{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38647237", "kind": "science-record", "revision": 3, "content_hash": "sha256:d6d62247a7a6e01eeb39f106f37849264531cefb65d30dc1e66b13797a84a3ce", "created_at": "2026-11-01T19:20:37Z", "updated_at": "2026-11-01T22:11:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development of m6A/m5C/m1A regulated lncRNA signature for prognostic prediction, personalized immune intervention and drug selection in LUAD.", "doi": "10.1111/jcmm.18282", "pmid": "38647237", "authors": ["Chao Ma", "Zhuoyu Gu", "Yang Yang"], "journal": "Journal of cellular and molecular medicine", "year": 2024, "abstract": "Research indicates that there are links between m6A, m5C and m1A modifications and the development of different types of tumours. However, it is not yet clear if these modifications are involved in the prognosis of LUAD. The TCGA-LUAD dataset was used as for signature training, while the validation cohort was created by amalgamating publicly accessible GEO datasets including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081. The study focused on 33 genes that are regulated by m6A, m5C or m1A (mRG), which were used to form mRGs clusters and clusters of mRG differentially expressed genes clusters (mRG-DEG clusters). Our subsequent LASSO regression analysis trained the signature of m6A/m5C/m1A-related lncRNA (mRLncSig) using lncRNAs that exhibited differential expression among mRG-DEG clusters and had prognostic value. The model's accuracy underwent validation via Kaplan-Meier analysis, Cox regression, ROC analysis, tAUC evaluation, PCA examination and nomogram predictor validation. In evaluating the immunotherapeutic potential of the signature, we employed multiple bioinformatics algorithms and concepts through various analyses. These included seven newly developed immunoinformatic algorithms, as well as evaluations of TMB, TIDE and immune checkpoints. Additionally, we identified and validated promising agents that target the high-risk mRLncSig in LUAD. To validate the real-world expression pattern of mRLncSig, real-time PCR was carried out on human LUAD tissues. The signature's ability to perform in pan-cancer settings was also evaluated. The study created a 10-lncRNA signature, mRLncSig, which was validated to have prognostic power in the validation cohort. Real-time PCR was applied to verify the actual manifestation of each gene in the signature in the real world. Our immunotherapy analysis revealed an association between mRLncSig and immune status. mRLncSig was found to be closely linked to several checkpoints, such as IL10, IL2, CD40LG, SELP, BTLA and CD28, which could be appropriate immunotherapy targets for LUAD. Among the high-risk patients, our study identified 12 candidate drugs and verified gemcitabine as the most significant one that could target our signature and be effective in treating LUAD. Additionally, we discovered that some of the lncRNAs in mRLncSig could play a crucial role in certain cancer types, and thus, may require further attention in future studies. According to the findings of this study, the use of mRLncSig has the potential to aid in forecasting the prognosis of LUAD and could serve as a potential target for immunotherapy. Moreover, our signature may assist in identifying targets and therapeutic agents more effectively.", "claims": [{"id": "claim-method", "statement": "To further refine our findings, we carried out LASSO analysis using these 18 DELs for selection and shrinkage.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38647237", "locator": "sections[16] \"Two mRG‐DEG clusters constructed and a mRLncSig generated\" paragraph 4", "quote": "To further refine our findings, we carried out LASSO analysis using these 18 DELs for selection and shrinkage."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38647237", "locator": "sections[31] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study created a 10‐lncRNA signature, mRLncSig, which was validated to have prognostic power in the validation cohort.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38647237", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The study created a 10‐lncRNA signature, mRLncSig, which was validated to have prognostic power in the validation cohort."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study created a 10‐lncRNA signature, mRLncSig, which was validated to have prognostic power in the validation cohort.", "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:38647237"], "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:GSE29013"], "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:GSE29013"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38647237", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/jcmm.18282", "sha256": "sha256:343bd3f2c5330671a8da424a013523b23e7b85a242bdd8bcd7768934eacb884c", "bytes": 99227, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/jcmm.18282", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11034373", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29013", "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=GSE29013", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29013", "version": null, "note": "The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. 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The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. 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experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM773540", "GSM773541", "GSM773542", "GSM773543", "GSM773544", "GSM773545", "GSM773546", "GSM773547", "GSM773548", "GSM773549", "GSM773550", "GSM773551", "GSM773552", "GSM773553", "GSM773554", "GSM773555", "GSM773556", "GSM773557", "GSM773558", "GSM773559", "GSM773560", "GSM773561", "GSM773562", "GSM773563", "GSM773564", "GSM773565", "GSM773566", "GSM773567", "GSM773568", "GSM773569", "GSM773570", "GSM773571", "GSM773572", "GSM773573", "GSM773574", "GSM773575", "GSM773576", "GSM773577", "GSM773578", "GSM773579", "GSM773580", "GSM773581", "GSM773582", "GSM773583", "GSM773584", "GSM773585", "GSM773586", "GSM773587", "GSM773588", "GSM773589", "GSM773590", "GSM773591", "GSM773592", "GSM773593", "GSM773594", "GSM773595", "GSM773596", "GSM773597", "GSM773598", "GSM773599", "GSM773600", "GSM773601", "GSM773602", "GSM773603", "GSM773604", "GSM773605", "GSM773606", "GSM773607", "GSM773608", "GSM773609", "GSM773610", "GSM773611", "GSM773612", "GSM773613", "GSM773614", "GSM773615", "GSM773616", "GSM773617", "GSM773618", "GSM773619", "GSM773620", "GSM773621", "GSM773622", "GSM773623", "GSM773624", "GSM773625", "GSM773626", "GSM773627", "GSM773628", "GSM773629", "GSM773630", "GSM773631", "GSM773632", "GSM773633", "GSM773634", "GSM773635", "GSM773636", "GSM773637", "GSM773638", "GSM773639", "GSM773640", "GSM773641", "GSM773642", "GSM773643", "GSM773644", "GSM773645", "GSM773646", "GSM773647", "GSM773648", "GSM773649", "GSM773650", "GSM773651", "GSM773652", "GSM773653", "GSM773654", "GSM773655", "GSM773656", "GSM773657", "GSM773658", "GSM773659", "GSM773660", "GSM773661", "GSM773662", "GSM773663", "GSM773664", "GSM773665", "GSM773666", "GSM773667", "GSM773668", "GSM773669", "GSM773670", "GSM773671", "GSM773672", "GSM773673", "GSM773674", "GSM773675", "GSM773676", "GSM773677", "GSM773678", "GSM773679", "GSM773680", "GSM773681", "GSM773682", "GSM773683", "GSM773684", "GSM773685", "GSM773686", "GSM773687", "GSM773688", "GSM773689", "GSM773690", "GSM773691", "GSM773692", "GSM773693", "GSM773694", "GSM773695", "GSM773696", "GSM773697", "GSM773698", "GSM773699", "GSM773700", "GSM773701", "GSM773702", "GSM773703", "GSM773704", "GSM773705", "GSM773706", "GSM773707", "GSM773708", "GSM773709", "GSM773710", "GSM773711", "GSM773712", "GSM773713", "GSM773714", "GSM773715", "GSM773716", "GSM773717", "GSM773718", "GSM773719", "GSM773720", "GSM773721", "GSM773722", "GSM773723", "GSM773724", "GSM773725", "GSM773726", "GSM773727", "GSM773728", "GSM773729", "GSM773730", "GSM773731", "GSM773732", "GSM773733", "GSM773734", "GSM773735", "GSM773736", "GSM773737", "GSM773738", "GSM773739", "GSM773740", "GSM773741", "GSM773742", "GSM773743", "GSM773744", "GSM773745", "GSM773746", "GSM773747", "GSM773748", "GSM773749", "GSM773750", "GSM773751", "GSM773752", "GSM773753", "GSM773754", "GSM773755", "GSM773756", "GSM773757", "GSM773758", "GSM773759", "GSM773760", "GSM773761", "GSM773762", "GSM773763", "GSM773764", "GSM773765", "GSM773766", "GSM773767", "GSM773768", "GSM773769", "GSM773770", "GSM773771", "GSM773772", "GSM773773", "GSM773774", "GSM773775", "GSM773776", "GSM773777", "GSM773778", "GSM773779", "GSM773780", "GSM773781", "GSM773782", "GSM773783", "GSM773784", "GSM773785"], "sample_count": 246, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data for pathological stage I-II lung adenocarcinomas", "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:GSE37745", "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=GSE37745", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37745", "version": null, "note": "The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1019138", "GSM1019139", "GSM1019140", "GSM1019141", "GSM1019142", "GSM1019143", "GSM1019144", "GSM1019145", "GSM1019146", "GSM1019147", "GSM1019148", "GSM1019149", "GSM1019150", "GSM1019151", "GSM1019152", "GSM1019153", "GSM1019154", "GSM1019155", "GSM1019156", "GSM1019157", "GSM1019158", "GSM1019159", "GSM1019160", "GSM1019161", "GSM1019162", "GSM1019163", "GSM1019164", "GSM1019165", "GSM1019166", "GSM1019167", "GSM1019168", "GSM1019169", "GSM1019170", "GSM1019171", "GSM1019172", "GSM1019173", "GSM1019174", "GSM1019175", "GSM1019176", "GSM1019177", "GSM1019178", "GSM1019179", "GSM1019180", "GSM1019181", "GSM1019182", "GSM1019183", "GSM1019184", "GSM1019185", "GSM1019186", "GSM1019187", "GSM1019188", "GSM1019189", "GSM1019190", "GSM1019191", "GSM1019192", "GSM1019193", "GSM1019194", "GSM1019195", "GSM1019196", "GSM1019197", "GSM1019198", "GSM1019199", "GSM1019200", "GSM1019201", "GSM1019202", "GSM1019203", "GSM1019204", "GSM1019205", "GSM1019206", "GSM1019207", "GSM1019208", "GSM1019209", "GSM1019210", "GSM1019211", "GSM1019212", "GSM1019213", "GSM1019214", "GSM1019215", "GSM1019216", "GSM1019217", "GSM1019218", "GSM1019219", "GSM1019220", "GSM1019221", "GSM1019222", "GSM1019223", "GSM1019224", "GSM1019225", "GSM1019226", "GSM1019227", "GSM1019228", "GSM1019229", "GSM1019230", "GSM1019231", "GSM1019232", "GSM1019233", "GSM1019234", "GSM1019235", "GSM1019236", "GSM1019237", "GSM1019238", "GSM1019239", "GSM1019240", "GSM1019241", "GSM1019242", "GSM1019243", "GSM1019244", "GSM1019245", "GSM1019246", "GSM1019247", "GSM1019248", "GSM1019249", "GSM1019250", "GSM1019251", "GSM1019252", "GSM1019253", "GSM1019254", "GSM1019255", "GSM1019256", "GSM1019257", "GSM1019258", "GSM1019259", "GSM1019260", "GSM1019261", "GSM1019262", "GSM1019263", "GSM1019264", "GSM1019265", "GSM1019266", "GSM1019267", "GSM1019268", "GSM1019269", "GSM1019270", "GSM1019271", "GSM1019272", "GSM1019273", "GSM1019274", "GSM1019275", "GSM1019276", "GSM1019277", "GSM1019278", "GSM1019279", "GSM1019280", "GSM1019281", "GSM1019282", "GSM1019283", "GSM1019284", "GSM1019285", "GSM1019286", "GSM1019287", "GSM1019288", "GSM1019289", "GSM1019290", "GSM1019291", "GSM1019292", "GSM1019293", "GSM1019294", "GSM1019295", "GSM1019296", "GSM1019297", "GSM1019298", "GSM1019299", "GSM1019300", "GSM1019301", "GSM1019302", "GSM1019303", "GSM1019304", "GSM1019305", "GSM1019306", "GSM1019307", "GSM1019308", "GSM1019309", "GSM1019310", "GSM1019311", "GSM1019312", "GSM1019313", "GSM1019314", "GSM1019315", "GSM1019316", "GSM1019317", "GSM1019318", "GSM1019319", "GSM1019320", "GSM1019321", "GSM1019322", "GSM1019323", "GSM1019324", "GSM1019325", "GSM1019326", "GSM1019327", "GSM1019328", "GSM1019329", "GSM1019330", "GSM1019331", "GSM1019332", "GSM1019333"], "sample_count": 196, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis and tissue microarray validation", "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:GSE50081", "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=GSE50081", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE50081", "version": null, "note": "The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1213669", "GSM1213670", "GSM1213671", "GSM1213672", "GSM1213673", "GSM1213674", "GSM1213675", "GSM1213676", "GSM1213677", "GSM1213678", "GSM1213679", "GSM1213680", "GSM1213681", "GSM1213682", "GSM1213683", "GSM1213684", "GSM1213685", "GSM1213686", "GSM1213687", "GSM1213688", "GSM1213689", "GSM1213690", "GSM1213691", "GSM1213692", "GSM1213693", "GSM1213694", "GSM1213695", "GSM1213696", "GSM1213697", "GSM1213698", "GSM1213699", "GSM1213700", "GSM1213701", "GSM1213702", "GSM1213703", "GSM1213704", "GSM1213705", "GSM1213706", "GSM1213707", "GSM1213708", "GSM1213709", "GSM1213710", "GSM1213711", "GSM1213712", "GSM1213713", "GSM1213714", "GSM1213715", "GSM1213716", "GSM1213717", "GSM1213718", "GSM1213719", "GSM1213720", "GSM1213721", "GSM1213722", "GSM1213723", "GSM1213724", "GSM1213725", "GSM1213726", "GSM1213727", "GSM1213728", "GSM1213729", "GSM1213730", "GSM1213731", "GSM1213732", "GSM1213733", "GSM1213734", "GSM1213735", "GSM1213736", "GSM1213737", "GSM1213738", "GSM1213739", "GSM1213740", "GSM1213741", "GSM1213742", "GSM1213743", "GSM1213744", "GSM1213745", "GSM1213746", "GSM1213747", "GSM1213748", "GSM1213749", "GSM1213750", "GSM1213751", "GSM1213752", "GSM1213753", "GSM1213754", "GSM1213755", "GSM1213756", "GSM1213757", "GSM1213758", "GSM1213759", "GSM1213760", "GSM1213761", "GSM1213762", "GSM1213763", "GSM1213764", "GSM1213765", "GSM1213766", "GSM1213767", "GSM1213768", "GSM1213769", "GSM1213770", "GSM1213771", "GSM1213772", "GSM1213773", "GSM1213774", "GSM1213775", "GSM1213776", "GSM1213777", "GSM1213778", "GSM1213779", "GSM1213780", "GSM1213781", "GSM1213782", "GSM1213783", "GSM1213784", "GSM1213785", "GSM1213786", "GSM1213787", "GSM1213788", "GSM1213789", "GSM1213790", "GSM1213791", "GSM1213792", "GSM1213793", "GSM1213794", "GSM1213795", "GSM1213796", "GSM1213797", "GSM1213798", "GSM1213799", "GSM1213800", "GSM1213801", "GSM1213802", "GSM1213803", "GSM1213804", "GSM1213805", "GSM1213806", "GSM1213807", "GSM1213808", "GSM1213809", "GSM1213810", "GSM1213811", "GSM1213812", "GSM1213813", "GSM1213814", "GSM1213815", "GSM1213816", "GSM1213817", "GSM1213818", "GSM1213819", "GSM1213820", "GSM1213821", "GSM1213822", "GSM1213823", "GSM1213824", "GSM1213825", "GSM1213826", "GSM1213827", "GSM1213828", "GSM1213829", "GSM1213830", "GSM1213831", "GSM1213832", "GSM1213833", "GSM1213834", "GSM1213835", "GSM1213836", "GSM1213837", "GSM1213838", "GSM1213839", "GSM1213840", "GSM1213841", "GSM1213842", "GSM1213843", "GSM1213844", "GSM1213845", "GSM1213846", "GSM1213847", "GSM1213848", "GSM1213849"], "sample_count": 181, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Validation of a histology-independent prognostic gene signature for early stage, non-small cell lung cancer including stage IA patients", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE29013 not downloaded", "asset:data:geo:GSE29013 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE31210 not downloaded", "asset:data:geo:GSE31210 licence not read", "asset:data:geo:GSE37745 not downloaded", "asset:data:geo:GSE37745 licence not read", "asset:data:geo:GSE50081 not downloaded", "asset:data:geo:GSE50081 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-3", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "PCA"}}, {"id": "method-4", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}, {"id": "method-5", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC analysis"}}, {"id": "method-6", "family": null, "specific": null, "label": "LASSO analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To further refine our findings, we carried out LASSO analysis using these 18 DELs for selection and shrinkage."}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE29013", "GSE30219", "GSE31210", "GSE37745", "GSE50081"], "resolved_accessions": ["GSE29013", "GSE30219", "GSE31210", "GSE37745", "GSE50081"], "statements": ["The study utilized data from both public databases and laboratory experiments. The sources of publicly available data are listed below. Model training utilized data from the TCGA and pan‐cancer TCGA TARGET GTEx, which were obtained from https://xenabrowser.net. The validation data came from GEO datasets, including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081, which were downloaded from https://www.ncbi.nlm.nih.gov/geo. For drug prediction, the CTRP and PRISM databases were used and obtained from https://portals.broadinstitute.org/ctrp and https://depmap.org/portal/prism, respectively. To obtain the laboratory data used in this study, please contact the corresponding author."], "basis": "The paper names GSE29013, GSE30219, GSE31210, GSE37745, GSE50081 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:38647237", "data:geo:GSE29013"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29013"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:16:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 27216, "completion_tokens": 3184, "cached_tokens": 256}}, "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:38647237", "type": "paper", "label": "pmid:38647237"}, {"id": "source:pmid:38647237", "type": "manuscript", "label": "PMID 38647237 full text"}, {"id": "data:geo:GSE29013", "type": "dataset", "label": "GEO GSE29013"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38647237", "type": "paper", "label": "pmid:38647237"}, {"id": "source:pmid:38647237", "type": "manuscript", "label": "PMID 38647237 full text"}, {"id": "data:geo:GSE29013", "type": "dataset", "label": "GEO GSE29013"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38647237", "type": "extraction", "used": ["source:pmid:38647237"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29013", "type": "accession_resolution", "used": ["data:geo:GSE29013"], "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:38647237", "parent_hash": "sha256:3749a6e69addbf0adb4a850a395cec991690a4acb1c2948b2bf4fc3f64d9f671", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE29013 licence not read", "asset:data:geo:GSE29013 not downloaded", "asset:data:geo:GSE30219 licence not read", "asset:data:geo:GSE30219 not downloaded", "asset:data:geo:GSE31210 licence not read", "asset:data:geo:GSE31210 not downloaded", "asset:data:geo:GSE37745 licence not read", "asset:data:geo:GSE37745 not downloaded", "asset:data:geo:GSE50081 licence not read", "asset:data:geo:GSE50081 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["e real-world expression pattern of mRLncSig, real-time PCR was carried out on human LUAD tissues. The s", "e prognostic power in the validation cohort. Real-time PCR was applied to verify the actual manifestati"], "order_basis": "paper_text_order:1532", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:16:28+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}