← All .science files
pmid:41162968
BRCAGenie: A machine learning-driven 43-gene polygenic risk score model for precision prediction of breast cancer survival.
Journal of translational medicine · 2025 doi:10.1186/s12967-025-07100-2
Paper
partial
Experiment
partial
Data
partial
Analysis
absent
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
generator object · 3 fields
paper object · 10 fields
claims array · 1 item
gaps array · 2 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 · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
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 · 3 items
data object · 3 fields
assets array · 8 items
[0] object · 15 fields
structure object · 1 field
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 9 items
[0] array · 3 items
[1] array · 1 item
[2] array · 3 items
[3] array · 2 items
[4] array · 2 items
[5] array · 3 items
[6] array · 2 items
[7] array · 3 items
[8] array · 2 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 7 items
[0] array · 3 items
[1] array · 3 items
[2] array · 2 items
[3] array · 3 items
[4] array · 2 items
[5] array · 3 items
[6] array · 2 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 7 items
[0] array · 3 items
[1] array · 3 items
[2] array · 2 items
[3] array · 3 items
[4] array · 2 items
[5] array · 3 items
[6] array · 2 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 44 items
[0] array · 3 items
[1] array · 3 items
[2] array · 3 items
[3] array · 3 items
[4] array · 3 items
[5] array · 3 items
[6] array · 3 items
[7] array · 3 items
[8] array · 3 items
[9] array · 3 items
[10] array · 3 items
[11] array · 3 items
[12] array · 3 items
[13] array · 3 items
[14] array · 3 items
[15] array · 3 items
[16] array · 3 items
[17] array · 3 items
[18] array · 3 items
[19] array · 3 items
[20] array · 3 items
[21] array · 3 items
[22] array · 3 items
[23] array · 3 items
[24] array · 3 items
[25] array · 3 items
[26] array · 3 items
[27] array · 3 items
[28] array · 3 items
[29] array · 3 items
[30] array · 3 items
[31] array · 3 items
[32] array · 3 items
[33] array · 3 items
[34] array · 3 items
[35] array · 3 items
[36] array · 3 items
[37] array · 3 items
[38] array · 3 items
[39] array · 3 items
[40] array · 3 items
[41] array · 3 items
[42] array · 3 items
[43] array · 3 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 45 items
[0] array · 3 items
[1] array · 3 items
[2] array · 3 items
[3] array · 3 items
[4] array · 3 items
[5] array · 3 items
[6] array · 3 items
[7] array · 3 items
[8] array · 3 items
[9] array · 3 items
[10] array · 3 items
[11] array · 3 items
[12] array · 3 items
[13] array · 3 items
[14] array · 3 items
[15] array · 3 items
[16] array · 3 items
[17] array · 3 items
[18] array · 3 items
[19] array · 3 items
[20] array · 3 items
[21] array · 3 items
[22] array · 3 items
[23] array · 3 items
[24] array · 3 items
[25] array · 3 items
[26] array · 3 items
[27] array · 3 items
[28] array · 3 items
[29] array · 3 items
[30] array · 3 items
[31] array · 3 items
[32] array · 3 items
[33] array · 3 items
[34] array · 3 items
[35] array · 3 items
[36] array · 3 items
[37] array · 3 items
[38] array · 3 items
[39] array · 3 items
[40] array · 3 items
[41] array · 3 items
[42] array · 3 items
[43] array · 3 items
[44] array · 3 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 14 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
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 44 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
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 6 items
[23] array · 6 items
[24] array · 6 items
[25] array · 6 items
[26] array · 6 items
[27] array · 6 items
[28] array · 6 items
[29] array · 6 items
[30] array · 6 items
[31] array · 6 items
[32] array · 6 items
[33] array · 6 items
[34] array · 6 items
[35] array · 6 items
[36] array · 6 items
[37] array · 6 items
[38] array · 6 items
[39] array · 6 items
[40] array · 6 items
[41] array · 6 items
[42] array · 6 items
[43] array · 6 items
gaps array · 1 item
capability object · 3 fields
readiness object · 8 fields
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 8 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 7 fields
providers array · 0 items
target_providers array · 0 items
disagreements array · 0 items
agreement_basis object · 2 fields
decisive_fields array · 4 items
human_critique object · 5 fields
stages array · 7 items
[0] object · 4 fields
[1] object · 4 fields
evidence object · 1 field
provider_errors array · 4 items
[0] object · 4 fields
[1] object · 4 fields
[2] object · 4 fields
[3] object · 4 fields
[2] object · 4 fields
[3] object · 4 fields
[4] object · 4 fields
[5] object · 4 fields
[6] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 1 item
activities array · 1 item
agents array · 1 item
lineage object · 4 fields
gaps array · 14 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41162968", "kind": "science-record", "revision": 2, "content_hash": "sha256:06728b9ca02129ab744cd7d0aed4848e97b3e704b05eb1c4aa6c4c835577ef62", "created_at": "2026-11-01T10:25:53Z", "updated_at": "2026-11-01T14:01:50Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "BRCAGenie: A machine learning-driven 43-gene polygenic risk score model for precision prediction of breast cancer survival.", "doi": "10.1186/s12967-025-07100-2", "pmid": "41162968", "authors": null, "journal": "Journal of translational medicine", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41162968"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:41162968", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41162968' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41162968", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12967-025-07100-2", "sha256": "sha256:b29e9dd000caf4b41afc4594c8eb87c921d4c16b9510daa5c2cdd78e2088574e", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12967-025-07100-2", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:41162968:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c89f91c9866cfca4bf2c20c4409c90961a05403401705f624c7ffbcfc34e8f2e", "bytes": 655, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#Tab1", "version": null, "note": "Clinical and demographic characteristics of the 1031 subjects in The Cancer Genome Atlas Breast Cancer (TCGA-BRCA) cohort", "structure": {"pmcid": "PMC12574034", "section_index": 4, "section_title": "Data pre-processing", "row_count": 9, "column_count": 3}, "table": {"label": "Table 1", "caption": "Clinical and demographic characteristics of the 1031 subjects in The Cancer Genome Atlas Breast Cancer (TCGA-BRCA) cohort", "rows": [["Variables", "Characteristics", "Overall"], ["(N = 1031)"], ["Age at diagnosis", "Mean (SD)", "58.7 (12.9)"], ["Median [Min, Max]", "58.9 [26.6, 90.0]"], ["Missing", "14 (1.4%)"], ["Three year survival", "Survival Time ≤ 3 years", "603 (58.5%)"], ["Survival Time > 3 years", "428 (41.5%)"], ["Five year survival", "Survival Time ≤ 5 years", "784 (76.0%)"], ["Survival Time > 5 years", "247 (24.0%)"]], "row_count": 9, "column_count": 3, "numeric_cells": 12, "header_rows": 2, "locator": "section[4]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:41162968:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:842481048ba15bfe02bec228e77010bd9f397be01362b2dfe094cc9d1ada3c89", "bytes": 656, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab2", "version": null, "note": "Clinical and demographic characteristics of the 1904 subjects in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort", "structure": {"pmcid": "PMC12574034", "section_index": 10, "section_title": "External validation", "row_count": 7, "column_count": 3}, "table": {"label": "Table 2", "caption": "Clinical and demographic characteristics of the 1904 subjects in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort", "rows": [["Variables", "Characteristics", "Overall (N = 1904)"], ["Age at diagnosis", "Mean (SD)", "61.1 (13.0)"], ["Median [Min, Max]", "61.8 [21.9, 96.3]"], ["Three year survival", "Survival time ≤ 3 years", "253 (13.3%)"], ["Survival time > 3 years", "1651 (86.7%)"], ["Five year survival", "Survival time ≤ 5 years", "472 (24.8%)"], ["Survival time > 5 years", "1432 (75.2%)"]], "row_count": 7, "column_count": 3, "numeric_cells": 11, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:41162968:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ce7a179f1bf5e9ccbb0b10bc6bb8310be4421e01f86ac63439bfdf6965453b12", "bytes": 620, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#Tab3", "version": null, "note": "Clinical and demographic characteristics of the 2969 subjects in the Gene Expression Omnibus (GSE96058) cohort", "structure": {"pmcid": "PMC12574034", "section_index": 10, "section_title": "External validation", "row_count": 7, "column_count": 3}, "table": {"label": "Table 3", "caption": "Clinical and demographic characteristics of the 2969 subjects in the Gene Expression Omnibus (GSE96058) cohort", "rows": [["Variables", "Characteristics", "Overall (N = 2969)"], ["Age at diagnosis", "Mean (SD)", "62.8 (13.1)"], ["Median [Min, Max]", "64.0 [24.0, 96.0]"], ["Three year survival", "Survival Time ≤ 3 years", "465 (15.7%)"], ["Survival Time > 3 years", "2504 (84.3%)"], ["Five year survival", "Survival Time ≤ 5 years", "1882 (63.4%)"], ["Survival Time > 5 years", "1087 (36.6%)"]], "row_count": 7, "column_count": 3, "numeric_cells": 11, "header_rows": 1, "locator": "section[10]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:41162968:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1885b79945d1ebe6522b5fca641acffea6aaa46701a108ca5ec9510089107eaf", "bytes": 2564, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab4", "version": null, "note": "Final set of 43 genes selected to be included in the PRS after forward stepwise selection", "structure": {"pmcid": "PMC12574034", "section_index": 14, "section_title": "Development of PRS with machine learning", "row_count": 44, "column_count": 3}, "table": {"label": "Table 4", "caption": "Final set of 43 genes selected to be included in the PRS after forward stepwise selection", "rows": [["Gene name", "Gene symbol", "Multivariate cox coefficient"], ["Endoplasmic reticulum protein 27", "ERP27", "− 2.6490"], ["NUMB like endocytic adaptor protein", "NUMBL", "− 2.6098"], ["Ribosomal protein S6 Kinase B1", "RPS6KB1", "− 2.0842"], ["Brain expressed X-Linked 5", "BEX5", "− 1.7170"], ["Transmembrane Protein 14B", "TMEM14B", "− 1.6914"], ["Solute carrier family 16 member 13", "SLC16A13", "− 1.5049"], ["Cytochrome P450 family 4 subfamily F Member 11", "CYP4F11", "− 1.4646"], ["Growth regulation by estrogen in breast cancer 1 like", "GREB1L", "− 1.2990"], ["Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3F", "APOBEC3F", "− 1.2551"], ["Ribosomal protein S29", "RPS29", "− 1.1681"], ["5'-nucleotidase domain containing 3", "NT5DC3", "− 1.1261"], ["Prostaglandin E synthase 3", "PTGES3", "− 0.9675"], ["Zinc finger protein 326", "ZNF326", "− 0.8347"], ["Metastasis associated 1 family member 2", "MTA2", "− 0.8020"], ["Syndecan 3", "SDC3", "− 0.6365"], ["Xg Glycoprotein", "XG", "− 0.4343"], ["Secretogranin II", "SCG2", "0.3120"], ["3-Hydroxybutyrate dehydrogenase 1", "BDH1", "0.6032"], ["ALX Homeobox 4", "ALX4", "0.6334"], ["Cytokine Like 1", "CYTL1", "0.6467"], ["ATPase H + Transporting V1 Subunit E1", "ATP6V1E1", "0.6498"], ["Surfeit 6", "SURF6", "0.6566"], ["Transmembrane Protein 41A", "TMEM41A", "0.6600"], ["HOX Transcript Antisense RNA", "HOTAIR", "0.6655"], ["PPFIA Binding Protein 2", "PPFIBP2", "0.6724"], ["Complement C6", "C6", "0.7013"], ["Malignant T-Cell Amplified Sequence 1", "MCTS1", "0.7264"], ["5'-Nucleotidase Ecto", "NT5E", "0.7425"], ["Argininosuccinate Synthase 1", "ASS1", "0.7785"], ["Transmembrane And Coiled-Coil Domains 1", "TMCO1", "0.7987"], ["P21 (RAC1) Activated Kinase 6", "PAK6", "0.8609"], ["Ring Finger Protein 135", "RNF135", "0.9085"], ["Globoside Alpha-1,3-N-Acetylgalactosaminyltransferase 1", "GBGT1", "0.9389"], ["Transient Receptor Potential Cation Channel Subfamily M Member 2", "TRPM2", "1.0328"], ["Exocyst Complex Component 1", "EXOC1", "1.0401"], ["Phosphoglycerate Kinase 1", "PGK1", "1.1237"], ["Cation Channel Sperm Associated 3", "CATSPER3", "1.1537"], ["Peroxidasin Like", "PXDNL", "1.2026"], ["Phosphofructokinase, Liver Type", "PFKL", "1.2867"], ["Ectodysplasin A2 Receptor", "EDA2R", "1.2898"], ["Inorganic Pyrophosphatase 2", "PPA2", "1.4623"], ["Tubulin Delta 1", "TUBD1", "2.0995"], ["C–C Motif Chemokine Receptor 7", "CCR7", "3.3420"]], "row_count": 44, "column_count": 3, "numeric_cells": 84, "header_rows": 1, "locator": "section[14]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:41162968:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:978fe78c3ea9c5c6b2d9051344d3d2f00ff1b57b55d990699405a648b6835e92", "bytes": 1748, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#Tab5", "version": null, "note": "Genetic and clinical features included in the PRS model", "structure": {"pmcid": "PMC12574034", "section_index": 20, "section_title": "Incorporation of clinical data", "row_count": 45, "column_count": 3}, "table": {"label": "Table 5", "caption": "Genetic and clinical features included in the PRS model", "rows": [["Variable", "Multivariate coefficient", "P-value"], ["RPS6KB1", "− 1.0039", "3.68E−03"], ["TUBD1", "0.9280", "1.07E−02"], ["PXDNL", "0.5045", "1.17E−07"], ["NUMBL", "− 0.9295", "1.55E−05"], ["CCR7", "0.4976", "2.98E−03"], ["PPA2", "0.1377", "4.25E−01"], ["ALX4", "0.3286", "8.36E−07"], ["PFKL", "0.5750", "3.32E−03"], ["RNF135", "0.4621", "8.77E−05"], ["EXOC1", "0.4085", "1.73E−02"], ["APOBEC3F", "− 0.7288", "1.16E−07"], ["EDA2R", "0.6618", "1.33E−05"], ["PGK1", "0.5598", "1.83E−04"], ["CATSPER3", "0.8440", "2.44E−09"], ["SLC16A13", "− 0.6982", "3.31E−04"], ["TRPM2", "0.2822", "3.62E−02"], ["GBGT1", "0.7154", "5.28E−07"], ["TMEM14B", "− 0.4823", "2.32E−02"], ["PTGES3", "0.0636", "6.82E−01"], ["ERP27", "− 1.1711", "1.83E−04"], ["NT5E", "0.2645", "3.37E−02"], ["BEX5", "− 0.6013", "1.33E−03"], ["C6", "0.3617", "1.37E−04"], ["ASS1", "0.0170", "8.97E−01"], ["PAK6", "0.4733", "3.96E−05"], ["TMCO1", "− 0.0133", "9.29E−01"], ["CYTL1", "0.5822", "1.15E−06"], ["PPFIBP2", "0.3625", "4.37E−04"], ["NT5DC3", "− 0.7307", "3.33E−03"], ["MTA2", "− 0.3961", "6.30E−03"], ["RPS29", "− 0.7609", "5.95E−05"], ["GREB1L", "− 0.7856", "2.12E−04"], ["TMEM41A", "0.5451", "1.18E−04"], ["ATP6V1E1", "0.1664", "2.53E−01"], ["HOTAIR", "0.3975", "2.92E−04"], ["SCG2", "0.2105", "4.62E−05"], ["SURF6", "0.3467", "1.60E−02"], ["ZNF326", "− 0.6445", "3.16E−04"], ["SDC3", "− 0.3120", "5.36E−02"], ["MCTS1", "0.5090", "2.62E−03"], ["XG", "− 0.0445", "6.93E−01"], ["BDH1", "0.2874", "3.09E−02"], ["CYP4F11", "− 0.9185", "1.21E−03"], ["Age at Diagnosis", "0.0107", "2.88E−01"]], "row_count": 45, "column_count": 3, "numeric_cells": 96, "header_rows": 1, "locator": "section[20]/table-wrap[1]#Tab5"}}, {"id": "asset:table:pmid:41162968:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a23e69f697e32081442e5a86f8df5ecbd170e1334d78373cf9e992785db12185", "bytes": 2347, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[1]#Tab6", "version": null, "note": "Model performance of our 43-gene risk score model compared with other published studies", "structure": {"pmcid": "PMC12574034", "section_index": 25, "section_title": "Discussion", "row_count": 14, "column_count": 4}, "table": {"label": "Table 6", "caption": "Model performance of our 43-gene risk score model compared with other published studies", "rows": [["Study", "Gene Number", "Three-year AUC(t)", "Five-year AUC(t)"], ["Construct ceRNA network and risk model of breast cancer using machine learning methods under the mechanism of Cuproptosis [19]", "4", "0.604", "0.550"], ["Establishment of a novel CNV-related prognostic signature predicting prognosis in patients with breast cancer [59]", "9", "0.630", "0.580"], ["Construction and validation of a newly prognostic signature for CRISPR-Cas9-based cancer dependency map genes in breast cancer [27]", "6", "0.649", "0.618"], ["Identification of a 6-gene signature for the survival prediction of breast cancer patients based on integrated multi-omics data analysis [60]", "6", "0.660", "0.630"], ["A novel hypoxia- and lactate metabolism-related signature to predict prognosis and immunotherapy responses for breast cancer by integrating machine learning and bioinformatic analyses [26]", "5", "0.671", "0.638"], ["A novel disulfidptosis-associated expression pattern in breast cancer based on machine learning [22]", "4", "0.687", "0.644"], ["Insights into a Machine Learning-Based Palmitoylation-Related Gene Model for Predicting the Prognosis and Treatment Response of Breast Cancer Patients [28]", "11", "0.743", "0.644"], ["Identification of prognostic genes for breast cancer related to systemic lupus erythematosus by integrated analysis and machine learning [32]", "3", "0.690", "0.690"], ["Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database [61]", "10", "0.717", "0.717"], ["A six-long non-coding RNAs signature as a potential prognostic marker for survival prediction of ER-positive breast cancer patients [62]", "6", "0.725", "0.717"], ["Integration of Bioinformatics and Machine Learning to Identify CD8 + T Cell-Related Prognostic Signature to Predict Clinical Outcomes and Treatment Response in Breast Cancer Patients [23]", "2", "0.754", "0.727"], ["Development and validation of a prognostic model and gene co-expression networks for breast carcinoma based on scRNA-seq and bulk-seq data [34]", "10", "0.772", "0.736"], ["43-gene risk score model in our study", "43", "0.736", "0.751"]], "row_count": 14, "column_count": 4, "numeric_cells": 52, "header_rows": 1, "locator": "section[25]/table-wrap[1]#Tab6"}}, {"id": "asset:table:pmid:41162968:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a1696a43bd8c9b558a3f90395df74bbaead69378d6e3bdb01ee5e6d2d9d98011", "bytes": 3369, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[2]#Tab7", "version": null, "note": "Summary of literature review of the 43 genes identified in our study", "structure": {"pmcid": "PMC12574034", "section_index": 25, "section_title": "Discussion", "row_count": 44, "column_count": 6}, "table": {"label": "Table 7", "caption": "Summary of literature review of the 43 genes identified in our study", "rows": [["Gene name", "Gene Symbol", "PRSCoefficient", "Good/poor prognostic marker (PRS)", "Good/poor prognostic marker (Lit search)", "References"], ["C–C Motif Chemokine Receptor 7", "CCR7", "3.3420", "", "", "[70–72]"], ["Tubulin Delta 1", "TUBD1", "2.0995", "", "", "[73, 74]"], ["Inorganic Pyrophosphatase 2", "PPA2", "1.4623", "", "", "[75, 76]"], ["Ectodysplasin A2 Receptor", "EDA2R", "1.2898", "", "", "[77, 78]"], ["Phosphofructokinase, Liver Type", "PFKL", "1.2867", "", "", "[79, 80]"], ["Peroxidasin Like", "PXDNL", "1.2026", "", "", "[81, 82]"], ["Cation Channel Sperm Associated 3", "CATSPER3", "1.1537", "", "", "[83]"], ["Phosphoglycerate Kinase 1", "PGK1", "1.1237", "", "", "[84–88]"], ["Exocyst Complex Component 1", "EXOC1", "1.0401", "", "", "[27, 89]"], ["Transient Receptor Potential Cation Channel Subfamily M Member 2", "TRPM2", "1.0328", "", "", "[90–92]"], ["Globoside Alpha-1,3-N-Acetylgalactosaminyltransferase 1", "GBGT1", "0.9389", "", "", "[93]"], ["Ring Finger Protein 135", "RNF135", "0.9085", "", "", "[94, 95]"], ["P21 (RAC1) Activated Kinase 6", "PAK6", "0.8609", "", "", "[96, 97]"], ["Transmembrane And Coiled-Coil Domains 1", "TMCO1", "0.7987", "", "", "[98, 99]"], ["Argininosuccinate Synthase 1", "ASS1", "0.7785", "", "", "[100–103]"], ["5'-Nucleotidase Ecto", "NT5E", "0.7425", "", "", "[104–107]"], ["Malignant T-Cell Amplified Sequence 1", "MCTS1", "0.7264", "", "", "[108–110]"], ["Complement C6", "C6", "0.7013", "", "", "[111]"], ["PPFIA Binding Protein 2", "PPFIBP2", "0.6724", "", "", "[112–114]"], ["HOX Transcript Antisense RNA", "HOTAIR", "0.6655", "", "", "[115–119]"], ["Transmembrane Protein 41A", "TMEM41A", "0.6600", "", "", "[120]"], ["Surfeit 6", "SURF6", "0.6566", "", "", "[121]"], ["ATPase H + Transporting V1 Subunit E1", "ATP6V1E1", "0.6498", "", "", "[122]"], ["Cytokine Like 1", "CYTL1", "0.6467", "", "", "[123–125]"], ["ALX Homeobox 4", "ALX4", "0.6334", "", "", "[126–130]"], ["3-Hydroxybutyrate Dehydrogenase 1", "BDH1", "0.6032", "", "", "[131, 132]"], ["Secretogranin II", "SCG2", "0.3120", "", "", "[133–136]"], ["Xg Glycoprotein", "XG", "− 0.4343", "", "", ""], ["Syndecan 3", "SDC3", "− 0.6365", "", "", "[137]"], ["Metastasis Associated 1 Family Member 2", "MTA2", "− 0.8020", "", "", "[138–141]"], ["Zinc Finger Protein 326", "ZNF326", "− 0.8347", "", "", "[142–146]"], ["Prostaglandin E Synthase 3", "PTGES3", "− 0.9675", "", "", "[147–150]"], ["5'-Nucleotidase Domain Containing 3", "NT5DC3", "− 1.1261", "", "", "[151, 152]"], ["Ribosomal Protein S29", "RPS29", "− 1.1681", "", "", "[153, 154]"], ["Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3F", "APOBEC3F", "− 1.2551", "", "", "[155, 156]"], ["Growth Regulation By Estrogen In Breast Cancer 1 Like", "GREB1L", "− 1.2990", "", "", "[157]"], ["Cytochrome P450 Family 4 Subfamily F Member 11", "CYP4F11", "− 1.4646", "", "", "[158–160]"], ["Solute Carrier Family 16 Member 13", "SLC16A13", "− 1.5049", "", "", "[161, 162]"], ["Transmembrane Protein 14B", "TMEM14B", "− 1.6914", "", "", "[34, 163]"], ["Brain Expressed X-Linked 5", "BEX5", "− 1.7170", "", "", "[164]"], ["Ribosomal Protein S6 Kinase B1", "RPS6KB1", "− 2.0842", "", "", "[165–167]"], ["NUMB Like Endocytic Adaptor Protein", "NUMBL", "− 2.6098", "", "", "[168]"], ["Endoplasmic Reticulum Protein 27", "ERP27", "− 2.6490", "", "", "[169–172]"]], "row_count": 44, "column_count": 6, "numeric_cells": 126, "header_rows": 1, "locator": "section[25]/table-wrap[2]#Tab7"}}], "gaps": ["asset:source:pmid:41162968 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41162968", "asset:table:pmid:41162968:1", "asset:table:pmid:41162968:2", "asset:table:pmid:41162968:3", "asset:table:pmid:41162968:4", "asset:table:pmid:41162968:5", "asset:table:pmid:41162968:6", "asset:table:pmid:41162968:7"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41162968"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:9c51aef71106c06759f1e65e8ae2eba45994a011695979f083f2a0ce689b1457", "type": "sep_package", "label": "SEP v1 package for pmid:41162968"}], "activities": [{"id": "activity:conversion:pmid:41162968", "type": "conversion", "used": ["package:9c51aef71106c06759f1e65e8ae2eba45994a011695979f083f2a0ce689b1457"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:41162968", "parent_hash": "sha256:15f35e134b4d8b4a3198922effc99acc0f80786ae7c76f12ab42d44ae32ad6f6", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:41162968 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41162968' does not resolve to a declared asset", "targets"]}