Comparative proteogenomics profiling of non-small and small lung carcinoma cell lines using mass spectrometry.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32351780", "kind": "science-record", "revision": 6, "content_hash": "sha256:8a0d3be46fab9696d39f3d404a6972698b13b60a0969edf2400f50a387ead2a4", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T21:23:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative proteogenomics profiling of non-small and small lung carcinoma cell lines using mass spectrometry.", "doi": "10.7717/peerj.8779", "pmid": "32351780", "authors": ["Jingyu Wu", "Zhifang Hao", "Chen Ma", "Pengfei Li", "Liuyi Dang", "Shisheng Sun"], "journal": "PeerJ", "year": 2020, "abstract": "BACKGROUND: Evidences indicated that non-small-cell lung cancer (NSCLC) and small-cell lung cancer (SCLC) might originate from the same cell type, which however ended up to be two different subtypes of lung carcinoma, requiring different therapeutic regimens. We aimed to identify the differences between these two subtypes of lung cancer by using integrated proteome and genome approaches.\nMETHODS AND MATERIALS: Two representative cell lines for each lung cancer subtype were comparatively analysed by quantitative proteomics, and their corresponding transcriptomics data were obtained from the Gene Expression Omnibus database. The integrated analyses of proteogenomic data were performed to determine key differentially expressed proteins that were positively correlated between proteomic and transcriptomic data.\nRESULT: The proteomics analysis revealed 147 differentially expressed proteins between SCLC and NSCLC from a total of 3,970 identified proteins. Combined with available transcriptomics data, we further confirmed 14 differentially expressed proteins including six known and eight new lung cancer related proteins that were positively correlated with their transcriptomics data. These proteins are mainly involved in cell migration, proliferation, and invasion.\nCONCLUSION: The proteogenomic data on both NSCLC and SCLC cell lines presented in this manuscript is complementary to existing genomic and proteomic data related to lung cancers and will be crucial for a systems biology-level understanding of the molecular mechanism of lung cancers. The raw mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD015270.", "claims": [{"id": "claim-method", "statement": "Linear Models for Microarray Analysis package in R language was employed to screen DEGs between NSCLC samples and SCLC samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32351780", "locator": "sections[8] \"Determination and hierarchical clustering analysis of DEGs\" paragraph 2", "quote": "Linear Models for Microarray Analysis package in R language was employed to screen DEGs between NSCLC samples and SCLC samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe proteomic data are available from the PRIDE Archive: PXD015270.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32351780", "locator": "sections[33] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nThe proteomic data are available from the PRIDE Archive: PXD015270."}], "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:32351780"], "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:GSE36133"], "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:GSE36133"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32351780", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.8779", "sha256": "sha256:45b12218b14f61344b4b76a2bc10a9108f9d90cf48cebfc36b1812bf954098df", "bytes": 48462, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.8779", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7183755", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE36133", "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=GSE36133", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE36133", "version": null, "note": "The following information was supplied regarding data availability:\nThe proteomic data are available from the PRIDE Archive: PXD015270.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe proteomic data are available from the PRIDE Archive: PXD015270.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM886835", "GSM886836", "GSM886837", "GSM886838", "GSM886839", "GSM886840", "GSM886841", "GSM886842", "GSM886843", "GSM886844", "GSM886845", "GSM886846", "GSM886847", "GSM886848", "GSM886849", "GSM886850", "GSM886851", "GSM886852", "GSM886853", "GSM886854", "GSM886855", "GSM886856", "GSM886857", "GSM886858", "GSM886859", "GSM886860", "GSM886861", "GSM886862", "GSM886863", "GSM886864", "GSM886865", "GSM886866", "GSM886867", "GSM886868", "GSM886869", "GSM886870", "GSM886871", "GSM886872", "GSM886873", "GSM886874", "GSM886875", "GSM886876", "GSM886877", "GSM886878", "GSM886879", "GSM886880", "GSM886881", "GSM886882", "GSM886883", "GSM886884", "GSM886885", "GSM886886", "GSM886887", "GSM886888", "GSM886889", "GSM886890", "GSM886891", "GSM886892", "GSM886893", "GSM886894", "GSM886895", "GSM886896", "GSM886897", "GSM886898", "GSM886899", "GSM886900", "GSM886901", "GSM886902", "GSM886903", "GSM886904", "GSM886905", "GSM886906", "GSM886907", "GSM886908", "GSM886909", "GSM886910", "GSM886911", "GSM886912", "GSM886913", "GSM886914", "GSM886915", "GSM886916", "GSM886917", "GSM886918", "GSM886919", "GSM886920", "GSM886921", "GSM886922", "GSM886923", "GSM886924", "GSM886925", "GSM886926", "GSM886927", "GSM886928", "GSM886929", "GSM886930", "GSM886931", "GSM886932", "GSM886933", "GSM886934", "GSM886935", "GSM886936", "GSM886937", "GSM886938", "GSM886939", "GSM886940", "GSM886941", "GSM886942", "GSM886943", "GSM886944", "GSM886945", "GSM886946", "GSM886947", "GSM886948", "GSM886949", "GSM886950", "GSM886951", "GSM886952", "GSM886953", "GSM886954", "GSM886955", "GSM886956", "GSM886957", "GSM886958", "GSM886959", "GSM886960", "GSM886961", "GSM886962", "GSM886963", "GSM886964", "GSM886965", "GSM886966", "GSM886967", "GSM886968", "GSM886969", "GSM886970", "GSM886971", "GSM886972", "GSM886973", "GSM886974", "GSM886975", "GSM886976", "GSM886977", "GSM886978", "GSM886979", "GSM886980", "GSM886981", "GSM886982", "GSM886983", "GSM886984", "GSM886985", "GSM886986", "GSM886987", "GSM886988", "GSM886989", "GSM886990", "GSM886991", "GSM886992", "GSM886993", "GSM886994", "GSM886995", "GSM886996", "GSM886997", "GSM886998", "GSM886999", "GSM887000", "GSM887001", "GSM887002", "GSM887003", "GSM887004", "GSM887005", "GSM887006", "GSM887007", "GSM887008", "GSM887009", "GSM887010", "GSM887011", "GSM887012", "GSM887013", "GSM887014", "GSM887015", "GSM887016", "GSM887017", "GSM887018", "GSM887019", "GSM887020", "GSM887021", "GSM887022", "GSM887023", "GSM887024", "GSM887025", "GSM887026", "GSM887027", "GSM887028", "GSM887029", "GSM887030", "GSM887031", "GSM887032", "GSM887033", "GSM887034", "GSM887035", "GSM887036", "GSM887037", "GSM887038", "GSM887039", "GSM887040", "GSM887041", "GSM887042", "GSM887043", "GSM887044", "GSM887045", "GSM887046", "GSM887047", "GSM887048", "GSM887049", "GSM887050", "GSM887051", "GSM887052", "GSM887053", "GSM887054", "GSM887055", "GSM887056", "GSM887057", "GSM887058", "GSM887059", "GSM887060", "GSM887061", "GSM887062", "GSM887063", "GSM887064", "GSM887065", "GSM887066", "GSM887067", "GSM887068", "GSM887069", "GSM887070", "GSM887071", "GSM887072", "GSM887073", "GSM887074", "GSM887075", "GSM887076", "GSM887077", "GSM887078", "GSM887079", "GSM887080", "GSM887081", "GSM887082", "GSM887083", "GSM887084", "GSM887085", "GSM887086", "GSM887087", "GSM887088", "GSM887089", "GSM887090", "GSM887091", "GSM887092", "GSM887093", "GSM887094", "GSM887095", "GSM887096", "GSM887097", "GSM887098", "GSM887099", "GSM887100", "GSM887101", "GSM887102", "GSM887103", "GSM887104", "GSM887105", "GSM887106", "GSM887107", "GSM887108", "GSM887109", "GSM887110", "GSM887111", "GSM887112", "GSM887113", "GSM887114", "GSM887115", "GSM887116", "GSM887117", "GSM887118", "GSM887119", "GSM887120", "GSM887121", "GSM887122", "GSM887123", "GSM887124", "GSM887125", "GSM887126", "GSM887127", "GSM887128", "GSM887129", "GSM887130", "GSM887131", "GSM887132", "GSM887133", "GSM887134", "GSM887135", "GSM887136", "GSM887137", "GSM887138", "GSM887139", "GSM887140", "GSM887141", "GSM887142", "GSM887143", "GSM887144", "GSM887145", "GSM887146", "GSM887147", "GSM887148", "GSM887149", "GSM887150", "GSM887151", "GSM887152", "GSM887153", "GSM887154", "GSM887155", "GSM887156", "GSM887157", "GSM887158", "GSM887159", "GSM887160", "GSM887161", "GSM887162", "GSM887163", "GSM887164", "GSM887165", "GSM887166", "GSM887167", "GSM887168", "GSM887169", "GSM887170", "GSM887171", "GSM887172", "GSM887173", "GSM887174", "GSM887175", "GSM887176", "GSM887177", "GSM887178", "GSM887179", "GSM887180", "GSM887181", "GSM887182", "GSM887183", "GSM887184", "GSM887185", "GSM887186", "GSM887187", "GSM887188", "GSM887189", "GSM887190", "GSM887191", "GSM887192", "GSM887193", "GSM887194", "GSM887195", "GSM887196", "GSM887197", "GSM887198", "GSM887199", "GSM887200", "GSM887201", "GSM887202", "GSM887203", "GSM887204", "GSM887205", "GSM887206", "GSM887207", "GSM887208", "GSM887209", "GSM887210", "GSM887211", "GSM887212", "GSM887213", "GSM887214", "GSM887215", "GSM887216", "GSM887217", "GSM887218", "GSM887219", "GSM887220", "GSM887221", "GSM887222", "GSM887223", "GSM887224", "GSM887225", "GSM887226", "GSM887227", "GSM887228", "GSM887229", "GSM887230", "GSM887231", "GSM887232", "GSM887233", "GSM887234", "GSM887235", "GSM887236", "GSM887237", "GSM887238", "GSM887239", "GSM887240", "GSM887241", "GSM887242", "GSM887243", "GSM887244", "GSM887245", "GSM887246", "GSM887247", "GSM887248", "GSM887249", "GSM887250", "GSM887251", "GSM887252", "GSM887253", "GSM887254", "GSM887255", "GSM887256", "GSM887257", "GSM887258", "GSM887259", "GSM887260", "GSM887261", "GSM887262", "GSM887263", "GSM887264", "GSM887265", "GSM887266", "GSM887267", "GSM887268", "GSM887269", "GSM887270", "GSM887271", "GSM887272", "GSM887273", "GSM887274", "GSM887275", "GSM887276", "GSM887277", "GSM887278", "GSM887279", "GSM887280", "GSM887281", "GSM887282", "GSM887283", "GSM887284", "GSM887285", "GSM887286", "GSM887287", "GSM887288", "GSM887289", "GSM887290", "GSM887291", "GSM887292", "GSM887293", "GSM887294", "GSM887295", "GSM887296", "GSM887297", "GSM887298", "GSM887299", "GSM887300", "GSM887301", "GSM887302", "GSM887303", "GSM887304", "GSM887305", "GSM887306", "GSM887307", "GSM887308", "GSM887309", "GSM887310", "GSM887311", "GSM887312", "GSM887313", "GSM887314", "GSM887315", "GSM887316", "GSM887317", "GSM887318", "GSM887319", "GSM887320", "GSM887321", "GSM887322", "GSM887323", "GSM887324", "GSM887325", "GSM887326", "GSM887327", "GSM887328", "GSM887329", "GSM887330", "GSM887331", "GSM887332", "GSM887333", "GSM887334", "GSM887335", "GSM887336", "GSM887337", "GSM887338", "GSM887339", "GSM887340", "GSM887341", "GSM887342", "GSM887343", "GSM887344", "GSM887345", "GSM887346", "GSM887347", "GSM887348", "GSM887349", "GSM887350", "GSM887351", "GSM887352", "GSM887353", "GSM887354", "GSM887355", "GSM887356", "GSM887357", "GSM887358", "GSM887359", "GSM887360", "GSM887361", "GSM887362", "GSM887363", "GSM887364", "GSM887365", "GSM887366", "GSM887367", "GSM887368", "GSM887369", "GSM887370", "GSM887371", "GSM887372", "GSM887373", "GSM887374", "GSM887375", "GSM887376", "GSM887377", "GSM887378", "GSM887379", "GSM887380", "GSM887381", "GSM887382", "GSM887383", "GSM887384", "GSM887385", "GSM887386", "GSM887387", "GSM887388", "GSM887389", "GSM887390", "GSM887391", "GSM887392", "GSM887393", "GSM887394", "GSM887395", "GSM887396", "GSM887397", "GSM887398", "GSM887399", "GSM887400", "GSM887401", "GSM887402", "GSM887403", "GSM887404", "GSM887405", "GSM887406", "GSM887407", "GSM887408", "GSM887409", "GSM887410", "GSM887411", "GSM887412", "GSM887413", "GSM887414", "GSM887415", "GSM887416", "GSM887417", "GSM887418", "GSM887419", "GSM887420", "GSM887421", "GSM887422", "GSM887423", "GSM887424", "GSM887425", "GSM887426", "GSM887427", "GSM887428", "GSM887429", "GSM887430", "GSM887431", "GSM887432", "GSM887433", "GSM887434", "GSM887435", "GSM887436", "GSM887437", "GSM887438", "GSM887439", "GSM887440", "GSM887441", "GSM887442", "GSM887443", "GSM887444", "GSM887445", "GSM887446", "GSM887447", "GSM887448", "GSM887449", "GSM887450", "GSM887451", "GSM887452", "GSM887453", "GSM887454", "GSM887455", "GSM887456", "GSM887457", "GSM887458", "GSM887459", "GSM887460", "GSM887461", "GSM887462", "GSM887463", "GSM887464", "GSM887465", "GSM887466", "GSM887467", "GSM887468", "GSM887469", "GSM887470", "GSM887471", "GSM887472", "GSM887473", "GSM887474", "GSM887475", "GSM887476", "GSM887477", "GSM887478", "GSM887479", "GSM887480", "GSM887481", "GSM887482", "GSM887483", "GSM887484", "GSM887485", "GSM887486", "GSM887487", "GSM887488", "GSM887489", "GSM887490", "GSM887491", "GSM887492", "GSM887493", "GSM887494", "GSM887495", "GSM887496", "GSM887497", "GSM887498", "GSM887499", "GSM887500", "GSM887501", "GSM887502", "GSM887503", "GSM887504", "GSM887505", "GSM887506", "GSM887507", "GSM887508", "GSM887509", "GSM887510", "GSM887511", "GSM887512", "GSM887513", "GSM887514", "GSM887515", "GSM887516", "GSM887517", "GSM887518", "GSM887519", "GSM887520", "GSM887521", "GSM887522", "GSM887523", "GSM887524", "GSM887525", "GSM887526", "GSM887527", "GSM887528", "GSM887529", "GSM887530", "GSM887531", "GSM887532", "GSM887533", "GSM887534", "GSM887535", "GSM887536", "GSM887537", "GSM887538", "GSM887539", "GSM887540", "GSM887541", "GSM887542", "GSM887543", "GSM887544", "GSM887545", "GSM887546", "GSM887547", "GSM887548", "GSM887549", "GSM887550", "GSM887551", "GSM887552", "GSM887553", "GSM887554", "GSM887555", "GSM887556", "GSM887557", "GSM887558", "GSM887559", "GSM887560", "GSM887561", "GSM887562", "GSM887563", "GSM887564", "GSM887565", "GSM887566", "GSM887567", "GSM887568", "GSM887569", "GSM887570", "GSM887571", "GSM887572", "GSM887573", "GSM887574", "GSM887575", "GSM887576", "GSM887577", "GSM887578", "GSM887579", "GSM887580", "GSM887581", "GSM887582", "GSM887583", "GSM887584", "GSM887585", "GSM887586", "GSM887587", "GSM887588", "GSM887589", "GSM887590", "GSM887591", "GSM887592", "GSM887593", "GSM887594", "GSM887595", "GSM887596", "GSM887597", "GSM887598", "GSM887599", "GSM887600", "GSM887601", "GSM887602", "GSM887603", "GSM887604", "GSM887605", "GSM887606", "GSM887607", "GSM887608", "GSM887609", "GSM887610", "GSM887611", "GSM887612", "GSM887613", "GSM887614", "GSM887615", "GSM887616", "GSM887617", "GSM887618", "GSM887619", "GSM887620", "GSM887621", "GSM887622", "GSM887623", "GSM887624", "GSM887625", "GSM887626", "GSM887627", "GSM887628", "GSM887629", "GSM887630", "GSM887631", "GSM887632", "GSM887633", "GSM887634", "GSM887635", "GSM887636", "GSM887637", "GSM887638", "GSM887639", "GSM887640", "GSM887641", "GSM887642", "GSM887643", "GSM887644", "GSM887645", "GSM887646", "GSM887647", "GSM887648", "GSM887649", "GSM887650", "GSM887651", "GSM887652", "GSM887653", "GSM887654", "GSM887655", "GSM887656", "GSM887657", "GSM887658", "GSM887659", "GSM887660", "GSM887661", "GSM887662", "GSM887663", "GSM887664", "GSM887665", "GSM887666", "GSM887667", "GSM887668", "GSM887669", "GSM887670", "GSM887671", "GSM887672", "GSM887673", "GSM887674", "GSM887675", "GSM887676", "GSM887677", "GSM887678", "GSM887679", "GSM887680", "GSM887681", "GSM887682", "GSM887683", "GSM887684", "GSM887685", "GSM887686", "GSM887687", "GSM887688", "GSM887689", "GSM887690", "GSM887691", "GSM887692", "GSM887693", "GSM887694", "GSM887695", "GSM887696", "GSM887697", "GSM887698", "GSM887699", "GSM887700", "GSM887701", "GSM887702", "GSM887703", "GSM887704", "GSM887705", "GSM887706", "GSM887707", "GSM887708", "GSM887709", "GSM887710", "GSM887711", "GSM887712", "GSM887713", "GSM887714", "GSM887715", "GSM887716", "GSM887717", "GSM887718", "GSM887719", "GSM887720", "GSM887721", "GSM887722", "GSM887723", "GSM887724", "GSM887725", "GSM887726", "GSM887727", "GSM887728", "GSM887729", "GSM887730", "GSM887731", "GSM887732", "GSM887733", "GSM887734", "GSM887735", "GSM887736", "GSM887737", "GSM887738", "GSM887739", "GSM887740", "GSM887741", "GSM887742", "GSM887743", "GSM887744", "GSM887745", "GSM887746", "GSM887747", "GSM887748", "GSM887749", "GSM887750", "GSM887751"], "sample_count": 917, "group_sizes": null, "group_sizes_basis": null, "platform": "15308", "taxon": "Homo sapiens", "title": "Expression data from the Cancer Cell Line Encyclopedia (CCLE)", "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:PXD015270", "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=PXD015270", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD015270", "version": null, "note": "The following information was supplied regarding data availability:\nThe proteomic data are available from the PRIDE Archive: PXD015270.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe proteomic data are available from the PRIDE Archive: PXD015270.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "comparative proteomics of non-small cell lung cancer and small cell lung cancer", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32351780:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:560c4e8124de4335d7e839ce3c033a99d5d013d812c4efe2cbe490b825b8ce45", "bytes": 1188, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#table-1", "version": null, "note": "The profiling of differentially expressed proteins and mRNA.", "structure": {"pmcid": "PMC7183755", "section_index": 19, "section_title": "Determination of key proteins by combined use of proteomics and transcriptomics", "row_count": 15, "column_count": 5}, "table": {"label": "Table 1", "caption": "The profiling of differentially expressed proteins and mRNA.", "rows": [["Protein name", "Description", "Gene name", "Ratio", "PSM"], ["P04083", "Annexin A1", "ANXA1", "0.072", "761"], ["P07355", "Annexin A2", "ANXA2", "0.314", "1,364"], ["O75369", "Filamin-B", "FLNB", "0.106", "1,816"], ["Q9BW1", "Acetyl-CoA acetyltransferase 2", "ACAT2", "7.92", "112"], ["O75475", "PC4 and SFRS1-interacting protein", "PSIP1", "15.25", "266"], ["O14776", "Transcription elongation regulator 1", "TCERG1", "7.166", "101"], ["P07741", "Adenine phosphoribosyl transferase", "APRT", "0.262", "160"], ["Q9BP6", "Dihydropyrimidinase-related protein 5", "DPYSL5", "3.058", "173"], ["Q71U36", "Tubulin alpha-1A", "TUBA1A", "2.969", "244"], ["P23368", "NAD-dependent malic enzyme 2", "ME2", "3.614", "252"], ["P22626", "Heterogeneous nuclear ribonucleoproteins A2/B1", "HNRNPA21", "2.924", "1,600"], ["P15121", "Aldose reductase", "AKR1B1", "0.179", "461"], ["Q9BTT0", "Acidic leucine-rich nuclear phosphoprotein 32 family member E", "ANP32E", "3.249", "61"], ["Q9BR2", "Thioredoxin domain-containing protein 17", "TXNDC17", "0.294", "109"]], "row_count": 15, "column_count": 5, "numeric_cells": 48, "header_rows": 1, "locator": "section[19]/table-wrap[1]#table-1"}}], "gaps": ["asset:data:geo:GSE36133 not downloaded", "asset:data:geo:GSE36133 licence not read", "asset:data:geo:PXD015270 not downloaded", "asset:data:geo:PXD015270 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"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": "GO enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Linear Models for Microarray Analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Linear Models for Microarray Analysis package in R language was employed to screen DEGs between NSCLC samples and SCLC samples."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["hierarchical_cluster"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: hierarchical."}, "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": ["GSE36133", "PXD015270"], "resolved_accessions": ["GSE36133", "PXD015270"], "statements": ["The following information was supplied regarding data availability:\nThe proteomic data are available from the PRIDE Archive: PXD015270."], "basis": "The paper names GSE36133, PXD015270 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": ["hierarchical_cluster"], "assets": ["source:pmid:32351780", "data:geo:GSE36133", "asset:table:pmid:32351780:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE36133"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 40156, "completion_tokens": 2072, "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:32351780", "type": "paper", "label": "pmid:32351780"}, {"id": "source:pmid:32351780", "type": "manuscript", "label": "PMID 32351780 full text"}, {"id": "data:geo:GSE36133", "type": "dataset", "label": "GEO GSE36133"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32351780", "type": "paper", "label": "pmid:32351780"}, {"id": "source:pmid:32351780", "type": "manuscript", "label": "PMID 32351780 full text"}, {"id": "data:geo:GSE36133", "type": "dataset", "label": "GEO GSE36133"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32351780", "type": "extraction", "used": ["source:pmid:32351780"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE36133", "type": "accession_resolution", "used": ["data:geo:GSE36133"], "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:32351780", "parent_hash": "sha256:5a4fd36fecddfe528b192874a274fc096b8627eb3762590c79dee1a317476d9a", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE36133 licence not read", "asset:data:geo:GSE36133 not downloaded", "asset:data:geo:PXD015270 licence not read", "asset:data:geo:PXD015270 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ll and small lung carcinoma cell lines using mass spectrometry.", "molecular mechanism of lung cancers. The raw mass spectrometry data have been deposited to the ProteomeXcha", "were comparatively analysed by quantitative proteomics, and their corresponding transcriptomics dat", "eins that were positively correlated between proteomic and transcriptomic data. RESULT: The proteom"], "order_basis": "paper_text_order:47", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["37 °C and 5% CO2. The NSCLC cell lines were cultivated with adherent method and SCLC cell lines wer", "ls Cell culture Two NSCLC cell lines (H1975, A549) and two SCLC cell lines (H69, H446) were ob"], "order_basis": "paper_text_order:1849", "id": "assay:2"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["lustering analysis of DEGs Linear Models for Microarray Analysis package in R language was employed"], "order_basis": "paper_text_order:2690", "id": "assay:3"}, {"role": "analysis", "definition_id": "clustering", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["hierarchical_cluster"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["hierarchical clustering"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}