← All .science files
pmid:30747226
A 6‑gene risk score system constructed for predicting the clinical prognosis of pancreatic adenocarcinoma patients.
Yan Liu · Dongyan Zhu · Hongjian Xing · Yi Hou · Yan Sun
Oncology reports · 2019 doi:10.3892/or.2019.6979
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 · 5 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 130 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 51 items
gaps array · 4 items
analysis object · 4 fields
methods array · 3 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
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 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 · 2 items
resolved_accessions array · 2 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 · 9 items
assays array · 1 item
[0] 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:30747226", "kind": "science-record", "revision": 8, "content_hash": "sha256:42607e58ad3783a2106ae28001c473f88ffd7b63d14b669c6c37bb6494fd9888", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:43:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A 6‑gene risk score system constructed for predicting the clinical prognosis of pancreatic adenocarcinoma patients.", "doi": "10.3892/or.2019.6979", "pmid": "30747226", "authors": ["Yan Liu", "Dongyan Zhu", "Hongjian Xing", "Yi Hou", "Yan Sun"], "journal": "Oncology reports", "year": 2019, "abstract": "Pancreatic adenocarcinoma (PAC) is the most common type of pancreatic cancer, which commonly has an unfavorable prognosis. The present study aimed to develop a novel prognostic prediction strategy for PAC patients. mRNA sequencing data of PAC (the training dataset) were extracted from The Cancer Genome Atlas database, and the validation datasets (GSE62452 and GSE79668) were acquired from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) between good and poor prognosis groups were analyzed by limma package, and then prognosis‑associated genes were screened using Cox regression analysis. Subsequently, the risk score system was constructed and confirmed using Kaplan‑Meier (KM) survival analysis. After the survival associated‑clinical factors were screened using Cox regression analysis, they were performed with stratified analysis. Using DAVID tool, the DEGs correlated with risk scores were conducted with enrichment analysis. The results revealed that there were a total of 242 DEGs between the poor and good prognosis groups. Afterwards, a risk score system was constructed based on 6 prognosis‑associated genes (CXCL11, FSTL4, SEZ6L, SPRR1B, SSTR2 and TINAG), which was confirmed in both the training and validation datasets. Cox regression analysis showed that risk score, targeted molecular therapy, and new tumor (the new tumor event days after the initial treatment according to the TCGA database) were significantly related to clinical prognosis. Under the same clinical condition, 6 clinical factors (age, history of chronic pancreatitis, alcohol consumption, radiation therapy, targeted molecular therapy and new tumor (event days) had significant associations with clinical prognosis. Under the same risk condition, only targeted molecular therapy was significantly correlated with clinical prognosis. In conclusion, the 6‑gene risk score system may be a promising strategy for predicting the outcome of PAC patients.", "claims": [{"id": "claim-method", "statement": "Under the thresholds of false discovery rate (FDR) <0.05 and |logfold change (FC)| >0.585, the differentially expressed genes (DEGs) between the good and poor prognosis groups were analyzed using the R package limma (http://www.bioconductor.org/packages/release/bioc/html/limma.html) (19).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30747226", "locator": "sections[5] \"Differential expression analysis\" paragraph 2", "quote": "Under the thresholds of false discovery rate (FDR) <0.05 and |logfold change (FC)| >0.585, the differentially expressed genes (DEGs) between the good and poor prognosis groups were analyzed using the R package limma (http://www.bioconductor.org/packages/release/bioc/html/limma.html) (19)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used during the present study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30747226", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used during the present study are available from the corresponding author upon reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30747226"], "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:GSE62452"], "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:GSE62452"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30747226", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/or.2019.6979", "sha256": "sha256:8dd62bb23db81825447e71bf881310facbb24b182b57eda7f78a6b820fab474a", "bytes": 21365, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/or.2019.6979", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6365694", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62452", "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=GSE62452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62452", "version": null, "note": "The datasets used during the present study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used during the present study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1527105", "GSM1527106", "GSM1527107", "GSM1527108", "GSM1527109", "GSM1527110", "GSM1527111", "GSM1527112", "GSM1527113", "GSM1527114", "GSM1527115", "GSM1527116", "GSM1527117", "GSM1527118", "GSM1527119", "GSM1527120", "GSM1527121", "GSM1527122", "GSM1527123", "GSM1527124", "GSM1527125", "GSM1527126", "GSM1527127", "GSM1527128", "GSM1527129", "GSM1527130", "GSM1527131", "GSM1527132", "GSM1527133", "GSM1527134", "GSM1527135", "GSM1527136", "GSM1527137", "GSM1527138", "GSM1527139", "GSM1527140", "GSM1527141", "GSM1527142", "GSM1527143", "GSM1527144", "GSM1527145", "GSM1527146", "GSM1527147", "GSM1527148", "GSM1527149", "GSM1527150", "GSM1527151", "GSM1527152", "GSM1527153", "GSM1527154", "GSM1527155", "GSM1527156", "GSM1527157", "GSM1527158", "GSM1527159", "GSM1527160", "GSM1527161", "GSM1527162", "GSM1527163", "GSM1527164", "GSM1527165", "GSM1527166", "GSM1527167", "GSM1527168", "GSM1527169", "GSM1527170", "GSM1527171", "GSM1527172", "GSM1527173", "GSM1527174", "GSM1527175", "GSM1527176", "GSM1527177", "GSM1527178", "GSM1527179", "GSM1527180", "GSM1527181", "GSM1527182", "GSM1527183", "GSM1527184", "GSM1527185", "GSM1527186", "GSM1527187", "GSM1527188", "GSM1527189", "GSM1527190", "GSM1527191", "GSM1527192", "GSM1527193", "GSM1527194", "GSM1527195", "GSM1527196", "GSM1527197", "GSM1527198", "GSM1527199", "GSM1527200", "GSM1527201", "GSM1527202", "GSM1527203", "GSM1527204", "GSM1527205", "GSM1527206", "GSM1527207", "GSM1527208", "GSM1527209", "GSM1527210", "GSM1527211", "GSM1527212", "GSM1527213", "GSM1527214", "GSM1527215", "GSM1527216", "GSM1527217", "GSM1527218", "GSM1527219", "GSM1527220", "GSM1527221", "GSM1527222", "GSM1527223", "GSM1527224", "GSM1527225", "GSM1527226", "GSM1527227", "GSM1527228", "GSM1527229", "GSM1527230", "GSM1527231", "GSM1527232", "GSM1527233", "GSM1527234"], "sample_count": 130, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Microarray gene-expression profiles of 69 pancreatic tumors and 61 adjacent non-tumor tissue from patients with pancreatic ductal adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE79668", "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=GSE79668", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE79668", "version": null, "note": "The datasets used during the present study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used during the present study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2100851", "GSM2100852", "GSM2100853", "GSM2100854", "GSM2100855", "GSM2100856", "GSM2100857", "GSM2100858", "GSM2100859", "GSM2100860", "GSM2100861", "GSM2100862", "GSM2100863", "GSM2100864", "GSM2100865", "GSM2100866", "GSM2100867", "GSM2100868", "GSM2100869", "GSM2100870", "GSM2100871", "GSM2100872", "GSM2100873", "GSM2100874", "GSM2100875", "GSM2100876", "GSM2100877", "GSM2100878", "GSM2100879", "GSM2100880", "GSM2100881", "GSM2100882", "GSM2100883", "GSM2100884", "GSM2100885", "GSM2100886", "GSM2100887", "GSM2100888", "GSM2100889", "GSM2100890", "GSM2100891", "GSM2100892", "GSM2100893", "GSM2100894", "GSM2100895", "GSM2100896", "GSM2100897", "GSM2100898", "GSM2100899", "GSM2100900", "GSM2100901"], "sample_count": 51, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "RNA-sequencing of human pancreatic adenocarcinoma cancer tissues", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE62452 not downloaded", "asset:data:geo:GSE62452 licence not read", "asset:data:geo:GSE79668 not downloaded", "asset:data:geo:GSE79668 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": "Under the thresholds of false discovery rate (FDR) <0.05 and |logfold change (FC)| >0.585, the differentially expressed genes (DEGs) between the good and poor prognosis groups were analyzed using the R package limma (http://www.bioconductor.org/packages/release/bioc/html/limma.html) (19)."}}, {"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": "KM"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}], "targets": [], "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": ["GSE79668", "GSE62452"], "resolved_accessions": ["GSE79668", "GSE62452"], "statements": ["The datasets used during the present study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE79668, GSE62452 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:30747226", "data:geo:GSE62452"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE62452"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:48Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 16050, "completion_tokens": 1501, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:30747226", "type": "paper", "label": "pmid:30747226"}, {"id": "source:pmid:30747226", "type": "manuscript", "label": "PMID 30747226 full text"}, {"id": "data:geo:GSE62452", "type": "dataset", "label": "GEO GSE62452"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30747226", "type": "paper", "label": "pmid:30747226"}, {"id": "source:pmid:30747226", "type": "manuscript", "label": "PMID 30747226 full text"}, {"id": "data:geo:GSE62452", "type": "dataset", "label": "GEO GSE62452"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30747226", "type": "extraction", "used": ["source:pmid:30747226"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE62452", "type": "accession_resolution", "used": ["data:geo:GSE62452"], "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:30747226", "parent_hash": "sha256:31f47b75fa29c031665a7d6ceec2eb81cdd85236451ec1331e2d6f8de00eadb4", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE62452 licence not read", "asset:data:geo:GSE62452 not downloaded", "asset:data:geo:GSE79668 licence not read", "asset:data:geo:GSE79668 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Under the thresholds of false discovery rate (FDR) <0.05 and |logfold change (FC)| >0.585, the differentially expressed genes (DEGs) between the good and poor prognosis groups were analyzed using the R package limma (http://www.bioconductor.org/packages/release/bioc/html/limma.html) (19)."], "order_basis": "analysis_only", "id": "assay:1"}]}