Integrated expression profiles analysis reveals novel predictive biomarker in pancreatic ductal adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28881752", "kind": "science-record", "revision": 8, "content_hash": "sha256:d8bb264d5a325dbc5a39ea052ac4d813fdcaf6e856d0b78872bbae89cd740bf2", "created_at": "2026-11-01T15:40:28Z", "updated_at": "2026-11-01T22:43:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated expression profiles analysis reveals novel predictive biomarker in pancreatic ductal adenocarcinoma.", "doi": "10.18632/oncotarget.16732", "pmid": "28881752", "authors": ["Hongzhe Li", "Xinjing Wang", "Yuan Fang", "Zhen Huo", "Xiongxiong Lu", "Xi Zhan", "Xiaxin Deng", "Chenghong Peng", "Baiyong Shen"], "journal": "Oncotarget", "year": 2017, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) is the most lethal human malignant tumor, with a dismal 5-year survival rate of less than 5%. The lack of specific symptoms at early tumor stages and the paucity of biomarkers contribute to the poor diagnosis of pancreatic ductal adenocarcinoma. To improve prognosis, a screening biomarker for early diagnosis of pancreatic cancer is in urgent need. We searched the databases of expression profiling by array on GEO, aiming at comparing gene expression profile of matched pairs of pancreatic tumor and adjacent non-tumor tissues, and we screen out 4 suitable series of gene expression microarray data (\"GSE15471\", \"GSE18670\", \"GSE28735\" and \"GSE58561\"). After carefully analyzing, 13 DEGs (MYOF, SLC6A6, S100P, HK2, IFI44L, OSBPL3, IGF2BP3, PDK4, IL1R2, ERO1A, EGLN3, PLAC8 and ACSL5) are significantly differentially expressed in four microarray databases in common. After analyzing mRNA expression data and clinical follow-up survey provided in the TCGA database and clinicopathological data of 137 pancreatic ductal adenocarcinoma patients, we carefully demonstrated that three of these differentially expressed genes (ERO1A, OSBPL3 and IFI44L) are correlated with poor prognosis of pancreatic ductal adenocarcinoma patients. In addition, we revealed that cell-matrix adhesion and extracellular matrix were top significantly regulated pathways in pancreatic ductal adenocarcinoma and depicted two protein-protein interactions networks of extracellular matrix related Genes which are dysregulated according to 4 gene expression microarray data mentioned above (\"GSE15471\", \"GSE18670\", \"GSE28735\" and \"GSE58561\"), hoping to shed light on the etiology of PDAC and mechanisms of drug resistance in PDAC in this study.", "claims": [{"id": "claim-method", "statement": "The postoperative survival of patients with PDAC was analyzed by the Kaplan-Meier estimator and tested by the log rank.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28881752", "locator": "sections[15] \"Algorithm and Statistical analysis\" paragraph 3", "quote": "The postoperative survival of patients with PDAC was analyzed by the Kaplan-Meier estimator and tested by the log rank."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All mRNA expression profiling data series involved in this study were available to public.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28881752", "locator": "sections[12] \"Data source\" paragraph 2", "quote": "All mRNA expression profiling data series involved in this study were available to public."}], "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:28881752"], "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:GSE15471"], "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:GSE15471"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28881752", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.16732", "sha256": 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PMID: 25148029 [25]"]], "row_count": 5, "column_count": 6, "numeric_cells": 20, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:28881752:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:696284a1f853b95676dbc7a9fb101fe1da40eec1ffb0514e28963f09c8e1e115", "bytes": 1114, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T2", "version": null, "note": "Overall survival (OS), disease free survival (DFS) and median month's survival of ERO1A, OSBPL3 and IFI44L", "structure": {"pmcid": "PMC5581051", "section_index": 5, "section_title": "ERO1A, OSBPL3 and IFI44L are potential marker for PDAC", "row_count": 16, "column_count": 5}, "table": {"label": "Table 2", "caption": "Overall survival (OS), disease free survival (DFS) and median month's survival of ERO1A, OSBPL3 and IFI44L", "rows": [["", "Overall 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"locator": "section[5]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:28881752:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:21cc1210478b4222d24056ddfc22af0ed96b211168ade88ea64d11ed35073094", "bytes": 1911, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#T3", "version": null, "note": "Correlation between ERO1A, OSBPL3 and IFI44L expression and clinicopathological characteristics of PDAC patients (n=137). *P<0.05,**P<0.01,***p<0.001", "structure": {"pmcid": "PMC5581051", "section_index": 5, "section_title": "ERO1A, OSBPL3 and IFI44L are potential marker for PDAC", "row_count": 26, "column_count": 11}, "table": {"label": "Table 3", "caption": "Correlation between ERO1A, OSBPL3 and IFI44L expression and clinicopathological characteristics of PDAC patients (n=137). *P<0.05,**P<0.01,***p<0.001", "rows": [["Variables", "Number of cases", "ERO1A immunostaining", "P value", "OSBPL3 immunostaining", "P value", "IFI44L immunostaining", "P value"], ["", "", "“++or+” n=89", "“±or-” n=48", "", "“++or+” n=98", "“±or-” n=39", "", "“++or+” n=88", "“±or-” n=49", ""], ["Gender", "", "", "", "", "", "", "", "", "", ""], ["male", "76", "48", "28", "0.621", "53", "23", "0.603", "46", "30", "0.312"], ["female", "61", "41", "20", "42", "19", "45", "16"], ["Age(years)", "", "", "", "", "", "", "", "", "", ""], ["<60", "45", "25", "20", "0.106", "31", "14", "0.631", "34", "11", "0.053"], ["≥60", "92", "64", "28", "67", "25", "54", "38"], ["Tumor size(cm)", "", "", "", "", "", "", "", "", "", ""], ["<5", "56", "55", "26", "0.386", "52", "29", "0.022*", "55", "26", "0.281"], ["≥5", "81", "34", "22", "46", "10", "33", "23"], ["Differentiation", "", "", "", "", "", "", "", "", "", ""], ["Poorly, undifferentiated (G3+G4)", "39", "24", "15", "0.596", "27", "12", "0.706", "20", "19", "0.046*"], ["Well, moderately (G1+G2)", "98", "65", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE15471", "GSE18670", "GSE28735", "GSE58561"], "resolved_accessions": ["GSE15471", "GSE18670", "GSE28735", "GSE58561"], "statements": ["All mRNA expression profiling data series involved in this study were available to public."], "basis": "The paper names GSE15471, GSE18670, GSE28735, GSE58561 in National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:28881752", "data:geo:GSE15471", "asset:table:pmid:28881752:1", "asset:table:pmid:28881752:2", "asset:table:pmid:28881752:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15471"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:28881752", "type": "paper", "label": "pmid:28881752"}, {"id": "source:pmid:28881752", "type": "manuscript", "label": "PMID 28881752 full text"}, {"id": "data:geo:GSE15471", "type": "dataset", "label": "GEO GSE15471"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28881752", "type": "paper", "label": "pmid:28881752"}, {"id": "source:pmid:28881752", "type": "manuscript", "label": "PMID 28881752 full text"}, {"id": "data:geo:GSE15471", "type": "dataset", "label": "GEO GSE15471"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28881752", "type": "extraction", "used": ["source:pmid:28881752"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15471", "type": "accession_resolution", "used": ["data:geo:GSE15471"], "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:28881752", "parent_hash": "sha256:13f1245b0bd51a182aad78944bd7aca8decf60f697d2f6d827e61ff4ae77f668", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE15471 licence not read", "asset:data:geo:GSE15471 not downloaded", "asset:data:geo:GSE18670 licence not read", "asset:data:geo:GSE18670 not downloaded", "asset:data:geo:GSE28735 licence not read", "asset:data:geo:GSE28735 not downloaded", "asset:data:geo:GSE58561 licence not read", "asset:data:geo:GSE58561 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": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["een out 4 suitable series of gene expression microarray data (\"GSE15471\", \"GSE18670\", \"GSE28735\" and", "gnificantly differentially expressed in four microarray databases in common. After analyzing mRNA ex", "dysregulated according to 4 gene expression microarray data mentioned above (\"GSE15471\", \"GSE18670\"", "tissues with normal, we ulteriorly studied 4 microarray databases previously mentioned (GSE15471, GS"], "order_basis": "paper_text_order:692", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["dded by paraffin to produce tissue chips for immunohistochemistry. Algorithm and Statistical analysis Due to u", "rom Affymetrix data. The distribution of the IHC scoring results for each protein was analyze"], "order_basis": "paper_text_order:6026", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The postoperative survival of patients with PDAC was analyzed by the Kaplan-Meier estimator and tested by the log rank."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}