{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28058013", "kind": "science-record", "revision": 3, "content_hash": "sha256:11170bca20d9330df2ced8c32521176c01f76d1d799f0a4a4e6a9415e9ad83e3", "created_at": "2026-11-01T15:40:22Z", "updated_at": "2026-11-01T18:48:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Aging related methylation influences the gene expression of key control genes in colorectal cancer and adenoma.", "doi": "10.3748/wjg.v22.i47.10325", "pmid": "28058013", "authors": ["Orsolya Galamb", "Alexandra Kalmár", "Barbara Kinga Barták", "Árpád V Patai", "Katalin Leiszter", "Bálint Péterfia", "Barnabás Wichmann", "Gábor Valcz", "Gábor Veres", "Zsolt Tulassay", "Béla Molnár"], "journal": "World journal of gastroenterology", "year": 2016, "abstract": "AIM: To analyze colorectal carcinogenesis and age-related DNA methylation alterations of gene sequences associated with epigenetic clock CpG sites.\nMETHODS: In silico DNA methylation analysis of 353 epigenetic clock CpG sites published by Steve Horvath was performed using methylation array data for a set of 123 colonic tissue samples [64 colorectal cancer (CRC), 42 adenoma, 17 normal; GEO accession number: GSE48684]. Among the differentially methylated age-related genes, secreted frizzled related protein 1 (SFRP1) promoter methylation was further investigated in colonic tissue from 8 healthy adults, 19 normal children, 20 adenoma and 8 CRC patients using bisulfite-specific PCR followed by methylation-specific high resolution melting (MS-HRM) analysis. mRNA expression of age-related \"epigenetic clock\" genes was studied using Affymetrix HGU133 Plus2.0 whole transcriptome data of 153 colonic biopsy samples (49 healthy adult, 49 adenoma, 49 CRC, 6 healthy children) (GEO accession numbers: GSE37364, GSE10714, GSE4183, GSE37267). Whole promoter methylation analysis of genes showing inverse DNA methylation-gene expression data was performed on 30 colonic samples using methyl capture sequencing.\nRESULTS: Fifty-seven age-related CpG sites including hypermethylated PPP1R16B, SFRP1, SYNE1 and hypomethylated MGP, PIPOX were differentially methylated between CRC and normal tissues (P < 0.05, Δβ ≥ 10%). In the adenoma vs normal comparison, 70 CpG sites differed significantly, including hypermethylated DKK3, SDC2, SFRP1, SYNE1 and hypomethylated CEMIP, SPATA18 (P < 0.05, Δβ ≥ 10%). In MS-HRM analysis, the SFRP1 promoter region was significantly hypermethylated in CRC (55.0% ± 8.4 %) and adenoma tissue samples (49.9% ± 18.1%) compared to normal adult (5.2% ± 2.7%) and young (2.2% ± 0.7%) colonic tissue (P < 0.0001). DNA methylation of SFRP1 promoter was slightly, but significantly increased in healthy adults compared to normal young samples (P < 0.02). This correlated with significantly increased SFRP1 mRNA levels in children compared to normal adult samples (P < 0.05). In CRC tissue the mRNA expression of 117 age-related genes were changed, while in adenoma samples 102 genes showed differential expression compared with normal colonic tissue (P < 0.05, logFC > 0.5). The change of expression for several genes including SYNE1, CLEC3B, LTBP3 and SFRP1, followed the same pattern in aging and carcinogenesis, though not for all genes (e.g., MGP).\nCONCLUSION: Several age-related DNA methylation alterations can be observed during CRC development and progression affecting the mRNA expression of certain CRC- and adenoma-related key control genes.", "claims": [{"id": "claim-data-access", "statement": "Additional data are available in a supplementary file.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28058013", "locator": "sections[26] \"fn-group\" paragraph 1", "quote": "Additional data are available in a supplementary file."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using in silico methylation-array data from GSE48684 and Affymetrix whole-transcriptome data from GSE37364, GSE10714, GSE4183, and GSE37267, analyzed with Student’s t-test or Welch’s test/ANOVA as appropriate and Benjamini–Hochberg correction, the study found that age-related DNA methylation alterations during colorectal cancer development and progression affect the mRNA expression of key CRC- and adenoma-related control genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28058013", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "In silico DNA methylation analysis of 353 epigenetic clock CpG sites published by Steve Horvath was performed using methylation array data for a set of 123 colonic tissue samples [64 colorectal cancer (CRC), 42 adenoma, 17 normal; GEO accession number: GSE48684]."}, {"asset": "source:pmid:28058013", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "mRNA expression of age-related “epigenetic clock” genes was studied using Affymetrix HGU133 Plus2.0 whole transcriptome data of 153 colonic biopsy samples (49 healthy adult, 49 adenoma, 49 CRC, 6 healthy children) (GEO accession numbers: GSE37364, GSE10714, GSE4183, GSE37267)."}, {"asset": "source:pmid:28058013", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Several age-related DNA methylation alterations can be observed during CRC development and progression affecting the mRNA expression of certain CRC- and adenoma-related key control genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using in silico methylation-array data from GSE48684 and Affymetrix whole-transcriptome data from GSE37364, GSE10714, GSE4183, and GSE37267, analyzed with Student’s t-test or Welch’s test/ANOVA as appropriate and Benjamini–Hochberg correction, the study found that age-related DNA methylation alterations during colorectal cancer development and progression affect the mRNA expression of key CRC- and adenoma-related control genes.", "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:28058013"], "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:GSE10714"], "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:GSE10714"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28058013", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3748/wjg.v22.i47.10325", "sha256": 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"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:28058013:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:20cd261fbf59241c17fb5759d12ede044171c638358360a1120cad73ed659dad", "bytes": 2839, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T2", "version": null, "note": "Significant DNA methylation alterations of age-related CpG sites in CRC samples compared to normal tissue", "structure": {"pmcid": "PMC5175245", "section_index": 4, "section_title": "In silico DNA methylation analysis", "row_count": 58, "column_count": 4}, "table": {"label": "Table 2", "caption": "Significant DNA methylation alterations of age-related CpG sites in CRC samples compared to normal tissue", "rows": [["cgID", "Gene symbol", "P value", "Δβ (CRC - N)"], ["cg06462291", "NT5DC3", "3.81 × 10-6", "-0.27"], ["cg06144905", "PIPOX", "1.81 × 10-7", "-0.22"], ["cg10345936", "SLC36A2", "2.49 × 10-5", "-0.18"], ["cg13828047", "MPI", "1.78 × 10-5", "-0.17"], ["cg11314684", "AKT3", "4.55 × 10-5", "-0.16"], ["cg00431549", "MGP", "0.020", "-0.12"], ["cg14409958", "ENPP2", "0.021", "-0.11"], ["cg00091693", "KRT20", "0.010", "-0.11"], ["cg17274064", "ERG", "1.48 × 10-4", "-0.11"], ["cg22809047", "RPL31", "1.91 × 10-3", "-0.10"], ["cg00075967", "STRA6", "0.010", "-0.10"], ["cg06952310", "NCAN", "7.13 × 10-3", "-0.10"], ["cg02388150", "SFRP1", "3.33 × 10-3", "0.10"], ["cg03588357", "GPR68", "7.72 × 10-3", "0.10"], ["cg26297688", "TMEM263", "6.21 × 10-3", "0.10"], ["cg04528819", "KLF14", "0.036", "0.10"], ["cg26372517", "TFAP2E", "9.23 × 10-3", "0.11"], ["cg08030082", "POMC", "1.93 × 10-3", "0.11"], ["cg05675373", "KCNC4", "7.80 × 10-3", "0.11"], ["cg10281002", "TBX5", "0.012", "0.11"], ["cg06117855", "CLEC3B", "1.87 × 10-3", "0.11"], ["cg09509673", "CCR10", "1.91 × 10-4", "0.11"], ["cg14597908", "GNAS", "1.48 × 10-4", "0.11"], ["cg27494383", "LTK", "9.32 × 10-3", "0.12"], ["cg21870884", "GPR25", "5.77 × 10-3", "0.13"], ["cg25657834", "NTSR2", "4.43 × 10-3", "0.13"], ["cg22449114", "TCF15", "3.48 × 10-5", "0.13"], ["cg04126866", "C10orf99", "4.52 × 10-4", "0.13"], ["cg25552492", "LGI3", "9.44 × 10-3", "0.14"], ["cg08965235", "LTBP3", "3.12 × 10-3", "0.14"], ["cg06836772", "PRKAA2", "0.013", "0.14"], ["cg02364642", "ARHGEF25", "1.20 × 10-3", "0.16"], ["cg18573383", "KCNC2", "1.38 × 10-3", "0.16"], ["cg12616277", "ESYT3", "0.015", "0.16"], ["cg17729667", "NINL", "3.46 × 10-3", "0.16"], ["cg04999691", "ZBED6CL", "3.32 × 10-11", "0.16"], ["cg12373771", "CECR6", "3.70 × 10-3", "0.17"], ["cg02489552", "CCDC105", "8.91 × 10-8", "0.17"], ["cg25148589", "GRIA2", "7.77 × 10-6", "0.19"], ["cg21096399", "MCAM", "5.47 × 10-6", "0.19"], ["cg20914508", "GAP43", "4.24 × 10-4", "0.20"], ["cg12768605", "LYPD5", "1.85 × 10-4", "0.21"], ["cg13216057", "DKK3", "2.10 × 10-4", "0.21"], ["cg12351433", "LHCGR", "4.97 × 10-7", "0.22"], ["cg08434234", "DGKI", "5.16 × 10-5", "0.23"], ["cg10920957", "JPH3", "3.00 × 10-4", "0.26"], ["cg27092035", "ARL10", "3.73 × 10-5", "0.27"], ["cg06557358", "TMEM132E", "3.17 × 10-6", "0.27"], ["cg26620959", "SYNE1", "1.32 × 10-6", "0.30"], ["cg07663789", "NPR3", "8.73 × 10-6", "0.31"], ["cg09191327", "PRDM12", "1.79 × 10-6", "0.31"], ["cg25070637", "SDC2", "1.64 × 10-6", "0.34"], ["cg10486998", "GALR1", "1.81 × 10-8", "0.35"], ["cg24834740", "PPP1R16B", "3.56 × 10-12", "0.37"], ["cg27319898", "ZNF804B", "5.41 × 10-8", "0.38"], ["cg08090772", "ADHFE1", "7.18 × 10-14", "0.39"], ["cg02217159", "KHDRBS2", "6.67 × 10-13", "0.43"]], "row_count": 58, "column_count": 4, "numeric_cells": 189, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:28058013:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:83e5dc3e8abdd936fef47e96530d4453de209c1fa7e8c17eee165ed1a99ee9cd", "bytes": 3495, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#T3", "version": null, "note": "Significant DNA methylation changes of age-related CpG sites in adenoma samples compared to normal tissue", "structure": {"pmcid": "PMC5175245", "section_index": 4, "section_title": "In silico DNA methylation analysis", "row_count": 71, "column_count": 4}, "table": {"label": "Table 3", "caption": "Significant DNA methylation changes of age-related CpG sites in adenoma samples compared to normal tissue", "rows": [["cgID", "Gene symbol", "P value", "Δβ (AD - N)"], ["cg10345936", "SLC36A2", "3.49 × 10-10", "-0.34"], ["cg00091693", "KRT20", "2.49 × 10-12", "-0.30"], ["cg00075967", "STRA6", "2.58 × 10-9", "-0.26"], ["cg11314684", "AKT3", "1.03 × 10-9", "-0.26"], ["cg06462291", "NT5DC3", "7.45 × 10-5", "-0.25"], ["cg17099569", "GLI2", "1.25 × 10-10", "-0.23"], ["cg00168942", "GJD4", "2.48 × 10-7", "-0.20"], ["cg20828084", "CEMIP", "1.33 × 10-9", "-0.19"], ["cg17274064", "ERG", "1.82 × 10-10", "-0.19"], ["cg07408456", "PGLYRP2", "2.41 × 10-12", "-0.19"], ["cg03019000", "TEX264", "2.25 × 10-7", "-0.19"], ["cg17589341", "SLC14A1", "1.42 × 10-9", "-0.19"], ["cg02580606", "KRT33B", "9.08 × 10-5", "-0.17"], ["cg00436603", "CYP2E1", "1.37 × 10-8", "-0.16"], ["cg19346193", "UROS", "6.59 × 10-7", "-0.15"], ["cg03103192", "SPATA18", "1.39 × 10-7", "-0.15"], ["cg25564800", "KPNA1", "2.18 × 10-8", "-0.14"], ["cg06144905", "PIPOX", "3.63 × 10-7", "-0.14"], ["cg06952310", "NCAN", "2.72 × 10-4", "-0.14"], ["cg13038560", "C2orf47", "2.13 × 10-5", "-0.13"], ["cg22190114", "NLRP8", "1.67 × 10-4", "-0.13"], ["cg13302154", "MGP", "7.27 × 10-6", "-0.13"], ["cg01262913", "DSCR9", "2.67 × 10-6", "-0.13"], ["cg14258236", "OR5V1", "3.71 × 10-4", "-0.12"], ["cg13828047", "MPI", "1.01 × 10-3", "-0.12"], ["cg01459453", "SELP", "1.65 × 10-4", "-0.12"], ["cg14894144", "LAMA3", "2.29 × 10-4", "-0.12"], ["cg07337598", "ANXA9", "2.02 × 10-5", "-0.12"], ["cg03270204", "DDR1", "7.47 × 10-5", "-0.12"], ["cg12946225", "HMG20B", "1.37 × 10-6", "-0.11"], ["cg09646392", "TNFSF13B", "2.66 × 10-5", "-0.10"], ["cg19305227", "SLC28A2", "0.033", "-0.10"], ["cg03578041", "LARP6", "2.22 × 10-5", "-0.10"], ["cg07455279", "NDUFA3", "0.013", "-0.10"], ["cg13899108", "PDE4C", "5.00 × 10-6", "0.10"], ["cg04999691", "ZBED6CL", "4.92 × 10-5", "0.10"], ["cg14597908", "GNAS", "9.38 × 10-5", "0.10"], ["cg21870884", "GPR25", "9.49 × 10-3", "0.11"], ["cg12616277", "ESYT3", "0.022", "0.12"], ["cg12373771", "CECR6", "3.55 × 10-3", "0.12"], ["cg17729667", "NINL", "4.43 × 10-3", "0.13"], ["cg02364642", "ARHGEF25", "2.33 × 10-3", "0.14"], ["cg22449114", "TCF15", "2.39 × 10-5", "0.14"], ["cg03565323", "ZNF287", "4.52 × 10-3", "0.14"], ["cg02388150", "SFRP1", "1.20 × 10-7", "0.15"], ["cg12768605", "LO×L2", "8.01 × 10-3", "0.15"], ["cg25657834", "NTSR2", "1.46 × 10-4", "0.16"], ["cg20914508", "GAP43", "9.41 × 10-4", "0.16"], ["cg10281002", "TBX5", "1.26 × 10-5", "0.17"], ["cg02489552", "CCDC105", "7.16 × 10-8", "0.18"], ["cg05675373", "KCNC4", "1.82 × 10-6", "0.18"], ["cg25148589", "GRIA2", "6.11 × 10-7", "0.18"], ["cg13216057", "DKK3", "9.64 × 10-4", "0.18"], ["cg27092035", "ARL10", "8.81 × 10-4", "0.19"], ["cg12351433", "LHCGR", "2.20 × 10-6", "0.20"], ["cg18573383", "KCNC2", "5.43 × 10-7", "0.21"], ["cg08434234", "DGKI", "6.60 × 10-5", "0.22"], ["cg21096399", "MCAM", "5.20 × 10-8", "0.22"], ["cg10920957", "JPH3", "1.03 × 10-4", "0.25"], ["cg08965235", "LTBP3", "6.03 × 10-10", "0.25"], ["cg27319898", "ZNF804B", "5.48 × 10-5", "0.26"], ["cg26620959", "SYNE1", "3.89 × 10-6", "0.29"], ["cg25070637", "SDC2", "1.82 × 10-5", "0.30"], ["cg07663789", "NPR3", "6.41 × 10-7", "0.31"], ["cg09191327", "PRDM12", "4.08 × 10-7", "0.31"], ["cg06557358", "TMEM132E", "2.04 × 10-8", "0.33"], ["cg10486998", "GALR1", "2.61 × 10-9", "0.36"], ["cg24834740", "PPP1R16B", "2.23 × 10-9", "0.36"], ["cg08090772", "ADHFE1", "5.19 × 10-11", "0.39"], ["cg02217159", "KHDRBS2", "1.87 × 10-11", "0.41"]], "row_count": 71, "column_count": 4, "numeric_cells": 231, "header_rows": 1, "locator": "section[14]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:28058013:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dfe56e44def883fe30c4474c2fff8dd3d8baeec55270b5ba54f99f6d51a7d788", "bytes": 1869, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[3]#T4", "version": null, "note": "Significant DNA methylation alterations of age-related CpG sites in colorectal cancer samples compared to adenoma tissue", "structure": {"pmcid": "PMC5175245", "section_index": 4, "section_title": "In silico DNA methylation analysis", "row_count": 35, "column_count": 4}, "table": {"label": "Table 4", "caption": "Significant DNA methylation alterations of age-related CpG sites in colorectal cancer samples compared to adenoma tissue", "rows": [["cgID", "Gene symbol", "P value", "Δβ (CRC - AD)"], ["cg08965235", "LTBP3", "9.09 × 10-4", "-0.11"], ["cg00945507", "SEC61G", "1.64 × 10-5", "0.10"], ["cg15974053", "HSD17B14", "2.27 × 10-3", "0.10"], ["cg24262469", "TIPARP", "5.33 × 10-8", "0.10"], ["cg07158339", "FXN", "1.84 × 10-7", "0.10"], ["cg11314684", "AKT3", "4.52 × 10-4", "0.10"], ["cg03578041", "LARP6", "2.57 × 10-9", "0.10"], ["cg17853587", "NDST3", "5.94 × 10-4", "0.10"], ["cg07408456", "PGLYRP2", "1.51 × 10-7", "0.11"], ["cg02580606", "KRT33B", "1.22 × 10-4", "0.11"], ["cg03019000", "TEX264", "5.39 × 10-5", "0.11"], ["cg27319898", "ZNF804B", "0.023", "0.12"], ["cg00436603", "CYP2E1", "1.97 × 10-6", "0.12"], ["cg15804973", "MAP3K5", "6.27 × 10-12", "0.12"], ["cg06117855", "CLEC3B", "1.73 × 10-7", "0.13"], ["cg24126851", "DCHS1", "3.58 × 10-8", "0.13"], ["cg16034652", "UNC79", "4.23 × 10-11", "0.13"], ["cg01262913", "DSCR9", "1.64 × 10-8", "0.13"], ["cg26372517", "TFAP2E", "9.80 × 10-6", "0.13"], ["cg03270204", "DDR1", "4.24 × 10-7", "0.13"], ["cg17589341", "SLC14A1", "7.35 × 10-10", "0.13"], ["cg22679120", "SNX8", "8.16 × 10-9", "0.14"], ["cg20828084", "CEMIP", "2.00 × 10-8", "0.14"], ["cg19305227", "SLC28A2", "1.11 × 10-6", "0.14"], ["cg00168942", "GJD4", "1.18 × 10-7", "0.14"], ["cg13038560", "C2orf47", "8.96 × 10-8", "0.15"], ["cg26614073", "SCAP", "1.33 × 10-9", "0.15"], ["cg19346193", "UROS", "2.09 × 10-8", "0.16"], ["cg00075967", "STRA6", "4.87 × 10-7", "0.16"], ["cg03103192", "SPATA18", "6.07 × 10-12", "0.16"], ["cg10345936", "SLC36A2", "4.09 × 10-6", "0.16"], ["cg17099569", "GLI2", "9.04 × 10-7", "0.16"], ["cg04126866", "C10orf99", "4.23 × 10-10", "0.18"], ["cg00091693", "KRT20", "1.17 × 10-8", "0.19"]], "row_count": 35, "column_count": 4, "numeric_cells": 115, "header_rows": 1, "locator": "section[14]/table-wrap[3]#T4"}}, {"id": "asset:table:pmid:28058013:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1d36878879ff10c4aeea5833f8f4fe985b3ea50461f42971a512d30207f8b4b9", "bytes": 3802, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T5", "version": null, "note": "Genes showing inverse DNA methylation and gene expression data", "structure": {"pmcid": "PMC5175245", "section_index": 5, "section_title": "In silico gene expression analysis", "row_count": 46, "column_count": 8}, "table": {"label": "Table 5", "caption": "Genes showing inverse DNA methylation and gene expression data", "rows": [["Gene symbol", "Gene name", "DNA methylation", "Gene expression"], ["cg ID", "P value", "Δβ", "Affymetrix ID", "P value", "LogFC"], ["CRC vs N", "", "", "", "", "", "", ""], ["AKT3", "AKT serine/threonine kinase 3", "cg11314684", "4.55 × 10-5", "-0.16", "224229_s_at", "0.015", "0.07"], ["222880_at", "2.26 × 10-3", "0.61"], ["212609_s_at", "4.72 × 10-4", "0.62"], ["212607_at", "9.76 × 10-4", "0.64"], ["ERG", "v-ets avian erythroblastosis virus E26 oncogene homolog", "cg17274064", "1.48 × 10-4", "-0.11", "211626_x_at", "5.84 × 10-4", "0.20"], ["241926_s_at", "2.05 × 10-5", "0.64"], ["213541_s_at", "4.69 × 10-9", "1.08"], ["MGP", "Matrix Gla protein", "cg00431549", "0.020", "-0.12", "202291_s_at", "2.34 × 10-11", "1.97"], ["PIPOX", "Pipecolic acid and sarcosine oxidase", "cg06144905", "1.81 × 10-7", "-0.22", "221605_s_at", "0.019", "0.50"], ["CCR10", "C-C motif chemokine receptor 10", "cg09509673", "1.91 × 10-4", "0.11", "220565_at", "0.010", "-0.51"], ["CLEC3B", "C-type lectin domain family 3 member B", "cg06117855", "1.88 × 10-3", "0.11", "205200_at", "1.45 × 10-13", "-1.79"], ["LTK", "Leukocyte receptor tyrosine kinase", "cg27494383", "9.32 × 10-3", "0.12", "217184_s_at", "2.14 × 10-11", "-1.32"], ["207106_s_at", "2.00 × 10-5", "-0.75"], ["PPP1R16B", "Protein phosphatase 1 regulatory subunit 16B", "cg24834740", "3.56 × 10-12", "0.37", "41577_at", "1.76 × 10-4", "-0.79"], ["212750_at", "7.68 × 10-3", "-0.48"], ["PRKAA2", "Protein kinase AMP-activated catalytic subunit alpha 2", "cg06836772", "0.013", "0.14", "227892_at", "4.15 × 10-3", "-0.87"], ["238489_at", "4.67 × 10-3", "-0.22"], ["SFRP1", "Secreted frizzled related protein 1", "cg02388150", "3.33 × 10-3", "0.10", "202036_s_at", "8.66 × 10-8", "-1.47"], ["202037_s_at", "3.98 × 10-5", "-1.11"], ["202035_s_at", "0.039", "-0.28"], ["SYNE1", "Spectrin repeat containing nuclear envelope protein 1", "cg26620959", "1.32 × 10-6", "0.30", "209447_at", "4.27 × 10-5", "-0.63"], ["AD vs N", "", "", "", "", "", "", ""], ["CEMIP", "Cell migration inducing hyaluronan binding protein", "cg20828084", "1.33 × 10-9", "-0.17", "1554685_a_at", "1.71 × 10-11", "1.12"], ["212942_s_at", "2.41 × 10-43", "6.88"], ["NT5DC3", "5'-nucleotidase domain containing 3", "cg06462291", "7.45 × 10-5", "-0.25", "218786_at", "6.83 × 10-9", "0.76"], ["SPATA18", "Spermatogenesis associated 18", "cg03103192", "1.39 × 10-7", "-0.15", "230723_at", "4.41 × 10-5", "0.45"], ["229331_at", "1.20 × 10-10", "1.50"], ["DKK3", "Dickkopf WNT signaling pathway inhibitor 3", "cg13216057", "9.64 × 10-4", "0.18", "202196_s_at", "9.82 × 10-5", "-0.65"], ["214247_s_at", "1.52 × 10-4", "-0.50"], ["PPP1R16B", "Protein phosphatase 1 regulatory subunit 16B", "cg24834740", "2.23 × 10-9", "0.36", "41577_at", "1.20 × 10-10", "-1.44"], ["212750_at", "3.28 × 10-7", "-0.81"], ["SDC2", "Syndecan 2", "cg25070637", "1.82 × 10-5", "0.30", "212158_at", "1.74 × 10-10", "-1.17"], ["212157_at", "2.14 × 10-8", "-0.66"], ["212154_at", "9.19 × 10-5", "-0.64"], ["SFRP1", "Secreted frizzled related protein 1", "cg02388150", "1.20 × 10-7", "0.15", "202036_s_at", "3.62 × 10-13", "-1.79"], ["202037_s_at", "4.43 × 10-11", "-1.48"], ["202035_s_at", "0.016", "-0.32"], ["SYNE1", "Spectrin repeat containing nuclear envelope protein 1", "cg26620959", "3.89 × 10-6", "0.29", "209447_at", "5.76 × 10-15", "-1.19"], ["CRC vs AD", "", "", "", "", "", "", ""], ["CEMIP", "Cell migration inducing hyaluronan binding protein", "cg20828084", "2.00 × 10-8", "0.14", "212942_s_at", "9.88 × 10-3", "-1.17"], ["SLC28A2", "Solute carrier family 28 member 2", "cg19305227", "1.11 × 10-6", "0.14", "207249_s_at", "0.027", "-1.24"], ["SPATA18", "Spermatogenesis associated 18", "cg03103192", "6.07 × 10-12", "0.16", "229331_at", "3.52 × 10-9", "-1.73"], ["230723_at", "7.35 × 10-4", "-0.41"]], "row_count": 46, "column_count": 8, "numeric_cells": 212, "header_rows": 2, "locator": "section[15]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:28058013:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a66388e612c930fddc008187678513e6d9bf9327c2bd3f85d3972c496e3bb6d2", "bytes": 4446, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T1", "version": null, "note": "Clinical data of samples involved in the high resolution melting study", "structure": {"pmcid": "PMC5175245", "section_index": 7, "section_title": "Clinical samples", "row_count": 57, "column_count": 11}, "table": {"label": "Table 1", "caption": "Clinical data of samples involved in the high resolution melting study", "rows": [["Sample ID", "Age", "Gender", "Localization", "Histology", "TNM", "Grade", "Dukes’ stage (MAC)", "Dysplasia", "Adenoma size", "Sample type"], ["Ch1", "4", "M", "Colon", "Normal", "", "", "", "", "", "FFPE"], ["Ch2", "7", "F", "Cecum", "Normal", "", "", "", "", "", "FFPE"], ["Ch3", "11", "M", "Colon", "Normal", "", "", "", "", "", "FFPE"], ["Ch4", "14", "M", "Transverse", "Normal", "", "", "", "", "", "FFPE"], ["Ch5", "5", "F", "Sigmoid", "Normal", "", "", "", "", "", "FFPE"], ["Ch6", "7", "F", "Descendent", "Normal", "", "", "", "", "", "FFPE"], ["Ch7", "1", "M", "Descendent", "Normal", "", "", "", "", "", "FFPE"], ["Ch8", "1", "M", "Sigmoid", "Normal", "", "", "", "", "", "FFPE"], ["Ch9", "10", "M", "Cecum", "Normal", "", "", "", "", "", "FFPE"], ["Ch10", "3", "M", "Sigmoid", "Normal", "", "", "", "", "", "FFPE"], ["Ch11", "17", "F", "Cecum", "Normal", "", "", "", "", "", "FFPE"], ["Ch12", "17", "F", "Sigmoid", "Normal", "", "", "", "", "", "FFPE"], ["Ch13", "16", "F", "Sigmoid", "Normal", "", "", "", "", "", "FFPE"], ["Ch14", "16", "F", "Cecum", "Normal", "", "", "", "", "", "FFPE"], ["Ch15", "1", "M", "Left colon", "Normal", "", "", "", "", "", "FF"], ["Ch16", "3", "F", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["Ch17", "6", "M", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["Ch18", "9", "M", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["Ch19", "17", "M", "Colon", "Normal", "", "", "", "", "", "FF"], ["N1", "44", "F", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["N2", "31", "F", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["N3", "59", "F", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["N4", "54", "M", "Colon", "Normal", "", "", "", "", "", "FF"], ["N5", "68", "F", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["N6", "71", "F", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["N7", "69", "F", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["N8", "57", "F", "Sigmoid", "Normal", "", "", "", "", "", "FF"], ["AD1", "78", "M", "Asc, sigmoid, rectum", "Tubulovillous adenoma", "", "", "", "Low-grade", "30 mm, 3 mm, 15 mm", "FF"], ["AD2", "60", "M", "Sigmoid", "Tubular adenoma", "", "", "", "Low-grade", "6 mm", "FF"], ["AD3", "88", "M", "Asc, transv, sigmoid", "Tubular adenoma", "", "", "", "Low-grade", "4 mm, 3 mm, 7-8 mm", "FF"], ["AD4", "72", "F", "Rectum", "Tubular adenoma", "", "", "", "Low-grade", "10 mm", "FF"], ["AD5", "45", "F", "Descendent", "Tubular adenoma", "", "", "", "High-grade", "5-6 mm", "FF"], ["AD6", "68", "F", "Rectum", "Tubular adenoma", "", "", "", "Low-grade", "5 mm", "FF"], ["AD7", "63", "F", "Sigmoid", "Tubular adenoma", "", "", "", "Low-grade", "8 mm", "FF"], ["AD8", "65", "F", "Asc, transv, rectum", "Tubular adenoma", "", "", "", "Low-grade", "2-3 mm, 2-3 mm, 2-3 mm", "FF"], ["AD9", "60", "F", "Sigmoid", "Tubular adenoma", "", "", "", "Low-grade", "5 mm, 4 mm", "FF"], ["AD10", "77", "F", "Rectosigmoid", "Tubular adenoma", "", "", "", "Low-grade", "5 mm", "FF"], ["AD11", "55", "F", "Asc colon", "Tubular adenoma", "", "", "", "Low-grade", "10 mm", "FF"], ["AD12", "76", "M", "Cecum, sigmoid", "Tubular adenoma", "", "", "", "Low-grade", "5 mm, 8-10 mm", "FF"], ["AD13", "62", "F", "Sigmoid", "Tubular adenoma", "", "", "", "High-grade", "30 mm", "FF"], ["AD14", "83", "M", "Asc colon", "Tubulovillous adenoma", "", "", "", "High-grade", "50-60 mm", "FF"], ["AD15", "73", "M", "Cecum, asc, desc", "Tubular adenoma", "", "", "", "Low-grade", "12 mm, 10 mm, 6-8 mm", "FF"], ["AD16", "64", "M", "Transv, sigmoid, rectum", "Tubular adenoma", "", "", "", "Low-grade", "5 mm, 25 mm, 15 mm", "FF"], ["AD17", "63", "M", "Asc, transv, rectum", "Tubular adenoma", "", "", "", "Low-grade", "2-3 mm, 5 mm, 5-6 mm, 15 mm", "FF"], ["AD18", "63", "F", "Sigmoid", "Tubulovillous adenoma", "", "", "", "Low-grade", "25 mm", "FF"], ["AD19", "63", "M", "Rectum", "Tubulovillous and tubular adenoma", "", "", "", "Low-grade", "25 mm, 30 mm", "FF"], ["AD20", "87", "M", "Sigmoid, rectum", "Tubulovillous adenoma", "", "", "", "Low-grade", "20 mm, 15 mm", "FF"], ["AD21", "63", "F", "Sigmoid", "Tubulovillous adenoma", "", "", "", "Low-grade", "25 mm", "FF"], ["CRC1", "67", "F", "Sigmoid", "Adenocarcinoma", "Unknown", "Unknown", "Unknown", "", "", "FF"], ["CRC2", "76", "F", "Hepatic flexure", "Adenocarcinoma", "T2N0M0", "2", "B1", "", "", "FF"], ["CRC3", "73", "F", "Sigmoid", "Adenocarcinoma", "T3N2M1", "2", "D", "", "", "FF"], ["CRC4", "65", "M", "Sigmoid", "Adenocarcinoma", "T2N0M0", "1", "B1", "", "", "FF"], ["CRC5", "85", "F", "Cecum", "Adenocarcinoma", "T2N0M0", "2", "B1", "", "", "FF"], ["CRC6", "60", "M", "Hepatic flexure", "Adenocarcinoma", "", "unknown", "D", "", "", "FF"], ["CRC7", "68", "M", "Sigmoid, rectum", "Adenocarcinoma", "T3N0M0", "1", "B2", "", "", "FF"], ["CRC8", "87", "F", "Sigmoid", "Adenocarcinoma", "T3N0M0", "2", "B2", "", "", "FF"]], "row_count": 57, "column_count": 11, "numeric_cells": 105, "header_rows": 1, "locator": "section[7]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:28058013:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:20cd261fbf59241c17fb5759d12ede044171c638358360a1120cad73ed659dad", "bytes": 2839, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T2", "version": null, "note": "Significant DNA methylation alterations of age-related CpG sites in CRC samples compared to normal tissue", "structure": {"pmcid": "PMC5175245", "section_index": 14, "section_title": "In silico DNA methylation analysis", "row_count": 58, "column_count": 4}, "table": {"label": "Table 2", "caption": "Significant DNA methylation alterations of age-related CpG sites in CRC samples compared to normal tissue", "rows": [["cgID", "Gene symbol", "P value", "Δβ (CRC - N)"], ["cg06462291", "NT5DC3", "3.81 × 10-6", "-0.27"], ["cg06144905", "PIPOX", "1.81 × 10-7", "-0.22"], ["cg10345936", "SLC36A2", "2.49 × 10-5", "-0.18"], ["cg13828047", "MPI", "1.78 × 10-5", "-0.17"], ["cg11314684", "AKT3", "4.55 × 10-5", "-0.16"], ["cg00431549", "MGP", "0.020", "-0.12"], ["cg14409958", "ENPP2", "0.021", "-0.11"], ["cg00091693", "KRT20", "0.010", "-0.11"], ["cg17274064", "ERG", "1.48 × 10-4", "-0.11"], ["cg22809047", "RPL31", "1.91 × 10-3", "-0.10"], ["cg00075967", "STRA6", "0.010", "-0.10"], ["cg06952310", "NCAN", "7.13 × 10-3", "-0.10"], ["cg02388150", "SFRP1", "3.33 × 10-3", "0.10"], ["cg03588357", "GPR68", "7.72 × 10-3", "0.10"], ["cg26297688", "TMEM263", "6.21 × 10-3", "0.10"], ["cg04528819", "KLF14", "0.036", "0.10"], ["cg26372517", "TFAP2E", "9.23 × 10-3", "0.11"], ["cg08030082", "POMC", "1.93 × 10-3", "0.11"], ["cg05675373", "KCNC4", "7.80 × 10-3", "0.11"], ["cg10281002", "TBX5", "0.012", "0.11"], ["cg06117855", "CLEC3B", "1.87 × 10-3", "0.11"], ["cg09509673", "CCR10", "1.91 × 10-4", "0.11"], ["cg14597908", "GNAS", "1.48 × 10-4", "0.11"], ["cg27494383", "LTK", "9.32 × 10-3", "0.12"], ["cg21870884", "GPR25", "5.77 × 10-3", "0.13"], ["cg25657834", "NTSR2", "4.43 × 10-3", "0.13"], ["cg22449114", "TCF15", "3.48 × 10-5", "0.13"], ["cg04126866", "C10orf99", "4.52 × 10-4", "0.13"], ["cg25552492", "LGI3", "9.44 × 10-3", "0.14"], ["cg08965235", "LTBP3", "3.12 × 10-3", "0.14"], ["cg06836772", "PRKAA2", "0.013", "0.14"], ["cg02364642", "ARHGEF25", "1.20 × 10-3", "0.16"], ["cg18573383", "KCNC2", "1.38 × 10-3", "0.16"], ["cg12616277", "ESYT3", "0.015", "0.16"], ["cg17729667", "NINL", "3.46 × 10-3", "0.16"], ["cg04999691", "ZBED6CL", "3.32 × 10-11", "0.16"], ["cg12373771", "CECR6", "3.70 × 10-3", "0.17"], ["cg02489552", "CCDC105", "8.91 × 10-8", "0.17"], ["cg25148589", "GRIA2", "7.77 × 10-6", "0.19"], ["cg21096399", "MCAM", "5.47 × 10-6", "0.19"], ["cg20914508", "GAP43", "4.24 × 10-4", "0.20"], ["cg12768605", "LYPD5", "1.85 × 10-4", "0.21"], ["cg13216057", "DKK3", "2.10 × 10-4", "0.21"], ["cg12351433", "LHCGR", "4.97 × 10-7", "0.22"], ["cg08434234", "DGKI", "5.16 × 10-5", "0.23"], ["cg10920957", "JPH3", "3.00 × 10-4", "0.26"], ["cg27092035", "ARL10", "3.73 × 10-5", "0.27"], ["cg06557358", "TMEM132E", "3.17 × 10-6", "0.27"], ["cg26620959", "SYNE1", "1.32 × 10-6", "0.30"], ["cg07663789", "NPR3", "8.73 × 10-6", "0.31"], ["cg09191327", "PRDM12", "1.79 × 10-6", "0.31"], ["cg25070637", "SDC2", "1.64 × 10-6", "0.34"], ["cg10486998", "GALR1", "1.81 × 10-8", "0.35"], ["cg24834740", "PPP1R16B", "3.56 × 10-12", "0.37"], ["cg27319898", "ZNF804B", "5.41 × 10-8", "0.38"], ["cg08090772", "ADHFE1", "7.18 × 10-14", "0.39"], ["cg02217159", "KHDRBS2", "6.67 × 10-13", "0.43"]], "row_count": 58, "column_count": 4, "numeric_cells": 189, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:28058013:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:83e5dc3e8abdd936fef47e96530d4453de209c1fa7e8c17eee165ed1a99ee9cd", "bytes": 3495, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#T3", "version": null, "note": "Significant DNA methylation changes of age-related CpG sites in adenoma samples compared to normal tissue", "structure": {"pmcid": "PMC5175245", "section_index": 14, "section_title": "In silico DNA methylation analysis", "row_count": 71, "column_count": 4}, "table": {"label": "Table 3", "caption": "Significant DNA methylation changes of age-related CpG sites in adenoma samples compared to normal tissue", "rows": [["cgID", "Gene symbol", "P value", "Δβ (AD - N)"], ["cg10345936", "SLC36A2", "3.49 × 10-10", "-0.34"], ["cg00091693", "KRT20", "2.49 × 10-12", "-0.30"], ["cg00075967", "STRA6", "2.58 × 10-9", "-0.26"], ["cg11314684", "AKT3", "1.03 × 10-9", "-0.26"], ["cg06462291", "NT5DC3", "7.45 × 10-5", "-0.25"], ["cg17099569", "GLI2", "1.25 × 10-10", "-0.23"], ["cg00168942", "GJD4", "2.48 × 10-7", "-0.20"], ["cg20828084", "CEMIP", "1.33 × 10-9", "-0.19"], ["cg17274064", "ERG", "1.82 × 10-10", "-0.19"], ["cg07408456", "PGLYRP2", "2.41 × 10-12", "-0.19"], ["cg03019000", "TEX264", "2.25 × 10-7", "-0.19"], ["cg17589341", "SLC14A1", "1.42 × 10-9", "-0.19"], ["cg02580606", "KRT33B", "9.08 × 10-5", "-0.17"], ["cg00436603", "CYP2E1", "1.37 × 10-8", "-0.16"], ["cg19346193", "UROS", "6.59 × 10-7", "-0.15"], ["cg03103192", "SPATA18", "1.39 × 10-7", "-0.15"], ["cg25564800", "KPNA1", "2.18 × 10-8", "-0.14"], ["cg06144905", "PIPOX", "3.63 × 10-7", "-0.14"], ["cg06952310", "NCAN", "2.72 × 10-4", "-0.14"], ["cg13038560", "C2orf47", "2.13 × 10-5", "-0.13"], ["cg22190114", "NLRP8", "1.67 × 10-4", "-0.13"], ["cg13302154", "MGP", "7.27 × 10-6", "-0.13"], ["cg01262913", "DSCR9", "2.67 × 10-6", "-0.13"], ["cg14258236", "OR5V1", "3.71 × 10-4", "-0.12"], ["cg13828047", "MPI", "1.01 × 10-3", "-0.12"], ["cg01459453", "SELP", "1.65 × 10-4", "-0.12"], ["cg14894144", "LAMA3", "2.29 × 10-4", "-0.12"], ["cg07337598", "ANXA9", "2.02 × 10-5", "-0.12"], ["cg03270204", "DDR1", "7.47 × 10-5", "-0.12"], ["cg12946225", "HMG20B", "1.37 × 10-6", "-0.11"], ["cg09646392", "TNFSF13B", "2.66 × 10-5", "-0.10"], ["cg19305227", "SLC28A2", "0.033", "-0.10"], ["cg03578041", "LARP6", "2.22 × 10-5", "-0.10"], ["cg07455279", "NDUFA3", "0.013", "-0.10"], ["cg13899108", "PDE4C", "5.00 × 10-6", "0.10"], ["cg04999691", "ZBED6CL", "4.92 × 10-5", "0.10"], ["cg14597908", "GNAS", "9.38 × 10-5", "0.10"], ["cg21870884", "GPR25", "9.49 × 10-3", "0.11"], ["cg12616277", "ESYT3", "0.022", "0.12"], ["cg12373771", "CECR6", "3.55 × 10-3", "0.12"], ["cg17729667", "NINL", "4.43 × 10-3", "0.13"], ["cg02364642", "ARHGEF25", "2.33 × 10-3", "0.14"], ["cg22449114", "TCF15", "2.39 × 10-5", "0.14"], ["cg03565323", "ZNF287", "4.52 × 10-3", "0.14"], ["cg02388150", "SFRP1", "1.20 × 10-7", "0.15"], ["cg12768605", "LO×L2", "8.01 × 10-3", "0.15"], ["cg25657834", "NTSR2", "1.46 × 10-4", "0.16"], ["cg20914508", "GAP43", "9.41 × 10-4", "0.16"], ["cg10281002", "TBX5", "1.26 × 10-5", "0.17"], ["cg02489552", "CCDC105", "7.16 × 10-8", "0.18"], ["cg05675373", "KCNC4", "1.82 × 10-6", "0.18"], ["cg25148589", "GRIA2", "6.11 × 10-7", "0.18"], ["cg13216057", "DKK3", "9.64 × 10-4", "0.18"], ["cg27092035", "ARL10", "8.81 × 10-4", "0.19"], ["cg12351433", "LHCGR", "2.20 × 10-6", "0.20"], ["cg18573383", "KCNC2", "5.43 × 10-7", "0.21"], ["cg08434234", "DGKI", "6.60 × 10-5", "0.22"], ["cg21096399", "MCAM", "5.20 × 10-8", "0.22"], ["cg10920957", "JPH3", "1.03 × 10-4", "0.25"], ["cg08965235", "LTBP3", "6.03 × 10-10", "0.25"], ["cg27319898", "ZNF804B", "5.48 × 10-5", "0.26"], ["cg26620959", "SYNE1", "3.89 × 10-6", "0.29"], ["cg25070637", "SDC2", "1.82 × 10-5", "0.30"], ["cg07663789", "NPR3", "6.41 × 10-7", "0.31"], ["cg09191327", "PRDM12", "4.08 × 10-7", "0.31"], ["cg06557358", "TMEM132E", "2.04 × 10-8", "0.33"], ["cg10486998", "GALR1", "2.61 × 10-9", "0.36"], ["cg24834740", "PPP1R16B", "2.23 × 10-9", "0.36"], ["cg08090772", "ADHFE1", "5.19 × 10-11", "0.39"], ["cg02217159", "KHDRBS2", "1.87 × 10-11", "0.41"]], "row_count": 71, "column_count": 4, "numeric_cells": 231, "header_rows": 1, "locator": "section[14]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:28058013:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dfe56e44def883fe30c4474c2fff8dd3d8baeec55270b5ba54f99f6d51a7d788", "bytes": 1869, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[3]#T4", "version": null, "note": "Significant DNA methylation alterations of age-related CpG sites in colorectal cancer samples compared to adenoma tissue", "structure": {"pmcid": "PMC5175245", "section_index": 14, "section_title": "In silico DNA methylation analysis", "row_count": 35, "column_count": 4}, "table": {"label": "Table 4", "caption": "Significant DNA methylation alterations of age-related CpG sites in colorectal cancer samples compared to adenoma tissue", "rows": [["cgID", "Gene symbol", "P value", "Δβ (CRC - AD)"], ["cg08965235", "LTBP3", "9.09 × 10-4", "-0.11"], ["cg00945507", "SEC61G", "1.64 × 10-5", "0.10"], ["cg15974053", "HSD17B14", "2.27 × 10-3", "0.10"], ["cg24262469", "TIPARP", "5.33 × 10-8", "0.10"], ["cg07158339", "FXN", "1.84 × 10-7", "0.10"], ["cg11314684", "AKT3", "4.52 × 10-4", "0.10"], ["cg03578041", "LARP6", "2.57 × 10-9", "0.10"], ["cg17853587", "NDST3", "5.94 × 10-4", "0.10"], ["cg07408456", "PGLYRP2", "1.51 × 10-7", "0.11"], ["cg02580606", "KRT33B", "1.22 × 10-4", "0.11"], ["cg03019000", "TEX264", "5.39 × 10-5", "0.11"], ["cg27319898", "ZNF804B", "0.023", "0.12"], ["cg00436603", "CYP2E1", "1.97 × 10-6", "0.12"], ["cg15804973", "MAP3K5", "6.27 × 10-12", "0.12"], ["cg06117855", "CLEC3B", "1.73 × 10-7", "0.13"], ["cg24126851", "DCHS1", "3.58 × 10-8", "0.13"], ["cg16034652", "UNC79", "4.23 × 10-11", "0.13"], ["cg01262913", "DSCR9", "1.64 × 10-8", "0.13"], ["cg26372517", "TFAP2E", "9.80 × 10-6", "0.13"], ["cg03270204", "DDR1", "4.24 × 10-7", "0.13"], ["cg17589341", "SLC14A1", "7.35 × 10-10", "0.13"], ["cg22679120", "SNX8", "8.16 × 10-9", "0.14"], ["cg20828084", "CEMIP", "2.00 × 10-8", "0.14"], ["cg19305227", "SLC28A2", "1.11 × 10-6", "0.14"], ["cg00168942", "GJD4", "1.18 × 10-7", "0.14"], ["cg13038560", "C2orf47", "8.96 × 10-8", "0.15"], ["cg26614073", "SCAP", "1.33 × 10-9", "0.15"], ["cg19346193", "UROS", "2.09 × 10-8", "0.16"], ["cg00075967", "STRA6", "4.87 × 10-7", "0.16"], ["cg03103192", "SPATA18", "6.07 × 10-12", "0.16"], ["cg10345936", "SLC36A2", "4.09 × 10-6", "0.16"], ["cg17099569", "GLI2", "9.04 × 10-7", "0.16"], ["cg04126866", "C10orf99", "4.23 × 10-10", "0.18"], ["cg00091693", "KRT20", "1.17 × 10-8", "0.19"]], "row_count": 35, "column_count": 4, "numeric_cells": 115, "header_rows": 1, "locator": "section[14]/table-wrap[3]#T4"}}, {"id": "asset:table:pmid:28058013:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1d36878879ff10c4aeea5833f8f4fe985b3ea50461f42971a512d30207f8b4b9", "bytes": 3802, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T5", "version": null, "note": "Genes showing inverse DNA methylation and gene expression data", "structure": {"pmcid": "PMC5175245", "section_index": 15, "section_title": "In silico gene expression analysis", "row_count": 46, "column_count": 8}, "table": {"label": "Table 5", "caption": "Genes showing inverse DNA methylation and gene expression data", "rows": [["Gene symbol", "Gene name", "DNA methylation", "Gene expression"], ["cg ID", "P value", "Δβ", "Affymetrix ID", "P value", "LogFC"], ["CRC vs N", "", "", "", "", "", "", ""], ["AKT3", "AKT serine/threonine kinase 3", "cg11314684", "4.55 × 10-5", "-0.16", "224229_s_at", "0.015", "0.07"], ["222880_at", "2.26 × 10-3", "0.61"], ["212609_s_at", "4.72 × 10-4", "0.62"], ["212607_at", "9.76 × 10-4", "0.64"], ["ERG", "v-ets avian erythroblastosis virus E26 oncogene homolog", "cg17274064", "1.48 × 10-4", "-0.11", "211626_x_at", "5.84 × 10-4", "0.20"], ["241926_s_at", "2.05 × 10-5", "0.64"], ["213541_s_at", "4.69 × 10-9", "1.08"], ["MGP", "Matrix Gla protein", "cg00431549", "0.020", "-0.12", "202291_s_at", "2.34 × 10-11", "1.97"], ["PIPOX", "Pipecolic acid and sarcosine oxidase", "cg06144905", "1.81 × 10-7", "-0.22", "221605_s_at", "0.019", "0.50"], ["CCR10", "C-C motif chemokine receptor 10", "cg09509673", "1.91 × 10-4", "0.11", "220565_at", "0.010", "-0.51"], ["CLEC3B", "C-type lectin domain family 3 member B", "cg06117855", "1.88 × 10-3", "0.11", "205200_at", "1.45 × 10-13", "-1.79"], ["LTK", "Leukocyte receptor tyrosine kinase", "cg27494383", "9.32 × 10-3", "0.12", "217184_s_at", "2.14 × 10-11", "-1.32"], ["207106_s_at", "2.00 × 10-5", "-0.75"], ["PPP1R16B", "Protein phosphatase 1 regulatory subunit 16B", "cg24834740", "3.56 × 10-12", "0.37", "41577_at", "1.76 × 10-4", "-0.79"], ["212750_at", "7.68 × 10-3", "-0.48"], ["PRKAA2", "Protein kinase AMP-activated catalytic subunit alpha 2", "cg06836772", "0.013", "0.14", "227892_at", "4.15 × 10-3", "-0.87"], ["238489_at", "4.67 × 10-3", "-0.22"], ["SFRP1", "Secreted frizzled related protein 1", "cg02388150", "3.33 × 10-3", "0.10", "202036_s_at", "8.66 × 10-8", "-1.47"], ["202037_s_at", "3.98 × 10-5", "-1.11"], ["202035_s_at", "0.039", "-0.28"], ["SYNE1", "Spectrin repeat containing nuclear envelope protein 1", "cg26620959", "1.32 × 10-6", "0.30", "209447_at", "4.27 × 10-5", "-0.63"], ["AD vs N", "", "", "", "", "", "", ""], ["CEMIP", "Cell migration inducing hyaluronan binding protein", "cg20828084", "1.33 × 10-9", "-0.17", "1554685_a_at", "1.71 × 10-11", "1.12"], ["212942_s_at", "2.41 × 10-43", "6.88"], ["NT5DC3", "5'-nucleotidase domain containing 3", "cg06462291", "7.45 × 10-5", "-0.25", "218786_at", "6.83 × 10-9", "0.76"], ["SPATA18", "Spermatogenesis associated 18", "cg03103192", "1.39 × 10-7", "-0.15", "230723_at", "4.41 × 10-5", "0.45"], ["229331_at", "1.20 × 10-10", "1.50"], ["DKK3", "Dickkopf WNT signaling pathway inhibitor 3", "cg13216057", "9.64 × 10-4", "0.18", "202196_s_at", "9.82 × 10-5", "-0.65"], ["214247_s_at", "1.52 × 10-4", "-0.50"], ["PPP1R16B", "Protein phosphatase 1 regulatory subunit 16B", "cg24834740", "2.23 × 10-9", "0.36", "41577_at", "1.20 × 10-10", "-1.44"], ["212750_at", "3.28 × 10-7", "-0.81"], ["SDC2", "Syndecan 2", "cg25070637", "1.82 × 10-5", "0.30", "212158_at", "1.74 × 10-10", "-1.17"], ["212157_at", "2.14 × 10-8", "-0.66"], ["212154_at", "9.19 × 10-5", "-0.64"], ["SFRP1", "Secreted frizzled related protein 1", "cg02388150", "1.20 × 10-7", "0.15", "202036_s_at", "3.62 × 10-13", "-1.79"], ["202037_s_at", "4.43 × 10-11", "-1.48"], ["202035_s_at", "0.016", "-0.32"], ["SYNE1", "Spectrin repeat containing nuclear envelope protein 1", "cg26620959", "3.89 × 10-6", "0.29", "209447_at", "5.76 × 10-15", "-1.19"], ["CRC vs AD", "", "", "", "", "", "", ""], ["CEMIP", "Cell migration inducing hyaluronan binding protein", "cg20828084", "2.00 × 10-8", "0.14", "212942_s_at", "9.88 × 10-3", "-1.17"], ["SLC28A2", "Solute carrier family 28 member 2", "cg19305227", "1.11 × 10-6", "0.14", "207249_s_at", "0.027", "-1.24"], ["SPATA18", "Spermatogenesis associated 18", "cg03103192", "6.07 × 10-12", "0.16", "229331_at", "3.52 × 10-9", "-1.73"], ["230723_at", "7.35 × 10-4", "-0.41"]], "row_count": 46, "column_count": 8, "numeric_cells": 212, "header_rows": 2, "locator": "section[15]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:28058013:10", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:55ba367b53d2b79ff42408e3b93d43ee86beb69d6e18667a79b73c7cae3fd693", "bytes": 4548, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T6", "version": null, "note": "Whole promoter methylation status of genes with inverse age-related CpG site DNA methylation and gene expression data", "structure": {"pmcid": "PMC5175245", "section_index": 16, "section_title": "Whole promoter methylation status of genes showing inverse relationship between gene expression and DNA methylation", "row_count": 78, "column_count": 7}, "table": {"label": "Table 6", "caption": "Whole promoter methylation status of genes with inverse age-related CpG site DNA methylation and gene expression data", "rows": [["Gene symbol", "DNA methylation on age-related CpG site", "Whole promoter DNA methylation status"], ["cg ID", "P value", "Δβ", "Start-Stop position", "P value", "Δβ"], ["CRC vs N", "", "", "", "", "", ""], ["AKT3", "cg11314684", "4.55 × 10-5", "-0.16", "chr1:244005801-244005900", "6.56 × 10-3", "-0.33"], ["ERG", "cg17274064", "1.48 × 10-4", "-0.11", "chr21:39871501-39871600", "0.044", "-0.21"], ["MGP", "cg00431549", "0.020", "-0.12", "chr12:15038501-15038600", "0.030", "-0.27"], ["CCR10", "cg09509673", "1.91 × 10-4", "0.11", "chr17:40835101-40835200", "0.045", "0.18"], ["chr17:40835201-40835300", "0.022", "0.26"], ["PPP1R16B", "cg24834740", "3.56 × 10-12", "0.37", "chr20:37433201-37433300", "3.76 × 10-3", "0.35"], ["chr20:37434701-37434800", "0.048", "0.40"], ["chr20:37435301-37435400", "0.042", "0.37"], ["SFRP1", "cg02388150", "3.33 × 10-3", "0.10", "chr8:41166001-41166100", "0.017", "0.44"], ["chr8:41166101-41166200", "1.31 × 10-4", "0.56"], ["chr8:41166201-41166300", "3.40 × 10-3", "0.49"], ["chr8:41166301-41166400", "0.014", "0.27"], ["chr8:41166401-41166500", "1.28 × 10-3", "0.53"], ["chr8:41166501-41166600", "0.027", "0.44"], ["chr8:41166601-41166700", "0.034", "0.39"], ["chr8:41166901-41167000", "0.042", "0.41"], ["SYNE1", "cg26620959", "1.32 × 10-6", "0.30", "chr6:152622201-152622300", "0.027", "0.35"], ["chr6:152957601-152957700", "0.032", "0.39"], ["chr6:152957701-152957800", "0.043", "0.40"], ["chr6:152958101-152958200", "2.86 × 10-4", "0.65"], ["AD vs N", "", "", "", "", "", ""], ["CEMIP", "cg20828084", "1.33 × 10-9", "-0.17", "chr15: 81070701-81070800", "0.028", "-0.25"], ["SPATA18", "cg03103192", "1.39 × 10-7", "-0.15", "chr4:52915901-52916000", "0.042", "-0.23"], ["DKK3", "cg13216057", "9.64 × 10-4", "0.18", "chr11:12029701-12029800", "3.11 × 10-3", "0.26"], ["chr11:12029801-12029900", "1.67 × 10-3", "0.33"], ["chr11:12029901-12030000", "8.08 × 10-5", "0.56"], ["chr11:12030001-12030100", "0.047", "0.15"], ["chr11:12030401-12030500", "7.38 × 10-3", "0.28"], ["chr11: 12030501-12030600", "0.012", "0.28"], ["PPP1R16B", "cg24834740", "2.23 × 10-9", "0.36", "chr20:37434201-37434300", "0.045", "0.26"], ["chr20:37434601-37434700", "0.022", "0.39"], ["chr20:37434701-37434800", "0.013", "0.39"], ["chr20:37434801-37434900", "6.87 × 10-3", "0.30"], ["chr20:37434901-37435000", "1.70 × 10-3", "0.44"], ["chr20:37435001-37435100", "1.93 × 10-3", "0.45"], ["chr20:37435101-37435200", "6.49 × 10-3", "0.35"], ["chr20:37435201-37435300", "8.93 × 10-4", "0.51"], ["chr20:37435301-37435400", "0.014", "0.42"], ["SDC2", "cg25070637", "1.82 × 10-5", "0.30", "chr8:97505901-97506000", "2.30 × 10-3", "0.59"], ["chr8:97506101-97506200", "1.96 × 10-4", "0.65"], ["chr8:97506201-97506300", "8.43 × 10-4", "0.63"], ["chr8:97506301-97506400", "0.012", "0.49"], ["chr8:97506401-97506500", "0.019", "0.47"], ["chr8:97506601-97506700", "3.99 × 10-3", "0.51"], ["chr8:97506701-97506800", "0.021", "0.45"], ["chr8:97506801-97506900", "0.014", "0.52"], ["chr8:97507101-97507200", "0.015", "0.44"], ["chr8:97507201-97507300", "0.010", "0.52"], ["chr8:97507301-97507400", "3.47 × 10-3", "0.59"], ["SFRP1", "cg02388150", "1.20 × 10-7", "0.15", "chr8:41165901-41166000", "2.30 × 10-3", "0.59"], ["chr8:41166001-41166100", "1.57 × 10-3", "0.59"], ["chr8:41166101-41166200", "3.54 × 10-4", "0.56"], ["chr8:41166201-41166300", "1.49 × 10-4", "0.60"], ["chr8:41166301-41166400", "6.54 × 10-3", "0.27"], ["chr8:41166401-41166500", "1.32 × 10-5", "0.55"], ["chr8: 41166501-41166600", "2.30 × 10-3", "0.60"], ["chr8:41166601-41166700", "5.45 × 10-3", "0.57"], ["chr8:41166701-41166800", "8.15 × 10-3", "0.51"], ["chr8:41166801-41166900", "0.032", "0.39"], ["chr8:41166901-41167000", "0.019", "0.45"], ["chr8:41167001-41167100", "0.046", "0.34"], ["chr8:41167101-41167200", "0.025", "0.41"], ["chr8:41167201-41167300", "0.024", "0.40"], ["SYNE1", "cg26620959", "3.89 × 10-6", "0.29", "chr6:152702701-152702800", "0.012", "0.20"], ["chr6:152702801-152702900", "0.035", "0.21"], ["chr6:152957501-152957600", "6.05 × 10-4", "0.37"], ["chr6:152957601-152957700", "2.34 × 10-4", "0.60"], ["chr6:152957701-152957800", "0.017", "0.51"], ["chr6:152957801-152957900", "1.09 × 10-3", "0.42"], ["chr6:152957901-152958000", "1.03 × 10-4", "0.57"], ["chr6:152958001-152958100", "7.13 × 10-4", "0.43"], ["chr6:152958101-152958200", "1.72 × 10-5", "0.72"], ["CRC vs AD", "", "", "", "", "", ""], ["CEMIP", "cg20828084", "2.00 × 10-8", "0.14", "chr15:81070701-81070800", "7.59 × 10-4", "0.31"], ["chr15:81070801-81070900", "0.011", "0.36"]], "row_count": 78, "column_count": 7, "numeric_cells": 268, "header_rows": 2, "locator": "section[16]/table-wrap[1]#T6"}}], "gaps": ["asset:data:geo:GSE10714 not downloaded", "asset:data:geo:GSE10714 licence not read", "asset:data:geo:GSE37267 not downloaded", "asset:data:geo:GSE37267 licence not read", "asset:data:geo:GSE37364 not downloaded", "asset:data:geo:GSE37364 licence not read", "asset:data:geo:GSE4183 not downloaded", "asset:data:geo:GSE4183 licence not read", "asset:data:geo:GSE48684 not downloaded", "asset:data:geo:GSE48684 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE48684", "GSE37364", "GSE10714", "GSE4183", "GSE37267"], "resolved_accessions": ["GSE48684", "GSE37364", "GSE10714", "GSE4183", "GSE37267"], "statements": ["Additional data are available in a supplementary file."], "basis": "The paper names GSE48684, GSE37364, GSE10714, GSE4183, GSE37267 in NCBI Gene Expression Database (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28058013", "data:geo:GSE10714", "asset:table:pmid:28058013:1", "asset:table:pmid:28058013:2", "asset:table:pmid:28058013:3", "asset:table:pmid:28058013:4", "asset:table:pmid:28058013:5", "asset:table:pmid:28058013:6", "asset:table:pmid:28058013:7", "asset:table:pmid:28058013:8", "asset:table:pmid:28058013:9", "asset:table:pmid:28058013:10"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10714"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:34Z", "independence": "same_provider"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 74980, "completion_tokens": 4457, "cached_tokens": 10928}}, "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:28058013", "type": "paper", "label": "pmid:28058013"}, {"id": "source:pmid:28058013", "type": "manuscript", "label": "PMID 28058013 full text"}, {"id": "data:geo:GSE10714", "type": "dataset", "label": "GEO GSE10714"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28058013", "type": "paper", "label": "pmid:28058013"}, {"id": "source:pmid:28058013", "type": "manuscript", "label": "PMID 28058013 full text"}, {"id": "data:geo:GSE10714", "type": "dataset", "label": "GEO GSE10714"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28058013", "type": "extraction", "used": ["source:pmid:28058013"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10714", "type": "accession_resolution", "used": ["data:geo:GSE10714"], "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:28058013", "parent_hash": "sha256:ebfeec3b3a1022d7e1d4a82f684f8272419b1c6c30a4145c630c17d1a0716354", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE10714 licence not read", "asset:data:geo:GSE10714 not downloaded", "asset:data:geo:GSE37267 licence not read", "asset:data:geo:GSE37267 not downloaded", "asset:data:geo:GSE37364 licence not read", "asset:data:geo:GSE37364 not downloaded", "asset:data:geo:GSE4183 licence not read", "asset:data:geo:GSE4183 not downloaded", "asset:data:geo:GSE48684 licence not read", "asset:data:geo:GSE48684 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "methylation_array", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["blished by Steve Horvath was performed using methylation array data for a set of 123 colonic tissue samples", "hildren, 20 adenoma and 8 CRC patients using bisulfite-specific PCR followed by methylation-specifi"], "order_basis": "paper_text_order:340", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["d \"epigenetic clock\" genes was studied using Affymetrix HGU133 Plus2.0 whole transcriptome data of 1"], "order_basis": "paper_text_order:903", "id": "assay:2"}]},"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":"2026-11-04T14:24:55+00:00","generated_at":"2026-11-05T02:17:40+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}}}