{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28627654", "kind": "science-record", "revision": 9, "content_hash": "sha256:b777c0ea2237fa1b34ed8c48e41a7fcd60e9320fe610ac582844e1c1b1ac6142", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T22:43:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of transcription profiling of solid pseudopapillary neoplasm of the pancreas.", "doi": "10.3892/mmr.2017.6800", "pmid": "28627654", "authors": ["Yongping Zhang", "Xu Han", "Hao Wu", "Yifeng Zhou"], "journal": "Molecular medicine reports", "year": 2017, "abstract": "Solid pseudopapillary neoplasm (SPN) of the pancreas is a low-grade malignant neoplasm that accounts for ~5% of cystic pancreatic tumors and ~0.9‑2.7% of exocrine pancreatic tumors. The transcription profiling data (GSE43795) of 14 SPN and 6 control samples were downloaded from the Gene Expression Omnibus (GEO) database. Using the Limma package, Student's t‑tests were performed to identify differentially expressed genes (DEGs) between SPN and control samples [with the following criterion: False discovery rate (FDR)<0.01 and log2 fold‑change (FC)≥3]. Pathway and functional enrichment analyses were performed to investigate the biological processes that the DEGs were involved in. Protein‑protein interaction (PPI) network and sub‑network analyses were conducted to comprehensively understand the interactions between DEGs. The screened DEGs were further annotated according to information relating to transcription factors and tumor associated genes (TAGs). A total of 710 upregulated and 710 downregulated DEGs were observed, including 74 transcriptional factors and 124 TAGs. Membrane metallo‑endopeptidase (MME), matrix metalloproteinase (MMP)-2 and MMP‑9 were also identified as key TAGs. Following PPI network analysis, hub nodes of epidermal growth factor receptor (EGFR), proto‑oncogene tyrosine protein kinase Fyn (FYN), c‑JUN (JUN), glucagon (GCG), c‑Myc (MYC) and CD44 were identified, the majority of which participate in the epidermal growth factor receptor (ErbB) and gonadotropin-releasing hormone (GnRH) signaling pathways. A sub‑network involving 70 gene nodes was also identified, with EGFR as the central gene. MME, MMP‑2 and MMP‑9 contribute to proliferative diabetic retinopathy and also involved in SPN. The genes EGFR, FYN, JUN, GCG, MYC and CD44 may therefore be key genes in SPN, and the ErbB and GnRH signaling pathways may be an important contributor to SPN progression.", "claims": [{"id": "claim-method", "statement": "Bayesian analysis was performed using the Limma package (15), to identify DEGs between SPN and control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28627654", "locator": "sections[5] \"DEGs screening\" paragraph 2", "quote": "Bayesian analysis was performed using the Limma package (15), to identify DEGs between SPN and control samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA expression profiles of SPN and non-neoplastic pancreatic tissues were obtained from the National Center of Biotechnology Information Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database. The access number was GSE43795 (14), and datasets from 14 SPN samples and 6 control samples were used for further analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28627654", "locator": "sections[4] \"Obtaining and preprocessing of mRNA expression profile data\" paragraph 2", "quote": "The mRNA expression profiles of SPN and non-neoplastic pancreatic tissues were obtained from the National Center of Biotechnology Information Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database. The access number was GSE43795 (14), and datasets from 14 SPN samples and 6 control samples were used for further analysis."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used Bayesian analysis with the Limma package (FDR<0.01 and log2 FC≥3) to analyze GSE43795 mRNA expression profiles downloaded from the Gene Expression Omnibus, comprising 14 SPN and 6 control samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28627654", "locator": "sections[5] \"DEGs screening\" paragraph 2", "quote": "Bayesian analysis was performed using the Limma package (15), to identify DEGs between SPN and control samples. FDR<0.01 and log2 FC≥3 were used as the thresholds."}, {"asset": "source:pmid:28627654", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The transcription profiling data (GSE43795) of 14 SPN and 6 control samples were downloaded from the Gene Expression Omnibus (GEO) database."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used Bayesian analysis with the Limma package (FDR<0.01 and log2 FC≥3) to analyze GSE43795 mRNA expression profiles downloaded from the Gene Expression Omnibus, comprising 14 SPN and 6 control samples.", "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:28627654"], "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:GSE43795"], "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:GSE43795"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28627654", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/mmr.2017.6800", "sha256": "sha256:34eb3544ea4805837bbf05531b28e1e08212c2c8d08f0caa539e75429edb157b", "bytes": 29637, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/mmr.2017.6800", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5562055", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE43795", "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=GSE43795", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43795", "version": null, "note": "The mRNA expression profiles of SPN and non-neoplastic pancreatic tissues were obtained from the National Center of Biotechnology Information Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database. The access number was GSE43795 (14), and datasets from 14 SPN samples and 6 control samples were used for further analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mRNA expression profiles of SPN and non-neoplastic pancreatic tissues were obtained from the National Center of Biotechnology Information Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database. The access number was GSE43795 (14), and datasets from 14 SPN samples and 6 control samples were used for further analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1071356", "GSM1071357", "GSM1071358", "GSM1071359", "GSM1071360", "GSM1071361", "GSM1071362", "GSM1071363", "GSM1071364", "GSM1071365", "GSM1071366", "GSM1071367", "GSM1071368", "GSM1071369", "GSM1071370", "GSM1071371", "GSM1071372", "GSM1071373", "GSM1071374", "GSM1071375", "GSM1071376", "GSM1071377", "GSM1071378", "GSM1071379", "GSM1071380", "GSM1071381", "GSM1071382", "GSM1071383", "GSM1071384", "GSM1071385", "GSM1071386"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Gene expression of pancreatic tumors", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:28627654:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:836b99d5813f94f4c2d7d99f5337e621a5f994689a4b50012a43a4e7e27b3e34", "bytes": 1294, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tI-mmr-16-02-1635", "version": null, "note": "KEGG pathway analysis of differentially expressed genes.", "structure": {"pmcid": "PMC5562055", "section_index": 6, "section_title": "Enrichment analysis of DEGs", "row_count": 21, "column_count": 4}, "table": {"label": "Table I.", "caption": "KEGG pathway analysis of differentially expressed genes.", "rows": [["Pattern", "KEGG pathway", "Gene counts", "P-value"], ["Down", "Pancreatic secretion", "28", "2.55E-15"], ["", "Maturity onset diabetes of the young", "12", "1.97E-10"], ["", "Protein digestion and absorption", "19", "2.12E-09"], ["", "Drug metabolism-cytochrome P450", "14", "3.98E-06"], ["", "Proximal tubule bicarbonate reclamation", "7", "4.99E-05"], ["", "Metabolism of xenobiotics by cytochrome P450", "12", "7.35E-05"], ["", "Fat digestion and absorption", "8", "9.77E-04"], ["", "Glutathione metabolism", "8", "1.72E-03"], ["", "Tyrosine metabolism", "7", "2.26E-03"], ["", "Starch and sucrose metabolism", "8", "2.84E-03"], ["Up", "Wnt signaling pathway", "15", "3.92E-04"], ["", "Melanogenesis", "11", "1.16E-03"], ["", "Axon guidance", "12", "2.77E-03"], ["", "Protein digestion and absorption", "9", "2.82E-03"], ["", "Leukocyte transendothelial migration", "11", "3.54E-03"], ["", "Cell adhesion molecules (CAMs)", "12", "3.56E-03"], ["", "Basal cell carcinoma", "7", "3.84E-03"], ["", "Pathways in cancer", "22", "4.23E-03"], ["", "Arrhythmogenic right ventricular cardiomyopathy", "8", "5.66E-03"], ["", "Tight junction", "11", "9.33E-03"]], "row_count": 21, "column_count": 4, "numeric_cells": 42, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tI-mmr-16-02-1635"}}, {"id": "asset:table:pmid:28627654:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a777323ceb711e34f19d1ff741436cbb9531d43b6b9ee1b1bbaef5299febad8a", "bytes": 1564, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#tII-mmr-16-02-1635", "version": null, "note": "Significantly enriched biological process function of differentially expressed genes.", "structure": {"pmcid": "PMC5562055", "section_index": 6, "section_title": "Enrichment analysis of DEGs", "row_count": 21, "column_count": 5}, "table": {"label": "Table II.", "caption": "Significantly enriched biological process function of differentially expressed genes.", "rows": [["Pattern", "GO ID", "Term", "Gene counts", "P-value"], ["Down", "GO:0007586", "Digestion", "31", "1.11E-16"], ["", "GO:0046903", "Secretion", "72", "6.84E-10"], ["", "GO:0071294", "Cellular response to zinc ion", "8", "9.69E-10"], ["", "GO:0031018", "Endocrine pancreas development", "15", "1.10E-09"], ["", "GO:0035270", "Endocrine system development", "22", "1.16E-08"], ["", "GO:0001525", "Angiogenesis", "39", "4.71E-08"], ["", "GO:0010038", "Response to metal ion", "28", "9.86E-08"], ["", "GO:0030001", "Metal ion transport", "48", "4.77E-07"], ["", "GO:0042593", "Glucose homeostasis", "20", "9.07E-07"], ["", "GO:0071248", "Cellular response to metal ion", "15", "1.11E-06"], ["Up", "GO:0007399", "Nervous system development", "119", "5.82E-10"], ["", "GO:0030154", "Cell differentiation", "168", "8.72E-10"], ["", "GO:0030182", "Neuron differentiation", "79", "3.39E-09"], ["", "GO:0001501", "Skeletal system development", "42", "5.94E-09"], ["", "GO:0043392", "Negative regulation of DNA binding", "9", "1.01E-05"], ["", "GO:0046189", "Phenol-containing compound biosynthetic process", "7", "6.87E-05"], ["", "GO:0060412", "Ventricular septum morphogenesis", "7", "8.76E-05"], ["", "GO:0007268", "Synaptic transmission", "46", "9.26E-05"], ["", "GO:0002720", "Positive regulation of cytokine production involved in immune response", "6", "1.02E-04"], ["", "GO:0007155", "Cell adhesion", "59", "3.00E-04"]], "row_count": 21, "column_count": 5, "numeric_cells": 60, "header_rows": 1, "locator": "section[12]/table-wrap[2]#tII-mmr-16-02-1635"}}, {"id": "asset:table:pmid:28627654:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a31e546f33cadd3e90bb8429965e03fb04b4d448d9902e6960a3dfc8f6824f35", "bytes": 1841, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tIII-mmr-16-02-1635", "version": null, "note": "Functional statistics of differentially expressed genes between solid pseudopapillary neoplasm and control samples.", "structure": {"pmcid": "PMC5562055", "section_index": 7, "section_title": "Gene functional annotation analysis", "row_count": 6, "column_count": 5}, "table": {"label": "Table III.", "caption": "Functional statistics of differentially expressed genes between solid pseudopapillary neoplasm and control samples.", "rows": [["Pattern", "TF counts", "TF genes", "TAG counts", "TAG genes"], ["Down", "31", "CDX2, EHF, ELF3, FOSB, FOXA2, FOXA3, FOXC1, FOXQ1, GATA4, HEYL, HHEX, HNF4G", "73", "Oncogene: CD24, CXCL1, EGFR, ELF3, ERBB3, FGFR1, FGFR3, GATA4, GFI1, GPX2, JUN, LCN2, MEIS1, MYC, SPHK1"], ["", "", "INSM1, ISL1, KCNIP3, KLF5, LMO3, MEIS1, NKX2.2, NKX2.5, NR4A2, NR5A2, ONECUT1, PAX6, PBX3, PDX1, PKNOX2, PLAGL1, SOX9, TEAD4, XBP1", "", "Tumor suppressor: WNK2, VIL1, UCHL1, TPM1, TFPI2, SYT13, STEAP3, SRPX, SIK1, SFRP5, SERPINI2, RAP1GAP, RAB25, PTPRK, PRKCDBP, PLK2, PLAGL1, PDX1, PDGFRL, PAX6, ONECUT1, NRCAM, MUC1, MTUS1, MT1G, MEG3, LPL, KLF5, KLF10, ID4, GNMT, GAS1, FOXC1, FOXA2, ERRFI1, EPHA1, ENC1, EHF, DEFB1, DAPK1, CLDN23, CEBPA, CDH1, C2orf40, BTG2, BMP2, BIN1, ADAMTS9 Other: TACC2, SLC43A1, RRAS2, PBX3, NR4A2, MAP3K5, GRB7, CHRM3, CDX2, CD44"], ["Up", "43", "TWIST2, TFAP2C, TCF7, TBX3, T, SOX11, SIM2, SHOX2, RUVBL1", "51", "Oncogene: RUNX2, NRAS, NOV, NET1, MME, MLLT11, MAP3K8, MAFG, LAMC2, GNA12, FYN, FGF20"], ["", "", "RUNX2, REST, PRDM1, PITX2, PGR, NR0B1, NFAT5, MAFG, MAF, LEF1, KLF12, HOXC9, HOXC8, HOXC6, HOXC5, HOXC4, HOXB8, HOXB7, HOXB3, HEY2, HEY1, HAND2, HAND1, GTF2H2, GLI2", "", "Tumor Suppressor: ZBTB7C, WNT5A, WIF1, TWIST2, TMEM127, TMEFF2, THSD1, SOX11, RASL10B, PTPRG, PRDM1, PPP1R1B, MIR185, MCPH1, LSAMP, ISG15, HPGD, GLIPR1, FANCD2, DKK3, CSMD1, CNTNAP2, CDKN2D, CDH11, CABLES2, C10orf90, BIK, AXIN2, ARHGAP29, ARHGAP20"], ["", "", "GATA1, FUBP1, ETV5, ESRRG, EMX2, DR1, DBP, BARX2, AR", "", "Other: WNT2B, TPH1, TPD52L1, TFAP2C, PITPNA, OGG1, MCC, MAF, HOXC6"]], "row_count": 6, "column_count": 5, "numeric_cells": 12, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tIII-mmr-16-02-1635"}}, {"id": "asset:table:pmid:28627654:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:53462491fc70de5c930c1ced381ad2874e2eec6226cf09e1a6373a301dac4ac8", "bytes": 1116, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tIV-mmr-16-02-1635", "version": null, "note": "Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes in the identified sub-network.", "structure": {"pmcid": "PMC5562055", "section_index": 8, "section_title": "PPI network construction and sub-network detection", "row_count": 11, "column_count": 4}, "table": {"label": "Table IV.", "caption": "Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes in the identified sub-network.", "rows": [["KEGG pathway", "Gene counts", "P-value", "Gene"], ["Bladder cancer", "7", "2.11E-08", "MYC, EGFR, EGF, CDH1, MMP9, NRAS, MMP2"], ["Endometrial cancer", "5", "4.19E-05", "MYC, EGFR, EGF, CDH1, NRAS"], ["Melanoma", "5", "0.0001884", "EGFR, EGF, CDH1, NRAS, FGF13"], ["Cell cycle", "6", "0.0003266", "CDC20, CCNB1, CDC7, MYC, ANAPC7, MCM2"], ["Prostate cancer", "5", "0.0005422", "AR, KLK3, EGFR, EGF, NRAS"], ["ErbB signaling pathway", "6", "4.57E-05", "JUN, MYC, EGFR, EGF, ERBB3, NRAS"], ["GnRH signaling pathway", "5", "0.0009664", "JUN, EGFR, PLA2G1B, NRAS, MMP2"], ["T cell receptor signaling pathway", "6", "0.0001534", "JUN, CD4, FYN, ZAP70, NRAS, ITK"], ["Axon guidance", "7", "4.76E-05", "CXCR4, FYN, EFNB3, CXCL12, EPHB1, NRAS, EPHB3"], ["Pathways in cancer", "12", "3.841E-06", "AR, JUN, KLK3, MYC, EGFR, EGF, CDH1, MMP9, PTGS2, NRAS, MMP2, FGF13"]], "row_count": 11, "column_count": 4, "numeric_cells": 25, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tIV-mmr-16-02-1635"}}, {"id": "asset:table:pmid:28627654:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:836b99d5813f94f4c2d7d99f5337e621a5f994689a4b50012a43a4e7e27b3e34", "bytes": 1294, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tI-mmr-16-02-1635", "version": null, "note": "KEGG pathway analysis of differentially expressed genes.", "structure": {"pmcid": "PMC5562055", "section_index": 12, "section_title": "Enrichment analysis of DEGs", "row_count": 21, "column_count": 4}, "table": {"label": "Table I.", "caption": "KEGG pathway analysis of differentially expressed genes.", "rows": [["Pattern", "KEGG pathway", "Gene counts", "P-value"], ["Down", "Pancreatic secretion", "28", "2.55E-15"], ["", "Maturity onset diabetes of the young", "12", "1.97E-10"], ["", "Protein digestion and absorption", "19", "2.12E-09"], ["", "Drug metabolism-cytochrome P450", "14", "3.98E-06"], ["", "Proximal tubule bicarbonate reclamation", "7", "4.99E-05"], ["", "Metabolism of xenobiotics by cytochrome P450", "12", "7.35E-05"], ["", "Fat digestion and absorption", "8", "9.77E-04"], ["", "Glutathione metabolism", "8", "1.72E-03"], ["", "Tyrosine metabolism", "7", "2.26E-03"], ["", "Starch and sucrose metabolism", "8", "2.84E-03"], ["Up", "Wnt signaling pathway", "15", "3.92E-04"], ["", "Melanogenesis", "11", "1.16E-03"], ["", "Axon guidance", "12", "2.77E-03"], ["", "Protein digestion and absorption", "9", "2.82E-03"], ["", "Leukocyte transendothelial migration", "11", "3.54E-03"], ["", "Cell adhesion molecules (CAMs)", "12", "3.56E-03"], ["", "Basal cell carcinoma", "7", "3.84E-03"], ["", "Pathways in cancer", "22", "4.23E-03"], ["", "Arrhythmogenic right ventricular cardiomyopathy", "8", "5.66E-03"], ["", "Tight junction", "11", "9.33E-03"]], "row_count": 21, "column_count": 4, "numeric_cells": 42, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tI-mmr-16-02-1635"}}, {"id": "asset:table:pmid:28627654:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a777323ceb711e34f19d1ff741436cbb9531d43b6b9ee1b1bbaef5299febad8a", "bytes": 1564, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#tII-mmr-16-02-1635", "version": null, "note": "Significantly enriched biological process function of differentially expressed genes.", "structure": {"pmcid": "PMC5562055", "section_index": 12, "section_title": "Enrichment analysis of DEGs", "row_count": 21, "column_count": 5}, "table": {"label": "Table II.", "caption": "Significantly enriched biological process function of differentially expressed genes.", "rows": [["Pattern", "GO ID", "Term", "Gene counts", "P-value"], ["Down", "GO:0007586", "Digestion", "31", "1.11E-16"], ["", "GO:0046903", "Secretion", "72", "6.84E-10"], ["", "GO:0071294", "Cellular response to zinc ion", "8", "9.69E-10"], ["", "GO:0031018", "Endocrine pancreas development", "15", "1.10E-09"], ["", "GO:0035270", "Endocrine system development", "22", "1.16E-08"], ["", "GO:0001525", "Angiogenesis", "39", "4.71E-08"], ["", "GO:0010038", "Response to metal ion", "28", "9.86E-08"], ["", "GO:0030001", "Metal ion transport", "48", "4.77E-07"], ["", "GO:0042593", "Glucose homeostasis", "20", "9.07E-07"], ["", "GO:0071248", "Cellular response to metal ion", "15", "1.11E-06"], ["Up", "GO:0007399", "Nervous system development", "119", "5.82E-10"], ["", "GO:0030154", "Cell differentiation", "168", "8.72E-10"], ["", "GO:0030182", "Neuron differentiation", "79", "3.39E-09"], ["", "GO:0001501", "Skeletal system development", "42", "5.94E-09"], ["", "GO:0043392", "Negative regulation of DNA binding", "9", "1.01E-05"], ["", "GO:0046189", "Phenol-containing compound biosynthetic process", "7", "6.87E-05"], ["", "GO:0060412", "Ventricular septum morphogenesis", "7", "8.76E-05"], ["", "GO:0007268", "Synaptic transmission", "46", "9.26E-05"], ["", "GO:0002720", "Positive regulation of cytokine production involved in immune response", "6", "1.02E-04"], ["", "GO:0007155", "Cell adhesion", "59", "3.00E-04"]], "row_count": 21, "column_count": 5, "numeric_cells": 60, "header_rows": 1, "locator": "section[12]/table-wrap[2]#tII-mmr-16-02-1635"}}, {"id": "asset:table:pmid:28627654:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a31e546f33cadd3e90bb8429965e03fb04b4d448d9902e6960a3dfc8f6824f35", "bytes": 1841, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tIII-mmr-16-02-1635", "version": null, "note": "Functional statistics of differentially expressed genes between solid pseudopapillary neoplasm and control samples.", "structure": {"pmcid": "PMC5562055", "section_index": 13, "section_title": "Gene functional annotation analysis", "row_count": 6, "column_count": 5}, "table": {"label": "Table III.", "caption": "Functional statistics of differentially expressed genes between solid pseudopapillary neoplasm and control samples.", "rows": [["Pattern", "TF counts", "TF genes", "TAG counts", "TAG genes"], ["Down", "31", "CDX2, EHF, ELF3, FOSB, FOXA2, FOXA3, FOXC1, FOXQ1, GATA4, HEYL, HHEX, HNF4G", "73", "Oncogene: CD24, CXCL1, EGFR, ELF3, ERBB3, FGFR1, FGFR3, GATA4, GFI1, GPX2, JUN, LCN2, MEIS1, MYC, SPHK1"], ["", "", "INSM1, ISL1, KCNIP3, KLF5, LMO3, MEIS1, NKX2.2, NKX2.5, NR4A2, NR5A2, ONECUT1, PAX6, PBX3, PDX1, PKNOX2, PLAGL1, SOX9, TEAD4, XBP1", "", "Tumor suppressor: WNK2, VIL1, UCHL1, TPM1, TFPI2, SYT13, STEAP3, SRPX, SIK1, SFRP5, SERPINI2, RAP1GAP, RAB25, PTPRK, PRKCDBP, PLK2, PLAGL1, PDX1, PDGFRL, PAX6, ONECUT1, NRCAM, MUC1, MTUS1, MT1G, MEG3, LPL, KLF5, KLF10, ID4, GNMT, GAS1, FOXC1, FOXA2, ERRFI1, EPHA1, ENC1, EHF, DEFB1, DAPK1, CLDN23, CEBPA, CDH1, C2orf40, BTG2, BMP2, BIN1, ADAMTS9 Other: TACC2, SLC43A1, RRAS2, PBX3, NR4A2, MAP3K5, GRB7, CHRM3, CDX2, CD44"], ["Up", "43", "TWIST2, TFAP2C, TCF7, TBX3, T, SOX11, SIM2, SHOX2, RUVBL1", "51", "Oncogene: RUNX2, NRAS, NOV, NET1, MME, MLLT11, MAP3K8, MAFG, LAMC2, GNA12, FYN, FGF20"], ["", "", "RUNX2, REST, PRDM1, PITX2, PGR, NR0B1, NFAT5, MAFG, MAF, LEF1, KLF12, HOXC9, HOXC8, HOXC6, HOXC5, HOXC4, HOXB8, HOXB7, HOXB3, HEY2, HEY1, HAND2, HAND1, GTF2H2, GLI2", "", "Tumor Suppressor: ZBTB7C, WNT5A, WIF1, TWIST2, TMEM127, TMEFF2, THSD1, SOX11, RASL10B, PTPRG, PRDM1, PPP1R1B, MIR185, MCPH1, LSAMP, ISG15, HPGD, GLIPR1, FANCD2, DKK3, CSMD1, CNTNAP2, CDKN2D, CDH11, CABLES2, C10orf90, BIK, AXIN2, ARHGAP29, ARHGAP20"], ["", "", "GATA1, FUBP1, ETV5, ESRRG, EMX2, DR1, DBP, BARX2, AR", "", "Other: WNT2B, TPH1, TPD52L1, TFAP2C, PITPNA, OGG1, MCC, MAF, HOXC6"]], "row_count": 6, "column_count": 5, "numeric_cells": 12, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tIII-mmr-16-02-1635"}}, {"id": "asset:table:pmid:28627654:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:53462491fc70de5c930c1ced381ad2874e2eec6226cf09e1a6373a301dac4ac8", "bytes": 1116, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tIV-mmr-16-02-1635", "version": null, "note": "Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes in the identified sub-network.", "structure": {"pmcid": "PMC5562055", "section_index": 14, "section_title": "PPI network construction and sub-network detection", "row_count": 11, "column_count": 4}, "table": {"label": "Table IV.", "caption": "Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes in the identified sub-network.", "rows": [["KEGG pathway", "Gene counts", "P-value", "Gene"], ["Bladder cancer", "7", "2.11E-08", "MYC, EGFR, EGF, CDH1, MMP9, NRAS, MMP2"], ["Endometrial cancer", "5", "4.19E-05", "MYC, EGFR, EGF, CDH1, NRAS"], ["Melanoma", "5", "0.0001884", "EGFR, EGF, CDH1, NRAS, FGF13"], ["Cell cycle", "6", "0.0003266", "CDC20, CCNB1, CDC7, MYC, ANAPC7, MCM2"], ["Prostate cancer", "5", "0.0005422", "AR, KLK3, EGFR, EGF, NRAS"], ["ErbB signaling pathway", "6", "4.57E-05", "JUN, MYC, EGFR, EGF, ERBB3, NRAS"], ["GnRH signaling pathway", "5", "0.0009664", "JUN, EGFR, PLA2G1B, NRAS, MMP2"], ["T cell receptor signaling pathway", "6", "0.0001534", "JUN, CD4, FYN, ZAP70, NRAS, ITK"], ["Axon guidance", "7", "4.76E-05", "CXCR4, FYN, EFNB3, CXCL12, EPHB1, NRAS, EPHB3"], ["Pathways in cancer", "12", "3.841E-06", "AR, JUN, KLK3, MYC, EGFR, EGF, CDH1, MMP9, PTGS2, NRAS, MMP2, FGF13"]], "row_count": 11, "column_count": 4, "numeric_cells": 25, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tIV-mmr-16-02-1635"}}], "gaps": ["asset:data:geo:GSE43795 not downloaded", "asset:data:geo:GSE43795 licence not read"]}, "analysis": {"state": "complete", "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": "Bayesian analysis was performed using the Limma package (15), to identify DEGs between SPN and control samples."}}, {"id": "method-2", "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": "PPI"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}], "targets": [], "gaps": []}, "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": ["GSE43795"], "resolved_accessions": ["GSE43795"], "statements": ["The mRNA expression profiles of SPN and non-neoplastic pancreatic tissues were obtained from the National Center of Biotechnology Information Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database. The access number was GSE43795 (14), and datasets from 14 SPN samples and 6 control samples were used for further analysis."], "basis": "The paper names GSE43795 in National Center of Biotechnology Information Gene Expression Omnibus (GEO) database 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:28627654", "data:geo:GSE43795", "asset:table:pmid:28627654:1", "asset:table:pmid:28627654:2", "asset:table:pmid:28627654:3", "asset:table:pmid:28627654:4", "asset:table:pmid:28627654:5", "asset:table:pmid:28627654:6", "asset:table:pmid:28627654:7", "asset:table:pmid:28627654:8"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE43795"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:23Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 67768, "completion_tokens": 2502, "cached_tokens": 1840}}, "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:28627654", "type": "paper", "label": "pmid:28627654"}, {"id": "source:pmid:28627654", "type": "manuscript", "label": "PMID 28627654 full text"}, {"id": "data:geo:GSE43795", "type": "dataset", "label": "GEO GSE43795"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28627654", "type": "paper", "label": "pmid:28627654"}, {"id": "source:pmid:28627654", "type": "manuscript", "label": "PMID 28627654 full text"}, {"id": "data:geo:GSE43795", "type": "dataset", "label": "GEO GSE43795"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28627654", "type": "extraction", "used": ["source:pmid:28627654"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE43795", "type": "accession_resolution", "used": ["data:geo:GSE43795"], "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:28627654", "parent_hash": "sha256:dd64f93e0d4ba38d2033ca84dbc847a92ea114f4ec419f4eb8b42b4b18ac25f1", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE43795 licence not read", "asset:data:geo:GSE43795 not downloaded", "execution.not_run", "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": ["Bayesian analysis was performed using the Limma package (15), to identify DEGs between SPN and control samples."], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T04:15:42+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}