← All .science files
pmid:33614483
Identification and Validation of an Autophagy-Related lncRNA Signature for Patients With Breast Cancer.
Ruyue Zhang · Qingwen Zhu · Detao Yin · Zhe Yang · Jinxiu Guo · Jingmin Zhang · Yubing Zhou · Jane J Yu
Frontiers in oncology · 2020 doi:10.3389/fonc.2020.597569
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 · 8 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
evidence array · 1 item
[0] 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 · 9 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 327 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 26 items
[0] array · 9 items
[1] array · 9 items
[2] array · 9 items
[3] array · 9 items
[4] array · 9 items
[5] array · 9 items
[6] array · 9 items
[7] array · 9 items
[8] array · 9 items
[9] array · 9 items
[10] array · 9 items
[11] array · 9 items
[12] array · 9 items
[13] array · 9 items
[14] array · 9 items
[15] array · 9 items
[16] array · 9 items
[17] array · 9 items
[18] array · 9 items
[19] array · 9 items
[20] array · 9 items
[21] array · 9 items
[22] array · 9 items
[23] array · 9 items
[24] array · 9 items
[25] array · 9 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 11 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
[9] array · 2 items
[10] array · 2 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 62 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
[17] array · 4 items
[18] array · 4 items
[19] array · 4 items
[20] array · 4 items
[21] array · 4 items
[22] array · 4 items
[23] array · 4 items
[24] array · 4 items
[25] array · 4 items
[26] array · 4 items
[27] array · 4 items
[28] array · 4 items
[29] array · 4 items
[30] array · 4 items
[31] array · 4 items
[32] array · 4 items
[33] array · 4 items
[34] array · 4 items
[35] array · 4 items
[36] array · 4 items
[37] array · 4 items
[38] array · 4 items
[39] array · 4 items
[40] array · 4 items
[41] array · 4 items
[42] array · 4 items
[43] array · 4 items
[44] array · 4 items
[45] array · 4 items
[46] array · 4 items
[47] array · 4 items
[48] array · 4 items
[49] array · 4 items
[50] array · 4 items
[51] array · 4 items
[52] array · 4 items
[53] array · 4 items
[54] array · 4 items
[55] array · 4 items
[56] array · 4 items
[57] array · 4 items
[58] array · 4 items
[59] array · 4 items
[60] array · 4 items
[61] array · 4 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 10 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 16 items
[0] array · 3 items
[1] array · 6 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 20 items
[0] array · 3 items
[1] array · 4 items
[2] array · 6 items
[3] array · 6 items
[4] array · 3 items
[5] array · 6 items
[6] array · 6 items
[7] array · 3 items
[8] array · 6 items
[9] array · 6 items
[10] array · 3 items
[11] array · 6 items
[12] array · 6 items
[13] array · 3 items
[14] array · 6 items
[15] array · 6 items
[16] array · 3 items
[17] array · 6 items
[18] array · 6 items
[19] array · 3 items
[8] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 26 items
[0] array · 9 items
[1] array · 9 items
[2] array · 9 items
[3] array · 9 items
[4] array · 9 items
[5] array · 9 items
[6] array · 9 items
[7] array · 9 items
[8] array · 9 items
[9] array · 9 items
[10] array · 9 items
[11] array · 9 items
[12] array · 9 items
[13] array · 9 items
[14] array · 9 items
[15] array · 9 items
[16] array · 9 items
[17] array · 9 items
[18] array · 9 items
[19] array · 9 items
[20] array · 9 items
[21] array · 9 items
[22] array · 9 items
[23] array · 9 items
[24] array · 9 items
[25] array · 9 items
gaps array · 2 items
analysis object · 4 fields
methods array · 4 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 · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 2 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 6 items
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 · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 9 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 · 6 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[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 · 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:33614483", "kind": "science-record", "revision": 7, "content_hash": "sha256:356fb138f2a285e8310ba64b4bd7c4dea700d98fb78b03b40f61259f0afa898a", "created_at": "2026-11-01T15:41:26Z", "updated_at": "2026-11-01T22:03:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Validation of an Autophagy-Related lncRNA Signature for Patients With Breast Cancer.", "doi": "10.3389/fonc.2020.597569", "pmid": "33614483", "authors": ["Ruyue Zhang", "Qingwen Zhu", "Detao Yin", "Zhe Yang", "Jinxiu Guo", "Jingmin Zhang", "Yubing Zhou", "Jane J Yu"], "journal": "Frontiers in oncology", "year": 2020, "abstract": "BACKGROUND: Autophagy is a \"self-feeding\" phenomenon of cells, which is crucial in mammalian development. Long non-coding RNA (lncRNA) is a new regulatory factor for cell autophagy, which can regulate the process of autophagy to affect tumor progression. However, poor attention has been paid to the roles of autophagy-related lncRNAs in breast cancer.\nOBJECTIVE: This study aimed to construct an autophagy-related lncRNA signature that can effectively predict the prognosis of breast cancer patients and explore the potential functions of these lncRNAs.\nMETHODS: The RNA sequencing (RNA-Seq) data of breast cancer patients was collected from The Cancer Genome Atlas (TCGA) database and the GSE20685 database. Multivariate Cox analysis was implemented to produce an autophagy-related lncRNA signature in the TCGA cohort. The signature was then validated in the GSE20685 cohort. The receiver operator characteristic (ROC) curve was performed to evaluate the predictive ability of the signature. Gene set enrichment analysis (GSEA) was used to explore the potential functions based on the signature. Finally, the study developed a nomogram and internal verification based on the autophagy-related lncRNAs.\nRESULTS: A signature composed of 9 autophagy-related lncRNAs was determined as a prognostic model, and 1,109 breast cancer patients were divided into high-risk group and low-risk group based on median risk score of the signature. Further analysis demonstrated that the over survival (OS) of breast cancer patients in the high-risk group was poorer than that in the low-risk group based on the prognostic signature. The area under the curve (AUC) of ROC curve verified the sensitivity and specificity of this signature. Additionally, we confirmed the signature is an independent factor and found it may be correlated to the progression of breast cancer. GSEA showed gene sets were notably enriched in carcinogenic activation pathways and autophagy-related pathways. The qRT-PCR identified 5 lncRNAs with significantly differential expression in breast cancer cells based on the 9 lncRNAs of the prognostic model, and the results were consistent with the tissues.\nCONCLUSION: In summary, our signature has potential predictive value in the prognosis of breast cancer and these autophagy-related lncRNAs may play significant roles in the diagnosis and treatment of breast cancer.", "claims": [{"id": "claim-method", "statement": "Stepwise multivariable cox proportional hazards regression analysis were carried out to identify the optimal prognostic lncRNAs among the 25 candidate lncRNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33614483", "locator": "sections[12] \"Identification of an Autophagy-Related lncRNA Signature in Breast Cancer\" paragraph 2", "quote": "Stepwise multivariable cox proportional hazards regression analysis were carried out to identify the optimal prognostic lncRNAs among the 25 candidate lncRNAs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.cancergenome.nih.gov/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20685, http://www.autophagy.lu/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33614483", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.cancergenome.nih.gov/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20685, http://www.autophagy.lu/."}], "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:33614483"], "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:GSE20685"], "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:GSE20685"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33614483", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2020.597569", "sha256": "sha256:9007b18b6c433cff0897cafff8e48d5162a51ba3892e163684eadb0724c55efc", "bytes": 32356, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2020.597569", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7892971", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20685", "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=GSE20685", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20685", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.cancergenome.nih.gov/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20685, http://www.autophagy.lu/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.cancergenome.nih.gov/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20685, http://www.autophagy.lu/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM519117", "GSM519118", "GSM519119", "GSM519120", "GSM519121", "GSM519122", "GSM519123", "GSM519124", "GSM519125", "GSM519126", "GSM519127", "GSM519128", "GSM519129", "GSM519130", "GSM519131", "GSM519132", "GSM519133", "GSM519134", "GSM519135", "GSM519136", "GSM519137", "GSM519138", "GSM519139", "GSM519140", "GSM519141", "GSM519142", "GSM519143", "GSM519144", "GSM519145", "GSM519146", "GSM519147", "GSM519148", "GSM519149", "GSM519150", "GSM519151", "GSM519152", "GSM519153", "GSM519154", "GSM519155", "GSM519156", "GSM519157", "GSM519158", "GSM519159", "GSM519160", "GSM519161", "GSM519162", "GSM519163", "GSM519164", "GSM519165", "GSM519166", "GSM519167", "GSM519168", "GSM519169", "GSM519170", "GSM519171", "GSM519172", "GSM519173", "GSM519174", "GSM519175", "GSM519176", "GSM519177", "GSM519178", "GSM519179", "GSM519180", "GSM519181", "GSM519182", "GSM519183", "GSM519184", "GSM519185", "GSM519186", "GSM519187", "GSM519188", "GSM519189", "GSM519190", "GSM519191", "GSM519192", "GSM519193", "GSM519194", "GSM519195", "GSM519196", "GSM519197", "GSM519198", "GSM519199", "GSM519200", "GSM519201", "GSM519202", "GSM519203", "GSM519204", "GSM519205", "GSM519206", "GSM519207", "GSM519208", "GSM519209", "GSM519210", "GSM519211", "GSM519212", "GSM519213", "GSM519214", "GSM519215", "GSM519216", "GSM519217", "GSM519218", "GSM519219", "GSM519220", "GSM519221", "GSM519222", "GSM519223", "GSM519224", "GSM519225", "GSM519226", "GSM519227", "GSM519228", "GSM519229", "GSM519230", "GSM519231", "GSM519232", "GSM519233", "GSM519234", "GSM519235", "GSM519236", "GSM519237", "GSM519238", "GSM519239", "GSM519240", "GSM519241", "GSM519242", "GSM519243", "GSM519244", "GSM519245", "GSM519246", "GSM519247", "GSM519248", "GSM519249", "GSM519250", "GSM519251", "GSM519252", "GSM519253", "GSM519254", "GSM519255", "GSM519256", "GSM519257", "GSM519258", "GSM519259", "GSM519260", "GSM519261", "GSM519262", "GSM519263", "GSM519264", "GSM519265", "GSM519266", "GSM519267", "GSM519268", "GSM519269", "GSM519270", "GSM519271", "GSM519272", "GSM519273", "GSM519274", "GSM519275", "GSM519276", "GSM519277", "GSM519278", "GSM519279", "GSM519280", "GSM519281", "GSM519282", "GSM519283", "GSM519284", "GSM519285", "GSM519286", "GSM519287", "GSM519288", "GSM519289", "GSM519290", "GSM519291", "GSM519292", "GSM519293", "GSM519294", "GSM519295", "GSM519296", "GSM519297", "GSM519298", "GSM519299", "GSM519300", "GSM519301", "GSM519302", "GSM519303", "GSM519304", "GSM519305", "GSM519306", "GSM519307", "GSM519308", "GSM519309", "GSM519310", "GSM519311", "GSM519312", "GSM519313", "GSM519314", "GSM519315", "GSM519316", "GSM519317", "GSM519318", "GSM519319", "GSM519320", "GSM519321", "GSM519322", "GSM519323", "GSM519324", "GSM519325", "GSM519326", "GSM519327", "GSM519328", "GSM519329", "GSM519330", "GSM519331", "GSM519332", "GSM519333", "GSM519334", "GSM519335", "GSM519336", "GSM519337", "GSM519338", "GSM519339", "GSM519340", "GSM519341", "GSM519342", "GSM519343", "GSM519344", "GSM519345", "GSM519346", "GSM519347", "GSM519348", "GSM519349", "GSM519350", "GSM519351", "GSM519352", "GSM519353", "GSM519354", "GSM519355", "GSM519356", "GSM519357", "GSM519358", "GSM519359", "GSM519360", "GSM519361", "GSM519362", "GSM519363", "GSM519364", "GSM519365", "GSM519366", "GSM519367", "GSM519368", "GSM519369", "GSM519370", "GSM519371", "GSM519372", "GSM519373", "GSM519374", "GSM519375", "GSM519376", "GSM519377", "GSM519378", "GSM519379", "GSM519380", "GSM519381", "GSM519382", "GSM519383", "GSM519384", "GSM519385", "GSM519386", "GSM519387", "GSM519388", "GSM519389", "GSM519390", "GSM519391", "GSM519392", "GSM519393", "GSM519394", "GSM519395", "GSM519396", "GSM519397", "GSM519398", "GSM519399", "GSM519400", "GSM519401", "GSM519402", "GSM519403", "GSM519404", "GSM519405", "GSM519406", "GSM519407", "GSM519408", "GSM519409", "GSM519410", "GSM519411", "GSM519412", "GSM519413", "GSM519414", "GSM519415", "GSM519416", "GSM519417", "GSM519418", "GSM519419", "GSM519420", "GSM519421", "GSM519422", "GSM519423", "GSM519424", "GSM519425", "GSM519426", "GSM519427", "GSM519428", "GSM519429", "GSM519430", "GSM519431", "GSM519432", "GSM519433", "GSM519434", "GSM519435", "GSM519436", "GSM519437", "GSM519438", "GSM519439", "GSM519440", "GSM519441", "GSM519442", "GSM519443"], "sample_count": 327, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Microarray-based molecular subtyping of 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": "asset:table:pmid:33614483:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3a1fbcccf55cd87096d1e1c3e88b60d0529650f1bae24c530ea9a7b234205509", "bytes": 3421, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T6", "version": null, "note": "Gene set enrichment analysis based on the signature of 9 autophagy-related lncRNAs.", "structure": {"pmcid": "PMC7892971", "section_index": 6, "section_title": "Gene Set Enrichment Analysis", "row_count": 26, "column_count": 9}, "table": {"label": "Table 6", "caption": "Gene set enrichment analysis based on the signature of 9 autophagy-related lncRNAs.", "rows": [["Name", "Size", "ES", "NES", "NOM P-val", "FDRq-val", "FWERP-val", "Rank at max", "Leading edge"], ["oocyte_meiosis", "112.000", "0.536", "2.039", "0.000", "0.047", "0.066", "4649.000", "tags=39%, list=8%, signal=43%"], ["vibrio_cholerae_infection", "54.000", "0.570", "1.956", "0.002", "0.087", "0.150", "8855.000", "tags=52%, list=16%, signal=62%"], ["gap_junction", "90.000", "0.449", "1.760", "0.002", "0.138", "0.414", "6344.000", "tags=39%, list=11%, signal=44%"], ["citrate_cycle_tca_cycle", "31.000", "0.718", "2.040", "0.006", "0.095", "0.066", "4597.000", "tags=55%, list=8%, signal=60%"], ["pathogenic_escherichia_coli_infection", "56.000", "0.546", "1.789", "0.006", "0.217", "0.363", "6053.000", "tags=43%, list=11%, signal=48%"], ["o_glycan_biosynthesis", "30.000", "0.534", "1.758", "0.010", "0.127", "0.417", "7284.000", "tags=50%, list=13%, signal=58%"], ["steroid_biosynthesis", "17.000", "0.700", "1.776", "0.011", "0.151", "0.384", "2995.000", "tags=53%, list=5%, signal=56%"], ["tgf_beta_signaling_pathway", "85.000", "0.469", "1.752", "0.012", "0.112", "0.427", "3973.000", "tags=31%, list=7%, signal=33%"], ["glycolysis_gluconeogenesis", "62.000", "0.488", "1.771", "0.013", "0.140", "0.396", "5471.000", "tags=34%, list=10%, signal=38%"], ["terpenoid_backbone_biosynthesis", "15.000", "0.705", "1.786", "0.015", "0.186", "0.368", "5030.000", "tags=40%, list=9%, signal=44%"], ["n_glycan_biosynthesis", "46.000", "0.548", "1.783", "0.016", "0.163", "0.371", "4408.000", "tags=39%, list=8%, signal=42%"], ["regulation_of_actin_cytoskeleton", "213.000", "0.401", "1.643", "0.016", "0.161", "0.576", "6127.000", "tags=35%, list=11%, signal=39%"], ["adherens_junction", "73.000", "0.497", "1.836", "0.017", "0.192", "0.291", "9394.000", "tags=52%, list=17%, signal=63%"], ["renal_cell_carcinoma", "70.000", "0.435", "1.643", "0.023", "0.170", "0.575", "5850.000", "tags=37%, list=11%, signal=41%"], ["progesterone_mediated_oocyte_maturation", "85.000", "0.434", "1.621", "0.026", "0.173", "0.611", "4505.000", "tags=33%, list=8%, signal=36%"], ["starch_and_sucrose_metabolism", "52.000", "0.468", "1.568", "0.028", "0.202", "0.684", "9541.000", "tags=44%, list=17%, signal=53%"], ["protein_export", "24.000", "0.643", "1.687", "0.029", "0.137", "0.514", "4379.000", "tags=50%, list=8%, signal=54%"], ["dorso_ventral_axis_formation", "24.000", "0.549", "1.717", "0.029", "0.122", "0.473", "5696.000", "tags=42%, list=10%, signal=46%"], ["epithelial_cell_signaling_in_helicobacter_pylori_infection", "68.000", "0.416", "1.538", "0.035", "0.209", "0.728", "3970.000", "tags=29%, list=7%, signal=32%"], ["arrhythmogenic_right_ventricular_cardiomyopathy_arvc", "74.000", "0.450", "1.596", "0.038", "0.180", "0.651", "6112.000", "tags=35%, list=11%, signal=39%"], ["long_term_potentiation", "70.000", "0.387", "1.557", "0.040", "0.197", "0.697", "6344.000", "tags=31%, list=11%, signal=35%"], ["ecm_receptor_interaction", "84.000", "0.536", "1.726", "0.040", "0.122", "0.454", "4669.000", "tags=36%, list=8%, signal=39%"], ["focal_adhesion", "199.000", "0.433", "1.610", "0.046", "0.175", "0.628", "6112.000", "tags=36%, list=11%, signal=41%"], ["prostate_cancer", "89.000", "0.405", "1.534", "0.046", "0.206", "0.730", "4558.000", "tags=33%, list=8%, signal=35%"], ["amino_sugar_and_nucleotide_sugar_metabolism", "43", "0.476", "1.568", "0.047", "0.194", "0.684", "5323", "tags=37%, list=10%, signal=41%"]], "row_count": 26, "column_count": 9, "numeric_cells": 200, "header_rows": 1, "locator": "section[15]/table-wrap[1]#T6"}}, {"id": "asset:table:pmid:33614483:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:104c602cdff0537fe33aa99baaf309df25dde831b22c2466749f58f21464994b", "bytes": 693, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T1", "version": null, "note": "Primer sequences for RT-PCR analysis.", "structure": {"pmcid": "PMC7892971", "section_index": 8, "section_title": "LncRNAs Validation Using qRT-PCR", "row_count": 11, "column_count": 2}, "table": {"label": "Table 1", "caption": "Primer sequences for RT-PCR analysis.", "rows": [["", "Primer sequences"], ["USP30-AS1-F", "5’-TGAAACCGTCTCCTCCGCTACC-3’"], ["USP30-AS1-R", "5’-TGTCCTGCGGTCTACGTTCCC-3’"], ["TFAP2A-AS1-F", "5’-CTTGACAGCTCCAGGGGTTA-3’"], ["TFAP2A-AS1-R", "5’-TCTAGACTTGCAGGCACACA-3’"], ["MAPT-AS1-F", "5’-AGATGCACCTGCAGCCC-3’"], ["MAPT-AS1-R", "5’-CCCGTCCTTGTTCTGACTCC-3’"], ["LINC01087-F", "5’-CCACCAACCTCACCCACTCAAAG-3’"], ["LINC01087-R", "5’-TCCTCACGCCTCTGCTCCATC-3’"], ["GAPDH-F", "5’-CAGGAGGCATTGCTGATGAT-3’"], ["GAPDH-R", "5’-GAAGGCTGGGGCTCATTT-3’"]], "row_count": 11, "column_count": 2, "numeric_cells": 14, "header_rows": 1, "locator": "section[8]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33614483:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:44bcd7bfb1678b72c97033363503b59e01e92b4269452394351e4718f6c96e5e", "bytes": 2727, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T2", "version": null, "note": "Correlation between autophagy genes and lncRNAs in breast cancer.", "structure": {"pmcid": "PMC7892971", "section_index": 12, "section_title": "Identification of an Autophagy-Related lncRNA Signature in Breast Cancer", "row_count": 62, "column_count": 4}, "table": {"label": "Table 2", "caption": "Correlation between autophagy genes and lncRNAs in breast cancer.", "rows": [["Autophagy genes", "lncRNAs", "Correlation", "P value"], ["ARSA", "KMT2E-AS1", "0.38", "7.24E-40"], ["ARSB", "KMT2E-AS1", "-0.33", "2.06E-30"], ["ATF6", "KMT2E-AS1", "-0.31", "2.37E-26"], ["ATG16L2", "KMT2E-AS1", "0.30", "9.31E-25"], ["ATG4B", "KMT2E-AS1", "0.50", "2.12E-72"], ["ATG4D", "KMT2E-AS1", "0.30", "4.97E-25"], ["BAX", "KMT2E-AS1", "0.46", "2.74E-60"], ["BNIP1", "KMT2E-AS1", "0.31", "3.85E-26"], ["CANX", "KMT2E-AS1", "-0.32", "1.44E-27"], ["CAPN10", "KMT2E-AS1", "0.51", "2.75E-75"], ["CLN3", "KMT2E-AS1", "0.35", "5.52E-33"], ["DDIT3", "KMT2E-AS1", "0.30", "1.24E-24"], ["HSPA8", "KMT2E-AS1", "-0.30", "3.95E-25"], ["ITGB1", "KMT2E-AS1", "-0.43", "1.63E-51"], ["MAP2K7", "KMT2E-AS1", "0.32", "2.21E-27"], ["MAPK1", "KMT2E-AS1", "-0.33", "4.61E-29"], ["MLST8", "KMT2E-AS1", "0.36", "2.58E-35"], ["NCKAP1", "KMT2E-AS1", "-0.40", "1.48E-43"], ["PELP1", "KMT2E-AS1", "0.37", "2.15E-36"], ["PEX14", "KMT2E-AS1", "0.35", "8.71E-33"], ["PIK3R4", "KMT2E-AS1", "-0.33", "4.89E-30"], ["RAB24", "KMT2E-AS1", "0.50", "6.73E-72"], ["RB1", "KMT2E-AS1", "-0.37", "1.37E-37"], ["SH3GLB1", "KMT2E-AS1", "-0.33", "8.19E-29"], ["STK11", "KMT2E-AS1", "0.38", "6.93E-39"], ["WDR45", "KMT2E-AS1", "0.42", "6.34E-49"], ["APOL1", "USP30-AS1", "0.65", "2.41E-136"], ["BAK1", "USP30-AS1", "0.36", "3.89E-35"], ["BAX", "USP30-AS1", "0.30", "5.64E-25"], ["CASP1", "USP30-AS1", "0.63", "4.65E-122"], ["CASP4", "USP30-AS1", "0.51", "7.21E-74"], ["CCR2", "USP30-AS1", "0.51", "4.73E-74"], ["CFLAR", "USP30-AS1", "0.37", "2.25E-36"], ["FAS", "USP30-AS1", "0.42", "4.41E-48"], ["IKBKE", "USP30-AS1", "0.44", "7.15E-55"], ["NLRC4", "USP30-AS1", "0.31", "1.82E-26"], ["PRKCQ", "USP30-AS1", "0.48", "6.54E-66"], ["RGS19", "USP30-AS1", "0.41", "7.33E-46"], ["EGFR", "ST7-AS1", "0.38", "4.60E-39"], ["ATF4", "VPS9D1-AS1", "0.33", "8.33E-29"], ["ATG12", "VPS9D1-AS1", "-0.33", "1.00E-28"], ["BID", "VPS9D1-AS1", "0.37", "1.14E-37"], ["BIRC5", "VPS9D1-AS1", "0.32", "1.29E-28"], ["CD46", "VPS9D1-AS1", "-0.33", "5.24E-30"], ["CDKN2A", "VPS9D1-AS1", "0.33", "3.76E-30"], ["GAPDH", "VPS9D1-AS1", "0.36", "7.50E-36"], ["MYC", "VPS9D1-AS1", "0.45", "1.57E-56"], ["RHEB", "VPS9D1-AS1", "0.32", "1.27E-28"], ["ZFYVE1", "VPS9D1-AS1", "-0.36", "4.51E-35"], ["ATG16L2", "TFAP2A-AS1", "0.34", "4.47E-31"], ["BIRC6", "TFAP2A-AS1", "0.36", "2.32E-35"], ["TSC1", "TFAP2A-AS1", "0.40", "5.96E-45"], ["WDFY3", "TFAP2A-AS1", "0.35", "3.17E-34"], ["KIF5B", "OTUD6B-AS1", "0.31", "1.60E-26"], ["MAPK1", "OTUD6B-AS1", "0.33", "5.57E-30"], ["RB1CC1", "OTUD6B-AS1", "0.59", "1.86E-104"], ["CAPN2", "HOXB-AS1", "0.32", "1.41E-28"], ["ATG2B", "LINC01087", "0.31", "2.52E-25"], ["BIRC6", "LINC01087", "0.34", "4.44E-32"], ["WDFY3", "LINC01087", "0.40", "6.65E-44"], ["STK11", "MAPT-AS1", "0.32", "4.11E-27"]], "row_count": 62, "column_count": 4, "numeric_cells": 148, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:33614483:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8dbdf9d622e60c3ee5d2ab8cae03dd7fefbbda76f6977e3965836d480350bdef", "bytes": 831, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#T3", "version": null, "note": "The 9 autophagy-related lncRNAs significantly associated with OS in the training set.", "structure": {"pmcid": "PMC7892971", "section_index": 12, "section_title": "Identification of an Autophagy-Related lncRNA Signature in Breast Cancer", "row_count": 10, "column_count": 6}, "table": {"label": "Table 3", "caption": "The 9 autophagy-related lncRNAs significantly associated with OS in the training set.", "rows": [["LncRNAs", "β", "HR", "Lower 95%CI", "Upper 95%CI", "P-value"], ["KMT2E-AS1", "0.2520", "1.2866", "0.9278", "1.7840", "0.1308"], ["USP30-AS1", "-0.4604", "0.6310", "0.4794", "0.8305", "0.0010"], ["ST7-AS1", "-0.5304", "0.5884", "0.3985", "0.8687", "0.0076"], ["VPS9D1-AS1", "-0.2505", "0.7784", "0.6457", "0.9383", "0.0086"], ["TFAP2A-AS1", "-0.5438", "0.5805", "0.3770", "0.8940", "0.0136"], ["OTUD6B-AS1", "0.2797", "1.3227", "0.9840", "1.7779", "0.0638"], ["HOXB-AS1", "-0.1847", "0.8314", "0.6605", "1.0464", "0.1157"], ["LINC01087", "-0.0873", "0.9164", "0.8188", "1.0257", "0.1290"], ["MAPT-AS1", "-0.4423", "0.6426", "0.4955", "0.8334", "0.0009"]], "row_count": 10, "column_count": 6, "numeric_cells": 49, "header_rows": 1, "locator": "section[12]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:33614483:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2b0cb4af9885c5c2af4b4214d7f78f3ab93857440a29864dee9f6ca83cc18147", "bytes": 1331, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T4", "version": null, "note": "Predictive values of related clinical features and risk score in the training dataset and the testing dataset.", "structure": {"pmcid": "PMC7892971", "section_index": 13, "section_title": "Validation of Prognostic Performance of the Autophagy-Related lncRNA Signature in Breast Cancer", "row_count": 16, "column_count": 7}, "table": {"label": "Table 4", "caption": "Predictive values of related clinical features and risk score in the training dataset and the testing dataset.", "rows": [["Variables", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "P-value", "HR", "95% CI", "P-value"], ["Training dataset", "", "", "", "", "", ""], ["age", "1.035", "1.022–1.049", "<0.001", "1.035", "1.020–1.050", "<0.001"], ["gender", "0.830", "0.116–5.943", "0.853", "0.645", "0.089–4.672", "0.664"], ["stage", "2.205", "1.756–2.768", "<0.001", "1.461", "0.880–2.427", "0.143"], ["T", "1.461", "1.196–1.785", "<0.001", "1.070", "0.796–1.438", "0.654"], ["M", "4.935", "2.944–8.273", "<0.001", "1.908", "0.843–4.318", "0.121"], ["N", "1.620", "1.364–1.923", "<0.001", "1.294", "0.971–1.724", "0.079"], ["risk score", "1.794", "1.556–2.069", "<0.001", "1.787", "1.525–2.093", "<0.001"], ["Testing dataset", "", "", "", "", "", ""], ["age", "0.992", "0.971–1.014", "0.483", "0.996", "0.974–1.018", "0.697"], ["T", "1.863", "1.440–2.412", "<0.001", "1.288", "0.891–1.860", "0.178"], ["M", "5.204", "2.391–11.326", "<0.001", "1.202", "0.421–3.436", "0.731"], ["N", "1.757", "1.448–2.134", "<0.001", "1.633", "1.317–2.026", "<0.001"], ["risk score", "1.215", "1.105–1.336", "<0.001", "1.210", "1.083–1.351", "0.001"]], "row_count": 16, "column_count": 7, "numeric_cells": 74, "header_rows": 2, "locator": "section[13]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:33614483:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5f6456fd338391d2f0168af8110422fa2241d614df4c0b857404eb702f8114ed", "bytes": 863, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T5", "version": null, "note": "Clinical impact of risk score signature for the TCGA cohort.", "structure": {"pmcid": "PMC7892971", "section_index": 14, "section_title": "Clinical Value of the Prognostic Signature in Patients With Breast Cancer", "row_count": 20, "column_count": 6}, "table": {"label": "Table 5", "caption": "Clinical impact of risk score signature for the TCGA cohort.", "rows": [["Clinical Features", "n", "Risk Score"], ["Mean", "SD", "t", "P"], ["Age", "", "", "", "", ""], ["<=65 >65", "665", "1.270", "0.857", "-2.673", "0.008"], ["243", "1.452", "0.932"], ["Gender", "", "", "", "", ""], ["Female Male", "897", "1.319", "0.882", "0.314", "0.700"], ["11", "1.238", "0.853"], ["Stage", "", "", "", "", ""], ["I-II III-IV", "691", "1.277", "0.862", "-2.443", "0.000"], ["217", "1.451", "0.929"], ["T", "", "", "", "", ""], ["T1-2 T3-4", "774", "1.304", "0.870", "-1.169", "0.161"], ["134", "1.405", "0.938"], ["M", "", "", "", "", ""], ["M0 M1", "891", "1.310", "0.881", "-2.325", "0.186"], ["17", "1.746", "0.763"], ["N", "", "", "", "", ""], ["N0 N1-3", "449", "1.265", "0.867", "-1.799", "0.013"], ["459", "1.370", "0.892"]], "row_count": 20, "column_count": 6, "numeric_cells": 51, "header_rows": 2, "locator": "section[14]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:33614483:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3a1fbcccf55cd87096d1e1c3e88b60d0529650f1bae24c530ea9a7b234205509", "bytes": 3421, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T6", "version": null, "note": "Gene set enrichment analysis based on the signature of 9 autophagy-related lncRNAs.", "structure": {"pmcid": "PMC7892971", "section_index": 15, "section_title": "Gene Set Enrichment Analysis", "row_count": 26, "column_count": 9}, "table": {"label": "Table 6", "caption": "Gene set enrichment analysis based on the signature of 9 autophagy-related lncRNAs.", "rows": [["Name", "Size", "ES", "NES", "NOM P-val", "FDRq-val", "FWERP-val", "Rank at max", "Leading edge"], ["oocyte_meiosis", "112.000", "0.536", "2.039", "0.000", "0.047", "0.066", "4649.000", "tags=39%, list=8%, signal=43%"], ["vibrio_cholerae_infection", "54.000", "0.570", "1.956", "0.002", "0.087", "0.150", "8855.000", "tags=52%, list=16%, signal=62%"], ["gap_junction", "90.000", "0.449", "1.760", "0.002", "0.138", "0.414", "6344.000", "tags=39%, list=11%, signal=44%"], ["citrate_cycle_tca_cycle", "31.000", "0.718", "2.040", "0.006", "0.095", "0.066", "4597.000", "tags=55%, list=8%, signal=60%"], ["pathogenic_escherichia_coli_infection", "56.000", "0.546", "1.789", "0.006", "0.217", "0.363", "6053.000", "tags=43%, list=11%, signal=48%"], ["o_glycan_biosynthesis", "30.000", "0.534", "1.758", "0.010", "0.127", "0.417", "7284.000", "tags=50%, list=13%, signal=58%"], ["steroid_biosynthesis", "17.000", "0.700", "1.776", "0.011", "0.151", "0.384", "2995.000", "tags=53%, list=5%, signal=56%"], ["tgf_beta_signaling_pathway", "85.000", "0.469", "1.752", "0.012", "0.112", "0.427", "3973.000", "tags=31%, list=7%, signal=33%"], ["glycolysis_gluconeogenesis", "62.000", "0.488", "1.771", "0.013", "0.140", "0.396", "5471.000", "tags=34%, list=10%, signal=38%"], ["terpenoid_backbone_biosynthesis", "15.000", "0.705", "1.786", "0.015", "0.186", "0.368", "5030.000", "tags=40%, list=9%, signal=44%"], ["n_glycan_biosynthesis", "46.000", "0.548", "1.783", "0.016", "0.163", "0.371", "4408.000", "tags=39%, list=8%, signal=42%"], ["regulation_of_actin_cytoskeleton", "213.000", "0.401", "1.643", "0.016", "0.161", "0.576", "6127.000", "tags=35%, list=11%, signal=39%"], ["adherens_junction", "73.000", "0.497", "1.836", "0.017", "0.192", "0.291", "9394.000", "tags=52%, list=17%, signal=63%"], ["renal_cell_carcinoma", "70.000", "0.435", "1.643", "0.023", "0.170", "0.575", "5850.000", "tags=37%, list=11%, signal=41%"], ["progesterone_mediated_oocyte_maturation", "85.000", "0.434", "1.621", "0.026", "0.173", "0.611", "4505.000", "tags=33%, list=8%, signal=36%"], ["starch_and_sucrose_metabolism", "52.000", "0.468", "1.568", "0.028", "0.202", "0.684", "9541.000", "tags=44%, list=17%, signal=53%"], ["protein_export", "24.000", "0.643", "1.687", "0.029", "0.137", "0.514", "4379.000", "tags=50%, list=8%, signal=54%"], ["dorso_ventral_axis_formation", "24.000", "0.549", "1.717", "0.029", "0.122", "0.473", "5696.000", "tags=42%, list=10%, signal=46%"], ["epithelial_cell_signaling_in_helicobacter_pylori_infection", "68.000", "0.416", "1.538", "0.035", "0.209", "0.728", "3970.000", "tags=29%, list=7%, signal=32%"], ["arrhythmogenic_right_ventricular_cardiomyopathy_arvc", "74.000", "0.450", "1.596", "0.038", "0.180", "0.651", "6112.000", "tags=35%, list=11%, signal=39%"], ["long_term_potentiation", "70.000", "0.387", "1.557", "0.040", "0.197", "0.697", "6344.000", "tags=31%, list=11%, signal=35%"], ["ecm_receptor_interaction", "84.000", "0.536", "1.726", "0.040", "0.122", "0.454", "4669.000", "tags=36%, list=8%, signal=39%"], ["focal_adhesion", "199.000", "0.433", "1.610", "0.046", "0.175", "0.628", "6112.000", "tags=36%, list=11%, signal=41%"], ["prostate_cancer", "89.000", "0.405", "1.534", "0.046", "0.206", "0.730", "4558.000", "tags=33%, list=8%, signal=35%"], ["amino_sugar_and_nucleotide_sugar_metabolism", "43", "0.476", "1.568", "0.047", "0.194", "0.684", "5323", "tags=37%, list=10%, signal=41%"]], "row_count": 26, "column_count": 9, "numeric_cells": 200, "header_rows": 1, "locator": "section[15]/table-wrap[1]#T6"}}], "gaps": ["asset:data:geo:GSE20685 not downloaded", "asset:data:geo:GSE20685 licence not read"]}, "analysis": {"state": "complete", "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": "Stepwise multivariable cox proportional hazards regression analysis were carried out to identify the optimal prognostic lncRNAs among the 25 candidate lncRNAs."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan Meier"}}, {"id": "method-3", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "ncRNAs in view of |log2 fold change (FC)|≥1 and false disco", "fdr_threshold": "fold change (FC)|≥1 and false discovery rate (FDR)<0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "Limma"}}, {"id": "method-4", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}], "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": ["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": ["GSE20685"], "resolved_accessions": ["GSE20685"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: https://www.cancergenome.nih.gov/, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20685, http://www.autophagy.lu/."], "basis": "The paper names GSE20685 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": ["cox_ph"], "assets": ["source:pmid:33614483", "data:geo:GSE20685", "asset:table:pmid:33614483:1", "asset:table:pmid:33614483:2", "asset:table:pmid:33614483:3", "asset:table:pmid:33614483:4", "asset:table:pmid:33614483:5", "asset:table:pmid:33614483:6", "asset:table:pmid:33614483:7"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20685"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:12Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 23805, "completion_tokens": 1787, "cached_tokens": 784}}, "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:33614483", "type": "paper", "label": "pmid:33614483"}, {"id": "source:pmid:33614483", "type": "manuscript", "label": "PMID 33614483 full text"}, {"id": "data:geo:GSE20685", "type": "dataset", "label": "GEO GSE20685"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33614483", "type": "paper", "label": "pmid:33614483"}, {"id": "source:pmid:33614483", "type": "manuscript", "label": "PMID 33614483 full text"}, {"id": "data:geo:GSE20685", "type": "dataset", "label": "GEO GSE20685"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33614483", "type": "extraction", "used": ["source:pmid:33614483"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20685", "type": "accession_resolution", "used": ["data:geo:GSE20685"], "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:33614483", "parent_hash": "sha256:60336ff03af912536659c67a47677d0dc3a4f7dd9cdb25cc034f04a6ab03e32c", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE20685 licence not read", "asset:data:geo:GSE20685 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["these lncRNAs. METHODS: The RNA sequencing (RNA-Seq) data of breast cancer patients was collecte", "ial functions of these lncRNAs. METHODS: The RNA sequencing (RNA-Seq) data of breast cancer patients was"], "order_basis": "paper_text_order:627", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ast cells (HBL-100) and breast cancer cells (MCF-7 and T-47D) were purchased from the Cell Bank"], "order_basis": "paper_text_order:2536", "id": "assay:2"}, {"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": ["Stepwise multivariable cox proportional hazards regression analysis were carried out to identify the optimal prognostic lncRNAs among the 25 candidate lncRNAs."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}