← All .science files
pmid:36949939
Construction and validation of chemoresistance-associated tumor- infiltrating exhausted-like CD8+ T cell signature in breast cancer: cr-TILCD8TSig.
D Q Cai · Diankui Cai · Yiping Zou · Xumeng Chen · Zhixiang Jian · Mude Shi · Ye Lin · Jueming Chen
Frontiers in immunology · 2023 doi:10.3389/fimmu.2023.1120886
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 8 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
target object · 4 fields
evidence array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 18 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 10 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 12 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 508 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 11 items
[5] object · 15 fields
structure object · 15 fields
sample_accessions array · 12 items
[6] object · 15 fields
structure object · 15 fields
sample_accessions array · 32 items
[7] object · 15 fields
structure object · 15 fields
sample_accessions array · 47 items
[8] object · 15 fields
structure object · 15 fields
sample_accessions array · 6 items
[9] object · 15 fields
structure object · 15 fields
sample_accessions array · 28 items
[10] object · 15 fields
structure object · 15 fields
sample_accessions array · 26 items
[11] object · 15 fields
structure object · 15 fields
sample_accessions array · 16 items
[12] object · 15 fields
structure object · 15 fields
sample_accessions array · 8 items
[13] object · 15 fields
structure object · 15 fields
sample_accessions array · 46 items
[14] object · 15 fields
structure object · 15 fields
sample_accessions array · 18 items
[15] object · 15 fields
structure object · 15 fields
sample_accessions array · 18 items
[16] object · 15 fields
structure object · 15 fields
sample_accessions array · 6 items
[17] object · 15 fields
structure object · 15 fields
sample_accessions array · 6 items
gaps array · 34 items
analysis object · 4 fields
methods array · 3 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 1 item
[0] object · 8 fields
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 17 items
resolved_accessions array · 17 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 39 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36949939", "kind": "science-record", "revision": 3, "content_hash": "sha256:5cc10cc5d7f6567ee105d8cb7404efac12a285949fde76e1576a422fd95944dd", "created_at": "2026-11-01T19:01:35Z", "updated_at": "2026-11-01T22:09:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction and validation of chemoresistance-associated tumor- infiltrating exhausted-like CD8+ T cell signature in breast cancer: cr-TILCD8TSig.", "doi": "10.3389/fimmu.2023.1120886", "pmid": "36949939", "authors": ["D Q Cai", "Diankui Cai", "Yiping Zou", "Xumeng Chen", "Zhixiang Jian", "Mude Shi", "Ye Lin", "Jueming Chen"], "journal": "Frontiers in immunology", "year": 2023, "abstract": "Background: Accumulating evidence has revealed that CD8+ T cell exhaustion (Tex) results in worse immunotherapy outcomes. However, the molecular functions and mechanisms of action of Tex in chemoresistance needed to be elucidated.\nMethods: The populations of tumor-infiltrating CD8+ T cells (TILCD8Ts) in chemoresistant and chemosensitive groups of the GSE25066 dataset were calculated using CIBERSORT. Differentially expressed genes (DEGs) between TILCD8Ts and other immune cells were explored by integrating 16 immune cell datasets downloaded from the gene expression omnibus (GEO) database. Gene ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, univariate and multivariate Cox regression, and least absolute shrinkage and selection operator (LASSO) regression of TILCD8T-specific upregulated genes were used to construct a chemoresistant TILCD8T signature (cr-TILCD8TSig). Clinical prognostic data, genomic alterations, chemotherapy response, and immunotherapy response were compared between the different cr-TILCD8TSig subgroups in the GSE25066 and the cancer genome atlas breast cancer (TCGA-BRCA) cohorts.\nResults: A cr-TILCD8TSig with exhausted features was identified, consisting of seven genes (TCF7, RARRES3, ARL4C, ITK, CDH3, GZMB, and KLRD1), which were identified from 104 TILCD8Ts-specific DEGs. Our results showed that compared to the cr-TILCD8TSig-low subgroup, the -high subgroup had a poorer distant relapse-free survival (DRFS) in the GSE25066 cohort and worse progression-free survival (PFS) in the TCGA-BRCA cohort. Univariate and multivariate Cox regression analyses also demonstrated that cr-TILCD8TSig was an independent prognostic factor in the two independent cohorts. Furthermore, cr-TILCD8TSig-low patients benefited more from chemotherapy and immunotherapy than cr-TILCD8TSig-high patients. Besides, we found cell transmembrane signal transduction and the ECM may provide the molecular basis for resistance to antitumor agents in the cr-TILCD8Sig-high subgroup. For genomic alterations, we revealed that mutations in PIK3CA, DMD, and APOB were more common in the cr-TILCD8Sig-high subgroup than in the cr-TILCD8Sig-low subgroup. A nomogram was finally constructed with good discrimination and calibration.\nConclusions: cr-TILCD8TSig is a useful tool to independently predict prognosis, chemotherapy response, and immunotherapy outcomes in patients with breast cancer.", "claims": [{"id": "claim-method", "statement": "Cox proportional hazards regression analysis was performed to examine the correlation between gene expression and overall survival (OS).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36949939", "locator": "sections[6] \"Identification of differentially expressed and prognostic genes\" paragraph 2", "quote": "Cox proportional hazards regression analysis was performed to examine the correlation between gene expression and overall survival (OS)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36949939", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The seven-gene cr-TILCD8TSig independently predicted poorer survival in breast cancer, with the high-signature group having worse progression-free survival in TCGA-BRCA.", "kind": "quantitative", "target": {"value": 0.0054, "unit": "p-value", "tolerance": null, "source": "Patients in the cr-TILCD8TSig-high group exhibited a poorer progression-free survival (PFS) rate than those in the cr-TILCD8TSig-low group (P=0.0054, Figure 7D )."}, "evidence": [{"asset": "source:pmid:36949939", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A cr-TILCD8TSig with exhausted features was identified, consisting of seven genes (TCF7, RARRES3, ARL4C, ITK, CDH3, GZMB, and KLRD1), which were identified from 104 TILCD8Ts-specific DEGs."}, {"asset": "source:pmid:36949939", "locator": "sections[16] \"Evaluation and validation of the cr-TILCD8TSig scoring model for predicting prognosis in the GSE25066 and TCGA-BRCA cohorts\" paragraph 2", "quote": "Patients in the cr-TILCD8TSig-high group exhibited a poorer progression-free survival (PFS) rate than those in the cr-TILCD8TSig-low group (P=0.0054, Figure 7D )."}, {"asset": "source:pmid:36949939", "locator": "sections[16] \"Evaluation and validation of the cr-TILCD8TSig scoring model for predicting prognosis in the GSE25066 and TCGA-BRCA cohorts\" paragraph 4", "quote": "Univariate and multivariate Cox regression analyses also proved the independent prognostic value of the cr-TILCD8TSig scoring model in the GSE25066 and TCGA-BRCA cohorts ( Figure 9 )."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The seven-gene cr-TILCD8TSig independently predicted poorer survival in breast cancer, with the high-signature group having worse progression-free survival in TCGA-BRCA.", "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:36949939"], "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:GSE13906"], "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:GSE13906"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36949939", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2023.1120886", "sha256": "sha256:3340b3046f22cbee188d9b1d0985570bb3e3d9994f6818c23298bc36277f803e", "bytes": 36138, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2023.1120886", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10025395", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13906", "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=GSE13906", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13906", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM349848", "GSM349849", "GSM349850", "GSM349851", "GSM349852", "GSM349853", "GSM349854", "GSM349855", "GSM349856", "GSM349857"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "NK-cell associated receptors expression in EBV-positive gamma-delta T cell lines.", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE23371", "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=GSE23371", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23371", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM573357", "GSM573358", "GSM573359", "GSM573360", "GSM573361", "GSM573362", "GSM573363", "GSM573364", "GSM573365", "GSM573366", "GSM573367", "GSM573368"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Transcriptomes of monocyte-derived DCs stimulated with various compounds", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE25066", "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=GSE25066", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25066", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM615096", "GSM615097", "GSM615098", "GSM615099", "GSM615100", "GSM615101", "GSM615102", "GSM615103", "GSM615104", "GSM615105", "GSM615106", "GSM615107", "GSM615108", "GSM615109", "GSM615110", "GSM615111", "GSM615112", "GSM615113", "GSM615114", "GSM615115", "GSM615116", "GSM615117", "GSM615118", "GSM615119", "GSM615120", "GSM615121", "GSM615122", "GSM615123", "GSM615124", "GSM615125", "GSM615126", "GSM615127", "GSM615128", "GSM615129", "GSM615130", "GSM615131", "GSM615132", "GSM615133", "GSM615134", "GSM615135", "GSM615136", "GSM615137", "GSM615138", "GSM615139", "GSM615140", "GSM615141", "GSM615142", "GSM615143", "GSM615144", "GSM615145", "GSM615146", "GSM615147", "GSM615148", "GSM615149", "GSM615150", "GSM615151", "GSM615152", "GSM615153", "GSM615154", "GSM615155", "GSM615156", "GSM615157", "GSM615158", "GSM615159", "GSM615160", "GSM615161", "GSM615162", "GSM615163", "GSM615164", "GSM615165", "GSM615166", "GSM615167", "GSM615168", "GSM615169", "GSM615170", "GSM615171", "GSM615172", "GSM615173", "GSM615174", "GSM615175", "GSM615176", "GSM615177", "GSM615178", "GSM615179", "GSM615180", "GSM615181", "GSM615182", "GSM615183", "GSM615184", "GSM615185", "GSM615186", "GSM615187", "GSM615188", "GSM615189", "GSM615190", "GSM615191", "GSM615192", "GSM615193", "GSM615194", "GSM615195", "GSM615196", "GSM615197", "GSM615198", "GSM615199", "GSM615200", "GSM615201", "GSM615202", "GSM615203", "GSM615204", "GSM615205", "GSM615206", "GSM615207", "GSM615208", "GSM615209", "GSM615210", "GSM615211", "GSM615212", "GSM615213", "GSM615214", "GSM615215", "GSM615216", "GSM615217", "GSM615218", "GSM615219", "GSM615220", "GSM615221", "GSM615222", "GSM615223", "GSM615224", "GSM615225", "GSM615226", "GSM615227", "GSM615228", "GSM615229", "GSM615230", "GSM615231", "GSM615232", "GSM615233", "GSM615234", "GSM615235", "GSM615236", "GSM615237", "GSM615238", "GSM615239", "GSM615240", "GSM615241", "GSM615242", "GSM615243", "GSM615244", "GSM615245", "GSM615246", "GSM615247", "GSM615248", "GSM615249", "GSM615250", "GSM615251", "GSM615252", "GSM615253", "GSM615254", "GSM615255", "GSM615256", "GSM615257", "GSM615258", "GSM615259", "GSM615260", "GSM615261", "GSM615262", "GSM615263", "GSM615264", "GSM615265", "GSM615266", "GSM615267", "GSM615268", "GSM615269", "GSM615270", "GSM615271", "GSM615272", "GSM615273", "GSM615274", "GSM615275", "GSM615276", "GSM615277", "GSM615278", "GSM615279", "GSM615280", "GSM615281", "GSM615282", "GSM615283", "GSM615284", "GSM615285", "GSM615286", "GSM615287", "GSM615288", "GSM615289", "GSM615290", "GSM615291", "GSM615292", "GSM615293", "GSM615294", "GSM615295", "GSM615296", "GSM615297", "GSM615298", "GSM615299", "GSM615300", "GSM615301", "GSM615302", "GSM615303", "GSM615304", "GSM615305", "GSM615306", "GSM615307", "GSM615308", "GSM615309", "GSM615310", "GSM615311", "GSM615312", "GSM615313", "GSM615314", "GSM615315", "GSM615316", "GSM615317", "GSM615318", "GSM615319", "GSM615320", "GSM615321", "GSM615322", "GSM615323", "GSM615324", "GSM615325", "GSM615326", "GSM615327", "GSM615328", "GSM615329", "GSM615330", "GSM615331", "GSM615332", "GSM615333", "GSM615334", "GSM615335", "GSM615336", "GSM615337", "GSM615338", "GSM615339", "GSM615340", "GSM615341", "GSM615342", "GSM615343", "GSM615344", "GSM615345", "GSM615346", "GSM615347", "GSM615348", "GSM615349", "GSM615350", "GSM615351", "GSM615352", "GSM615353", "GSM615354", "GSM615355", "GSM615356", "GSM615357", "GSM615358", "GSM615359", "GSM615360", "GSM615361", "GSM615362", "GSM615363", "GSM615364", "GSM615365", "GSM615366", "GSM615367", "GSM615368", "GSM615369", "GSM615370", "GSM615371", "GSM615372", "GSM615373", "GSM615374", "GSM615375", "GSM615376", "GSM615377", "GSM615378", "GSM615379", "GSM615380", "GSM615381", "GSM615382", "GSM615383", "GSM615384", "GSM615385", "GSM615386", "GSM615387", "GSM615388", "GSM615389", "GSM615390", "GSM615391", "GSM615392", "GSM615393", "GSM615394", "GSM615395", "GSM615396", "GSM615397", "GSM615398", "GSM615399", "GSM615400", "GSM615401", "GSM615402", "GSM615403", "GSM615404", "GSM615405", "GSM615631", "GSM615632", "GSM615633", "GSM615634", "GSM615635", "GSM615636", "GSM615637", "GSM615638", "GSM615639", "GSM615640", "GSM615641", "GSM615642", "GSM615643", "GSM615644", "GSM615645", "GSM615646", "GSM615647", "GSM615648", "GSM615649", "GSM615650", "GSM615651", "GSM615652", "GSM615653", "GSM615654", "GSM615655", "GSM615656", "GSM615657", "GSM615658", "GSM615659", "GSM615660", "GSM615661", "GSM615662", "GSM615663", "GSM615664", "GSM615665", "GSM615666", "GSM615667", "GSM615668", "GSM615669", "GSM615670", "GSM615671", "GSM615672", "GSM615673", "GSM615674", "GSM615675", "GSM615676", "GSM615677", "GSM615678", "GSM615679", "GSM615680", "GSM615681", "GSM615682", "GSM615683", "GSM615684", "GSM615685", "GSM615686", "GSM615687", "GSM615688", "GSM615689", "GSM615690", "GSM615691", "GSM615692", "GSM615693", "GSM615694", "GSM615695", "GSM615696", "GSM615697", "GSM615698", "GSM615699", "GSM615700", "GSM615701", "GSM615702", "GSM615703", "GSM615704", "GSM615705", "GSM615706", "GSM615707", "GSM615708", "GSM615709", "GSM615710", "GSM615711", "GSM615712", "GSM615713", "GSM615714", "GSM615715", "GSM615716", "GSM615717", "GSM615718", "GSM615719", "GSM615720", "GSM615721", "GSM615722", "GSM615723", "GSM615724", "GSM615725", "GSM615726", "GSM615727", "GSM615728", "GSM615729", "GSM615730", "GSM615731", "GSM615732", "GSM615733", "GSM615734", "GSM615735", "GSM615736", "GSM615737", "GSM615738", "GSM615739", "GSM615740", "GSM615741", "GSM615742", "GSM615743", "GSM615744", "GSM615745", "GSM615746", "GSM615747", "GSM615748", "GSM615749", "GSM615750", "GSM615751", "GSM615752", "GSM615753", "GSM615754", "GSM615755", "GSM615756", "GSM615757", "GSM615758", "GSM615759", "GSM615760", "GSM615761", "GSM615762", "GSM615763", "GSM615764", "GSM615765", "GSM615766", "GSM615767", "GSM615768", "GSM615769", "GSM615770", "GSM615771", "GSM615772", "GSM615773", "GSM615774", "GSM615775", "GSM615776", "GSM615777", "GSM615778", "GSM615779", "GSM615780", "GSM615781", "GSM615782", "GSM615783", "GSM615784", "GSM615785", "GSM615786", "GSM615787", "GSM615788", "GSM615789", "GSM615790", "GSM615791", "GSM615792", "GSM615793", "GSM615794", "GSM615795", "GSM615796", "GSM615797", "GSM615798", "GSM615799", "GSM615800", "GSM615801", "GSM615802", "GSM615803", "GSM615804", "GSM615805", "GSM615806", "GSM615807", "GSM615808", "GSM615809", "GSM615810", "GSM615811", "GSM615812", "GSM615813", "GSM615814", "GSM615815", "GSM615816", "GSM615817", "GSM615818", "GSM615819", "GSM615820", "GSM615821", "GSM615822", "GSM615823", "GSM615824", "GSM615825", "GSM615826", "GSM615827", "GSM615828"], "sample_count": 508, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast 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": "data:geo:GSE25320", "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=GSE25320", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25320", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM622845", "GSM622846", "GSM622847", "GSM622848", "GSM622849", "GSM622850", "GSM622851", "GSM622852", "GSM623441", "GSM623442", "GSM623443"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "7724;570", "taxon": "Human alphaherpesvirus 1; human gammaherpesvirus 4; Betapolyomavirus macacae; Mus musculus; Human gammaherpesvirus 8; Homo sapiens; Human betaherpesvirus 5; Human immunodeficiency virus 1; Rattus norvegicus; JC polyomavirus; Betapolyomavirus hominis", "title": "Characterisation of mRNA and microRNA in human mast cell exosomes and their transfer to other mast cells and blood CD34 progenitor cells", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE27291", "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=GSE27291", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27291", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM674835", "GSM674836", "GSM674837", "GSM674838", "GSM674839", "GSM674840", "GSM674841", "GSM674842", "GSM674843", "GSM674844", "GSM674845", "GSM674846"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Microarray expression data from human TCRVg9-positive gamma delta T lymphocytes", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE27838", "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=GSE27838", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27838", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM687236", "GSM687237", "GSM687238", "GSM687239", "GSM687240", "GSM687241", "GSM687242", "GSM687243", "GSM687244", "GSM687245", "GSM687246", "GSM687247", "GSM687248", "GSM687249", "GSM687250", "GSM687251", "GSM687252", "GSM687253", "GSM687254", "GSM687255", "GSM687256", "GSM687257", "GSM687258", "GSM687259", "GSM687260", "GSM687261", "GSM687262", "GSM687263", "GSM687264", "GSM687265", "GSM687266", "GSM687267"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression of expanded and non-expanded natural killer cells from healthy donor and myeloma patients", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE28490", "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=GSE28490", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28490", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM705287", "GSM705288", "GSM705289", "GSM705290", "GSM705291", "GSM705292", "GSM705293", "GSM705294", "GSM705295", "GSM705296", "GSM705297", "GSM705298", "GSM705299", "GSM705300", "GSM705301", "GSM705302", "GSM705303", "GSM705304", "GSM705305", "GSM705306", "GSM705307", "GSM705308", "GSM705309", "GSM705310", "GSM705311", "GSM705312", "GSM705313", "GSM705314", "GSM705315", "GSM705316", "GSM705317", "GSM705318", "GSM705319", "GSM705320", "GSM705321", "GSM705322", "GSM705323", "GSM705324", "GSM705325", "GSM705326", "GSM705327", "GSM705328", "GSM705329", "GSM705330", "GSM705331", "GSM705332", "GSM705333"], "sample_count": 47, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "mRNA expression profiling of human immune cell subset (Roche)", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE28698", "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=GSE28698", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28698", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM710733", "GSM710734", "GSM710735", "GSM710736", "GSM710737", "GSM710738"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling of imatinib-treated and untreated human Hematopoetic progenitors expressing the ETV6-PDGFRB oncogene", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE28726", "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=GSE28726", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28726", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM710977", "GSM710979", "GSM711464", "GSM711481", "GSM711482", "GSM711608", "GSM711609", "GSM711610", "GSM711611", "GSM711612", "GSM711613", "GSM711614", "GSM711615", "GSM711616", "GSM711617", "GSM711618", "GSM711666", "GSM711685", "GSM711686", "GSM711687", "GSM711688", "GSM711689", "GSM711690", "GSM711691", "GSM711692", "GSM711693", "GSM711728", "GSM711729"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "NKT, CD1d-aGC+ Va24-, and CD4 T cell clones from human peripheral blood", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE37750", "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=GSE37750", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37750", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM926937", "GSM926938", "GSM926939", "GSM926940", "GSM926941", "GSM926942", "GSM926943", "GSM926944", "GSM926945", "GSM926946", "GSM926947", "GSM926948", "GSM926949", "GSM926950", "GSM926951", "GSM926952", "GSM926953", "GSM926954", "GSM926955", "GSM926956", "GSM926957", "GSM926958", "GSM926959", "GSM926960", "GSM926961", "GSM926962"], "sample_count": 26, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data: Plasmacytoid dendritic cells (pDCs) of healthy donors and MS patientes before and after IFN beta treatment", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE39889", "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=GSE39889", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39889", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM980734", "GSM980735", "GSM980736", "GSM980737", "GSM980738", "GSM980739", "GSM980740", "GSM980741", "GSM980742", "GSM980743", "GSM980744", "GSM980745", "GSM980746", "GSM980747", "GSM980748", "GSM980749"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Neutrophil gene expression in response to Mycobacterium abscessus", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE42058", "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=GSE42058", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42058", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1031685", "GSM1031686", "GSM1031687", "GSM1031688", "GSM1031689", "GSM1031690", "GSM1031691", "GSM1031692"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from CD11c+ mDCs in HIV infection", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE49910", "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=GSE49910", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE49910", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1209554", "GSM1209555", "GSM1209556", "GSM1209557", "GSM1209558", "GSM1209559", "GSM1209560", "GSM1209561", "GSM1209562", "GSM1209563", "GSM1209564", "GSM1209565", "GSM1209566", "GSM1209567", "GSM1209568", "GSM1209569", "GSM1209570", "GSM1209571", "GSM1209572", "GSM1209573", "GSM1209574", "GSM1209575", "GSM1209576", "GSM1209577", "GSM1209578", "GSM1209579", "GSM1209580", "GSM1209581", "GSM1209582", "GSM1209583", "GSM1209584", "GSM1209585", "GSM1209586", "GSM1209587", "GSM1209588", "GSM1209589", "GSM1209590", "GSM1209591", "GSM1209592", "GSM1209593", "GSM1209594", "GSM1209595", "GSM1209596", "GSM1209597", "GSM1209598", "GSM1209599"], "sample_count": 46, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "An Expression Atlas of Human Primary Cells: Inference of Gene Function from Coexpression Networks", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE51540", "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=GSE51540", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51540", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1247614", "GSM1247615", "GSM1247616", "GSM1247617", "GSM1247618", "GSM1247619", "GSM1247620", "GSM1247621", "GSM1247622", "GSM1247623", "GSM1247624", "GSM1247625", "GSM1247626", "GSM1247627", "GSM1247628", "GSM1247629", "GSM1247630", "GSM1247631"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "16268", "taxon": "Homo sapiens", "title": "Effects of TNF-alpha blocking in sorted Th17 cells from co-cultures of human CD4-positive and CD14-positive cells", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE59237", "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=GSE59237", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59237", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1431110", "GSM1431111", "GSM1431112", "GSM1431113", "GSM1431114", "GSM1431115", "GSM1431116", "GSM1431117", "GSM1431118", "GSM1431119", "GSM1431120", "GSM1431121", "GSM1431122", "GSM1431123", "GSM1431124", "GSM1431125", "GSM1431126", "GSM1431127"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "TSLP effects on primary human blood dendritic cells", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE6863", "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=GSE6863", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6863", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM158148", "GSM158182", "GSM158183", "GSM158184", "GSM158186", "GSM158187"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Immature dendritic cells under hypoxic condition", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE8059", "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=GSE8059", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE8059", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material .", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM198942", "GSM198943", "GSM198944", "GSM198945", "GSM198958", "GSM198959"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "resting and IL2 activated human natural killer cells", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE13906 not downloaded", "asset:data:geo:GSE13906 licence not read", "asset:data:geo:GSE23371 not downloaded", "asset:data:geo:GSE23371 licence not read", "asset:data:geo:GSE25066 not downloaded", "asset:data:geo:GSE25066 licence not read", "asset:data:geo:GSE25320 not downloaded", "asset:data:geo:GSE25320 licence not read", "asset:data:geo:GSE27291 not downloaded", "asset:data:geo:GSE27291 licence not read", "asset:data:geo:GSE27838 not downloaded", "asset:data:geo:GSE27838 licence not read", "asset:data:geo:GSE28490 not downloaded", "asset:data:geo:GSE28490 licence not read", "asset:data:geo:GSE28698 not downloaded", "asset:data:geo:GSE28698 licence not read", "asset:data:geo:GSE28726 not downloaded", "asset:data:geo:GSE28726 licence not read", "asset:data:geo:GSE37750 not downloaded", "asset:data:geo:GSE37750 licence not read", "asset:data:geo:GSE39889 not downloaded", "asset:data:geo:GSE39889 licence not read", "asset:data:geo:GSE42058 not downloaded", "asset:data:geo:GSE42058 licence not read", "asset:data:geo:GSE49910 not downloaded", "asset:data:geo:GSE49910 licence not read", "asset:data:geo:GSE51540 not downloaded", "asset:data:geo:GSE51540 licence not read", "asset:data:geo:GSE59237 not downloaded", "asset:data:geo:GSE59237 licence not read", "asset:data:geo:GSE6863 not downloaded", "asset:data:geo:GSE6863 licence not read", "asset:data:geo:GSE8059 not downloaded", "asset:data:geo:GSE8059 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Cox proportional hazards regression analysis was performed to examine the correlation between gene expression and overall survival (OS)."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-3", "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": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.0054, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE25066", "GSE42058", "GSE49910", "GSE51540", "GSE59237", "GSE6863", "GSE8059", "GSE13906", "GSE23371", "GSE25320", "GSE27291", "GSE27838", "GSE28490", "GSE28698", "GSE28726", "GSE37750", "GSE39889"], "resolved_accessions": ["GSE25066", "GSE42058", "GSE49910", "GSE51540", "GSE59237", "GSE6863", "GSE8059", "GSE13906", "GSE23371", "GSE25320", "GSE27291", "GSE27838", "GSE28490", "GSE28698", "GSE28726", "GSE37750", "GSE39889"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."], "basis": "The paper names GSE25066, GSE42058, GSE49910, GSE51540, GSE59237, GSE6863, GSE8059, GSE13906, GSE23371, GSE25320, GSE27291, GSE27838, GSE28490, GSE28698, GSE28726, GSE37750, GSE39889 in Gene Expression Omnibus (GEO) repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:36949939", "data:geo:GSE13906"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13906"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:34:18Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10719, "completion_tokens": 4902, "cached_tokens": 264}}, "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:36949939", "type": "paper", "label": "pmid:36949939"}, {"id": "source:pmid:36949939", "type": "manuscript", "label": "PMID 36949939 full text"}, {"id": "data:geo:GSE13906", "type": "dataset", "label": "GEO GSE13906"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36949939", "type": "paper", "label": "pmid:36949939"}, {"id": "source:pmid:36949939", "type": "manuscript", "label": "PMID 36949939 full text"}, {"id": "data:geo:GSE13906", "type": "dataset", "label": "GEO GSE13906"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36949939", "type": "extraction", "used": ["source:pmid:36949939"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13906", "type": "accession_resolution", "used": ["data:geo:GSE13906"], "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:36949939", "parent_hash": "sha256:c896b25a3eebe1669f32791fab0df6630399c3a5629400a294326010740fd972", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE13906 licence not read", "asset:data:geo:GSE13906 not downloaded", "asset:data:geo:GSE23371 licence not read", "asset:data:geo:GSE23371 not downloaded", "asset:data:geo:GSE25066 licence not read", "asset:data:geo:GSE25066 not downloaded", "asset:data:geo:GSE25320 licence not read", "asset:data:geo:GSE25320 not downloaded", "asset:data:geo:GSE27291 licence not read", "asset:data:geo:GSE27291 not downloaded", "asset:data:geo:GSE27838 licence not read", "asset:data:geo:GSE27838 not downloaded", "asset:data:geo:GSE28490 licence not read", "asset:data:geo:GSE28490 not downloaded", "asset:data:geo:GSE28698 licence not read", "asset:data:geo:GSE28698 not downloaded", "asset:data:geo:GSE28726 licence not read", "asset:data:geo:GSE28726 not downloaded", "asset:data:geo:GSE37750 licence not read", "asset:data:geo:GSE37750 not downloaded", "asset:data:geo:GSE39889 licence not read", "asset:data:geo:GSE39889 not downloaded", "asset:data:geo:GSE42058 licence not read", "asset:data:geo:GSE42058 not downloaded", "asset:data:geo:GSE49910 licence not read", "asset:data:geo:GSE49910 not downloaded", "asset:data:geo:GSE51540 licence not read", "asset:data:geo:GSE51540 not downloaded", "asset:data:geo:GSE59237 licence not read", "asset:data:geo:GSE59237 not downloaded", "asset:data:geo:GSE6863 licence not read", "asset:data:geo:GSE6863 not downloaded", "asset:data:geo:GSE8059 licence not read", "asset:data:geo:GSE8059 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Cox proportional hazards regression analysis was performed to examine the correlation between gene expression and overall survival (OS)."], "order_basis": "analysis_only", "id": "assay:1"}]}