← All .science files
pmid:36836779
In Silico Analysis of Publicly Available Transcriptomic Data for the Identification of Triple-Negative Breast Cancer-Specific Biomarkers.
Rachid Kaddoura · Fatma Alqutami · Mohamed Asbaita · Mahmood Hachim
Life (Basel, Switzerland) · 2023 doi:10.3390/life13020422
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 · 4 items
claims array · 3 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
[2] object · 6 fields
target object · 4 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 · 10 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 84 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 115 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 169 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 343 items
[5] object · 15 fields
structure object · 15 fields
sample_accessions array · 50 items
[6] object · 15 fields
structure object · 15 fields
sample_accessions array · 108 items
[7] object · 15 fields
structure object · 15 fields
sample_accessions array · 275 items
[8] object · 15 fields
structure object · 15 fields
sample_accessions array · 139 items
[9] object · 15 fields
structure object · 15 fields
sample_accessions array · 53 items
gaps array · 18 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
evidence object · 3 fields
[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 · 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 · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 9 items
resolved_accessions array · 9 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 · 23 items
assays array · 2 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 · 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:36836779", "kind": "science-record", "revision": 4, "content_hash": "sha256:71cddf92b9fed4f69fdd945a7c553539a90aa6f3bfe98c44502653adee8b820a", "created_at": "2026-11-01T19:01:27Z", "updated_at": "2026-11-01T22:51:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "In Silico Analysis of Publicly Available Transcriptomic Data for the Identification of Triple-Negative Breast Cancer-Specific Biomarkers.", "doi": "10.3390/life13020422", "pmid": "36836779", "authors": ["Rachid Kaddoura", "Fatma Alqutami", "Mohamed Asbaita", "Mahmood Hachim"], "journal": "Life (Basel, Switzerland)", "year": 2023, "abstract": "BACKGROUND: Breast cancer is the most common type of cancer among women and is classified into multiple subtypes. Triple-negative breast cancer (TNBC) is the most aggressive subtype, with high mortality rates and limited treatment options such as chemotherapy and radiation. Due to the heterogeneity and complexity of TNBC, there is a lack of reliable biomarkers that can be used to aid in the early diagnosis and prognosis of TNBC in a non-invasive screening method.\nAIM: This study aims to use in silico methods to identify potential biomarkers for TNBC screening and diagnosis, as well as potential therapeutic markers.\nMETHODS: Publicly available transcriptomic data of breast cancer patients published in the NCBI's GEO database were used in this analysis. Data were analyzed with the online tool GEO2R to identify differentially expressed genes (DEGs). Genes that were differentially expressed in more than 50% of the datasets were selected for further analysis. Metascape, Kaplan-Meier plotter, cBioPortal, and the online tool TIMER were used for functional pathway analysis to identify the biological role and functional pathways associated with these genes. Breast Cancer Gene-Expression Miner v4.7 was used to validify the obtained results in a larger cohort of datasets.\nRESULTS: A total of 34 genes were identified as differentially expressed in more than half of the datasets. The DEG GATA3 had the highest degree of regulation, and it plays a role in regulating other genes. The estrogen-dependent pathway was the most enriched pathway, involving four crucial genes, including GATA3. The gene FOXA1 was consistently down-regulated in TNBC in all datasets.\nCONCLUSIONS: The shortlisted 34 DEGs will aid clinicians in diagnosing TNBC more accurately as well as developing targeted therapies to improve patient prognosis. In vitro and in vivo studies are further recommended to validate the results of the current study.", "claims": [{"id": "claim-method", "statement": "Each dataset was processed individually to identify DEGs using the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/, accessed on 1 October 2021). Samples were assigned to groups based on their subtype and analyzed using the standardized parameters of the tool. These standardized parameters include automated log2 transformation of non-transformed data, empirical Bayes method of calculation through the limma statistical package, and adjustment of p value using the default Benjamini and Hochberg (false discovery rate) method. p-value < 0.05 was used to indicate statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36836779", "locator": "sections[4] \"2.2. Identification of Differentially Expressed Genes\" paragraph 2", "quote": "Each dataset was processed individually to identify DEGs using the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/, accessed on 1 October 2021). Samples were assigned to groups based on their subtype and analyzed using the standardized parameters of the tool. These standardized parameters include automated log2 transformation of non-transformed data, empirical Bayes method of calculation through the limma statistical package, and adjustment of p value using the default Benjamini and Hochberg (false discovery rate) method. p-value < 0.05 was used to indicate statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36836779", "locator": "sections[29] \"Data Availability Statement\" paragraph 2", "quote": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The re-analysis of these datasets revealed a total of 1217 DEGs in all datasets (Supplementary Files S1–S9), 34 of which are consistent across five of the nine datasets (50%) (Figure 2, Table 2, Supplementary File S10), with these genes being either up- or down-regulated.", "kind": "quantitative", "target": {"value": 50.0, "unit": "per cent", "tolerance": null, "source": "The re-analysis of these datasets revealed a total of 1217 DEGs in all datasets (Supplementary Files S1–S9), 34 of which are consistent across five of the nine datasets (50%) (Figure 2, Table 2, Supplementary File S10), with these genes being either up- or down-regulated."}, "evidence": [{"asset": "source:pmid:36836779", "locator": "sections[7] \"3. Results\" paragraph 2", "quote": "The re-analysis of these datasets revealed a total of 1217 DEGs in all datasets (Supplementary Files S1–S9), 34 of which are consistent across five of the nine datasets (50%) (Figure 2, Table 2, Supplementary File S10), with these genes being either up- or down-regulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The re-analysis of these datasets revealed a total of 1217 DEGs in all datasets (Supplementary Files S1–S9), 34 of which are consistent across five of the nine datasets (50%) (Figure 2, Table 2, Supplementary File S10), with these genes being either up- or down-regulated.", "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:36836779"], "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:GSE18864"], "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:GSE18864"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36836779", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/life13020422", "sha256": "sha256:1860cc3bc2d73688a9389ce9986ef4e7cb354e64acd5c9eee3ba4c0faed6f0d7", "bytes": 48365, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/life13020422", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9965976", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE18864", "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=GSE18864", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18864", "version": null, "note": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM467523", "GSM467524", "GSM467525", "GSM467526", "GSM467527", "GSM467528", "GSM467529", "GSM467530", "GSM467531", "GSM467532", "GSM467533", "GSM467534", "GSM467535", "GSM467536", "GSM467537", "GSM467538", "GSM467539", "GSM467540", "GSM467541", "GSM467542", "GSM467543", "GSM467544", "GSM467545", "GSM467546", "GSM467547", "GSM467548", "GSM467549", "GSM467550", "GSM467551", "GSM467552", "GSM467553", "GSM467554", "GSM467555", "GSM467556", "GSM467557", "GSM467558", "GSM467559", "GSM467560", "GSM467561", "GSM467562", "GSM467563", "GSM467564", "GSM467565", "GSM467566", "GSM467567", "GSM467568", "GSM467569", "GSM467570", "GSM467571", "GSM467572", "GSM467573", "GSM467574", "GSM467575", "GSM467576", "GSM467577", "GSM467578", "GSM467579", "GSM467580", "GSM467581", "GSM467582", "GSM467583", "GSM467584", "GSM467585", "GSM467586", "GSM467587", "GSM467588", "GSM467589", "GSM467590", "GSM467591", "GSM467592", "GSM467593", "GSM467594", "GSM467595", "GSM467596", "GSM467597", "GSM467598", "GSM467599", "GSM467600", "GSM467601", "GSM467602", "GSM467603", "GSM467604", "GSM467605", "GSM467606"], "sample_count": 84, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Tumor expression data from neoadjuvant trial of cisplatin monotherapy in triple negative breast cancer patients", "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:GSE19615", "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=GSE19615", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19615", "version": null, "note": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM491175", "GSM491176", "GSM491177", "GSM491178", "GSM491179", "GSM491180", "GSM491181", "GSM491182", "GSM491183", "GSM491184", "GSM491185", "GSM491186", "GSM491187", "GSM491188", "GSM491189", "GSM491190", "GSM491191", "GSM491192", "GSM491193", "GSM491194", "GSM491195", "GSM491196", "GSM491197", "GSM491198", "GSM491199", "GSM491200", "GSM491201", "GSM491202", "GSM491203", "GSM491204", "GSM491205", "GSM491206", "GSM491207", "GSM491208", "GSM491209", "GSM491210", "GSM491211", "GSM491212", "GSM491213", "GSM491214", "GSM491215", "GSM491216", "GSM491217", "GSM491218", "GSM491219", "GSM491220", "GSM491221", "GSM491222", "GSM491223", "GSM491224", "GSM491225", "GSM491226", "GSM491227", "GSM491228", "GSM491229", "GSM491230", "GSM491231", "GSM491232", "GSM491233", "GSM491234", "GSM491235", "GSM491236", "GSM491237", "GSM491238", "GSM491239", "GSM491240", "GSM491241", "GSM491242", "GSM491243", "GSM491244", "GSM491245", "GSM491246", "GSM491247", "GSM491248", "GSM491249", "GSM491250", "GSM491251", "GSM491252", "GSM491253", "GSM491254", "GSM491255", "GSM491256", "GSM491257", "GSM491258", "GSM491259", "GSM491260", "GSM491261", "GSM491262", "GSM491263", "GSM491264", "GSM491265", "GSM491266", "GSM491267", "GSM491268", "GSM491269", "GSM491270", "GSM491271", "GSM491272", "GSM491273", "GSM491274", "GSM491275", "GSM491276", "GSM491277", "GSM491278", "GSM491279", "GSM491280", "GSM491281", "GSM491282", "GSM491283", "GSM491284", "GSM491285", "GSM491286", "GSM491287", "GSM491288", "GSM491289"], "sample_count": 115, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Integrated genomic and function characterization of the 8q22 gain", "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:GSE2741", "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=GSE2741", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2741", "version": null, "note": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM34423", "GSM34424", "GSM34425", "GSM34426", "GSM34427", "GSM34428", "GSM34429", "GSM34430", "GSM34431", "GSM34432", "GSM34433", "GSM34434", "GSM34435", "GSM34436", "GSM34437", "GSM34438", "GSM34439", "GSM34440", "GSM34441", "GSM34442", "GSM34443", "GSM34444", "GSM34445", "GSM34446", "GSM34447", "GSM34448", "GSM34449", "GSM34450", "GSM34451", "GSM34452", "GSM34453", "GSM34454", "GSM34455", "GSM34456", "GSM34457", "GSM34458", "GSM34459", "GSM34460", "GSM34461", "GSM34462", "GSM34463", "GSM34464", "GSM34465", "GSM34466", "GSM34467", "GSM34468", "GSM34469", "GSM34470", "GSM34471", "GSM34472", "GSM34473", "GSM34474", "GSM34475", "GSM34476", "GSM34477", "GSM34478", "GSM34479", "GSM34480", "GSM34481", "GSM34482", "GSM34483", "GSM34484", "GSM34485", "GSM34486", "GSM34487", "GSM34488", "GSM34489", "GSM34490", "GSM34491", "GSM34492", "GSM34493", "GSM34494", "GSM34495", "GSM34496", "GSM34497", "GSM34498", "GSM34499", "GSM34500", "GSM34501", "GSM34502", "GSM34503", "GSM34504", "GSM34505", "GSM34506", "GSM34507", "GSM34508", "GSM34509", "GSM34510", "GSM34511", "GSM34512", "GSM34513", "GSM34514", "GSM34515", "GSM34516", "GSM34517", "GSM34518", "GSM34519", "GSM34520", "GSM34521", "GSM34522", "GSM34523", "GSM34524", "GSM34525", "GSM34526", "GSM34527", "GSM34528", "GSM34529", "GSM34530", "GSM34531", "GSM34532", "GSM34533", "GSM34534", "GSM34535", "GSM34536", "GSM34537", "GSM34538", "GSM34539", "GSM34540", "GSM34541", "GSM34542", "GSM34543", "GSM34544", "GSM34545", "GSM34546", "GSM34547", "GSM34548", "GSM34549", "GSM34550", "GSM34551", "GSM34552", "GSM34553", "GSM34554", "GSM34555", "GSM34556", "GSM34557", "GSM34558", "GSM34559", "GSM34560", "GSM34561", "GSM34562", "GSM34563", "GSM34564", "GSM34565", "GSM34566", "GSM34567", "GSM34568", "GSM52910", "GSM52911", "GSM52912", "GSM52913", "GSM52914", "GSM52915", "GSM52916", "GSM52917", "GSM52918", "GSM52919", "GSM52920", "GSM52921", "GSM52922", "GSM52923", "GSM52924", "GSM52925", "GSM52926", "GSM52927", "GSM52928", "GSM52929", "GSM52930", "GSM52931", "GSM52932"], "sample_count": 169, "group_sizes": null, "group_sizes_basis": null, "platform": "1390;887;885", "taxon": "Homo sapiens", "title": "Breast Tumor's study", "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:GSE30682", "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=GSE30682", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30682", "version": null, "note": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM760813", "GSM760814", "GSM760815", "GSM760816", "GSM760817", "GSM760818", "GSM760819", "GSM760820", "GSM760821", "GSM760822", "GSM760823", "GSM760824", "GSM760825", "GSM760826", "GSM760827", "GSM760828", "GSM760829", "GSM760830", "GSM760831", "GSM760832", "GSM760833", "GSM760834", "GSM760835", "GSM760836", "GSM760837", "GSM760838", "GSM760839", "GSM760840", "GSM760841", "GSM760842", "GSM760843", "GSM760844", "GSM760845", "GSM760846", "GSM760847", "GSM760848", "GSM760849", "GSM760850", "GSM760851", "GSM760852", "GSM760853", "GSM760854", "GSM760855", "GSM760856", "GSM760857", "GSM760858", "GSM760859", "GSM760860", "GSM760861", "GSM760862", "GSM760863", "GSM760864", "GSM760865", "GSM760866", "GSM760867", "GSM760868", "GSM760869", "GSM760870", "GSM760871", "GSM760872", "GSM760873", "GSM760874", "GSM760875", "GSM760876", "GSM760877", "GSM760878", "GSM760879", "GSM760880", "GSM760881", "GSM760882", "GSM760883", "GSM760884", "GSM760885", "GSM760886", "GSM760887", "GSM760888", "GSM760889", "GSM760890", "GSM760891", "GSM760892", "GSM760893", "GSM760894", "GSM760895", "GSM760896", "GSM760897", "GSM760898", "GSM760899", "GSM760900", "GSM760901", "GSM760902", "GSM760903", "GSM760904", "GSM760905", "GSM760906", "GSM760907", "GSM760908", "GSM760909", "GSM760910", "GSM760911", "GSM760912", "GSM760913", "GSM760914", "GSM760915", "GSM760916", "GSM760917", "GSM760918", "GSM760919", "GSM760920", "GSM760921", "GSM760922", "GSM760923", "GSM760924", "GSM760925", "GSM760926", "GSM760927", "GSM760928", "GSM760929", "GSM760930", "GSM760931", "GSM760932", "GSM760933", "GSM760934", "GSM760935", "GSM760936", "GSM760937", "GSM760938", "GSM760939", "GSM760940", "GSM760941", "GSM760942", "GSM760943", "GSM760944", "GSM760945", "GSM760946", "GSM760947", "GSM760948", "GSM760949", "GSM760950", "GSM760951", "GSM760952", "GSM760953", "GSM760954", "GSM760955", "GSM760956", "GSM760957", "GSM760958", "GSM760959", "GSM760960", "GSM760961", "GSM760962", "GSM760963", "GSM760964", "GSM760965", "GSM760966", "GSM760967", "GSM760968", "GSM760969", "GSM760970", "GSM760971", "GSM760972", "GSM760973", "GSM760974", "GSM760975", "GSM760976", "GSM760977", "GSM760978", "GSM760979", "GSM760980", "GSM760981", "GSM760982", "GSM760983", "GSM760984", "GSM760985", "GSM760986", "GSM760987", "GSM760988", "GSM760989", "GSM760990", "GSM760991", "GSM760992", "GSM760993", "GSM760994", "GSM760995", "GSM760996", "GSM760997", "GSM760998", "GSM760999", "GSM761000", "GSM761001", "GSM761002", "GSM761003", "GSM761004", "GSM761005", "GSM761006", "GSM761007", "GSM761008", "GSM761009", "GSM761010", "GSM761011", "GSM761012", "GSM761013", "GSM761014", "GSM761015", "GSM761016", "GSM761017", "GSM761018", "GSM761019", "GSM761020", "GSM761021", "GSM761022", "GSM761023", "GSM761024", "GSM761025", "GSM761026", "GSM761027", "GSM761028", "GSM761029", "GSM761030", "GSM761031", "GSM761032", "GSM761033", "GSM761034", "GSM761035", "GSM761036", "GSM761037", "GSM761038", "GSM761039", "GSM761040", "GSM761041", "GSM761042", "GSM761043", "GSM761044", "GSM761045", "GSM761046", "GSM761047", "GSM761048", "GSM761049", "GSM761050", "GSM761051", "GSM761052", "GSM761053", "GSM761054", "GSM761055", "GSM761056", "GSM761057", "GSM761058", "GSM761059", "GSM761060", "GSM761061", "GSM761062", "GSM761063", "GSM761064", "GSM761065", "GSM761066", "GSM761067", "GSM761068", "GSM761069", "GSM761070", "GSM761071", "GSM761072", "GSM761073", "GSM761074", "GSM761075", "GSM761076", "GSM761077", "GSM761078", "GSM761079", "GSM761080", "GSM761081", "GSM761082", "GSM761083", "GSM761084", "GSM761085", "GSM761086", "GSM761087", "GSM761088", "GSM761089", "GSM761090", "GSM761091", "GSM761092", "GSM761093", "GSM761094", "GSM761095", "GSM761096", "GSM761097", "GSM761098", "GSM761099", "GSM761100", "GSM761101", "GSM761102", "GSM761103", "GSM761104", "GSM761105", "GSM761106", "GSM761107", "GSM761108", "GSM761109", "GSM761110", "GSM761111", "GSM761112", "GSM761113", "GSM761114", "GSM761115", "GSM761116", "GSM761117", "GSM761118", "GSM761119", "GSM761120", "GSM761121", "GSM761122", "GSM761123", "GSM761124", "GSM761125", "GSM761126", "GSM761127", "GSM761128", "GSM761129", "GSM761130", "GSM761131", "GSM761132", "GSM761133", "GSM761134", "GSM761135", "GSM761136", "GSM761137", "GSM761138", "GSM761139", "GSM761140", "GSM761141", "GSM761142", "GSM761143", "GSM761144", "GSM761145", "GSM761146", "GSM761147", "GSM761148", "GSM761149", "GSM761150", "GSM761151", "GSM761152", "GSM761153", "GSM761154", "GSM761155"], "sample_count": 343, "group_sizes": null, "group_sizes_basis": null, "platform": "6884", "taxon": "Homo sapiens", "title": "Search for a gene-expression signature of breast cancer local recurrence in young women", "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:GSE36295", "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=GSE36295", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE36295", "version": null, "note": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM886560", "GSM886561", "GSM886562", "GSM886563", "GSM886564", "GSM886565", "GSM886566", "GSM886567", "GSM886568", "GSM886569", "GSM886570", "GSM886571", "GSM886572", "GSM886573", "GSM886574", "GSM886575", "GSM886576", "GSM886577", "GSM886578", "GSM886579", "GSM886580", "GSM886581", "GSM886582", "GSM886583", "GSM886584", "GSM886585", "GSM886586", "GSM886587", "GSM886588", "GSM886589", "GSM886590", "GSM886591", "GSM886592", "GSM886593", "GSM886594", "GSM886595", "GSM886596", "GSM886597", "GSM886598", "GSM886599", "GSM886600", "GSM886601", "GSM886602", "GSM886603", "GSM886604", "GSM886605", "GSM886606", "GSM886607", "GSM886608", "GSM886609"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Transcriptomic analysis 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": "data:geo:GSE37751", "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=GSE37751", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37751", "version": null, "note": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM926963", "GSM926964", "GSM926965", "GSM926966", "GSM926967", "GSM926968", "GSM926969", "GSM926970", "GSM926971", "GSM926972", "GSM926973", "GSM926974", "GSM926975", "GSM926976", "GSM926977", "GSM926978", "GSM926979", "GSM926980", "GSM926981", "GSM926982", "GSM926983", "GSM926984", "GSM926985", "GSM926986", "GSM926987", "GSM926988", "GSM926989", "GSM926990", "GSM926991", "GSM926992", "GSM926993", "GSM926994", "GSM926995", "GSM926996", "GSM926997", "GSM926998", "GSM926999", "GSM927000", "GSM927001", "GSM927002", "GSM927003", "GSM927004", "GSM927005", "GSM927006", "GSM927007", "GSM927008", "GSM927009", "GSM927010", "GSM927011", "GSM927012", "GSM927013", "GSM927014", "GSM927015", "GSM927016", "GSM927017", "GSM927018", "GSM927019", "GSM927020", "GSM927021", "GSM927022", "GSM927023", "GSM927024", "GSM927025", "GSM927026", "GSM927027", "GSM927028", "GSM927029", "GSM927030", "GSM927031", "GSM927032", "GSM927033", "GSM927034", "GSM927035", "GSM927036", "GSM927037", "GSM927038", "GSM927039", "GSM927040", "GSM927041", "GSM927042", "GSM927043", "GSM927044", "GSM927045", "GSM927046", "GSM927047", "GSM927048", "GSM927049", "GSM927050", "GSM927051", "GSM927052", "GSM927053", "GSM927054", "GSM927055", "GSM927056", "GSM927057", "GSM927058", "GSM927059", "GSM927060", "GSM927061", "GSM927062", "GSM927063", "GSM927064", "GSM927065", "GSM927066", "GSM927067", "GSM927068", "GSM927069", "GSM927070"], "sample_count": 108, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Molecular Profiles of Human Breast Cancer and Their Association with Tumor Subtypes and Disease Prognosis (Affymetrix)", "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:GSE40115", "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=GSE40115", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40115", "version": null, "note": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM985140", "GSM985141", "GSM985142", "GSM985143", "GSM985144", "GSM985145", "GSM985146", "GSM985147", "GSM985148", "GSM985149", "GSM985150", "GSM985151", "GSM985152", "GSM985153", "GSM985154", "GSM985155", "GSM985156", "GSM985157", "GSM985158", "GSM985159", "GSM985160", "GSM985161", "GSM985162", "GSM985163", "GSM985164", "GSM985165", "GSM985166", "GSM985167", "GSM985168", "GSM985169", "GSM985170", "GSM985171", "GSM985172", "GSM985173", "GSM985174", "GSM985175", "GSM985176", "GSM985177", "GSM985178", "GSM985179", "GSM985180", "GSM985181", "GSM985182", "GSM985183", "GSM985184", "GSM985185", "GSM985186", "GSM985187", "GSM985188", "GSM985189", "GSM985190", "GSM985191", "GSM985192", "GSM985193", "GSM985194", "GSM985195", "GSM985196", "GSM985197", "GSM985198", "GSM985199", "GSM985200", "GSM985201", "GSM985202", "GSM985203", "GSM985204", "GSM985205", "GSM985206", "GSM985207", "GSM985208", "GSM985209", "GSM985210", "GSM985211", "GSM985212", "GSM985213", "GSM985214", "GSM985215", "GSM985216", "GSM985217", "GSM985218", "GSM985219", "GSM985220", "GSM985221", "GSM985222", "GSM985223", "GSM985224", "GSM985225", "GSM985226", "GSM985227", "GSM985228", "GSM985229", "GSM985230", "GSM985231", "GSM985232", "GSM985233", "GSM985234", "GSM985235", "GSM985236", "GSM985237", "GSM985238", "GSM985239", "GSM985240", "GSM985241", "GSM985242", "GSM985243", "GSM985244", "GSM985245", "GSM985246", "GSM985247", "GSM985248", "GSM985249", "GSM985250", "GSM985251", "GSM985252", "GSM985253", "GSM985254", "GSM985255", "GSM985256", "GSM985257", "GSM985258", "GSM985259", "GSM985260", "GSM985261", "GSM985262", "GSM985263", "GSM985264", "GSM985265", "GSM985266", "GSM985267", "GSM985268", "GSM985269", "GSM985270", "GSM985271", "GSM985272", "GSM985273", "GSM985274", "GSM985275", "GSM985276", "GSM985277", "GSM985278", "GSM985279", "GSM985280", "GSM985281", "GSM985282", "GSM985283", "GSM985284", "GSM985285", "GSM985286", "GSM985287", "GSM985288", "GSM985289", "GSM985290", "GSM985291", "GSM985292", "GSM985293", "GSM985294", "GSM985295", "GSM985296", "GSM985297", "GSM985298", "GSM985299", "GSM985300", "GSM985301", "GSM985302", "GSM985303", "GSM985304", "GSM985305", "GSM985306", "GSM985307", "GSM985308", "GSM985309", "GSM985310", "GSM985311", "GSM985312", "GSM985313", "GSM985314", "GSM985315", "GSM985316", "GSM985317", "GSM985318", "GSM985319", "GSM985320", "GSM985321", "GSM985322", "GSM985335", "GSM985336", "GSM985337", "GSM985338", "GSM985339", "GSM985340", "GSM985341", "GSM985342", "GSM985343", "GSM985344", "GSM985345", "GSM985346", "GSM985347", "GSM985348", "GSM985349", "GSM985350", "GSM985351", "GSM985352", "GSM985353", "GSM985354", "GSM985355", "GSM985356", "GSM985357", "GSM985358", "GSM985359", "GSM985360", "GSM985361", "GSM985362", "GSM985363", "GSM985364", "GSM985365", "GSM985366", "GSM985367", "GSM985368", "GSM985369", "GSM985370", "GSM985371", "GSM985372", "GSM985373", "GSM985374", "GSM985375", "GSM985376", "GSM985377", "GSM985378", "GSM985379", "GSM985380", "GSM985381", "GSM985382", "GSM985383", "GSM985384", "GSM985385", "GSM985386", "GSM985387", "GSM985388", "GSM985389", "GSM985390", "GSM985391", "GSM985392", "GSM985393", "GSM985394", "GSM985395", "GSM985396", "GSM985397", "GSM985398", "GSM985399", "GSM985400", "GSM985401", "GSM985402", "GSM985403", "GSM985404", "GSM985405", "GSM985406", "GSM985407", "GSM985408", "GSM985409", "GSM985410", "GSM985411", "GSM985412", "GSM985413", "GSM985414", "GSM985415", "GSM985416", "GSM985417", "GSM985418", "GSM985419", "GSM985420", "GSM985421", "GSM985422", "GSM985423", "GSM985424", "GSM985425", "GSM985426"], "sample_count": 275, "group_sizes": null, "group_sizes_basis": null, "platform": "15932;15931", "taxon": "Homo sapiens", "title": "Classifications within Molecular Subtypes Enables Identification of BRCA1/BRCA2 Mutation Carriers by RNA Tumor Profiling", "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:GSE45255", "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=GSE45255", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45255", "version": null, "note": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1100037", "GSM1100038", "GSM1100039", "GSM1100040", "GSM1100041", "GSM1100042", "GSM1100043", "GSM1100044", "GSM1100045", "GSM1100046", "GSM1100047", "GSM1100048", "GSM1100049", "GSM1100050", "GSM1100051", "GSM1100052", "GSM1100053", "GSM1100054", "GSM1100055", "GSM1100056", "GSM1100057", "GSM1100058", "GSM1100059", "GSM1100060", "GSM1100061", "GSM1100062", "GSM1100063", "GSM1100064", "GSM1100065", "GSM1100066", "GSM1100067", "GSM1100068", "GSM1100069", "GSM1100070", "GSM1100071", "GSM1100072", "GSM1100073", "GSM1100074", "GSM1100075", "GSM1100076", "GSM1100077", "GSM1100078", "GSM1100079", "GSM1100080", "GSM1100081", "GSM1100082", "GSM1100083", "GSM1100084", "GSM1100085", "GSM1100086", "GSM1100087", "GSM1100088", "GSM1100089", "GSM1100090", "GSM1100091", "GSM1100092", "GSM1100093", "GSM1100094", "GSM1100095", "GSM1100096", "GSM1100097", "GSM1100098", "GSM1100099", "GSM1100100", "GSM1100101", "GSM1100102", "GSM1100103", "GSM1100104", "GSM1100105", "GSM1100106", "GSM1100107", "GSM1100108", "GSM1100109", "GSM1100110", "GSM1100111", "GSM1100112", "GSM1100113", "GSM1100114", "GSM1100115", "GSM1100116", "GSM1100117", "GSM1100118", "GSM1100119", "GSM1100120", "GSM1100121", "GSM1100122", "GSM1100123", "GSM1100124", "GSM1100125", "GSM1100126", "GSM1100127", "GSM1100128", "GSM1100129", "GSM1100130", "GSM1100131", "GSM1100132", "GSM1100133", "GSM1100134", "GSM1100135", "GSM1100136", "GSM1100137", "GSM1100138", "GSM1100139", "GSM1100140", "GSM1100141", "GSM1100142", "GSM1100143", "GSM1100144", "GSM1100145", "GSM1100146", "GSM1100147", "GSM1100148", "GSM1100149", "GSM1100150", "GSM1100151", "GSM1100152", "GSM1100153", "GSM1100154", "GSM1100155", "GSM1100156", "GSM1100157", "GSM1100158", "GSM1100159", "GSM1100160", "GSM1100161", "GSM1100162", "GSM1100163", "GSM1100164", "GSM1100165", "GSM1100166", "GSM1100167", "GSM1100168", "GSM1100169", "GSM1100170", "GSM1100171", "GSM1100172", "GSM1100173", "GSM1100174", "GSM1100175"], "sample_count": 139, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression Profiles of Breast Tumors from Singapore and Europe", "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:GSE97177", "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=GSE97177", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE97177", "version": null, "note": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2556314", "GSM2556316", "GSM2556318", "GSM2556319", "GSM2556321", "GSM2556323", "GSM2556324", "GSM2556326", "GSM2556327", "GSM2556329", "GSM2556331", "GSM2556332", "GSM2556334", "GSM2556336", "GSM2556337", "GSM2556339", "GSM2556341", "GSM2556342", "GSM2556344", "GSM2556346", "GSM2556347", "GSM2556349", "GSM2556351", "GSM2556352", "GSM2556354", "GSM2556356", "GSM2556357", "GSM2556359", "GSM2556361", "GSM2556363", "GSM2556364", "GSM2556366", "GSM2556368", "GSM2556369", "GSM2556371", "GSM2556373", "GSM2556374", "GSM2556376", "GSM2556378", "GSM2556379", "GSM2556381", "GSM2556383", "GSM2556385", "GSM2556386", "GSM2556388", "GSM2556390", "GSM2556392", "GSM2556393", "GSM2556395", "GSM2556397", "GSM2556399", "GSM2556401", "GSM2556403"], "sample_count": 53, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [expression]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE18864 not downloaded", "asset:data:geo:GSE18864 licence not read", "asset:data:geo:GSE19615 not downloaded", "asset:data:geo:GSE19615 licence not read", "asset:data:geo:GSE2741 not downloaded", "asset:data:geo:GSE2741 licence not read", "asset:data:geo:GSE30682 not downloaded", "asset:data:geo:GSE30682 licence not read", "asset:data:geo:GSE36295 not downloaded", "asset:data:geo:GSE36295 licence not read", "asset:data:geo:GSE37751 not downloaded", "asset:data:geo:GSE37751 licence not read", "asset:data:geo:GSE40115 not downloaded", "asset:data:geo:GSE40115 licence not read", "asset:data:geo:GSE45255 not downloaded", "asset:data:geo:GSE45255 licence not read", "asset:data:geo:GSE97177 not downloaded", "asset:data:geo:GSE97177 licence not read"]}, "analysis": {"state": "partial", "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": "Each dataset was processed individually to identify DEGs using the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/, accessed on 1 October 2021). Samples were assigned to groups based on their subtype and analyzed using the standardized parameters of the tool. These standardized parameters include automated log2 transformation of non-transformed data, empirical Bayes method of calculation through the limma statistical package, and adjustment of p value using the default Benjamini and Hochberg (false discovery rate) method. p-value < 0.05 was used to indicate statistical significance."}}, {"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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 50.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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": ["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": ["GSE2741", "GSE18864", "GSE19615", "GSE30682", "GSE36295", "GSE37751", "GSE40115", "GSE45255", "GSE97177"], "resolved_accessions": ["GSE2741", "GSE18864", "GSE19615", "GSE30682", "GSE36295", "GSE37751", "GSE40115", "GSE45255", "GSE97177"], "statements": ["The datasets supporting the conclusion of this article are available in the NCBI repository, (https://www.ncbi.nlm.nih.gov/geo/, accessed on 1 October 2021), with their accession codes in Table 1."], "basis": "The paper names GSE2741, GSE18864, GSE19615, GSE30682, GSE36295, GSE37751, GSE40115, GSE45255, GSE97177 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:36836779", "data:geo:GSE18864"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE18864"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:31:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14297, "completion_tokens": 2560, "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:36836779", "type": "paper", "label": "pmid:36836779"}, {"id": "source:pmid:36836779", "type": "manuscript", "label": "PMID 36836779 full text"}, {"id": "data:geo:GSE18864", "type": "dataset", "label": "GEO GSE18864"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36836779", "type": "paper", "label": "pmid:36836779"}, {"id": "source:pmid:36836779", "type": "manuscript", "label": "PMID 36836779 full text"}, {"id": "data:geo:GSE18864", "type": "dataset", "label": "GEO GSE18864"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36836779", "type": "extraction", "used": ["source:pmid:36836779"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE18864", "type": "accession_resolution", "used": ["data:geo:GSE18864"], "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:36836779", "parent_hash": "sha256:893df51cffd83ea6e32a034c0aaef4eca114311cc0aaa9be0e42e6e8ec3f36e0", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE18864 licence not read", "asset:data:geo:GSE18864 not downloaded", "asset:data:geo:GSE19615 licence not read", "asset:data:geo:GSE19615 not downloaded", "asset:data:geo:GSE2741 licence not read", "asset:data:geo:GSE2741 not downloaded", "asset:data:geo:GSE30682 licence not read", "asset:data:geo:GSE30682 not downloaded", "asset:data:geo:GSE36295 licence not read", "asset:data:geo:GSE36295 not downloaded", "asset:data:geo:GSE37751 licence not read", "asset:data:geo:GSE37751 not downloaded", "asset:data:geo:GSE40115 licence not read", "asset:data:geo:GSE40115 not downloaded", "asset:data:geo:GSE45255 licence not read", "asset:data:geo:GSE45255 not downloaded", "asset:data:geo:GSE97177 licence not read", "asset:data:geo:GSE97177 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["s to improve patient prognosis. In vitro and in vivo studies are further recommended to validate"], "order_basis": "paper_text_order:1939", "id": "assay:1"}, {"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": ["Each dataset was processed individually to identify DEGs using the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/, accessed on 1 October 2021). Samples were assigned to groups based on their subtype and analyzed using the standardized parameters of the tool. These standardized parameters include automated log2 transformation of non-transformed data, empirical Bayes method of calculation through the limma statistical package, and adjustment of p value using the default Benjamini and Hochberg (false discovery rate) method. p-value < 0.05 was used to indicate statistical significance."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}