← All .science files
pmid:30254489
Establishment and validation of a 7-microRNA prognostic signature for non-small cell lung cancer.
Nan Wang · Huihui Guo · Zhaohuo Dong · Qiuqiang Chen · Xilin Zhang · Weiyun Shen · Ying Bao · Xiang Wang
Cancer management and research · 2018 doi:10.2147/CMAR.S170481
Paper
complete
Experiment
partial
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 8 items
claims array · 1 item
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
data object · 3 fields
assets array · 9 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 6 items
[0] array · 3 items
[1] array · 6 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 6 items
[0] array · 4 items
[1] array · 6 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 21 items
[0] array · 3 items
[1] array · 2 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
[17] array · 4 items
[18] array · 4 items
[19] array · 4 items
[20] array · 4 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 5 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 5 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 25 items
[0] array · 3 items
[1] array · 3 items
[2] array · 2 items
[3] array · 2 items
[4] array · 3 items
[5] array · 2 items
[6] array · 2 items
[7] array · 3 items
[8] array · 2 items
[9] array · 2 items
[10] array · 3 items
[11] array · 2 items
[12] array · 2 items
[13] array · 3 items
[14] array · 2 items
[15] array · 2 items
[16] array · 3 items
[17] array · 2 items
[18] array · 2 items
[19] array · 3 items
[20] array · 2 items
[21] array · 2 items
[22] array · 3 items
[23] array · 2 items
[24] array · 2 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 5 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[8] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 25 items
[0] array · 3 items
[1] array · 3 items
[2] array · 2 items
[3] array · 2 items
[4] array · 3 items
[5] array · 2 items
[6] array · 2 items
[7] array · 3 items
[8] array · 2 items
[9] array · 2 items
[10] array · 3 items
[11] array · 2 items
[12] array · 2 items
[13] array · 3 items
[14] array · 2 items
[15] array · 2 items
[16] array · 3 items
[17] array · 2 items
[18] array · 2 items
[19] array · 3 items
[20] array · 2 items
[21] array · 2 items
[22] array · 3 items
[23] array · 2 items
[24] array · 2 items
gaps array · 0 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 0 items
resolved_accessions array · 0 items
statements array · 0 items
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 9 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 5 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[2] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30254489", "kind": "science-record", "revision": 6, "content_hash": "sha256:b108e94ba4535a0de6c946759bc0666e114e873c2c54fdba1e6746ae9ea4f32f", "created_at": "2026-11-01T15:40:37Z", "updated_at": "2026-11-01T21:21:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment and validation of a 7-microRNA prognostic signature for non-small cell lung cancer.", "doi": "10.2147/CMAR.S170481", "pmid": "30254489", "authors": ["Nan Wang", "Huihui Guo", "Zhaohuo Dong", "Qiuqiang Chen", "Xilin Zhang", "Weiyun Shen", "Ying Bao", "Xiang Wang"], "journal": "Cancer management and research", "year": 2018, "abstract": "PURPOSE: A series of microRNAs (miRNAs) have been identified as associated with the survival of patients with non-small-cell lung cancer (NSCLC). The aim of the present study was to explore whether combination of these experimentally validated individual miRNA biomarkers could be used to further increase their prognostic power in NSCLC.\nPATIENTS AND METHODS: Based on previously validated NSCLC prognostic miRNAs, gene signatures that could discriminate high-risk subgroups with poor clinical outcome in four NSCLC miRNA expression datasets (GSE13937, GSE16025, The Cancer Genome Atlas Lung Adenocarcinoma, and TCGA lung squamous cell carcinoma) were developed using the SurvMicro tool. The potential of the miRNA signature established was validated by quantitative real-time PCR analysis of clinical NSCLC samples, and its prognostic power evaluated using the survivalROC method.\nRESULTS: We developed two miRNA signatures with prognostic significance for NSCLC, comprising 12- and 7-miRNAs. The 7-miRNA signature (miR-148b, miR-365, miR-32, miR-375, miR-21, miR-125b, and miR-155) was a subset of a 12-miRNA set that retained prognostic power across NSCLC cohorts. Compared with previously established miRNA signatures, our 7-miRNA signature has similar potential, while comprising fewer miRNA components. The prognostic ability of the 7-miRNA signature was validated experimentally in an independent NSCLC cohort using real-time PCR (HR=3.4847, 95% CI=1.3693-8.8680, P=0.0092), and this signature, combined with tumor pathological stage, had superior prognostic ability compared with tumor stage alone.\nCONCLUSION: Our data indicate that the established 7-miRNA signature is simple, robust, and may have greater clinical prognostic utility for patients with NSCLC.", "claims": [{"id": "claim-method", "statement": "Survival was compared between high- and low-risk groups using Kaplan–Meier survival curves and the log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30254489", "locator": "sections[9] \"Statistics\" paragraph 2", "quote": "Survival was compared between high- and low-risk groups using Kaplan–Meier survival curves and the log-rank test."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:30254489"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30254489", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S170481", "sha256": "sha256:b493a8e3cbf01c55b6e1c55e8621ea43c2333f556ad582872d0e16de52d942d3", "bytes": 25479, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CMAR.S170481", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6140736", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:30254489:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cabf619b7ddd3597e0f116ef0104ffab6ca73e5f33f2a632cb093ee9434e9936", "bytes": 777, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t1-cmar-10-3463", "version": null, "note": "Prognostic significance of 12- and 7-miRNA signatures in four independent NSCLC cohorts", "structure": {"pmcid": "PMC6140736", "section_index": 10, "section_title": "Results", "row_count": 6, "column_count": 7}, "table": {"label": "Table 1", "caption": "Prognostic significance of 12- and 7-miRNA signatures in four independent NSCLC cohorts", "rows": [["Dataset", "12-miRNA signature", "7-miRNA signature"], ["Concordance index", "HR (95% CI)", "P-value", "Concordance index", "HR (95% CI)", "P-value"], ["Mathe Zhao lung GSE13937", "64.05", "2.32 (1.38–3.9)", "0.0014", "64.82", "2.6 (1.52–4.45)", "0.00027"], ["Raponi Beer lung GSE16025", "69.85", "2.49 (1.21–5/13)", "0.013", "63.76", "3.13 (1.52–6.42)", "0.0019"], ["TCGA LUAD", "63.98", "2.78 (1.58–4.9)", "0.0004", "67.71", "2.82 (1.57–5.05)", "0.00049"], ["TCGA LUSC", "59.89", "1.70 (0.95–3.04)", "0.071", "60.17", "2.1 (1.2–3.69)", "0.0097"]], "row_count": 6, "column_count": 7, "numeric_cells": 30, "header_rows": 2, "locator": "section[10]/table-wrap[1]#t1-cmar-10-3463"}}, {"id": "asset:table:pmid:30254489:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6573547fbeb23dd46ccaa49fbff6a6575031e4b872e328f7c28103fd333ee489", "bytes": 667, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#t2-cmar-10-3463", "version": null, "note": "Comparison of our 7-miRNA signature with two other miRNA signatures in NSCLC", "structure": {"pmcid": "PMC6140736", "section_index": 10, "section_title": "Results", "row_count": 6, "column_count": 7}, "table": {"label": "Table 2", "caption": "Comparison of our 7-miRNA signature with two other miRNA signatures in NSCLC", "rows": [["Dataset", "7-miRNA signature", "Raponi signature", "Yu signature"], ["Concordance index", "P-value", "Concordance index", "P-value", "Concordance index", "P-value"], ["Mathe Zhao", "64.82", "0.00027", "74.76", "1.063e-06", "59.75", "0.052"], ["Raponi Beer", "63.76", "0.0019", "77.56", "0.00016", "59.68", "0.1621"], ["TCGA LUAD", "67.71", "0.00049", "73.56", "8.741e-06", "58.36", "0.1149"], ["TCGA LUSC", "60.17", "0.0097", "63.63", "0.00086", "63.04", "0.1089"]], "row_count": 6, "column_count": 7, "numeric_cells": 25, "header_rows": 2, "locator": "section[10]/table-wrap[2]#t2-cmar-10-3463"}}, {"id": "asset:table:pmid:30254489:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b592e8f9d15b6cc33cc5c2418d5c1fb54b1e1ba17c043ed5b5997a83deaa8bb0", "bytes": 869, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[3]#t3-cmar-10-3463", "version": null, "note": "Association between miRNA signature risk with clinicopathological characteristics", "structure": {"pmcid": "PMC6140736", "section_index": 10, "section_title": "Results", "row_count": 21, "column_count": 4}, "table": {"label": "Table 3", "caption": "Association between miRNA signature risk with clinicopathological characteristics", "rows": [["Characteristics", "7-miRNA signature", "P-value"], ["High-risk(n=20)", "Low-risk(n=20)"], ["Age (years)", "", "", ""], ["<60 (n=20)", "7", "13", "0.1138"], ["≥60 (n=20)", "13", "7", ""], ["Gender", "", "", ""], ["Male (n=36)", "20", "16", "0.1138"], ["Female (n=4)", "0", "4", ""], ["Histology", "", "", ""], ["LUAD (n=17)", "10", "7", "0.5524"], ["LUSC (n=23)", "10", "13", ""], ["Tumor size", "", "", ""], ["T1–2 (n=30)", "14", "16", "0.7150"], ["T3–4 (n=10)", "6", "4", ""], ["Lymph node metastasis", "", "", ""], ["N0 (n=23)", "11", "12", "1.000"], ["N1 (n=17)", "9", "8", ""], ["Stage", "", "", ""], ["I (n=18)", "8", "10", ""], ["II (n=10)", "4", "6", "0.3761"], ["III (n=12)", "8", "4", ""]], "row_count": 21, "column_count": 4, "numeric_cells": 48, "header_rows": 2, "locator": "section[10]/table-wrap[3]#t3-cmar-10-3463"}}, {"id": "asset:table:pmid:30254489:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8de15a722c19498ebc7540283e1765641cc5a069aeb9240ca04aa998297f04b7", "bytes": 568, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[4]#t4-cmar-10-3463", "version": null, "note": "Multivariate Cox regression analysis of 7-miRNA signature risk score and clinicopathological factors with overall survival", "structure": {"pmcid": "PMC6140736", "section_index": 10, "section_title": "Results", "row_count": 5, "column_count": 4}, "table": {"label": "Table 4", "caption": "Multivariate Cox regression analysis of 7-miRNA signature risk score and clinicopathological factors with overall survival", "rows": [["Prognostic factors", "P-value", "Hazard ratio", "95% CI"], ["Grade", "0.7911", "1.1601", "0.3889–3.4606"], ["Lymph node metastasis", "0.0103", "3.2550", "1.3281–7.9774"], ["Tumor size", "0.5791", "0.7213", "0.2287–2.2747"], ["7-miRNA signature risk score", "0.0092", "3.4847", "1.3693–8.8680"]], "row_count": 5, "column_count": 4, "numeric_cells": 14, "header_rows": 1, "locator": "section[10]/table-wrap[4]#t4-cmar-10-3463"}}, {"id": "asset:table:pmid:30254489:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a12e354ad8fa751d5e28c4cbc5b08aba1f306625e1ffd73434eb9dc20d4ac820", "bytes": 507, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#ts1-cmar-10-3463", "version": null, "note": "NSCLC miRNA expression profiles datasets used in our analysis", "structure": {"pmcid": "PMC6140736", "section_index": 13, "section_title": "Supplementary materials", "row_count": 5, "column_count": 4}, "table": {"label": "Table S1", "caption": "NSCLC miRNA expression profiles datasets used in our analysis", "rows": [["Dataset", "Platform", "Samples", "Ref"], ["Mathe Zhao Lung GSE13937", "Microarray", "152 (64 ADC, 88 SCC)", "1"], ["Raponi Beer Lung GSE16025", "Microarray", "61 SCC", "2"], ["TCGA Lung Adenocarcinoma", "miRNA-Seq", "195 ADC", "3"], ["TCGA Lung Squamous Cell Carcinoma", "miRNA-Seq", "142 SCC", "3"]], "row_count": 5, "column_count": 4, "numeric_cells": 10, "header_rows": 1, "locator": "section[13]/table-wrap[1]#ts1-cmar-10-3463"}}, {"id": "asset:table:pmid:30254489:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:834a2c2d897d427fe80ff3d4fb559021603d8395721d3540793434bb33792c1e", "bytes": 1618, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#ts2-cmar-10-3463", "version": null, "note": "Primers for the signature miRNAs assays by real-time PCR", "structure": {"pmcid": "PMC6140736", "section_index": 13, "section_title": "Supplementary materials", "row_count": 25, "column_count": 3}, "table": {"label": "Table S2", "caption": "Primers for the signature miRNAs assays by real-time PCR", "rows": [["miRNA", "Primer", "Primer sequence"], ["hsa-miR-32", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGACTGGATACGACTGCAACTT-3′"], ["Forward", "5′-GTGCAGGGTCCGAGGTATT-3′"], ["Reverse", "5′-GCCGCTATTGCACATTACTAAGTT-3′"], ["hsa-miR-21", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTCAACA-3′"], ["Forward", "5′-GCCCGCTAGCTTATCAGACTGATG-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["hsa-miR-125b", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTCACAAG-3′"], ["Forward", "5′-GCGGCTCCCTGAGACCCTAAC-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["hsa-miR-155", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACCCCCTA-3′"], ["Forward", "5′-CTCGTGGTAATGCTAATTGTGA-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["hsa-mir-148b", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACGCCTGA-3′"], ["Forward", "5′-GGCGCAAGTTCTGTTATACAC-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["hsa-miR-365", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACATAAGG-3′"], ["Forward", "5′-CGTAATGCCCCTAAAAAT-3′"], ["Reverse", "5′-AGCCGTTTGTTCGTTCGGCT-3′"], ["hsa-miR-367", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTCACGC-3′"], ["Forward", "5′-AGCCGTTTGTTCGTTCGGCT-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["U6 snRNA", "RT", "5′-CGCTTCACGAATTTGCGTGTCAT-3′"], ["Forward", "5′-GCTTCGGCAGCACATATACTAAAAT-3′"], ["Reverse", "5′-CGCTTCACGAATTTGCGTGTCAT-3′"]], "row_count": 25, "column_count": 3, "numeric_cells": 31, "header_rows": 1, "locator": "section[13]/table-wrap[2]#ts2-cmar-10-3463"}}, {"id": "asset:table:pmid:30254489:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:61a27fb3ab3d8b46f25a9308abc52bc64d16136b6e637d4793bfd8b30ca96095", "bytes": 515, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#db_ds_table-wrap1_reqid_", "version": null, "note": "NSCLC miRNA expression profiles datasets used in our analysis", "structure": {"pmcid": "PMC6140736", "section_index": 21, "section_title": "Supplementary Materials", "row_count": 5, "column_count": 4}, "table": {"label": "Table S1", "caption": "NSCLC miRNA expression profiles datasets used in our analysis", "rows": [["Dataset", "Platform", "Samples", "Ref"], ["Mathe Zhao Lung GSE13937", "Microarray", "152 (64 ADC, 88 SCC)", "1"], ["Raponi Beer Lung GSE16025", "Microarray", "61 SCC", "2"], ["TCGA Lung Adenocarcinoma", "miRNA-Seq", "195 ADC", "3"], ["TCGA Lung Squamous Cell Carcinoma", "miRNA-Seq", "142 SCC", "3"]], "row_count": 5, "column_count": 4, "numeric_cells": 10, "header_rows": 1, "locator": "section[21]/table-wrap[1]#db_ds_table-wrap1_reqid_"}}, {"id": "asset:table:pmid:30254489:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e929fcf95eca40dedeccd333a4de722b82810c49dec5a3b3691b2a4665670139", "bytes": 1626, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[2]#db_ds_table-wrap2_reqid_", "version": null, "note": "Primers for the signature miRNAs assays by real-time PCR", "structure": {"pmcid": "PMC6140736", "section_index": 21, "section_title": "Supplementary Materials", "row_count": 25, "column_count": 3}, "table": {"label": "Table S2", "caption": "Primers for the signature miRNAs assays by real-time PCR", "rows": [["miRNA", "Primer", "Primer sequence"], ["hsa-miR-32", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGACTGGATACGACTGCAACTT-3′"], ["Forward", "5′-GTGCAGGGTCCGAGGTATT-3′"], ["Reverse", "5′-GCCGCTATTGCACATTACTAAGTT-3′"], ["hsa-miR-21", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTCAACA-3′"], ["Forward", "5′-GCCCGCTAGCTTATCAGACTGATG-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["hsa-miR-125b", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTCACAAG-3′"], ["Forward", "5′-GCGGCTCCCTGAGACCCTAAC-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["hsa-miR-155", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACCCCCTA-3′"], ["Forward", "5′-CTCGTGGTAATGCTAATTGTGA-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["hsa-mir-148b", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACGCCTGA-3′"], ["Forward", "5′-GGCGCAAGTTCTGTTATACAC-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["hsa-miR-365", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACATAAGG-3′"], ["Forward", "5′-CGTAATGCCCCTAAAAAT-3′"], ["Reverse", "5′-AGCCGTTTGTTCGTTCGGCT-3′"], ["hsa-miR-367", "RT", "5′-GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTCACGC-3′"], ["Forward", "5′-AGCCGTTTGTTCGTTCGGCT-3′"], ["Reverse", "5′-GTGCAGGGTCCGAGGT-3′"], ["U6 snRNA", "RT", "5′-CGCTTCACGAATTTGCGTGTCAT-3′"], ["Forward", "5′-GCTTCGGCAGCACATATACTAAAAT-3′"], ["Reverse", "5′-CGCTTCACGAATTTGCGTGTCAT-3′"]], "row_count": 25, "column_count": 3, "numeric_cells": 31, "header_rows": 1, "locator": "section[21]/table-wrap[2]#db_ds_table-wrap2_reqid_"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Survival was compared between high- and low-risk groups using Kaplan–Meier survival curves and the log-rank test."}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": [], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:30254489", "asset:table:pmid:30254489:1", "asset:table:pmid:30254489:2", "asset:table:pmid:30254489:3", "asset:table:pmid:30254489:4", "asset:table:pmid:30254489:5", "asset:table:pmid:30254489:6", "asset:table:pmid:30254489:7", "asset:table:pmid:30254489:8"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:36:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 22138, "completion_tokens": 2524, "cached_tokens": 648}}, "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:30254489", "type": "paper", "label": "pmid:30254489"}, {"id": "source:pmid:30254489", "type": "manuscript", "label": "PMID 30254489 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30254489", "type": "paper", "label": "pmid:30254489"}, {"id": "source:pmid:30254489", "type": "manuscript", "label": "PMID 30254489 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30254489", "type": "extraction", "used": ["source:pmid:30254489"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:30254489", "parent_hash": "sha256:90dbdcc00ac137a2ee94cb0097bc23568bc0a63a44e24d8c7d30fc931c2b2594", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["dentified as associated with the survival of patients with non-small-cell lung cancer (NSCLC). The aim", "have greater clinical prognostic utility for patients with NSCLC."], "order_basis": "paper_text_order:149", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["re established was validated by quantitative real-time PCR analysis of clinical NSCLC samples, and its", "entally in an independent NSCLC cohort using real-time PCR (HR=3.4847, 95% CI=1.3693-8.8680, P=0.0092),", "of the 7-miRNA signature using quantitative real-time PCR. The samples were collected from archived tu"], "order_basis": "paper_text_order:821", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Survival was compared between high- and low-risk groups using Kaplan–Meier survival curves and the log-rank test."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}