Robust Identification of Differential Gene Expression Patterns from Multiple Transcriptomics Datasets for Early Diagnosis, Prognosis, and Therapies for Breast Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37893423", "kind": "science-record", "revision": 4, "content_hash": "sha256:92d56fba0a4a20b244eadb1909e5e7bd1556d06222e73af35c1ed50eab2ed790", "created_at": "2026-11-01T19:02:45Z", "updated_at": "2026-11-01T22:10:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Robust Identification of Differential Gene Expression Patterns from Multiple Transcriptomics Datasets for Early Diagnosis, Prognosis, and Therapies for Breast Cancer.", "doi": "10.3390/medicina59101705", "pmid": "37893423", "authors": ["Khanis Farhana Tuly", "Md Bayazid Hossen", "Md Ariful Islam", "Md Kaderi Kibria", "Md Shahin Alam", "Md Harun-Or-Roshid", "Anjuman Ara Begum", "Sohel Hasan", "Rashidul Alam Mahumud", "Md Nurul Haque Mollah"], "journal": "Medicina (Kaunas, Lithuania)", "year": 2023, "abstract": "Background and Objectives: Breast cancer (BC) is one of the major causes of cancer-related death in women globally. Proper identification of BC-causing hub genes (HubGs) for prognosis, diagnosis, and therapies at an earlier stage may reduce such death rates. However, most of the previous studies detected HubGs through non-robust statistical approaches that are sensitive to outlying observations. Therefore, the main objectives of this study were to explore BC-causing potential HubGs from robustness viewpoints, highlighting their early prognostic, diagnostic, and therapeutic performance. Materials and Methods: Integrated robust statistics and bioinformatics methods and databases were used to obtain the required results. Results: We robustly identified 46 common differentially expressed genes (cDEGs) between BC and control samples from three microarrays (GSE26910, GSE42568, and GSE65194) and one scRNA-seq (GSE235168) dataset. Then, we identified eight cDEGs (COL11A1, COL10A1, CD36, ACACB, CD24, PLK1, UBE2C, and PDK4) as the BC-causing HubGs by the protein-protein interaction (PPI) network analysis of cDEGs. The performance of BC and survival probability prediction models with the expressions of HubGs from two independent datasets (GSE45827 and GSE54002) and the TCGA (The Cancer Genome Atlas) database showed that our proposed HubGs might be considered as diagnostic and prognostic biomarkers, where two genes, COL11A1 and CD24, exhibit better performance. The expression analysis of HubGs by Box plots with the TCGA database in different stages of BC progression indicated their early diagnosis and prognosis ability. The HubGs set enrichment analysis with GO (Gene ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways disclosed some BC-causing biological processes, molecular functions, and pathways. Finally, we suggested the top-ranked six drug molecules (Suramin, Rifaximin, Telmisartan, Tukysa Tucatinib, Lynparza Olaparib, and TG.02) for the treatment of BC by molecular docking analysis with the proposed HubGs-mediated receptors. Molecular docking analysis results also showed that these drug molecules may inhibit cancer-related post-translational modification (PTM) sites (Succinylation, phosphorylation, and ubiquitination) of hub proteins. Conclusions: This study's findings might be valuable resources for diagnosis, prognosis, and therapies at an earlier stage of BC.", "claims": [{"id": "claim-method", "statement": "The Bayesian robust inference for differential gene expression (BRIDGE) [20] approach with R-package ‘bridge’ was used to robustly identify DEGs between BC and control samples from three microarray datasets (GSE26910, GSE42568, and GSE65194), separately. To identify DEGs from scRNA-seq count data (GSE235168), an R package, Seurat [82] was used with the cutoff at adj. p-value < 0.05 and |logFC| > 0.5. The Seurat [82] R-package utilized the non-parametric Wilcoxon rank sum test [84] to calculate the p-values from the robustness viewpoints.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37893423", "locator": "sections[7] \"2.2. Identification of DEGs from Microarray Data\" paragraph 2", "quote": "The Bayesian robust inference for differential gene expression (BRIDGE) [20] approach with R-package ‘bridge’ was used to robustly identify DEGs between BC and control samples from three microarray datasets (GSE26910, GSE42568, and GSE65194), separately."}, {"asset": "source:pmid:37893423", "locator": "sections[8] \"2.3. Identification of DEGs from scRNA-seq Count Data\" paragraph 2", "quote": "To identify DEGs from scRNA-seq count data (GSE235168), an R package, Seurat [82] was used with the cutoff at adj. p-value < 0.05 and |logFC| > 0.5."}, {"asset": "source:pmid:37893423", "locator": "sections[8] \"2.3. Identification of DEGs from scRNA-seq Count Data\" paragraph 2", "quote": "The Seurat [82] R-package utilized the non-parametric Wilcoxon rank sum test [84] to calculate the p-values from the robustness viewpoints."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37893423", "locator": "sections[33] \"Data Availability Statement\" paragraph 2", "quote": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 46 cDEGs, including 18 up-regulated (CD24, BGN, GALNT10, CXCL10, NREP, COL11A1, CTTN, JPT1, IDH2, EPPK1, FN1, INHBA, SDC1, FAM83D, COL10A1, TRIM59, PLK1, UBE2C) and 28 down-regulated (NFIA, EIF1, SPTBN1, RBP7, PDK4, TACC1, CXCL2, PALMD, ADIRF, TFPI, AKR1C1, ACACB, NOVA1, ABCA5, PCOLCE2, SYNM, CD36, PLAGL1, NR3C1, SLIT3, ARRB1, PTX3, MGLL, ADAMTS1, LIFR, RASD1, SOCS2, FAM107A) as the BC-causing genes from three microarrays and one scRNA-seq count data and visualized them by the Venn diagram (see Figure 2).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37893423", "locator": "sections[19] \"3.3. Identification of Common DEGs (cDEGs)\" paragraph 2", "quote": "We identified 46 cDEGs, including 18 up-regulated (CD24, BGN, GALNT10, CXCL10, NREP, COL11A1, CTTN, JPT1, IDH2, EPPK1, FN1, INHBA, SDC1, FAM83D, COL10A1, TRIM59, PLK1, UBE2C) and 28 down-regulated (NFIA, EIF1, SPTBN1, RBP7, PDK4, TACC1, CXCL2, PALMD, ADIRF, TFPI, AKR1C1, ACACB, NOVA1, ABCA5, PCOLCE2, SYNM, CD36, PLAGL1, NR3C1, SLIT3, ARRB1, PTX3, MGLL, ADAMTS1, LIFR, RASD1, SOCS2, FAM107A) as the BC-causing genes from three microarrays and one scRNA-seq count data and visualized them by the Venn diagram (see Figure 2)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We identified 46 cDEGs, including 18 up-regulated (CD24, BGN, GALNT10, CXCL10, NREP, COL11A1, CTTN, JPT1, IDH2, EPPK1, FN1, INHBA, SDC1, FAM83D, COL10A1, TRIM59, PLK1, UBE2C) and 28 down-regulated (NFIA, EIF1, SPTBN1, RBP7, PDK4, TACC1, CXCL2, PALMD, ADIRF, TFPI, AKR1C1, ACACB, NOVA1, ABCA5, PCOLCE2, SYNM, CD36, PLAGL1, NR3C1, SLIT3, ARRB1, PTX3, MGLL, ADAMTS1, LIFR, RASD1, SOCS2, FAM107A) as the BC-causing genes from three microarrays and one scRNA-seq count data and visualized them by the Venn diagram (see Figure 2).", "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:37893423"], "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:GSE235168"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE235168"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37893423", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/medicina59101705", "sha256": "sha256:9fcbd34eb78f283cefc6c9fb835e68f2900282a17e66ace52caa62b626a1ba1c", "bytes": 88571, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/medicina59101705", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10608013", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE235168", "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=GSE235168", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE235168", "version": null, "note": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM7497157", "GSM7497158", "GSM7497159", "GSM7497160", "GSM7497161", "GSM7497162", "GSM7497163", "GSM7497164", "GSM7497165", "GSM7497166", "GSM7497167", "GSM7497168", "GSM7497169", "GSM7497170", "GSM7497171", "GSM7497172", "GSM7497173", "GSM7497174", "GSM7497175", "GSM7497176", "GSM7497177", "GSM7497178", "GSM7497179", "GSM7497180", "GSM7497181"], "sample_count": 25, "group_sizes": null, "group_sizes_basis": null, "platform": "30173;20301", "taxon": "Homo sapiens", "title": "Evaluation of breast cancer PDX tumor heterogeneity at single cell resolution [scRNA-seq]", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE26910", "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=GSE26910", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26910", "version": null, "note": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM662756", "GSM662757", "GSM662758", "GSM662759", "GSM662760", "GSM662761", "GSM662762", "GSM662763", "GSM662764", "GSM662765", "GSM662766", "GSM662767", "GSM662768", "GSM662769", "GSM662770", "GSM662771", "GSM662772", "GSM662773", "GSM662774", "GSM662775", "GSM662776", "GSM662777", "GSM662778", "GSM662779"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Stromal molecular signatures of breast and prostate 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:GSE42568", "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=GSE42568", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42568", "version": null, "note": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1045191", "GSM1045192", "GSM1045193", "GSM1045194", "GSM1045195", "GSM1045196", "GSM1045197", "GSM1045198", "GSM1045199", "GSM1045200", "GSM1045201", "GSM1045202", "GSM1045203", "GSM1045204", "GSM1045205", "GSM1045206", "GSM1045207", "GSM1045208", "GSM1045209", "GSM1045210", "GSM1045211", "GSM1045212", "GSM1045213", "GSM1045214", "GSM1045215", "GSM1045216", "GSM1045217", "GSM1045218", "GSM1045219", "GSM1045220", "GSM1045221", "GSM1045222", "GSM1045223", "GSM1045224", "GSM1045225", "GSM1045226", "GSM1045227", "GSM1045228", "GSM1045229", "GSM1045230", "GSM1045231", "GSM1045232", "GSM1045233", "GSM1045234", "GSM1045235", "GSM1045236", "GSM1045237", "GSM1045238", "GSM1045239", "GSM1045240", "GSM1045241", "GSM1045242", "GSM1045243", "GSM1045244", "GSM1045245", "GSM1045246", "GSM1045247", "GSM1045248", "GSM1045249", "GSM1045250", "GSM1045251", "GSM1045252", "GSM1045253", "GSM1045254", "GSM1045255", "GSM1045256", "GSM1045257", "GSM1045258", "GSM1045259", "GSM1045260", "GSM1045261", "GSM1045262", "GSM1045263", "GSM1045264", "GSM1045265", "GSM1045266", "GSM1045267", "GSM1045268", "GSM1045269", "GSM1045270", "GSM1045271", "GSM1045272", "GSM1045273", "GSM1045274", "GSM1045275", "GSM1045276", "GSM1045277", "GSM1045278", "GSM1045279", "GSM1045280", "GSM1045281", "GSM1045282", "GSM1045283", "GSM1045284", "GSM1045285", "GSM1045286", "GSM1045287", "GSM1045288", "GSM1045289", "GSM1045290", "GSM1045291", "GSM1045292", "GSM1045293", "GSM1045294", "GSM1045295", "GSM1045296", "GSM1045297", "GSM1045298", "GSM1045299", "GSM1045300", "GSM1045301", "GSM1045302", "GSM1045303", "GSM1045304", "GSM1045305", "GSM1045306", "GSM1045307", "GSM1045308", "GSM1045309", "GSM1045310", "GSM1045311"], "sample_count": 121, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Breast Cancer Gene Expression Analysis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65194", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65194", "version": null, "note": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1588970", "GSM1588971", "GSM1588972", "GSM1588973", "GSM1588974", "GSM1588975", "GSM1588976", "GSM1588977", "GSM1588978", "GSM1588979", "GSM1588980", "GSM1588981", "GSM1588982", "GSM1588983", "GSM1588984", "GSM1588985", "GSM1588986", "GSM1588987", "GSM1588988", "GSM1588989", "GSM1588990", "GSM1588991", "GSM1588992", "GSM1588993", "GSM1588994", "GSM1588995", "GSM1588996", "GSM1588997", "GSM1588998", "GSM1588999", "GSM1589000", "GSM1589001", "GSM1589002", "GSM1589003", "GSM1589004", "GSM1589005", "GSM1589006", "GSM1589007", "GSM1589008", "GSM1589009", "GSM1589010", "GSM1589011", "GSM1589012", "GSM1589013", "GSM1589014", "GSM1589015", "GSM1589016", "GSM1589017", "GSM1589018", "GSM1589019", "GSM1589020", "GSM1589021", "GSM1589022", "GSM1589023", "GSM1589024", "GSM1589025", "GSM1589026", "GSM1589027", "GSM1589028", "GSM1589029", "GSM1589030", "GSM1589031", "GSM1589032", "GSM1589033", "GSM1589034", "GSM1589035", "GSM1589036", "GSM1589037", "GSM1589038", "GSM1589039", "GSM1589040", "GSM1589041", "GSM1589042", "GSM1589043", "GSM1589044", "GSM1589045", "GSM1589046", "GSM1589047", "GSM1589048", "GSM1589049", "GSM1589050", "GSM1589051", "GSM1589052", "GSM1589053", "GSM1589054", "GSM1589055", "GSM1589056", "GSM1589057", "GSM1589058", "GSM1589059", "GSM1589060", "GSM1589061", "GSM1589062", "GSM1589063", "GSM1589064", "GSM1589065", "GSM1589066", "GSM1589067", "GSM1589068", "GSM1589069", "GSM1589070", "GSM1589071", "GSM1589072", "GSM1589073", "GSM1589074", "GSM1589075", "GSM1589076", "GSM1589077", "GSM1589078", "GSM1589079", "GSM1589080", "GSM1589081", "GSM1589082", "GSM1589083", "GSM1589084", "GSM1589085", "GSM1589086", "GSM1589087", "GSM1589088", "GSM1589089", "GSM1589090", "GSM1589091", "GSM1589092", "GSM1589093", "GSM1589094", "GSM1589095", "GSM1589097", "GSM1589098", "GSM1589099", "GSM1589101", "GSM1589103", "GSM1589105", "GSM1589107", "GSM1589109", "GSM1589110", "GSM1589111", "GSM1589112", "GSM1589113", "GSM1589114", "GSM1589115", "GSM1589116", "GSM1589117", "GSM1589118", "GSM1589119", "GSM1589120", "GSM1589121", "GSM1589122", "GSM1589123", "GSM1589124", "GSM1589125", "GSM1589126", "GSM1589127", "GSM1589128", "GSM1589129", "GSM1589130", "GSM1589131", "GSM1589132", "GSM1589133", "GSM1589134", "GSM1589135", "GSM1589136", "GSM1589137", "GSM1589138", "GSM1589139", "GSM1589140", "GSM1589141", "GSM1589142", "GSM1589143", "GSM1589144", "GSM1589145", "GSM1589146", "GSM1589147", "GSM1589148", "GSM1589149", "GSM1589150", "GSM1589151", "GSM1589152", "GSM1589153"], "sample_count": 178, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression profiling of breast cancer samples from Institut Curie (Maire cohort) --Affy CDF", "resolution_checked_at": "2026-11-01T11:38:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE235168 not downloaded", "asset:data:geo:GSE235168 licence not read", "asset:data:geo:GSE26910 not downloaded", "asset:data:geo:GSE26910 licence not read", "asset:data:geo:GSE42568 not downloaded", "asset:data:geo:GSE42568 licence not read", "asset:data:geo:GSE65194 not downloaded", "asset:data:geo:GSE65194 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The Bayesian robust inference for differential gene expression (BRIDGE) [20] approach with R-package ‘bridge’ was used to robustly identify DEGs between BC and control samples from three microarray datasets (GSE26910, GSE42568, and GSE65194), separately. To identify DEGs from scRNA-seq count data (GSE235168), an R package, Seurat [82] was used with the cutoff at adj. p-value < 0.05 and |logFC| > 0.5. The Seurat [82] R-package utilized the non-parametric Wilcoxon rank sum test [84] to calculate the p-values from the robustness viewpoints."}}, {"id": "method-2", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "Random Forest"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE26910", "GSE42568", "GSE65194", "GSE235168"], "resolved_accessions": ["GSE26910", "GSE42568", "GSE65194", "GSE235168"], "statements": ["The gene-expression profiles datasets were downloaded from the GEO platform in the NCBI database with accession numbers GSE26910, GSE42568, GSE65194, GSE45827, and GSE54002 weblinks: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26910, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42568, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65194, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002, respectively (accessed on 12 January 2023). Also, one scRNA-seq dataset (GSE235168) was downloaded from the NCBI database with the weblink https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE235168 (accessed on 22 August 2023). The other relevant data are given in the Supplementary Tables."], "basis": "The paper names GSE26910, GSE42568, GSE65194, GSE235168 in NCBI-GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:37893423", "data:geo:GSE235168"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE235168"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:57:47Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 27740, "completion_tokens": 3471, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37893423", "type": "paper", "label": "pmid:37893423"}, {"id": "source:pmid:37893423", "type": "manuscript", "label": "PMID 37893423 full text"}, {"id": "data:geo:GSE235168", "type": "dataset", "label": "GEO GSE235168"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37893423", "type": "paper", "label": "pmid:37893423"}, {"id": "source:pmid:37893423", "type": "manuscript", "label": "PMID 37893423 full text"}, {"id": "data:geo:GSE235168", "type": "dataset", "label": "GEO GSE235168"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37893423", "type": "extraction", "used": ["source:pmid:37893423"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE235168", "type": "accession_resolution", "used": ["data:geo:GSE235168"], "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:37893423", "parent_hash": "sha256:4d1e87339b5d1f086b8ca10a88a4c279d787cb6c4ebbde34077996ae9a5b8c96", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE235168 licence not read", "asset:data:geo:GSE235168 not downloaded", "asset:data:geo:GSE26910 licence not read", "asset:data:geo:GSE26910 not downloaded", "asset:data:geo:GSE42568 licence not read", "asset:data:geo:GSE42568 not downloaded", "asset:data:geo:GSE65194 licence not read", "asset:data:geo:GSE65194 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Bayesian robust inference for differential gene expression (BRIDGE) [20] approach with R-package ‘bridge’ was used to robustly identify DEGs between BC and control samples from three microarray datasets (GSE26910, GSE42568, and GSE65194), separately. To identify DEGs from scRNA-seq count data (GSE235168), an R package, Seurat [82] was used with the cutoff at adj. p-value < 0.05 and |logFC| > 0.5. The Seurat [82] R-package utilized the non-parametric Wilcoxon rank sum test [84] to calculate the p-values from the robustness viewpoints."], "order_basis": "analysis_only", "id": "assay:1"}]}