LTF, ANO5, ANO4, CHRNA1, SLC30A8, SCN5A, ADD2"], ["GO:0007268", "Synaptic transmission", "11", "1.44×10−4", "GABRG2, GABRA2, PNOC, GRIK2, OPRK1, SLC1A6, MYLK2, CARTPT, ATP1A2, CHRNA1, CTNNA2"], ["GO:0030182", "Neuron differentiation", "13", "2.09×10−4", "NCAM2, SLITRK4, SOX1, OPCML, FOXA2, PKHD1, EMX2, MDGA2, PTPRR, POU4F1, OLFM3, NEFL, CTNNA2"], ["GO:0019226", "Transmission of nerve impulse", "11", "5.20×10−4", "GABRG2, GABRA2, PNOC, GRIK2, OPRK1, SLC1A6, MYLK2, CARTPT, ATP1A2, CHRNA1, CTNNA2"], ["GO:0055082", "Cellular chemical homeostasis", "10", "3.60×10−3", "CALCA, CALCB, XIRP1, GRIK2, SLC1A6, LTF, CARTPT, ATP1A2, SLC30A8, CHRNA1"], ["GO:0019725", "Cellular homeostasis", "10", "1.29×10−2", "CALCA, CALCB, XIRP1, GRIK2, SLC1A6, LTF, CARTPT, ATP1A2, SLC30A8, CHRNA1"], ["GO:0048878", "Chemical homeostasis", "10", "2.24×10−2", "CALCA, CALCB, XIRP1, GRIK2, SLC1A6, LTF, CARTPT, ATP1A2, SLC30A8, CHRNA1"], ["GO:0007155", "Cell adhesion", "12", "2.54×10−2", "IBSP, FLRT3, CALCA, NCAM2, AMBN, OPCML, FAT3, PKHD1, CLDN6, CLDN22, CLDN10, CTNNA2"], ["GO:0022610", "Biological adhesion", "12", "2.56×10−2", "IBSP, FLRT3, CALCA, NCAM2, AMBN, OPCML, FAT3, PKHD1, CLDN6, CLDN22, CLDN10, CTNNA2"], ["GO:0050877", "Neurological system process", "17", "3.28×10−2", "GABRG2, GABRA2, MYO3A, GRIK2, OPRK1, MYLK2, ATP1A2, TAS1R1, CTNNA2, CALCA, NCAM2, PNOC, SLC1A6, CARTPT, POU4F1, CHRNA1, NEFL"], ["GO:0042592", "Homeostatic process", "12", "3.94×10−2", "CALCA, CALCB, XIRP1, GRIK2, PKHD1, SLC1A6, LTF, CARTPT, ATP1A2, SLC30A8, CHRNA1, EPO"]], "row_count": 17, "column_count": 5, "numeric_cells": 56, "header_rows": 1, "locator": "section[18]/table-wrap[2]#tIV-mmr-19-06-4806"}}, {"id": "asset:table:pmid:31059106:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a0a425653933efe6307dbac1bda838cce7ff5a31320b3ecfc57d3d80a5aa7667", "bytes": 1662, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#tI-mmr-19-06-4806", "version": null, "note": "Basic information of 32 optimal feature-coding genes, among the genes significantly differentially expressed between recurrent and nonrecurrent cancer samples.", "structure": {"pmcid": "PMC6522811", "section_index": 17, "section_title": "SVM classifier", "row_count": 33, "column_count": 5}, "table": {"label": "Table I.", "caption": "Basic information of 32 optimal feature-coding genes, among the genes significantly differentially expressed between recurrent and nonrecurrent cancer samples.", "rows": [["Gene symbol", "Betweenness centrality", "Number of interactions", "P-value", "Log2 fold-change"], ["SHISA6", "0.240", "4", "0.028", "0.544"], ["MAGEA2", "0.215", "5", "0.047", "−0.394"], ["TRDN", "0.156", "6", "0.002", "0.601"], ["RGS7", "0.149", "4", "0.001", "1.331"], ["CPNE4", "0.142", "4", "0.020", "0.657"], ["CALCA", "0.111", "3", "0.004", "1.214"], ["GABRG2", "0.101", "2", "0.035", "0.599"], ["TECRL", "0.083", "3", "0.043", "0.846"], ["MYLK2", "0.073", "3", "0.005", "0.543"], ["MYO3A", "0.058", "3", "0.048", "0.365"], ["ASB10", "0.057", "3", "0.001", "1.261"], ["WT1", "0.039", "4", "0.015", "0.712"], ["CALCB", "0.038", "2", "0.006", "0.986"], ["OPCML", "0.038", "2", "0.011", "0.693"], ["KY", "0.038", "2", "0.011", "0.502"], ["CYP3A43", "0.038", "2", "0.027", "−2.312"], ["EPHA6", "0.038", "2", "0.001", "1.216"], ["SLC6A20", "0.038", "2", "0.001", "0.583"], ["NCAM2", "0.036", "2", "0.026", "0.451"], ["FLRT3", "0.033", "2", "0.022", "0.312"], ["TMC5", "0.033", "2", "0.034", "−0.334"], ["AADACL3", "0.033", "2", "0.011", "0.983"], ["ANKRD1", "0.026", "6", "0.005", "0.520"], ["CLDN22", "0.020", "2", "0.005", "−1.662"], ["FGF5", "0.018", "2", "0.015", "0.593"], ["SCN5A", "0.016", "2", "0.009", "0.475"], ["PTPRR", "0.016", "2", "0.005", "0.561"], ["LDHC", "0.015", "2", "0.000", "−1.366"], ["OLFM3", "0.012", "2", "0.036", "1.283"], ["HRASLS5", "0.012", "2", "0.042", "−0.560"], ["SPINK6", "0.010", "2", "0.011", "−0.533"], ["SPESP1", "0.008", "2", "0.004", "0.499"]], "row_count": 33, "column_count": 5, "numeric_cells": 132, "header_rows": 1, "locator": "section[17]/table-wrap[1]#tI-mmr-19-06-4806"}}, {"id": "asset:table:pmid:31059106:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5734f893d821a46857a2bee7799ec63780011e9642e7dc1341759657ced2020e", "bytes": 638, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#tII-mmr-19-06-4806", "version": null, "note": "Classifying parameters of the support vector machine classifier for the three datasets analyzed.", "structure": {"pmcid": "PMC6522811", "section_index": 17, "section_title": "SVM classifier", "row_count": 4, "column_count": 8}, "table": {"label": "Table II.", "caption": "Classifying parameters of the support vector machine classifier for the three datasets analyzed.", "rows": [["Dataset", "Number of samples", "Accuracy", "Sensitivity", "Specificity", "Positive predictive value", "Negative predictive value", "Area under receiver operating characteristic curve"], ["TCGA", "84", "0.9410", "0.947", "0.938", "0.818", "0.984", "0.986"], ["GSE27020", "109", "0.9266", "0.882", "0.947", "0.882", "0.947", "0.946"], ["GSE25727", "56", "0.9107", "0.941", "0.897", "0.8", "0.972", "0.921"]], "row_count": 4, "column_count": 8, "numeric_cells": 23, "header_rows": 1, "locator": "section[17]/table-wrap[2]#tII-mmr-19-06-4806"}}, {"id": "asset:table:pmid:31059106:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a745b59a26bbb2d9807a265a8ce64efd9ff197b00c16e681b799431bab7d5ca1", "bytes": 1238, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#tIII-mmr-19-06-4806", "version": null, "note": "Significantly enriched pathways in the competing endogenous RNA regulatory network.", "structure": {"pmcid": "PMC6522811", "section_index": 18, "section_title": "Molecular function and pathway enrichment analysis", "row_count": 12, "column_count": 5}, "table": {"label": "Table III.", "caption": "Significantly enriched pathways in the competing endogenous RNA regulatory network.", "rows": [["KEGG pathway ID", "KEGG pathway name", "Gene count", "P-value", "Differentially expressed genes"], ["hsa04530", "Tight junction", "5", "0.001", "MYH1, CLDN6, MYH4, CTNNA2, CLDN10"], ["hsa04970", "Salivary secretion", "4", "0.001", "HTN3, ATP1B4, ATP1A2, STATH"], ["hsa04080", "Neuroactive ligand-receptor interaction", "6", "0.004", "GABRA2, GABRG2, PTH2R, OPRK1, CHRNA1, GRIK2"], ["hsa04918", "Thyroid hormone synthesis", "3", "0.007", "6528, ATP1B4, ATP1A2"], ["hsa04964", "Proximal tubule bicarbonate reclamation", "2", "0.008", "ATP1B4, ATP1A2"], ["hsa04960", "Aldosterone-regulated sodium reabsorption", "2", "0.020", "ATP1B4, ATP1A2"], ["hsa05033", "Nicotine addiction", "2", "0.020", "GABRA2, GABRG2"], ["hsa04973", "Carbohydrate digestion and absorption", "2", "0.025", "ATP1B4, ATP1A2"], ["hsa04670", "Leukocyte transendothelial migration", "3", "0.026", "CLDN6, CTNNA2, CLDN10"], ["hsa04978", "Mineral absorption", "2", "0.032", "ATP1B4, ATP1A2"], ["hsa04514", "Cell adhesion molecules (CAMs)", "3", "0.041", "CLDN6, NCAM2, CLDN10"]], "row_count": 12, "column_count": 5, "numeric_cells": 37, "header_rows": 1, "locator": "section[18]/table-wrap[1]#tIII-mmr-19-06-4806"}}, {"id": "asset:table:pmid:31059106:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2df3e319f66e1ea49df05d1e0275a1306a3c496d0fda80412c2746cd42e2d9b9", "bytes": 2665, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[2]#tIV-mmr-19-06-4806", "version": null, "note": "Significantly enriched molecular functions in the competing endogenous RNA regulatory network.", "structure": {"pmcid": "PMC6522811", "section_index": 18, "section_title": "Molecular function and pathway enrichment analysis", "row_count": 17, "column_count": 5}, "table": {"label": "Table IV.", "caption": "Significantly enriched molecular functions in the competing endogenous RNA regulatory network.", "rows": [["GO term ID", "GO term name", "Gene count", "P-value", "Genes"], ["GO:0006936", "Muscle contraction", "11", "4.17×10−7", "TRDN, ACTC1, MYH1, MYL1, MYLK2, MYH4, SMPX, TTN, CHRNA1, SCN5A, CASQ2"], ["GO:0003012", "Muscle system process", "11", "9.88×10−7", "TRDN, ACTC1, MYH1, MYL1, MYLK2, MYH4, SMPX, TTN, CHRNA1, SCN5A, CASQ2"], ["GO:0008015", "Blood circulation", "10", "1.89×10−5", "CALCA, CALCB, ACTC1, MYL1, MYLK2, CARTPT, ATP1A2, TAC4, SCN5A, EPO"], ["GO:0003013", "Circulatory system process", "10", "1.89×10−5", "CALCA, CALCB, ACTC1, MYL1, MYLK2, CARTPT, ATP1A2, TAC4, SCN5A, EPO"], ["GO:0007267", "Cell-cell signaling", "16", "9.03×10−5", "FGF5, GABRG2, GABRA2, GRIK2, OPRK1, MYLK2, ATP1A2, CXCL6, IL22, CTNNA2, CALCA, PNOC, SLC1A6, CARTPT, SLC30A8, CHRNA1"], ["GO:0006811", "Ion transport", "18", "1.32×10−4", "GABRG2, SLC5A5, GABRA2, GRIK2, ATP1B4, KCNA6, ATP1A2, TCN1, BEST3, SLC1A6, SLC5A8, LTF, ANO5, ANO4, CHRNA1, SLC30A8, SCN5A, ADD2"], ["GO:0007268", "Synaptic transmission", "11", "1.44×10−4", "GABRG2, GABRA2, PNOC, GRIK2, OPRK1, SLC1A6, MYLK2, CARTPT, ATP1A2, CHRNA1, CTNNA2"], ["GO:0030182", "Neuron differentiation", "13", "2.09×10−4", "NCAM2, SLITRK4, SOX1, OPCML, FOXA2, PKHD1, EMX2, MDGA2, PTPRR, POU4F1, OLFM3, NEFL, CTNNA2"], ["GO:0019226", "Transmission of nerve impulse", "11", "5.20×10−4", "GABRG2, GABRA2, PNOC, GRIK2, OPRK1, SLC1A6, MYLK2, CARTPT, ATP1A2, CHRNA1, CTNNA2"], ["GO:0055082", "Cellular chemical homeostasis", "10", "3.60×10−3", "CALCA, CALCB, XIRP1, GRIK2, SLC1A6, LTF, CARTPT, ATP1A2, SLC30A8, CHRNA1"], ["GO:0019725", "Cellular homeostasis", "10", "1.29×10−2", "CALCA, CALCB, XIRP1, GRIK2, SLC1A6, LTF, CARTPT, ATP1A2, SLC30A8, CHRNA1"], ["GO:0048878", "Chemical homeostasis", "10", "2.24×10−2", "CALCA, CALCB, XIRP1, GRIK2, SLC1A6, LTF, CARTPT, ATP1A2, SLC30A8, CHRNA1"], ["GO:0007155", "Cell adhesion", "12", "2.54×10−2", "IBSP, FLRT3, CALCA, NCAM2, AMBN, OPCML, FAT3, PKHD1, CLDN6, CLDN22, CLDN10, CTNNA2"], ["GO:0022610", "Biological adhesion", "12", "2.56×10−2", "IBSP, FLRT3, CALCA, NCAM2, AMBN, OPCML, FAT3, PKHD1, CLDN6, CLDN22, CLDN10, CTNNA2"], ["GO:0050877", "Neurological system process", "17", "3.28×10−2", "GABRG2, GABRA2, MYO3A, GRIK2, OPRK1, MYLK2, ATP1A2, TAS1R1, CTNNA2, CALCA, NCAM2, PNOC, SLC1A6, CARTPT, POU4F1, CHRNA1, NEFL"], ["GO:0042592", "Homeostatic process", "12", "3.94×10−2", "CALCA, CALCB, XIRP1, GRIK2, PKHD1, SLC1A6, LTF, CARTPT, ATP1A2, SLC30A8, CHRNA1, EPO"]], "row_count": 17, "column_count": 5, "numeric_cells": 56, "header_rows": 1, "locator": "section[18]/table-wrap[2]#tIV-mmr-19-06-4806"}}], "gaps": ["asset:data:geo:GSE25727 not downloaded", "asset:data:geo:GSE25727 licence not read", "asset:data:geo:GSE27020 not downloaded", "asset:data:geo:GSE27020 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The differentially expressed RNAs, including differentially expressed mRNAs (DEGs), differentially expressed lncRNAs (DE-lncRs) and differentially expressed miRNAs (DE-miRs), between recurrent and nonrecurrent laryngeal cancer samples were analyzed using the EdgeR package version 3.8.5, which adopted an overdispersed poisson model and an empirical Bayesian approach to improve the reliability of the prediction (23)."}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-3", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "support vector machine"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-5", "family": "network_analysis", "specific": "centrality", "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": "centrality"}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: edger."}, "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": ["GSE27020", "GSE25727"], "resolved_accessions": ["GSE27020", "GSE25727"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE27020, GSE25727 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:31059106", "data:geo:GSE25727", "asset:table:pmid:31059106:1", "asset:table:pmid:31059106:2", "asset:table:pmid:31059106:3", "asset:table:pmid:31059106:4", "asset:table:pmid:31059106:5", "asset:table:pmid:31059106:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE25727"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:14:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 39432, "completion_tokens": 1657, "cached_tokens": 520}}, "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:31059106", "type": "paper", "label": "pmid:31059106"}, {"id": "source:pmid:31059106", "type": "manuscript", "label": "PMID 31059106 full text"}, {"id": "data:geo:GSE25727", "type": "dataset", "label": "GEO GSE25727"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31059106", "type": "paper", "label": "pmid:31059106"}, {"id": "source:pmid:31059106", "type": "manuscript", "label": "PMID 31059106 full text"}, {"id": "data:geo:GSE25727", "type": "dataset", "label": "GEO GSE25727"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31059106", "type": "extraction", "used": ["source:pmid:31059106"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE25727", "type": "accession_resolution", "used": ["data:geo:GSE25727"], "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:31059106", "parent_hash": "sha256:2493d4020291801971eeac1502dc4525063d7e62f6d404757569eca75e7c6ca3", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE25727 licence not read", "asset:data:geo:GSE25727 not downloaded", "asset:data:geo:GSE27020 licence not read", "asset:data:geo:GSE27020 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["et was constructed using the RNA sequencing (RNA-seq) data downloaded from the TCGA database. The", "e training dataset was constructed using the RNA sequencing (RNA-seq) data downloaded from the TCGA data"], "order_basis": "paper_text_order:3172", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The differentially expressed RNAs, including differentially expressed mRNAs (DEGs), differentially expressed lncRNAs (DE-lncRs) and differentially expressed miRNAs (DE-miRs), between recurrent and nonrecurrent laryngeal cancer samples were analyzed using the EdgeR package version 3.8.5, which adopted an overdispersed poisson model and an empirical Bayesian approach to improve the reliability of the prediction (23)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}