← All .science files
pmid:32352014
Screening of a Novel Upregulated lncRNA, A2M-AS1, That Promotes Invasion and Migration and Signifies Poor Prognosis in Breast Cancer.
Kai Fang · Hu Caixia · Zhang Xiufen · Guo Zijian · Lihua Li
BioMed research international · 2020 doi:10.1155/2020/9747826
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
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 · 5 items
claims array · 2 items
[0] object · 6 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 · 6 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 683 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 155 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 178 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 178 items
[5] object · 15 fields
structure object · 15 fields
sample_accessions array · 356 items
gaps array · 10 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
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 · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 5 items
resolved_accessions array · 5 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
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 · 14 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 3 items
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:32352014", "kind": "science-record", "revision": 8, "content_hash": "sha256:dddb197f305ada0685008fd5d135ac16d37a9056054af6459dcd3ff702aa605d", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T22:44:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of a Novel Upregulated lncRNA, A2M-AS1, That Promotes Invasion and Migration and Signifies Poor Prognosis in Breast Cancer.", "doi": "10.1155/2020/9747826", "pmid": "32352014", "authors": ["Kai Fang", "Hu Caixia", "Zhang Xiufen", "Guo Zijian", "Lihua Li"], "journal": "BioMed research international", "year": 2020, "abstract": "Understanding of prognostic factors and therapeutic targets for breast cancer is imperative for guidance of patient care. We studied 1203 tumour samples from the Gene Expression Omnibus (GEO) to evaluate potential genes related to breast cancer. R software was used to analyse differentially expressed long noncoding RNAs (lncRNAs) in the RNA microarray expression profiles GSE45827 and GSE65216 and to identify a series of differentially expressed lncRNAs associated with human breast cancer. Of these lncRNAs, A2M-AS1, a lncRNA that has not been previously reported, was significantly upregulated in human breast cancer tissues compared with adjacent nontumour tissues. Importantly, A2M-AS1 upregulation was significantly associated with ER-negative, HER2-positive, and basal-like breast cancer and with poor recurrence-free survival and metastasis-free survival in breast cancer patients. After validating these results in 96 collected human breast cancer tissues and 64 paired adjacent noncancerous tissues, we further investigated the roles of A2M-AS1 in human ER-negative and basal-like breast cancer cells. The results revealed that A2M-AS1 significantly promotes human breast cancer cell proliferation, invasion, and migration. Additionally, bioinformatics analysis of genes coexpressed with A2M-AS1 in the context of human breast cancer combined with qRT-PCR and Western blot assays revealed that A2M-AS1 exerts regulatory effects on downstream factors in the cell adhesion molecule pathway, including CD2 and SELL. These results imply that A2M-AS1 might be a promising candidate prognostic factor and therapeutic target for breast cancer.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were analysed using the limma package in R version 3.5.1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32352014", "locator": "sections[11] \"2.9. Statistical Analysis\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were analysed using the limma package in R version 3.5.1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32352014", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The data sets used and analysed in the current study are available upon appropriate request from the authors."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32352014"], "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:GSE102484"], "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:GSE102484"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32352014", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/9747826", "sha256": "sha256:423871da8d11d9ed9b1b4e5677a4c56fd954916a58e4c61c3fee2f1cc04ba867", "bytes": 28193, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/9747826", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7171613", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102484", "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=GSE102484", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102484", "version": null, "note": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2738656", "GSM2738657", "GSM2738658", "GSM2738659", "GSM2738660", "GSM2738661", "GSM2738662", "GSM2738663", "GSM2738664", "GSM2738665", "GSM2738666", "GSM2738667", "GSM2738668", "GSM2738669", "GSM2738670", "GSM2738671", "GSM2738672", "GSM2738673", "GSM2738674", "GSM2738675", "GSM2738676", "GSM2738677", "GSM2738678", "GSM2738679", "GSM2738680", "GSM2738681", "GSM2738682", "GSM2738683", "GSM2738684", "GSM2738685", "GSM2738686", "GSM2738687", "GSM2738688", "GSM2738689", "GSM2738690", "GSM2738691", "GSM2738692", "GSM2738693", "GSM2738694", "GSM2738695", "GSM2738696", "GSM2738697", "GSM2738698", "GSM2738699", "GSM2738700", "GSM2738701", "GSM2738702", "GSM2738703", "GSM2738704", "GSM2738705", "GSM2738706", "GSM2738707", "GSM2738708", "GSM2738709", "GSM2738710", "GSM2738711", "GSM2738712", "GSM2738713", "GSM2738714", "GSM2738715", "GSM2738716", "GSM2738717", "GSM2738718", "GSM2738719", "GSM2738720", "GSM2738721", "GSM2738722", "GSM2738723", "GSM2738724", "GSM2738725", "GSM2738726", "GSM2738727", "GSM2738728", "GSM2738729", "GSM2738730", "GSM2738731", "GSM2738732", "GSM2738733", "GSM2738734", "GSM2738735", "GSM2738736", "GSM2738737", "GSM2738738", "GSM2738739", "GSM2738740", "GSM2738741", "GSM2738742", "GSM2738743", "GSM2738744", "GSM2738745", "GSM2738746", "GSM2738747", "GSM2738748", "GSM2738749", "GSM2738750", "GSM2738751", "GSM2738752", "GSM2738753", "GSM2738754", "GSM2738755", "GSM2738756", "GSM2738757", "GSM2738758", "GSM2738759", "GSM2738760", "GSM2738761", "GSM2738762", "GSM2738763", "GSM2738764", "GSM2738765", "GSM2738766", "GSM2738767", "GSM2738768", "GSM2738769", "GSM2738770", "GSM2738771", "GSM2738772", "GSM2738773", "GSM2738774", "GSM2738775", "GSM2738776", "GSM2738777", "GSM2738778", "GSM2738779", "GSM2738780", "GSM2738781", "GSM2738782", "GSM2738783", "GSM2738784", "GSM2738785", "GSM2738786", "GSM2738787", "GSM2738788", "GSM2738789", "GSM2738790", "GSM2738791", "GSM2738792", "GSM2738793", "GSM2738794", "GSM2738795", "GSM2738796", "GSM2738797", "GSM2738798", "GSM2738799", "GSM2738800", "GSM2738801", "GSM2738802", "GSM2738803", "GSM2738804", "GSM2738805", "GSM2738806", "GSM2738807", "GSM2738808", "GSM2738809", "GSM2738810", "GSM2738811", "GSM2738812", "GSM2738813", "GSM2738814", "GSM2738815", "GSM2738816", "GSM2738817", "GSM2738818", "GSM2738819", "GSM2738820", "GSM2738821", "GSM2738822", "GSM2738823", "GSM2738824", "GSM2738825", "GSM2738826", "GSM2738827", "GSM2738828", "GSM2738829", "GSM2738830", "GSM2738831", "GSM2738832", "GSM2738833", "GSM2738834", "GSM2738835", "GSM2738836", "GSM2738837", "GSM2738838", "GSM2738839", "GSM2738840", "GSM2738841", "GSM2738842", "GSM2738843", "GSM2738844", "GSM2738845", "GSM2738846", "GSM2738847", "GSM2738848", "GSM2738849", "GSM2738850", "GSM2738851", "GSM2738852", "GSM2738853", "GSM2738854", "GSM2738855", "GSM2738856", "GSM2738857", "GSM2738858", "GSM2738859", "GSM2738860", "GSM2738861", "GSM2738862", "GSM2738863", "GSM2738864", "GSM2738865", "GSM2738866", "GSM2738867", "GSM2738868", "GSM2738869", "GSM2738870", "GSM2738871", "GSM2738872", "GSM2738873", "GSM2738874", "GSM2738875", "GSM2738876", "GSM2738877", "GSM2738878", "GSM2738879", "GSM2738880", "GSM2738881", "GSM2738882", "GSM2738883", "GSM2738884", "GSM2738885", "GSM2738886", "GSM2738887", "GSM2738888", "GSM2738889", "GSM2738890", "GSM2738891", "GSM2738892", "GSM2738893", "GSM2738894", "GSM2738895", "GSM2738896", "GSM2738897", "GSM2738898", "GSM2738899", "GSM2738900", "GSM2738901", "GSM2738902", "GSM2738903", "GSM2738904", "GSM2738905", "GSM2738906", "GSM2738907", "GSM2738908", "GSM2738909", "GSM2738910", "GSM2738911", "GSM2738912", "GSM2738913", "GSM2738914", "GSM2738915", "GSM2738916", "GSM2738917", "GSM2738918", "GSM2738919", "GSM2738920", "GSM2738921", "GSM2738922", "GSM2738923", "GSM2738924", "GSM2738925", "GSM2738926", "GSM2738927", "GSM2738928", "GSM2738929", "GSM2738930", "GSM2738931", "GSM2738932", "GSM2738933", "GSM2738934", "GSM2738935", "GSM2738936", "GSM2738937", "GSM2738938", "GSM2738939", "GSM2738940", "GSM2738941", "GSM2738942", "GSM2738943", "GSM2738944", "GSM2738945", "GSM2738946", "GSM2738947", "GSM2738948", "GSM2738949", "GSM2738950", "GSM2738951", "GSM2738952", "GSM2738953", "GSM2738954", "GSM2738955", "GSM2738956", "GSM2738957", "GSM2738958", "GSM2738959", "GSM2738960", "GSM2738961", "GSM2738962", "GSM2738963", "GSM2738964", "GSM2738965", "GSM2738966", "GSM2738967", "GSM2738968", "GSM2738969", "GSM2738970", "GSM2738971", "GSM2738972", "GSM2738973", "GSM2738974", "GSM2738975", "GSM2738976", "GSM2738977", "GSM2738978", "GSM2738979", "GSM2738980", "GSM2738981", "GSM2738982", "GSM2738983", "GSM2738984", "GSM2738985", "GSM2738986", "GSM2738987", "GSM2738988", "GSM2738989", "GSM2738990", "GSM2738991", "GSM2738992", "GSM2738993", "GSM2738994", "GSM2738995", "GSM2738996", "GSM2738997", "GSM2738998", "GSM2738999", "GSM2739000", "GSM2739001", "GSM2739002", "GSM2739003", "GSM2739004", "GSM2739005", "GSM2739006", "GSM2739007", "GSM2739008", "GSM2739009", "GSM2739010", "GSM2739011", "GSM2739012", "GSM2739013", "GSM2739014", "GSM2739015", "GSM2739016", "GSM2739017", "GSM2739018", "GSM2739019", "GSM2739020", "GSM2739021", "GSM2739022", "GSM2739023", "GSM2739024", "GSM2739025", "GSM2739026", "GSM2739027", "GSM2739028", "GSM2739029", "GSM2739030", "GSM2739031", "GSM2739032", "GSM2739033", "GSM2739034", "GSM2739035", "GSM2739036", "GSM2739037", "GSM2739038", "GSM2739039", "GSM2739040", "GSM2739041", "GSM2739042", "GSM2739043", "GSM2739044", "GSM2739045", "GSM2739046", "GSM2739047", "GSM2739048", "GSM2739049", "GSM2739050", "GSM2739051", "GSM2739052", "GSM2739053", "GSM2739054", "GSM2739055", "GSM2739056", "GSM2739057", "GSM2739058", "GSM2739059", "GSM2739060", "GSM2739061", "GSM2739062", "GSM2739063", "GSM2739064", "GSM2739065", "GSM2739066", "GSM2739067", "GSM2739068", "GSM2739069", "GSM2739070", "GSM2739071", "GSM2739072", "GSM2739073", "GSM2739074", "GSM2739075", "GSM2739076", "GSM2739077", "GSM2739078", "GSM2739079", "GSM2739080", "GSM2739081", "GSM2739082", "GSM2739083", "GSM2739084", "GSM2739085", "GSM2739086", "GSM2739087", "GSM2739088", "GSM2739089", "GSM2739090", "GSM2739091", "GSM2739092", "GSM2739093", "GSM2739094", "GSM2739095", "GSM2739096", "GSM2739097", "GSM2739098", "GSM2739099", "GSM2739100", "GSM2739101", "GSM2739102", "GSM2739103", "GSM2739104", "GSM2739105", "GSM2739106", "GSM2739107", "GSM2739108", "GSM2739109", "GSM2739110", "GSM2739111", "GSM2739112", "GSM2739113", "GSM2739114", "GSM2739115", "GSM2739116", "GSM2739117", "GSM2739118", "GSM2739119", "GSM2739120", "GSM2739121", "GSM2739122", "GSM2739123", "GSM2739124", "GSM2739125", "GSM2739126", "GSM2739127", "GSM2739128", "GSM2739129", "GSM2739130", "GSM2739131", "GSM2739132", "GSM2739133", "GSM2739134", "GSM2739135", "GSM2739136", "GSM2739137", "GSM2739138", "GSM2739139", "GSM2739140", "GSM2739141", "GSM2739142", "GSM2739143", "GSM2739144", "GSM2739145", "GSM2739146", "GSM2739147", "GSM2739148", "GSM2739149", "GSM2739150", "GSM2739151", "GSM2739152", "GSM2739153", "GSM2739154", "GSM2739155", "GSM2739156", "GSM2739157", "GSM2739158", "GSM2739159", "GSM2739160", "GSM2739161", "GSM2739162", "GSM2739163", "GSM2739164", "GSM2739165", "GSM2739166", "GSM2739167", "GSM2739168", "GSM2739169", "GSM2739170", "GSM2739171", "GSM2739172", "GSM2739173", "GSM2739174", "GSM2739175", "GSM2739176", "GSM2739177", "GSM2739178", "GSM2739179", "GSM2739180", "GSM2739181", "GSM2739182", "GSM2739183", "GSM2739184", "GSM2739185", "GSM2739186", "GSM2739187", "GSM2739188", "GSM2739189", "GSM2739190", "GSM2739191", "GSM2739192", "GSM2739193", "GSM2739194", "GSM2739195", "GSM2739196", "GSM2739197", "GSM2739198", "GSM2739199", "GSM2739200", "GSM2739201", "GSM2739202", "GSM2739203", "GSM2739204", "GSM2739205", "GSM2739206", "GSM2739207", "GSM2739208", "GSM2739209", "GSM2739210", "GSM2739211", "GSM2739212", "GSM2739213", "GSM2739214", "GSM2739215", "GSM2739216", "GSM2739217", "GSM2739218", "GSM2739219", "GSM2739220", "GSM2739221", "GSM2739222", "GSM2739223", "GSM2739224", "GSM2739225", "GSM2739226", "GSM2739227", "GSM2739228", "GSM2739229", "GSM2739230", "GSM2739231", "GSM2739232", "GSM2739233", "GSM2739234", "GSM2739235", "GSM2739236", "GSM2739237", "GSM2739238", "GSM2739239", "GSM2739240", "GSM2739241", "GSM2739242", "GSM2739243", "GSM2739244", "GSM2739245", "GSM2739246", "GSM2739247", "GSM2739248", "GSM2739249", "GSM2739250", "GSM2739251", "GSM2739252", "GSM2739253", "GSM2739254", "GSM2739255", "GSM2739256", "GSM2739257", "GSM2739258", "GSM2739259", "GSM2739260", "GSM2739261", "GSM2739262", "GSM2739263", "GSM2739264", "GSM2739265", "GSM2739266", "GSM2739267", "GSM2739268", "GSM2739269", "GSM2739270", "GSM2739271", "GSM2739272", "GSM2739273", "GSM2739274", "GSM2739275", "GSM2739276", "GSM2739277", "GSM2739278", "GSM2739279", "GSM2739280", "GSM2739281", "GSM2739282", "GSM2739283", "GSM2739284", "GSM2739285", "GSM2739286", "GSM2739287", "GSM2739288", "GSM2739289", "GSM2739290", "GSM2739291", "GSM2739292", "GSM2739293", "GSM2739294", "GSM2739295", "GSM2739296", "GSM2739297", "GSM2739298", "GSM2739299", "GSM2739300", "GSM2739301", "GSM2739302", "GSM2739303", "GSM2739304", "GSM2739305", "GSM2739306", "GSM2739307", "GSM2739308", "GSM2739309", "GSM2739310", "GSM2739311", "GSM2739312", "GSM2739313", "GSM2739314", "GSM2739315", "GSM2739316", "GSM2739317", "GSM2739318", "GSM2739319", "GSM2739320", "GSM2739321", "GSM2739322", "GSM2739323", "GSM2739324", "GSM2739325", "GSM2739326", "GSM2739327", "GSM2739328", "GSM2739329", "GSM2739330", "GSM2739331", "GSM2739332", "GSM2739333", "GSM2739334", "GSM2739335", "GSM2739336", "GSM2739337", "GSM2739338"], "sample_count": 683, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from invasive breast cancer patient", "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:GSE45827", "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=GSE45827", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45827", "version": null, "note": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1116084", "GSM1116085", "GSM1116086", "GSM1116087", "GSM1116088", "GSM1116089", "GSM1116090", "GSM1116091", "GSM1116092", "GSM1116093", "GSM1116094", "GSM1116095", "GSM1116096", "GSM1116097", "GSM1116098", "GSM1116099", "GSM1116100", "GSM1116101", "GSM1116102", "GSM1116103", "GSM1116104", "GSM1116105", "GSM1116106", "GSM1116107", "GSM1116108", "GSM1116109", "GSM1116110", "GSM1116111", "GSM1116112", "GSM1116113", "GSM1116114", "GSM1116115", "GSM1116116", "GSM1116117", "GSM1116118", "GSM1116119", "GSM1116120", "GSM1116121", "GSM1116122", "GSM1116123", "GSM1116124", "GSM1116125", "GSM1116126", "GSM1116127", "GSM1116128", "GSM1116129", "GSM1116130", "GSM1116131", "GSM1116132", "GSM1116133", "GSM1116134", "GSM1116135", "GSM1116136", "GSM1116137", "GSM1116138", "GSM1116139", "GSM1116140", "GSM1116141", "GSM1116142", "GSM1116143", "GSM1116144", "GSM1116145", "GSM1116146", "GSM1116147", "GSM1116148", "GSM1116149", "GSM1116150", "GSM1116151", "GSM1116152", "GSM1116153", "GSM1116154", "GSM1116155", "GSM1116156", "GSM1116157", "GSM1116158", "GSM1116159", "GSM1116160", "GSM1116161", "GSM1116162", "GSM1116163", "GSM1116164", "GSM1116165", "GSM1116166", "GSM1116167", "GSM1116168", "GSM1116169", "GSM1116170", "GSM1116171", "GSM1116172", "GSM1116173", "GSM1116174", "GSM1116175", "GSM1116176", "GSM1116177", "GSM1116178", "GSM1116179", "GSM1116180", "GSM1116181", "GSM1116182", "GSM1116183", "GSM1116184", "GSM1116185", "GSM1116186", "GSM1116187", "GSM1116188", "GSM1116189", "GSM1116190", "GSM1116191", "GSM1116192", "GSM1116193", "GSM1116194", "GSM1116195", "GSM1116196", "GSM1116197", "GSM1116198", "GSM1116199", "GSM1116200", "GSM1116201", "GSM1116202", "GSM1116203", "GSM1116204", "GSM1116205", "GSM1116206", "GSM1116207", "GSM1116208", "GSM1116209", "GSM1116210", "GSM1116211", "GSM1116212", "GSM1116213", "GSM1116214", "GSM1116215", "GSM1116216", "GSM1116217", "GSM1116218", "GSM1116219", "GSM1116220", "GSM1116221", "GSM1116222", "GSM1116223", "GSM1116224", "GSM1116225", "GSM1116226", "GSM1116227", "GSM1116228", "GSM1116229", "GSM1116230", "GSM1116231", "GSM1116232", "GSM1116233", "GSM1116234", "GSM1116235", "GSM1116236", "GSM1116237", "GSM1116238"], "sample_count": 155, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from Breast cancer subtypes", "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:GSE65194", "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=GSE65194", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65194", "version": null, "note": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1588970", "GSM1588971", "GSM1588972", "GSM1588973", "GSM1588974", "GSM1588975", "GSM1588976", "GSM1588977", "GSM1588978", "GSM1588979", "GSM1588980", "GSM1588981", "GSM1588982", "GSM1588983", "GSM1588984", "GSM1588985", "GSM1588986", "GSM1588987", "GSM1588988", "GSM1588989", "GSM1588990", "GSM1588991", "GSM1588992", "GSM1588993", "GSM1588994", "GSM1588995", "GSM1588996", "GSM1588997", "GSM1588998", "GSM1588999", "GSM1589000", "GSM1589001", "GSM1589002", "GSM1589003", "GSM1589004", "GSM1589005", "GSM1589006", "GSM1589007", "GSM1589008", "GSM1589009", "GSM1589010", "GSM1589011", "GSM1589012", "GSM1589013", "GSM1589014", "GSM1589015", "GSM1589016", "GSM1589017", "GSM1589018", "GSM1589019", "GSM1589020", "GSM1589021", "GSM1589022", "GSM1589023", "GSM1589024", "GSM1589025", "GSM1589026", "GSM1589027", "GSM1589028", "GSM1589029", "GSM1589030", "GSM1589031", "GSM1589032", "GSM1589033", "GSM1589034", "GSM1589035", "GSM1589036", "GSM1589037", "GSM1589038", "GSM1589039", "GSM1589040", "GSM1589041", "GSM1589042", "GSM1589043", "GSM1589044", "GSM1589045", "GSM1589046", "GSM1589047", "GSM1589048", "GSM1589049", "GSM1589050", "GSM1589051", "GSM1589052", "GSM1589053", "GSM1589054", "GSM1589055", "GSM1589056", "GSM1589057", "GSM1589058", "GSM1589059", "GSM1589060", "GSM1589061", "GSM1589062", "GSM1589063", "GSM1589064", "GSM1589065", "GSM1589066", "GSM1589067", "GSM1589068", "GSM1589069", "GSM1589070", "GSM1589071", "GSM1589072", "GSM1589073", "GSM1589074", "GSM1589075", "GSM1589076", "GSM1589077", "GSM1589078", "GSM1589079", "GSM1589080", "GSM1589081", "GSM1589082", "GSM1589083", "GSM1589084", "GSM1589085", "GSM1589086", "GSM1589087", "GSM1589088", "GSM1589089", "GSM1589090", "GSM1589091", "GSM1589092", "GSM1589093", "GSM1589094", "GSM1589095", "GSM1589097", "GSM1589098", "GSM1589099", "GSM1589101", "GSM1589103", "GSM1589105", "GSM1589107", "GSM1589109", "GSM1589110", "GSM1589111", "GSM1589112", "GSM1589113", "GSM1589114", "GSM1589115", "GSM1589116", "GSM1589117", "GSM1589118", "GSM1589119", "GSM1589120", "GSM1589121", "GSM1589122", "GSM1589123", "GSM1589124", "GSM1589125", "GSM1589126", "GSM1589127", "GSM1589128", "GSM1589129", "GSM1589130", "GSM1589131", "GSM1589132", "GSM1589133", "GSM1589134", "GSM1589135", "GSM1589136", "GSM1589137", "GSM1589138", "GSM1589139", "GSM1589140", "GSM1589141", "GSM1589142", "GSM1589143", "GSM1589144", "GSM1589145", "GSM1589146", "GSM1589147", "GSM1589148", "GSM1589149", "GSM1589150", "GSM1589151", "GSM1589152", "GSM1589153"], "sample_count": 178, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression profiling of breast cancer samples from Institut Curie (Maire cohort) --Affy CDF", "resolution_checked_at": "2026-11-01T11:38:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65212", "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=GSE65212", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65212", "version": null, "note": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1589620", "GSM1589621", "GSM1589622", "GSM1589623", "GSM1589624", "GSM1589625", "GSM1589626", "GSM1589627", "GSM1589628", "GSM1589629", "GSM1589630", "GSM1589631", "GSM1589632", "GSM1589633", "GSM1589634", "GSM1589635", "GSM1589636", "GSM1589637", "GSM1589638", "GSM1589639", "GSM1589640", "GSM1589641", "GSM1589642", "GSM1589643", "GSM1589644", "GSM1589645", "GSM1589646", "GSM1589647", "GSM1589648", "GSM1589649", "GSM1589650", "GSM1589651", "GSM1589652", "GSM1589653", "GSM1589654", "GSM1589655", "GSM1589656", "GSM1589657", "GSM1589658", "GSM1589659", "GSM1589660", "GSM1589661", "GSM1589662", "GSM1589663", "GSM1589664", "GSM1589665", "GSM1589666", "GSM1589667", "GSM1589668", "GSM1589669", "GSM1589670", "GSM1589671", "GSM1589672", "GSM1589673", "GSM1589674", "GSM1589675", "GSM1589676", "GSM1589677", "GSM1589678", "GSM1589679", "GSM1589680", "GSM1589681", "GSM1589682", "GSM1589683", "GSM1589684", "GSM1589685", "GSM1589686", "GSM1589687", "GSM1589688", "GSM1589689", "GSM1589690", "GSM1589691", "GSM1589692", "GSM1589693", "GSM1589694", "GSM1589695", "GSM1589696", "GSM1589697", "GSM1589698", "GSM1589699", "GSM1589700", "GSM1589701", "GSM1589702", "GSM1589703", "GSM1589704", "GSM1589705", "GSM1589706", "GSM1589707", "GSM1589708", "GSM1589709", "GSM1589710", "GSM1589711", "GSM1589712", "GSM1589713", "GSM1589714", "GSM1589715", "GSM1589716", "GSM1589717", "GSM1589718", "GSM1589719", "GSM1589720", "GSM1589721", "GSM1589722", "GSM1589723", "GSM1589724", "GSM1589725", "GSM1589726", "GSM1589727", "GSM1589728", "GSM1589729", "GSM1589730", "GSM1589731", "GSM1589732", "GSM1589733", "GSM1589734", "GSM1589735", "GSM1589736", "GSM1589737", "GSM1589738", "GSM1589739", "GSM1589740", "GSM1589741", "GSM1589742", "GSM1589743", "GSM1589744", "GSM1589745", "GSM1589746", "GSM1589747", "GSM1589748", "GSM1589749", "GSM1589750", "GSM1589751", "GSM1589752", "GSM1589753", "GSM1589754", "GSM1589755", "GSM1589756", "GSM1589757", "GSM1589758", "GSM1589759", "GSM1589760", "GSM1589761", "GSM1589762", "GSM1589763", "GSM1589764", "GSM1589765", "GSM1589766", "GSM1589767", "GSM1589768", "GSM1589769", "GSM1589770", "GSM1589771", "GSM1589772", "GSM1589773", "GSM1589774", "GSM1589775", "GSM1589776", "GSM1589777", "GSM1589778", "GSM1589779", "GSM1589780", "GSM1589781", "GSM1589782", "GSM1589783", "GSM1589784", "GSM1589785", "GSM1589786", "GSM1589787", "GSM1589788", "GSM1589789", "GSM1589790", "GSM1589791", "GSM1589792", "GSM1589793", "GSM1589794", "GSM1589795", "GSM1589796", "GSM1589797"], "sample_count": 178, "group_sizes": null, "group_sizes_basis": null, "platform": "14877", "taxon": "Homo sapiens", "title": "Expression profiling of breast cancer samples from Institut Curie (Maire cohort) -- BrainArray CDF", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65216", "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=GSE65216", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65216", "version": null, "note": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data sets used and analysed in the current study are available upon appropriate request from the authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1588970", "GSM1588971", "GSM1588972", "GSM1588973", "GSM1588974", "GSM1588975", "GSM1588976", "GSM1588977", "GSM1588978", "GSM1588979", "GSM1588980", "GSM1588981", "GSM1588982", "GSM1588983", "GSM1588984", "GSM1588985", "GSM1588986", "GSM1588987", "GSM1588988", "GSM1588989", "GSM1588990", "GSM1588991", "GSM1588992", "GSM1588993", "GSM1588994", "GSM1588995", "GSM1588996", "GSM1588997", "GSM1588998", "GSM1588999", "GSM1589000", "GSM1589001", "GSM1589002", "GSM1589003", "GSM1589004", "GSM1589005", "GSM1589006", "GSM1589007", "GSM1589008", "GSM1589009", "GSM1589010", "GSM1589011", "GSM1589012", "GSM1589013", "GSM1589014", "GSM1589015", "GSM1589016", "GSM1589017", "GSM1589018", "GSM1589019", "GSM1589020", "GSM1589021", "GSM1589022", "GSM1589023", "GSM1589024", "GSM1589025", "GSM1589026", "GSM1589027", "GSM1589028", "GSM1589029", "GSM1589030", "GSM1589031", "GSM1589032", "GSM1589033", "GSM1589034", "GSM1589035", "GSM1589036", "GSM1589037", "GSM1589038", "GSM1589039", "GSM1589040", "GSM1589041", "GSM1589042", "GSM1589043", "GSM1589044", "GSM1589045", "GSM1589046", "GSM1589047", "GSM1589048", "GSM1589049", "GSM1589050", "GSM1589051", "GSM1589052", "GSM1589053", "GSM1589054", "GSM1589055", "GSM1589056", "GSM1589057", "GSM1589058", "GSM1589059", "GSM1589060", "GSM1589061", "GSM1589062", "GSM1589063", "GSM1589064", "GSM1589065", "GSM1589066", "GSM1589067", "GSM1589068", "GSM1589069", "GSM1589070", "GSM1589071", "GSM1589072", "GSM1589073", "GSM1589074", "GSM1589075", "GSM1589076", "GSM1589077", "GSM1589078", "GSM1589079", "GSM1589080", "GSM1589081", "GSM1589082", "GSM1589083", "GSM1589084", "GSM1589085", "GSM1589086", "GSM1589087", "GSM1589088", "GSM1589089", "GSM1589090", "GSM1589091", "GSM1589092", "GSM1589093", "GSM1589094", "GSM1589095", "GSM1589097", "GSM1589098", "GSM1589099", "GSM1589101", "GSM1589103", "GSM1589105", "GSM1589107", "GSM1589109", "GSM1589110", "GSM1589111", "GSM1589112", "GSM1589113", "GSM1589114", "GSM1589115", "GSM1589116", "GSM1589117", "GSM1589118", "GSM1589119", "GSM1589120", "GSM1589121", "GSM1589122", "GSM1589123", "GSM1589124", "GSM1589125", "GSM1589126", "GSM1589127", "GSM1589128", "GSM1589129", "GSM1589130", "GSM1589131", "GSM1589132", "GSM1589133", "GSM1589134", "GSM1589135", "GSM1589136", "GSM1589137", "GSM1589138", "GSM1589139", "GSM1589140", "GSM1589141", "GSM1589142", "GSM1589143", "GSM1589144", "GSM1589145", "GSM1589146", "GSM1589147", "GSM1589148", "GSM1589149", "GSM1589150", "GSM1589151", "GSM1589152", "GSM1589153", "GSM1589620", "GSM1589621", "GSM1589622", "GSM1589623", "GSM1589624", "GSM1589625", "GSM1589626", "GSM1589627", "GSM1589628", "GSM1589629", "GSM1589630", "GSM1589631", "GSM1589632", "GSM1589633", "GSM1589634", "GSM1589635", "GSM1589636", "GSM1589637", "GSM1589638", "GSM1589639", "GSM1589640", "GSM1589641", "GSM1589642", "GSM1589643", "GSM1589644", "GSM1589645", "GSM1589646", "GSM1589647", "GSM1589648", "GSM1589649", "GSM1589650", "GSM1589651", "GSM1589652", "GSM1589653", "GSM1589654", "GSM1589655", "GSM1589656", "GSM1589657", "GSM1589658", "GSM1589659", "GSM1589660", "GSM1589661", "GSM1589662", "GSM1589663", "GSM1589664", "GSM1589665", "GSM1589666", "GSM1589667", "GSM1589668", "GSM1589669", "GSM1589670", "GSM1589671", "GSM1589672", "GSM1589673", "GSM1589674", "GSM1589675", "GSM1589676", "GSM1589677", "GSM1589678", "GSM1589679", "GSM1589680", "GSM1589681", "GSM1589682", "GSM1589683", "GSM1589684", "GSM1589685", "GSM1589686", "GSM1589687", "GSM1589688", "GSM1589689", "GSM1589690", "GSM1589691", "GSM1589692", "GSM1589693", "GSM1589694", "GSM1589695", "GSM1589696", "GSM1589697", "GSM1589698", "GSM1589699", "GSM1589700", "GSM1589701", "GSM1589702", "GSM1589703", "GSM1589704", "GSM1589705", "GSM1589706", "GSM1589707", "GSM1589708", "GSM1589709", "GSM1589710", "GSM1589711", "GSM1589712", "GSM1589713", "GSM1589714", "GSM1589715", "GSM1589716", "GSM1589717", "GSM1589718", "GSM1589719", "GSM1589720", "GSM1589721", "GSM1589722", "GSM1589723", "GSM1589724", "GSM1589725", "GSM1589726", "GSM1589727", "GSM1589728", "GSM1589729", "GSM1589730", "GSM1589731", "GSM1589732", "GSM1589733", "GSM1589734", "GSM1589735", "GSM1589736", "GSM1589737", "GSM1589738", "GSM1589739", "GSM1589740", "GSM1589741", "GSM1589742", "GSM1589743", "GSM1589744", "GSM1589745", "GSM1589746", "GSM1589747", "GSM1589748", "GSM1589749", "GSM1589750", "GSM1589751", "GSM1589752", "GSM1589753", "GSM1589754", "GSM1589755", "GSM1589756", "GSM1589757", "GSM1589758", "GSM1589759", "GSM1589760", "GSM1589761", "GSM1589762", "GSM1589763", "GSM1589764", "GSM1589765", "GSM1589766", "GSM1589767", "GSM1589768", "GSM1589769", "GSM1589770", "GSM1589771", "GSM1589772", "GSM1589773", "GSM1589774", "GSM1589775", "GSM1589776", "GSM1589777", "GSM1589778", "GSM1589779", "GSM1589780", "GSM1589781", "GSM1589782", "GSM1589783", "GSM1589784", "GSM1589785", "GSM1589786", "GSM1589787", "GSM1589788", "GSM1589789", "GSM1589790", "GSM1589791", "GSM1589792", "GSM1589793", "GSM1589794", "GSM1589795", "GSM1589796", "GSM1589797"], "sample_count": 356, "group_sizes": null, "group_sizes_basis": null, "platform": "570;14877", "taxon": "Homo sapiens", "title": "Expression profiling of breast cancer samples from Institut Curie (Maire cohort)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE102484 not downloaded", "asset:data:geo:GSE102484 licence not read", "asset:data:geo:GSE45827 not downloaded", "asset:data:geo:GSE45827 licence not read", "asset:data:geo:GSE65194 not downloaded", "asset:data:geo:GSE65194 licence not read", "asset:data:geo:GSE65212 not downloaded", "asset:data:geo:GSE65212 licence not read", "asset:data:geo:GSE65216 not downloaded", "asset:data:geo:GSE65216 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed genes (DEGs) were analysed using the limma package in R version 3.5.1."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson's correlation"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE45827", "GSE65216", "GSE65194", "GSE65212", "GSE102484"], "resolved_accessions": ["GSE45827", "GSE65216", "GSE65194", "GSE65212", "GSE102484"], "statements": ["The data sets used and analysed in the current study are available upon appropriate request from the authors."], "basis": "The paper names GSE45827, GSE65216, GSE65194, GSE65212, GSE102484 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32352014", "data:geo:GSE102484"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102484"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22626, "completion_tokens": 2066, "cached_tokens": 7688}}, "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:32352014", "type": "paper", "label": "pmid:32352014"}, {"id": "source:pmid:32352014", "type": "manuscript", "label": "PMID 32352014 full text"}, {"id": "data:geo:GSE102484", "type": "dataset", "label": "GEO GSE102484"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32352014", "type": "paper", "label": "pmid:32352014"}, {"id": "source:pmid:32352014", "type": "manuscript", "label": "PMID 32352014 full text"}, {"id": "data:geo:GSE102484", "type": "dataset", "label": "GEO GSE102484"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32352014", "type": "extraction", "used": ["source:pmid:32352014"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102484", "type": "accession_resolution", "used": ["data:geo:GSE102484"], "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:32352014", "parent_hash": "sha256:a98d3187bee09be1bf0f4494733ddaf5e20c300075212ba44b2171634aa0ae24", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE102484 licence not read", "asset:data:geo:GSE102484 not downloaded", "asset:data:geo:GSE45827 licence not read", "asset:data:geo:GSE45827 not downloaded", "asset:data:geo:GSE65194 licence not read", "asset:data:geo:GSE65194 not downloaded", "asset:data:geo:GSE65212 licence not read", "asset:data:geo:GSE65212 not downloaded", "asset:data:geo:GSE65216 licence not read", "asset:data:geo:GSE65216 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["sed long noncoding RNAs (lncRNAs) in the RNA microarray expression profiles GSE45827 and GSE65216 an"], "order_basis": "paper_text_order:432", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["uman breast cancer combined with qRT-PCR and Western blot assays revealed that A2M-AS1 exerts regulato"], "order_basis": "paper_text_order:1461", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) were analysed using the limma package in R version 3.5.1."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}