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pmid:28058013
Aging related methylation influences the gene expression of key control genes in colorectal cancer and adenoma.
Orsolya Galamb · Alexandra Kalmár · Barbara Kinga Barták · Árpád V Patai · Katalin Leiszter · Bálint Péterfia · Barnabás Wichmann · Gábor Valcz · Gábor Veres · Zsolt Tulassay · Béla Molnár
World journal of gastroenterology · 2016 doi:10.3748/wjg.v22.i47.10325
Abstract
AIM: To analyze colorectal carcinogenesis and age-related DNA methylation alterations of gene sequences associated with epigenetic clock CpG sites. METHODS: 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. RESULTS: 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). CONCLUSION: 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.
The publication
- PubMed · PMID 28058013 The record in the National Library of Medicine.
- The publisher's article · doi:10.3748/wjg.v22.i47.10325 World journal of gastroenterology · 2016
- Orsolya Galamb · Alexandra Kalmár · Barbara Kinga Barták · Árpád V Patai · Katalin Leiszter · Bálint Péterfia · Barnabás Wichmann · Gábor Valcz · Gábor Veres · Zsolt Tulassay · Béla Molnár
Source data and code
- 10.3748/wjg.v22.i47.10325 manuscript · resolved
- GSE10714 raw · resolved
- GSE37267 raw · resolved
- GSE37364 raw · resolved
- GSE4183 raw · resolved
- GSE48684 raw · resolved
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Five-stage experiment
- 1 data generation Definition methylation_array · partial
- 2 data generation Definition microarray · partial
The order is the order the experiment runs them in. The full definitions, contracts and evidence are in the file below.
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Experiment
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Analysis
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Execution
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Complete file
{"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": 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