Common and distinct features of potentially predictive biomarkers in small cell lung carcinoma and large cell neuroendocrine carcinoma of the lung by systematic and integrated analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31981472", "kind": "science-record", "revision": 8, "content_hash": "sha256:26f7d5c92e0ebbf7aaa21ab1245459c7c3de0d4a138c6bba5cd406363e15b457", "created_at": "2026-11-01T15:40:55Z", "updated_at": "2026-11-01T22:01:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Common and distinct features of potentially predictive biomarkers in small cell lung carcinoma and large cell neuroendocrine carcinoma of the lung by systematic and integrated analysis.", "doi": "10.1002/mgg3.1126", "pmid": "31981472", "authors": ["Shenghua Dong", "Jun Liang", "Wenxin Zhai", "Zhuang Yu"], "journal": "Molecular genetics & genomic medicine", "year": 2020, "abstract": "BACKGROUND: Large-cell neuroendocrine carcinoma of the lung (LCNEC) and small-cell lung carcinoma (SCLC) are neuroendocrine neoplasms. However, the underlying mechanisms of common and distinct genetic characteristics between LCNEC and SCLC are currently unclear. Herein, protein expression profiles and possible interactions with miRNAs were provided by integrated bioinformatics analysis, in order to explore core genes associated with tumorigenesis and prognosis in SCLC and LCNEC.\nMETHODS: GSE1037 gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in LCNEC and SCLC, as compared with normal lung tissues, were selected using the GEO2R online analyzer and Venn diagram software. Gene ontology (GO) analysis was performed using Database for Annotation, Visualization and Integrated Discovery. The biological pathway analysis was performed using the FunRich database. Subsequently, a protein-protein interaction (PPI) network of DEGs was generated using Search Tool for the Retrieval of Interacting Genes and displayed via Cytoscape software. The PPI network was analyzed by the Molecular Complex Detection app from Cytoscape, and 16 upregulated hub genes were selected. The Oncomine database was used to detect expression patterns of hub genes for validation. Furthermore, the biological pathways of these 16 hub genes were re-analyzed, and potential interactions between these genes and miRNAs were explored via FunRich.\nRESULTS: A total of 384 DEGs were identified. A Venn diagram determined 88 common DEGs. The PPI network was constructed with 48 nodes and 221 protein pairs. Among them, 16 hub genes were extracted, 14 of which were upregulated in SCLC samples, as compared with normal lung specimens, and 10 were correlated with the cell cycle pathway. Furthermore, 57 target miRNAs for 8 hub genes were identified, among which 31 miRNAs were correlated with the progression of carcinoma, drug-resistance, radio-sensitivity, or autophagy in lung cancer.\nCONCLUSION: This study provided effective biomarkers and novel therapeutic targets for diagnosis and prognosis of SCLC and LCNEC.", "claims": [{"id": "claim-data-access", "statement": "Gene expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1037) were obtained from the GEO database, based on the GPL962 CHUGAI 41K platform. Data including 18 primary normal lung tissues, 8 primary LCNEC tissues, 15 primary small‐cell lung carcinoma tissues, and 9 small‐cell lung carcinoma cell lines were downloaded.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31981472", "locator": "sections[4] \"Gene expression profile data\" paragraph 2", "quote": "Gene expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1037) were obtained from the GEO database, based on the GPL962 CHUGAI 41K platform. Data including 18 primary normal lung tissues, 8 primary LCNEC tissues, 15 primary small‐cell lung carcinoma tissues, and 9 small‐cell lung carcinoma cell lines were downloaded."}], "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:31981472"], "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:GSE1037"], "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:GSE1037"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31981472", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/mgg3.1126", "sha256": "sha256:fb7f3b48eb1b331626dbfe0efcbefc8ee5a755a34f2516dd4b919c93672582c6", "bytes": 70667, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/mgg3.1126", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7057089", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE1037", "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=GSE1037", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1037", "version": null, "note": "Gene expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1037) were obtained from the GEO database, based on the GPL962 CHUGAI 41K platform. Data including 18 primary normal lung tissues, 8 primary LCNEC tissues, 15 primary small‐cell lung carcinoma tissues, and 9 small‐cell lung carcinoma cell lines were downloaded.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Gene expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1037) were obtained from the GEO database, based on the GPL962 CHUGAI 41K platform. Data including 18 primary normal lung tissues, 8 primary LCNEC tissues, 15 primary small‐cell lung carcinoma tissues, and 9 small‐cell lung carcinoma cell lines were downloaded.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM16557", "GSM16558", "GSM16559", "GSM16560", "GSM16561", "GSM16562", "GSM16563", "GSM16564", "GSM16565", "GSM16566", "GSM16567", "GSM16568", "GSM17195", "GSM17196", "GSM17287", "GSM17288", "GSM17289", "GSM17290", "GSM17291", "GSM17292", "GSM17293", "GSM17294", "GSM17295", "GSM17296", "GSM17297", "GSM17298", "GSM17299", "GSM17300", "GSM17301", "GSM17302", "GSM17303", "GSM17304", "GSM17305", "GSM17306", "GSM17307", "GSM17308", "GSM17309", "GSM17310", "GSM17311", "GSM17312", "GSM17313", "GSM17314", "GSM17315", "GSM17316", "GSM17317", "GSM17318", "GSM17319", "GSM17320", "GSM17321", "GSM17322", "GSM17323", "GSM17324", "GSM17325", "GSM17326", "GSM17327", "GSM17328", "GSM17329", "GSM17330", "GSM17331", "GSM17332", "GSM17333", "GSM17334", "GSM17335", "GSM17336", "GSM17337", "GSM17338", "GSM17339", "GSM17340", "GSM17341", "GSM17342", "GSM17343", "GSM17344", "GSM17345", "GSM17346", "GSM17347", "GSM17348", "GSM17349", "GSM17350", "GSM17351", "GSM17352", "GSM17353", "GSM17354", "GSM17355", "GSM17356", "GSM18306", "GSM18307", "GSM18308", "GSM18309", "GSM18310", "GSM18311", "GSM18312"], "sample_count": 91, "group_sizes": null, "group_sizes_basis": null, "platform": "962", "taxon": "Homo sapiens", "title": "Lung 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:31981472:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9786397856b13a122a79357fa9dc5a8e5fa2019cb1b822a8125dd9b8aeb01513", "bytes": 908, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#mgg31126-tbl-0001", "version": null, "note": "Commonly DEGs in the SCLC and LCNEC samples", "structure": {"pmcid": "PMC7057089", "section_index": 12, "section_title": "Identification of DEGs", "row_count": 3, "column_count": 2}, "table": {"label": "Table 1", "caption": "Commonly DEGs in the SCLC and LCNEC samples", "rows": [["DEGs", "Genes name"], ["Upregulated", "ZNF829 BCCIP PTTG1 CENPA FAM123A SESN2 CSE1L LOC256676///CDCA5 PBK UBE2TC5orf13 ZNF587 UNQ353///CSNK1G1///KIAA0101 HMGB3 SOX4 FARP1 C1orf215///STMN1 MLF1IP AURKA MYBL2 ZWINTAS///ZWINT UBE2C EZH2 RFC4 CDCA8 SLC2A1 LOC253012 TPX2 TTKCDCA7 TOP2A NUF2"], ["Downregulated", "ADH1B CAV1 WIF1 SFTPC FMO2 TSHZ2///ADAMTS8 USP42 MFAP4 SCGB1A1 IGSF10 TIMP3 CLDN18 OGN CAV2 MAOA FABP4 ZNF521 SVEP1 EPAS1 TPSB2///TPSAB1 FHL1 FAT4 CAB39L ADH1C PI4KAP1 C2orf34 AGER LOC144571///PZP///A2M AQP4 FAM75A1 SFTPH AQP1 CAMP HBE1 EMCN HNRNPH1 SLC39A8 SUSD2 FLJ44379 LIMCH1 SLPI CYBRD1 HOPX C13orf15 LOC100131277///TACC1 LYVE1 GPR116 MAOB SELENBP1 PGM5 EMP2 PMP22 S1PR1 ABCA8 ANGPTL1 RGS2"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[12]/table-wrap[1]#mgg31126-tbl-0001"}}, {"id": "asset:table:pmid:31981472:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b82744efdde33404a5809029f9f0d7e40ef5ade12d670f791c0a9ef31492a14e", "bytes": 5525, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#mgg31126-tbl-0002", "version": null, "note": "Enriched Go terms of the DEGs", "structure": {"pmcid": "PMC7057089", "section_index": 13, "section_title": "Enrichment analysis", "row_count": 52, "column_count": 7}, "table": {"label": "Table 2", "caption": "Enriched Go terms of the DEGs", "rows": [["", "Category", "Term", "Count", "%", "p‐Value", "FDR"], ["Up regulated", "GOTERM_BP_DIRECT", "GO:0051301~cell division", "6", "0.142993327", "4.04E‐06", "0.004971483"], ["GOTERM_BP_DIRECT", "GO:0006355~regulation of transcription DNA‐templated", "7", "0.166825548", "3.53E‐04", "0.432578524"], ["GOTERM_BP_DIRECT", "GO:0006281~DNA repair", "4", "0.095328885", "8.15E‐04", "0.997007591"], ["GOTERM_BP_DIRECT", "GO:0045143~homologous chromosome segregation", "2", "0.047664442", ".006639221", "7.86341138"], ["GOTERM_BP_DIRECT", "GO:0031536~positive regulation of exit from mitosis", "2", "0.047664442", ".008292426", "9.731016783"], ["GOTERM_BP_DIRECT", "GO:0007067~mitotic nuclear division", "3", "0.071496663", ".013030094", "14.89218414"], ["GOTERM_BP_DIRECT", "GO:0046323~glucose import", "2", "0.047664442", ".018156528", "20.17047326"], ["GOTERM_BP_DIRECT", "GO:0051276~chromosome organization", "2", "0.047664442", ".023053317", "24.9298377"], ["GOTERM_BP_DIRECT", "GO:0070979~protein K11‐linked ubiquitination", "2", "0.047664442", ".037603917", "37.57710332"], ["GOTERM_BP_DIRECT", "GO:0007052~mitotic spindle organization", "2", "0.047664442", ".037603917", "37.57710332"], ["GOTERM_BP_DIRECT", "GO:0090307~mitotic spindle assembly", "2", "0.047664442", ".045597774", "43.66110836"], ["GOTERM_CC_DIRECT", "GO:0005737~cytoplasm", "15", "0.357483317", "2.21E‐05", "0.022280174"], ["GOTERM_CC_DIRECT", "GO:0005634~nucleus", "14", "0.333651096", "5.40E‐05", "0.054460588"], ["GOTERM_CC_DIRECT", "GO:0043203~axon hillock", "2", "0.047664442", ".00741693", "7.237425098"], ["GOTERM_CC_DIRECT", "GO:0032133~chromosome passenger complex", "2", "0.047664442", ".00741693", "7.237425098"], ["GOTERM_CC_DIRECT", "GO:0005654~nucleoplasm", "7", "0.166825548", ".010502317", "10.10650713"], ["GOTERM_CC_DIRECT", "GO:0045120~pronucleus", "2", "0.047664442", ".013312558", "12.64989615"], ["GOTERM_CC_DIRECT", "GO:0051233~spindle midzone", "2", "0.047664442", ".022093237", "20.18460143"], ["GOTERM_MF_DIRECT", "GO:0031625~ubiquitin protein ligase binding", "3", "0.076628352", ".011662791", "10.93819391"], ["GOTERM_MF_DIRECT", "GO:0008301~DNA binding bending", "2", "0.051085568", ".015851015", "14.59560577"], ["GOTERM_MF_DIRECT", "GO:0005524~ATP binding", "6", "0.153256705", ".027091606", "23.75384229"], ["GOTERM_MF_DIRECT", "GO:0030414~peptidase inhibitor activity", "2", "0.051085568", ".030054212", "26.01571812"], ["GOTERM_MF_DIRECT", "GO:0061631~ubiquitin conjugating enzyme activity", "2", "0.051085568", ".038482685", "32.12464677"], ["Down regulated", "GOTERM_BP_DIRECT", "GO:0070836~caveola assembly", "3", "0.046260601", "6.99E−05", "0.098559412"], ["GOTERM_BP_DIRECT", "GO:0007155~cell adhesion", "6", "0.092521203", ".007419687", "9.977332032"], ["GOTERM_BP_DIRECT", "GO:0019065~receptor‐mediated endocytosis of virus by host cell", "2", "0.030840401", ".008018493", "10.74080337"], ["GOTERM_BP_DIRECT", "GO:0042420~dopamine catabolic process", "2", "0.030840401", ".013329193", "17.25342044"], ["GOTERM_BP_DIRECT", "GO:0042135~neurotransmitter catabolic process", "2", "0.030840401", ".021243157", "26.14357095"], ["GOTERM_BP_DIRECT", "GO:0050891~multicellular organismal water homeostasis", "2", "0.030840401", ".021243157", "26.14357095"], ["GOTERM_BP_DIRECT", "GO:0001525~angiogenesis", "4", "0.061680802", ".021777665", "26.71078904"], ["GOTERM_BP_DIRECT", "GO:0032060~bleb assembly", "2", "0.030840401", ".026484616", "31.53390357"], ["GOTERM_BP_DIRECT", "GO:0006069~ethanol oxidation", "2", "0.030840401", ".031698626", "36.53140253"], ["GOTERM_BP_DIRECT", "GO:0015793~glycerol transport", "2", "0.030840401", ".034295382", "38.89185575"], ["GOTERM_BP_DIRECT", "GO:0009992~cellular water homeostasis", "2", "0.030840401", ".034295382", "38.89185575"], ["GOTERM_CC_DIRECT", "GO:0070062~extracellular exosome", "16", "0.246723207", ".001317986", "1.408901211"], ["GOTERM_CC_DIRECT", "GO:0005886~plasma membrane", "19", "0.292983809", ".003743762", "3.955034143"], ["GOTERM_CC_DIRECT", "GO:0005901~caveola", "3", "0.046260601", ".010295194", "10.53630766"], ["GOTERM_CC_DIRECT", "GO:0005576~extracellular region", "10", "0.154202005", ".01150877", "11.70950819"], ["GOTERM_CC_DIRECT", "GO:0045121~membrane raft", "4", "0.061680802", ".012603718", "12.75603307"], ["GOTERM_CC_DIRECT", "GO:0045177~apical part of cell", "3", "0.046260601", ".013532583", "13.63498448"], ["GOTERM_CC_DIRECT", "GO:0016021~integral component of membrane", "20", "0.308404009", ".018955008", "18.60768595"], ["GOTERM_CC_DIRECT", "GO:0031012~extracellular matrix", "4", "0.061680802", ".032469722", "29.89178143"], ["GOTERM_CC_DIRECT", "GO:0005615~extracellular space", "8", "0.123361604", ".036771948", "33.17391345"], ["GOTERM_CC_DIRECT", "GO:0002080~acrosomal membrane", "2", "0.030840401", ".043912815", "38.31524409"], ["GOTERM_MF_DIRECT", "GO:0016491~oxidoreductase activity", "4", "0.061680802", ".014279333", "14.99791487"], ["GOTERM_MF_DIRECT", "GO:0005215~transporter activity", "4", "0.061680802", ".014662761", "15.37073704"], ["GOTERM_MF_DIRECT", "GO:0004024~alcohol dehydrogenase activity zinc‐dependent", "2", "0.030840401", ".015188693", "15.87969632"], ["GOTERM_MF_DIRECT", "GO:0005372~water transmembrane transporter activity", "2", "0.030840401", ".015188693", "15.87969632"], ["GOTERM_MF_DIRECT", "GO:0008131~primary amine oxidase activity", "2", "0.030840401", ".015188693", "15.87969632"], ["GOTERM_MF_DIRECT", "GO:0015254~glycerol channel activity", "2", "0.030840401", ".030151975", "29.24210187"], ["GOTERM_MF_DIRECT", "GO:0015250~water channel activity", "2", "0.030840401", ".040003884", "36.95130237"]], "row_count": 52, "column_count": 7, "numeric_cells": 255, "header_rows": 1, "locator": "section[13]/table-wrap[1]#mgg31126-tbl-0002"}}, {"id": "asset:table:pmid:31981472:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3581cf5f8d32afc3aa40cd62d3b39fe23a861884a472e25273b5004ed772775b", "bytes": 1601, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#mgg31126-tbl-0003", "version": null, "note": "Hub genes and corresponded target miRNAs", "structure": {"pmcid": "PMC7057089", "section_index": 17, "section_title": "Prediction of target miRNAs for hub genes", "row_count": 9, "column_count": 2}, "table": {"label": "Table 3", "caption": "Hub genes and corresponded target miRNAs", "rows": [["Gene", "miRNA"], ["TTK", "hsa‐miR‐101‐3p hsa‐miR‐212‐3p hsa‐miR‐132‐3p hsa‐miR‐140‐5p hsa‐miR‐455‐3p hsa‐miR‐582‐5p"], ["PTTG1", "hsa‐miR‐655‐3p hsa‐miR‐374c‐5p"], ["MYBL2", "hsa‐miR‐29a‐3p hsa‐miR‐29b‐3p hsa‐miR‐30c‐5p hsa‐miR‐30a‐5p hsa‐miR‐30b‐5p hsa‐miR‐30d‐5p hsa‐miR‐29c‐3p hsa‐miR‐30e‐5p hsa‐miR‐423‐5p hsa‐miR‐3184‐5p"], ["EZH2", "hsa‐miR‐101‐3p hsa‐miR‐124‐3p hsa‐miR‐137 hsa‐miR‐138‐5p"], ["CENPA", "hsa‐miR‐873‐5p"], ["CDCA8", "hsa‐let‐7a‐5p hsa‐let‐7b‐5p hsa‐let‐7c‐5p hsa‐let‐7d‐5p hsa‐let‐7e‐5p hsa‐let‐7f‐5p hsa‐miR‐98‐5p hsa‐let‐7g‐5p hsa‐let‐7i‐5p hsa‐miR‐133a‐3p hsa‐miR‐133b hsa‐miR‐4458 hsa‐miR‐4500"], ["CDCA7", "hsa‐miR‐30a‐5p hsa‐miR‐30b‐5p hsa‐miR‐30c‐5p hsa‐miR‐30d‐5p hsa‐miR‐30e‐5p hsa‐miR‐302a‐3p hsa‐miR‐302‐3p hsa‐miR‐302c‐3p hsa‐miR‐302d‐3p hsa‐miR‐372‐3p hsa‐miR‐373‐3p hsa‐miR‐520e hsa‐miR‐520b hsa‐miR‐520f‐3p hsa‐miR‐520a‐3p hsa‐miR‐520d‐3p hsa‐miR‐520c‐3p hsa‐miR‐499a‐5p hsa‐miR‐302e"], ["AURKA", "hsa‐miR‐25‐3p hsa‐miR‐92a‐3p hsa‐miR‐363‐3p hsa‐miR‐367‐3p hsa‐miR‐490‐3p hsa‐miR‐92b‐3p hsa‐miR‐421 hsa‐miR‐32‐5p"]], "row_count": 9, "column_count": 2, "numeric_cells": 8, "header_rows": 1, "locator": "section[17]/table-wrap[1]#mgg31126-tbl-0003"}}, {"id": "asset:table:pmid:31981472:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:18caefba689141877e0022338719ab5a1962a335c1e5a76734b7ee0962d571e9", "bytes": 1595, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#mgg31126-tbl-0004", "version": null, "note": "Functions of miRNAs in lung cancer", "structure": {"pmcid": "PMC7057089", "section_index": 17, "section_title": "Prediction of target miRNAs for hub genes", "row_count": 9, "column_count": 2}, "table": {"label": "Table 4", "caption": "Functions of miRNAs in lung cancer", "rows": [["Gene", "miRNA"], ["TTK", "hsa‐miR‐101‐3p hsa‐miR‐212‐3p hsa‐miR‐132‐3p hsa‐miR‐140‐5p hsa‐miR‐455‐3p hsa‐miR‐582‐5p"], ["PTTG1", "hsa‐miR‐655‐3p hsa‐miR‐374c‐5p"], ["MYBL2", "hsa‐miR‐29a‐3p hsa‐miR‐29b‐3p hsa‐miR‐30c‐5p hsa‐miR‐30a‐5p hsa‐miR‐30b‐5p hsa‐miR‐30d‐5p hsa‐miR‐29c‐3p hsa‐miR‐30e‐5p hsa‐miR‐423‐5p hsa‐miR‐3184‐5p"], ["EZH2", "hsa‐miR‐101‐3p hsa‐miR‐124‐3p hsa‐miR‐137 hsa‐miR‐138‐5p"], ["CENPA", "hsa‐miR‐873‐5p"], ["CDCA8", "hsa‐let‐7a‐5p hsa‐let‐7b‐5p hsa‐let‐7c‐5p hsa‐let‐7d‐5p hsa‐let‐7e‐5p hsa‐let‐7f‐5p hsa‐miR‐98‐5p hsa‐let‐7g‐5p hsa‐let‐7i‐5p hsa‐miR‐133a‐3p hsa‐miR‐133b hsa‐miR‐4458 hsa‐miR‐4500"], ["CDCA7", "hsa‐miR‐30a‐5p hsa‐miR‐30b‐5p hsa‐miR‐30c‐5p hsa‐miR‐30d‐5p hsa‐miR‐30e‐5p hsa‐miR‐302a‐3p hsa‐miR‐302‐3p hsa‐miR‐302c‐3p hsa‐miR‐302d‐3p hsa‐miR‐372‐3p hsa‐miR‐373‐3p hsa‐miR‐520e hsa‐miR‐520b hsa‐miR‐520f‐3p hsa‐miR‐520a‐3p hsa‐miR‐520d‐3p hsa‐miR‐520c‐3p hsa‐miR‐499a‐5p hsa‐miR‐302e"], ["AURKA", "hsa‐miR‐25‐3p hsa‐miR‐92a‐3p hsa‐miR‐363‐3p hsa‐miR‐367‐3p hsa‐miR‐490‐3p hsa‐miR‐92b‐3p hsa‐miR‐421 hsa‐miR‐32‐5p"]], "row_count": 9, "column_count": 2, "numeric_cells": 8, "header_rows": 1, "locator": "section[17]/table-wrap[2]#mgg31126-tbl-0004"}}], "gaps": ["asset:data:geo:GSE1037 not downloaded", "asset:data:geo:GSE1037 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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-2", "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": 0.8, "band": "high", "quote": "pathway enrichment"}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE1037"], "resolved_accessions": ["GSE1037"], "statements": ["Gene expression profiles (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1037) were obtained from the GEO database, based on the GPL962 CHUGAI 41K platform. Data including 18 primary normal lung tissues, 8 primary LCNEC tissues, 15 primary small‐cell lung carcinoma tissues, and 9 small‐cell lung carcinoma cell lines were downloaded."], "basis": "The paper names GSE1037 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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