Identification of a Potentially Functional microRNA-mRNA Regulatory Network in Lung Adenocarcinoma Using a Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33681226", "kind": "science-record", "revision": 8, "content_hash": "sha256:2a511163976e9c7c41cb60f814c433308c553f2dde468a6650386048d4aed3dd", "created_at": "2026-11-01T15:41:27Z", "updated_at": "2026-11-01T22:46:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a Potentially Functional microRNA-mRNA Regulatory Network in Lung Adenocarcinoma Using a Bioinformatics Analysis.", "doi": "10.3389/fcell.2021.641840", "pmid": "33681226", "authors": ["Xiao-Jun Wang", "Jing Gao", "Zhuo Wang", "Qin Yu"], "journal": "Frontiers in cell and developmental biology", "year": 2021, "abstract": "BACKGROUND: Lung adenocarcinoma (LUAD) is a common lung cancer with a high mortality, for which microRNAs (miRNAs) play a vital role in its regulation. Multiple messenger RNAs (mRNAs) may be regulated by miRNAs, involved in LUAD tumorigenesis and progression. However, the miRNA-mRNA regulatory network involved in LUAD has not been fully elucidated.\nMETHODS: Differentially expressed miRNAs and mRNA were derived from the Cancer Genome Atlas (TCGA) dataset in tissue samples and from our microarray data in plasma (GSE151963). Then, common differentially expressed (Co-DE) miRNAs were obtained through intersected analyses between the above two datasets. An overlap was applied to confirm the Co-DEmRNAs identified both in targeted mRNAs and DEmRNAs in TCGA. A miRNA-mRNA regulatory network was constructed using Cytoscape. The top five miRNA were identified as hub miRNA by degrees in the network. The functions and signaling pathways associated with the hub miRNA-targeted genes were revealed through Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The key mRNAs in the protein-protein interaction (PPI) network were identified using the STRING database and CytoHubba. Survival analyses were performed using Gene Expression Profiling Interactive Analysis (GEPIA).\nRESULTS: The miRNA-mRNA regulatory network consists of 19 Co-DEmiRNAs and 760 Co-DEmRNAs. The five miRNAs (miR-539-5p, miR-656-3p, miR-2110, let-7b-5p, and miR-92b-3p) in the network were identified as hub miRNAs by degrees (>100). The 677 Co-DEmRNAs were targeted mRNAs from the five hub miRNAs, showing the roles in the functional analyses of the GO analysis and KEGG pathways (inclusion criteria: 836 and 48, respectively). The PPI network and Cytoscape analyses revealed that the top ten key mRNAs were NOTCH1, MMP2, IGF1, KDR, SPP1, FLT1, HGF, TEK, ANGPT1, and PDGFB. SPP1 and HGF emerged as hub genes through survival analysis. A high SPP1 expression indicated a poor survival, whereas HGF positively associated with survival outcomes in LUAD.\nCONCLUSION: This study investigated a miRNA-mRNA regulatory network associated with LUAD, exploring the hub miRNAs and potential functions of mRNA in the network. These findings contribute to identify new prognostic markers and therapeutic targets for LUAD patients in clinical settings.", "claims": [{"id": "claim-method", "statement": "The differentially expressed miRNAs (DEmiRNAs) and mRNA (DEmRNAs) were analyzed comparing the LUAD and normal samples using the R package limma. The common consistently and differentially expressed (Co-DE) miRNAs were obtained using intersected analyses comparing TCGA and microarray datasets (Cojocneanu et al., 2020).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33681226", "locator": "sections[3] \"Construction of the miRNA–mRNA Regulatory Network\" paragraph 2", "quote": "The differentially expressed miRNAs (DEmiRNAs) and mRNA (DEmRNAs) were analyzed comparing the LUAD and normal samples using the R package limma."}, {"asset": "source:pmid:33681226", "locator": "sections[3] \"Construction of the miRNA–mRNA Regulatory Network\" paragraph 2", "quote": "The common consistently and differentially expressed (Co-DE) miRNAs were obtained using intersected analyses comparing TCGA and microarray datasets (Cojocneanu et al., 2020)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33681226", "locator": "sections[11] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "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:33681226"], "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:GSE151963"], "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:GSE151963"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33681226", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcell.2021.641840", "sha256": "sha256:c717b41a45ea170128ce6963f605692d7f386f10391ac94c6569c4c76f8240bf", "bytes": 43906, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcell.2021.641840", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7930498", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE151963", "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=GSE151963", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE151963", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4594400", "GSM4594401", "GSM4594402", "GSM4594403", "GSM4594404", "GSM4594405", "GSM4594406", "GSM4594407", "GSM4594408", "GSM4594409"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "Exploring differentially expressed miRNAs (DEmiRNAs) in plasma sample between lung adenocarcinoma patients and healthy people", "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:33681226:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fd37fcba321204606501bed47607199988b941e82cbfee37cd099e3f53a188d3", "bytes": 2452, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T1", "version": null, "note": "Common differentially expressed miRNAs (n = 30) in the GSE151963 and TCGA datasets.", "structure": {"pmcid": "PMC7930498", "section_index": 7, "section_title": "Constructing the miRNA–mRNA Regulatory Network", "row_count": 34, "column_count": 7}, "table": {"label": "TABLE 1", "caption": "Common differentially expressed miRNAs (n = 30) in the GSE151963 and TCGA datasets.", "rows": [["ID", "GSE151963", "TCGA"], ["", "log2 FC", "p-value", "Expression change", "log2 FC", "p-value", "Expression change"], ["Consistent (n = 19)"], ["hsa-miR-369-3p", "4.071", "2.38E-07", "Down", "1.434", "2.41E-03", "Down"], ["hsa-miR-539-5p", "3.966", "1.06E-07", "Down", "2.943", "6.00E-03", "Down"], ["hsa-miR-379-5p", "3.727", "1.04E-04", "Down", "1.69", "5.53E-03", "Down"], ["hsa-miR-494-3p", "2.999", "7.57E-04", "Down", "1.837", "3.53E-03", "Down"], ["hsa-miR-495-3p", "2.695", "1.06E-03", "Down", "2.12", "4.78E-02", "Down"], ["hsa-miR-337-3p", "2.634", "1.02E-04", "Down", "2.556", "1.69E-04", "Down"], ["hsa-miR-376c-3p", "2.552", "7.87E-06", "Down", "1.69", "3.42E-03", "Down"], ["hsa-miR-382-5p", "2.51", "6.23E-03", "Down", "1.644", "5.36E-03", "Down"], ["hsa-miR-154-5p", "2.4", "1.49E-05", "Down", "1.837", "1.09E-03", "Down"], ["hsa-miR-134-5p", "2.322", "6.94E-03", "Down", "1.599", "1.44E-03", "Down"], ["hsa-miR-656-3p", "1.914", "5.94E-03", "Down", "1.69", "2.61E-02", "Down"], ["hsa-miR-655-3p", "1.771", "8.56E-04", "Down", "2.184", "2.52E-03", "Down"], ["hsa-miR-496", "1.106", "6.55E-04", "Down", "1.396", "3.43E-02", "Down"], ["hsa-miR-184", "3.775", "2.44E-04", "Up", "2.06", "5.86E-11", "Up"], ["hsa-miR-486-5p", "3.552", "5.22E-05", "Up", "1.8", "8.87E-06", "Up"], ["hsa-miR-2110", "2.483", "1.12E-03", "Up", "1.28", "1.40E-09", "Up"], ["hsa-miR-92b-3p", "1.874", "1.41E-06", "Up", "1.49", "8.46E-06", "Up"], ["hsa-let-7b-5p", "1.806", "3.96E-04", "Up", "1.1", "3.26E-08", "Up"], ["hsa-miR-455-5p", "1.256", "4.60E-04", "Up", "2.566", "3.04E-03", "Up"], ["Inconsistent (n = 11)"], ["hsa-miR-20a-5p", "2.178", "3.21E-04", "Down", "2.63", "3.57E-05", "Up"], ["hsa-miR-556-5p", "2.175", "1.85E-04", "Down", "2.381", "1.83E-02", "Up"], ["hsa-miR-766-3p", "2.089", "1.60E-04", "Down", "1.362", "1.48E-02", "Up"], ["hsa-miR-146b-5p", "1.777", "7.07E-05", "Down", "1.45", "2.20E-16", "Up"], ["hsa-miR-362-5p", "1.661", "4.38E-04", "Down", "1.183", "2.23E-03", "Up"], ["hsa-miR-130a-3p", "1.583", "3.90E-05", "Down", "1.58", "2.89E-07", "Up"], ["hsa-miR-33a-5p", "1.447", "8.96E-04", "Down", "3.38", "1.66E-05", "Up"], ["hsa-miR-1296-5p", "1.439", "4.30E-03", "Down", "1.275", "8.47E-03", "Up"], ["hsa-miR-552-3p", "1.322", "1.03E-03", "Down", "1.49", "1.28E-07", "Up"], ["hsa-miR-122-5p", "4.746", "1.14E-05", "Up", "3.644", "3.83E-02", "Down"], ["hsa-miR-10b-5p", "3.323", "3.93E-04", "Up", "2.06", "3.95E-08", "Down"]], "row_count": 34, "column_count": 7, "numeric_cells": 153, "header_rows": 2, "locator": "section[7]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33681226:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:64edb96d39a49dfb184f94448ec3e4a75eb7d31c49828e001343fbb684e54ff1", "bytes": 7175, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T2", "version": null, "note": "Results from the Kyoto Encyclopedia of Genes and Genomes enrichment pathway analysis.", "structure": {"pmcid": "PMC7930498", "section_index": 8, "section_title": "GO and KEGG Analyses of Targeted mRNAs for Hub miRNAs", "row_count": 49, "column_count": 5}, "table": {"label": "TABLE 2", "caption": "Results from the Kyoto Encyclopedia of Genes and Genomes enrichment pathway analysis.", "rows": [["ID", "Description", "p-value", "Gene ID", "Count"], ["hsa04510", "Focal adhesion", "2.070E-09", "PXN/PIK3R3/LAMA4/SPP1/LAMC2/HGF/FYN/AKT3/SHC3/ITGA8/MAPK10/COL4A3/ROCK1/THBS1/IGF1/COL1A1/COL4A2/PPP1R12B/PDGFB/CCND2/PPP1R12C/ITGA5/LAMA2/PRKCB/FLT1/RAPGEF1/CAV2/KDR", "28"], ["hsa05205", "Proteoglycans in cancer", "5.760E-08", "WNT7B/PXN/FGFR1/PIK3R3/MMP2/HGF/AKT3/DDX5/ROCK1/WNT3/FZD4/THBS1/IGF1/CDKN1A/COL1A1/PPP1R12B/PPP1R12C/ITGA5/ITPR1/TLR4/WNT7A/PRKCB/TIMP3/HBEGF/CAV2/KDR", "26"], ["hsa04512", "Extracellular matrix–receptor interaction", "5.150E-06", "LAMA4/CD36/SPP1/LAMC2/FRAS1/ITGA8/FREM1/COL4A3/THBS1/COL1A1/COL4A2/ITGA5/NPNT/LAMA2", "14"], ["hsa04270", "Vascular smooth-muscle contraction", "1.340E-05", "MRVI1/PLA2G4A/GUCY1A2/ROCK1/PLA2G3/EDN1/PPP1R12B/PPP1R12C/ADM/ADCY3/ITPR1/PRKCE/PRKG1/CALCRL/PRKCB/CACNA1C/CACNA1D", "17"], ["hsa04022", "cGMP–PKG signaling pathway", "2.030E-04", "MRVI1/PIK3R5/PDE3B/AKT3/GUCY1A2/MEF2A/ROCK1/ADRB2/ADRB1/ADCY3/ITPR1/PRKCE/PRKG1/EDNRB/CACNA1C/PLN/CACNA1D", "17"], ["hsa04931", "Insulin resistance", "2.210E-04", "PYGM/PIK3R3/PPP1R3E/PTPN1/CD36/AKT3/PPARGC1A/MAPK10/PPAR GC1B/GFPT2/PRKCE/OGT/PRKCB", "13"], ["hsa04611", "Platelet activation", "2.530E-04", "PIK3R3/FCER1G/PIK3R5/PLA2G4A/FYN/AKT3/GUCY1A2/ROCK1/P2RX1/COL1A1/COL3A1/ADCY3/ITPR1/PRKG1", "14"], ["hsa04924", "Renin secretion", "2.590E-04", "AQP1/PDE3B/GUCY1A2/ADRB2/EDN1/ADRB1/ITPR1/PTGER4/CACNA1C/CACNA1D", "10"], ["hsa05414", "Dilated cardiomyopathy", "2.700E-04", "SGCD/ITGA8/IGF1/ADRB1/ITGA5/ADCY3/ACTC1/CACNB2/LAMA2/CACNA1C/PLN/CACNA1D", "12"], ["hsa04310", "Wnt signaling pathway", "3.810E-04", "WNT7B/NKD1/PRICKLE4/SFRP1/RSPO3/SOX17/RSPO2/PRICKLE2/MAPK10/WNT3/FZD4/CCND2/WNT7A/PRKCB/WIF1/AXIN2", "16"], ["hsa04933", "AGE–RAGE signaling pathway in diabetic complications", "3.960E-04", "PIK3R3/EGR1/MMP2/AKT3/MAPK10/COL4A3/EDN1/COL1A1/COL4A2/COL3A1/PRKCE/PRKCB", "12"], ["hsa04151", "PI3K–Akt signaling pathway", "4.370E-04", "FGFR1/PIK3R3/LAMA4/PIK3R5/SPP1/LAMC2/HGF/AKT3/ITGA8/COL4A3/FOXO3/THBS1/GHR/IGF1/CDKN1A/COL1A1/COL4A2/PDGFB/CCND2/ITGA5/TLR4/ANGPT1/NR4A1/LAMA2/TEK/FLT1/KDR", "27"], ["hsa05146", "Amebiasis", "4.760E-04", "PIK3R3/LAMA4/CXCL2/LAMC2/ITGAM/COL4A3/COL1A1/COL4A2/COL3A1/TLR4/LAMA2/PRKCB", "12"], ["hsa04360", "Axon guidance", "5.260E-04", "ROBO2/SEMA5A/SEMA6A/PIK3R3/FYN/DPYSL2/ABLIM2/ROCK1/SEMA3D/CFL2/LIMK2/BMPR2/SEMA6D/PLXNA2/SLIT2/SEMA3F/EFNB2", "17"], ["hsa04666", "Fc gamma R-mediated phagocytosis", "7.770E-04", "MARCKSL1/PIK3R3/PLA2G4A/AKT3/WASF3/CFL2/GAB2/LIMK2/ASAP1/PRKCE/PRKCB", "11"], ["hsa04912", "GnRH signaling pathway", "7.770E-04", "EGR1/MMP2/PLA2G4A/MAPK10/MAP3K3/ADCY3/ITPR1/PRKCB/CACNA1C/HBEGF/CACNA1D", "11"], ["hsa01521", "EGFR tyrosine kinase inhibitor resistance", "7.850E-04", "PIK3R3/HGF/AKT3/SHC3/FOXO3/IGF1/PDGFB/NRG1/PRKCB/KDR", "10"], ["hsa05418", "Fluid shear stress and atherosclerosis", "8.150E-04", "GSTM5/PIK3R3/MMP2/AKT3/NQO1/MEF2A/MAPK10/DUSP1/EDN1/PDGFB/KLF2/BMPR2/CAV2/KDR", "14"], ["hsa04015", "Rap1 signaling pathway", "1.075E-03", "FGFR1/PIK3R3/HGF/AKT3/ITGAM/THBS1/IGF1/PDGFB/ADCY3/DOCK4/ANGPT1/PRKCB/TEK/FLT1/RAPGEF5/RAPGEF1/CNR1/KDR", "18"], ["hsa01522", "Endocrine resistance", "1.206E-03", "PIK3R3/MMP2/AKT3/SHC3/MAPK10/IGF1/CDKN1A/NOTCH1/ADCY3/HBEGF/DLL4", "11"], ["hsa04072", "Phospholipase D signaling pathway", "1.504E-03", "AGPAT4/PIK3R3/FCER1G/PIK3R5/PLA2G4A/FYN/AKT3/SHC3/DGKH/DNM3/GAB2/PDGFB/ADCY3/MS4A2", "14"], ["hsa04935", "Growth hormone synthesis, secretion and action", "1.875E-03", "PIK3R3/AKT3/SHC3/MAPK10/GHR/IGF1/ADCY3/ITPR1/PRKCB/JUNB/CACNA1C/CACNA1D", "12"], ["hsa05410", "Hypertrophic cardiomyopathy", "2.154E-03", "SGCD/ITGA8/IGF1/EDN1/ITGA5/ACTC1/CACNB2/LAMA2/CACNA1C/CACNA1D", "10"], ["hsa04928", "Parathyroid hormone synthesis, secretion and action", "2.285E-03", "FGFR1/EGR1/AKAP13/MEF2A/PDE4B/CDKN1A/ADCY3/ITPR1/PRKCB/KL/HBEGF", "11"], ["hsa05412", "Arrhythmogenic right-ventricular cardiomyopathy", "2.504E-03", "SGCD/DSG2/ITGA8/ITGA5/DSC2/CACNB2/LAMA2/CACNA1C/CACNA1D", "9"], ["hsa04929", "GnRH secretion", "2.817E-03", "GABBR1/PIK3R3/SPP1/AKT3/ITPR1/PRKCB/CACNA1C/CACNA1D", "8"], ["hsa04066", "HIF-1 signaling pathway", "2.851E-03", "PIK3R3/EGLN3/AKT3/IGF1/EDN1/CDKN1A/TLR4/ANGPT1/PRKCB/TEK/FLT1", "11"], ["hsa04014", "Ras signaling pathway", "3.255E-03", "FGFR1/PIK3R3/SYNGAP1/HGF/PLA2G4A/AKT3/SHC3/MAPK10/IGF1/PLA2G3/GAB2/PDGFB/ANGPT1/PRKCB/TEK/FLT1/RAPGEF5/KDR", "18"], ["hsa04926", "Relaxin signaling pathway", "3.686E-03", "PIK3R3/MMP2/AKT3/SHC3/MAPK10/COL4A3/EDN1/COL1A1/COL4A2/COL3A1/ADCY3/EDNRB", "12"], ["hsa05165", "Human papillomavirus infection", "3.847E-03", "WNT7B/PXN/PIK3R3/LAMA4/SPP1/LAMC2/AKT3/ITGA8/COL4A3/WNT3/FZD4/THBS1/CDKN1A/COL1A1/COL4A2/CCND2/NOTCH1/ITGA5/PTGER4/WNT7A/DLG3/LAMA2/AXIN2", "23"], ["hsa05224", "Breast cancer", "3.960E-03", "WNT7B/FGFR1/PIK3R3/AKT3/SHC3/WNT3/FZD4/IGF1/CDKN1A/NOTCH1/WNT7A/AXIN2/DLL4", "13"], ["hsa05231", "Choline metabolism in cancer", "4.036E-03", "PIK3R3/PLA2G4A/AKT3/DGKH/WASF3/LYPLA1/MAPK10/PDGFB/GPCPD1/PRKCB", "10"], ["hsa04724", "Glutamatergic synapse", "4.041E-03", "SLC1A1/PLA2G4A/DLG4/GRIA1/ADCY3/ITPR1/SLC38A2/SHANK3/PRKCB/CACNA1C/CACNA1D", "11"], ["hsa04664", "Fc epsilon RI signaling pathway", "4.126E-03", "PIK3R3/FCER1G/PLA2G4A/FYN/AKT3/MAPK10/GAB2/MS4A2", "8"], ["hsa04392", "Hippo signaling pathway—multiple species", "4.366E-03", "DCHS1/FAT4/RASSF2/LIMD1/LATS2", "5"], ["hsa04923", "Regulation of lipolysis in adipocytes", "5.111E-03", "PIK3R3/PDE3B/AKT3/ADRB2/ADRB1/ADCY3/PRKG1", "7"], ["hsa04071", "Sphingolipid signaling pathway", "5.598E-03", "PIK3R3/FCER1G/SGPP2/FYN/AKT3/MAPK10/ROCK1/GAB2/PRKCE/MS4A2/PRKCB", "11"], ["hsa04921", "Oxytocin signaling pathway", "5.867E-03", "PIK3R5/PLA2G4A/GUCY1A2/ROCK1/CDKN1A/PPP1R12B/PPP1R12C/ADCY3/ITPR1/CACNB2/PRKCB/CACNA1C/CACNA1D", "13"], ["hsa04910", "Insulin signaling pathway", "5.979E-03", 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The common consistently and differentially expressed (Co-DE) miRNAs were obtained using intersected analyses comparing TCGA and microarray datasets (Cojocneanu et al., 2020)."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "sequence_alignment", "specific": "read_mapping", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "Bowtie"}}], "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: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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