Identification of aberrantly methylated differentially expressed genes in prostate carcinoma using integrated bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30872976", "kind": "science-record", "revision": 5, "content_hash": "sha256:203b97dc90df35e2d07088c6de1e54724ba06ce7c4b8c3ffb8ef137cf3227cff", "created_at": "2026-11-01T15:40:43Z", "updated_at": "2026-11-01T22:00:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of aberrantly methylated differentially expressed genes in prostate carcinoma using integrated bioinformatics.", "doi": "10.1186/s12935-019-0763-8", "pmid": "30872976", "authors": ["Kai Wu", "Xiaotao Yin", "Yipeng Jin", "Fangfang Liu", "Jiangping Gao"], "journal": "Cancer cell international", "year": 2019, "abstract": "BACKGROUND: Methylation plays a key role in the aetiology and pathogenesis of prostate cancer (PCa). This study aimed to identify aberrantly methylated differentially expressed genes (DEGs) and pathways in PCa and explore the underlying mechanisms of tumourigenesis.\nMETHODS: Expression profile (GSE29079) and methylation profile (GSE76938) datasets were obtained from the Gene Expression Omnibus (GEO). We used R 3.4.4 software to assess aberrantly methylated DEGs. The Cancer Genome Atlas (TCGA) RNA sequencing and Illumina HumanMethylation450 DNA methylation data were utilized to validate screened genes. Functional enrichment analysis of the screened genes was performed, and a protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Gens (STRING). The results were visualized in Cytoscape. After confirmation using TCGA, cBioPortal was used to examine alterations in genes of interest. Then, protein localization in PCa cells was observed using immunohistochemistry.\nRESULTS: Overall, 536 hypomethylated upregulated genes were identified that were enriched in biological processes such as negative regulation of transcription, osteoblast differentiation, intracellular signal transduction, and the Wnt signalling pathway. Pathway enrichment showed significant changes in factors involved in AMPK signalling, cancer, and adherens junction pathways. The hub oncogenes were AKT1, PRDM10, and FASN. Additionally, 322 hypermethylated downregulated genes were identified that demonstrated enrichment in biological processes including positive regulation of the MAPK cascade, muscle contraction, ageing, and signal transduction. Pathway analysis indicated enrichment in arrhythmogenic right ventricular cardiomyopathy (ARVC), focal adhesion, dilated cardiomyopathy, and PI3K-AKT signalling. The hub tumour suppressor gene was FLNA. Immunohistochemistry showed that AKT1, FASN, and FLNA were mainly expressed in PCa cell cytoplasm, while PRDM10 was mainly expressed in nuclei.\nCONCLUSIONS: Our results identify numerous novel genetic and epigenetic regulatory networks and offer molecular evidence crucial to understanding the pathogenesis of PCa. Aberrantly methylated hub genes, including AKT1, PRDM10, FASN, and FLNA, can be used as biomarkers for accurate PCa diagnosis and treatment. In conclusion, our study suggests that AKT1, PRDM10, and FASN may be tumour promoters and that FLNA may be a tumour suppressor in PCa. We hope these findings will draw more attention to these hub genes in future cancer studies.", "claims": [{"id": "claim-data-access", "statement": "The authors declare that the data supporting the findings of this study are available within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30872976", "locator": "sections[20] \"ack\" paragraph 1", "quote": "The authors declare that the data supporting the findings of this study are available within the article."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30872976"], "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:GSE29079"], "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:GSE29079"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30872976", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-019-0763-8", "sha256": "sha256:f0cf8a002229b8e9cbdcebf03967188f7fe1ece07cb119caaae235020dfc8ff1", "bytes": 41206, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-019-0763-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6402097", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29079", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29079", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29079", "version": null, "note": "The authors declare that the data supporting the findings of this study are available within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The authors declare that the data supporting the findings of this study are available within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM720503", "GSM720504", "GSM720505", "GSM720506", "GSM720507", "GSM720508", "GSM720509", "GSM720510", "GSM720511", "GSM720512", "GSM720513", "GSM720514", "GSM720515", "GSM720516", "GSM720517", "GSM720518", "GSM720519", "GSM720520", "GSM720521", "GSM720522", "GSM720523", "GSM720524", "GSM720525", "GSM720526", "GSM720527", "GSM720528", "GSM720529", "GSM720530", "GSM720531", "GSM720532", "GSM720533", "GSM720534", "GSM720535", "GSM720536", "GSM720537", "GSM720538", "GSM720539", "GSM720540", "GSM720541", "GSM720542", "GSM720543", "GSM720544", "GSM720545", "GSM720546", "GSM720547", "GSM720548", "GSM720549", "GSM720550", "GSM720551", "GSM720552", "GSM720553", "GSM720554", "GSM720555", "GSM720556", 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"GSM2041203", "GSM2041204", "GSM2041205", "GSM2041206", "GSM2041207", "GSM2041208", "GSM2041209", "GSM2041210", "GSM2041211", "GSM2041212", "GSM2041213", "GSM2041214", "GSM2041215", "GSM2041216", "GSM2041217", "GSM2041218", "GSM2041219", "GSM2041220", "GSM2041221", "GSM2041222", "GSM2041223", "GSM2041224", "GSM2041225", "GSM2041226", "GSM2041227", "GSM2041228", "GSM2041229", "GSM2041230", "GSM2041231", "GSM2041232", "GSM2041233", "GSM2041234", "GSM2041235", "GSM2041236", "GSM2041237", "GSM2041238", "GSM2041239", "GSM2041240", "GSM2041241", "GSM2041242", "GSM2041243", "GSM2041244", "GSM2041245"], "sample_count": 136, "group_sizes": null, "group_sizes_basis": null, "platform": "13534", "taxon": "Homo sapiens", "title": "Illumina M450 profiling of human prostate cancer tissue and benign prostate tissue", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30872976:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e290412c0fd98d2ffee0da2baf8641ef44fa9eb57d453f5086150f0130162af9", "bytes": 2755, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab1", "version": null, "note": "Gene Ontology analysis of aberrantly methylated differentially expressed genes in prostate cancer", "structure": {"pmcid": "PMC6402097", "section_index": 11, "section_title": "GO functional enrichment analysis", "row_count": 33, "column_count": 4}, "table": {"label": "Table 1", "caption": "Gene Ontology analysis of aberrantly methylated differentially expressed genes in prostate cancer", "rows": [["Category", "Term", "Count", "P value"], ["Hypomethylated with high expression"], ["GOTERM_BP_DIRECT", "GO:0000122 —negative regulation of transcription from RNA polymerase II promoter", "41", "5.49E−05"], ["GOTERM_BP_DIRECT", "GO:0001649 —osteoblast differentiation", "12", "1.99E−04"], ["GOTERM_BP_DIRECT", "GO:0035556 —intracellular signal transduction", "25", "6.61E−04"], ["GOTERM_BP_DIRECT", "GO:0007223 —Wnt signalling pathway, calcium-modulating pathway", "7", "8.00E−04"], ["GOTERM_BP_DIRECT", "GO:0030036 —actin cytoskeleton organization", "12", "0.0013"], ["GOTERM_CC_DIRECT", "GO:0005654 —nucleoplasm", "111", "8.73E−05"], ["GOTERM_CC_DIRECT", "GO:0005829 —cytosol", "126", "1.97E−04"], ["GOTERM_CC_DIRECT", "GO:0016604 —nuclear body", "6", "0.0021"], ["GOTERM_CC_DIRECT", "GO:0005737 —cytoplasm", "176", "0.0030"], ["GOTERM_CC_DIRECT", "GO:0032580 —Golgi cisterna membrane", "8", "0.0054"], ["GOTERM_MF_DIRECT", "GO:0005515 —protein binding", "297", "2.57E−04"], ["GOTERM_MF_DIRECT", "GO:0044212 —transcription regulatory region DNA-binding activity", "16", "0.0016"], ["GOTERM_MF_DIRECT", "GO:0016874 —ligase activity", "18", "0.0027"], ["GOTERM_MF_DIRECT", "GO:0005096 —GTPase activator activity", "18", "0.0037"], ["GOTERM_MF_DIRECT", "GO:0003713 —transcription coactivator activity", "16", "0.0066"], ["Hypermethylated with low expression"], ["GOTERM_BP_DIRECT", "GO:0043410 —positive regulation of MAPK cascade", "8", "8.37E−05"], ["GOTERM_BP_DIRECT", "GO:0006936 —muscle contraction", "9", "1.41E−04"], ["GOTERM_BP_DIRECT", "GO:0007568 —ageing", "11", "2.19E−04"], ["GOTERM_BP_DIRECT", "GO:0007165 —signal transduction", "37", "2.44E−04"], ["GOTERM_BP_DIRECT", "GO:0014068 —positive regulation of phosphatidylinositol 3-kinase signalling", "7", "3.77E−04"], ["GOTERM_CC_DIRECT", "GO:0005925 —focal adhesion", "24", "1.01E−03"], ["GOTERM_CC_DIRECT", "GO:0009986 —cell surface", "25", "1.34E−03"], ["GOTERM_CC_DIRECT", "GO:0070062 —extracellular exosome", "74", "2.77E−03"], ["GOTERM_CC_DIRECT", "GO:0042383 —sarcolemma", "9", "3.60E−03"], ["GOTERM_CC_DIRECT", "GO:0005615 —extracellular space", "41", "1.24E−02"], ["GOTERM_MF_DIRECT", "GO:0003779 —actin binding", "16", "1.37E−04"], ["GOTERM_MF_DIRECT", "GO:0005515 —protein binding", "184", "7.99E−04"], ["GOTERM_MF_DIRECT", "GO:0030165 —PDZ domain binding", "8", "8.30E−04"], ["GOTERM_MF_DIRECT", "GO:0005539 —glycosaminoglycan binding", "4", "0.0037"], ["GOTERM_MF_DIRECT", "GO:0004714 —transmembrane receptor protein tyrosine kinase activity", "5", "0.0044"]], "row_count": 33, "column_count": 4, "numeric_cells": 90, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:30872976:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:607a46af41f2ff9ed6057c01dd37618df4c43102a932168745f6a472830c13be", "bytes": 1600, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab2", "version": null, "note": "Kyoto Encyclopedia of Genes and Genomes pathway analysis of aberrantly methylated differentially expressed genes in prostate cancer", "structure": {"pmcid": "PMC6402097", "section_index": 12, "section_title": "KEGG pathway analysis", "row_count": 11, "column_count": 5}, "table": {"label": "Table 2", "caption": "Kyoto Encyclopedia of Genes and Genomes pathway analysis of aberrantly methylated differentially expressed genes in prostate cancer", "rows": [["Category", "Term", "Count", "P value", "Gene"], ["Hypomethylated with high expression"], ["KEGG_PATHWAY", "hsa04152: AMPK signalling pathway", "12", "0.0025", "AKT1, IGF1R, PDPK1, IRS2, CCND1, TSC2, ACACA, FASN, FBP1, EEF2, PPP2R2D, RPTOR"], ["KEGG_PATHWAY", "hsa05200: pathways in cancer", "24", "0.0062", "HSP90AB1, DVL3, CTBP1, ADCY1, COL4A1, ADCY7, RXRA, CREBBP, GNA12, LEF1, FZD4, TCF7L2, TPM3, DAPK1, AKT1, JUP, IGF1R, WNT7B, CBLB, CCND1, GNB2, GNB1, CASP8, GNG7"], ["KEGG_PATHWAY", "hsa04520: adherens junction", "8", "0.0094", "ACTG1, IGF1R, TJP1, WASF3, BAIAP2, CREBBP, LEF1, TCF7L2"], ["Hypermethylated with low expression"], ["KEGG_PATHWAY", "hsa05412: arrhythmogenic right ventricular cardiomyopathy (ARVC)", "8", "3.99E−04", "DES, SGCG, DMD, ITGA7, ITGA1, CACNB2, GJA1, CTNNB1"], ["KEGG_PATHWAY", "hsa04510: focal adhesion", "12", "0.0020", "CAV2, ITGA7, ITGA1, PDGFC, PTEN, FLNA, PIK3R1, MYLK, COL4A6, KDR, CTNNB1, PRKCB"], ["KEGG_PATHWAY", "hsa05410: hypertrophic cardiomyopathy (HCM)", "7", "0.0038", "DES, SGCG, DMD, ITGA7, ITGA1, CACNB2, TPM1 1"], ["KEGG_PATHWAY", "hsa05414: dilated cardiomyopathy", "7", "0.0054", "DES, SGCG, DMD, ITGA7, ITGA1, CACNB2, TPM1"], ["KEGG_PATHWAY", "hsa04151: PI3K-Akt signalling pathway", "15", "0.0063", "FGFR2, ITGA1, KITLG, KIT, LPAR1, PTEN, COL4A6, KDR, EIF4B, CDKN1B, ITGA7, ANGPT1, PDGFC, FGF2, PIK3R1"]], "row_count": 11, "column_count": 5, "numeric_cells": 26, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:30872976:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:08fd770e9675fb7c153aaf539f2917a76225ed4e2572e276b973789023d60c2c", "bytes": 2569, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab3", "version": null, "note": "Hub genes among the aberrantly methylated differentially expressed genes ranked in cytoHubba", "structure": {"pmcid": "PMC6402097", "section_index": 13, "section_title": "PPI network construction and cytoHubba analysis", "row_count": 11, "column_count": 3}, "table": {"label": "Table 3", "caption": "Hub genes among the aberrantly methylated differentially expressed genes ranked in cytoHubba", "rows": [["Category", "Rank method in cytoHubba", "Top 30 genes"], ["Hypomethylated with high expression", "Betweenness", "AKT1, PRDM10, ACACA, GNB1, DICER1, CTBP1, ACTG1, CREBBP, HSP90AB1, DCY7, GNG7, PXN, POLR2D, PPP3CA, EEF2, BGN, GNB2, EHMT2, FASN, CCND1 , OXA1L, SHMT2, CBLB, ATP5B, UBE4A, RPL6, SYNJ2, TCF7L2, EPHB2, FAF2"], ["Bottleneck", "AKT1, PRDM10 , ACACA, DICER1, GNB1, ADCY7, CTBP1, SH3RF1, EHMT2, CREBBP, PPP3CA, ACTG1, FASN , RPL6, JUP, OXA1L, BGN, HSP90AB1, PXN, ECHS1, ATP5B, GPT2, POLR2D, CCND1 , SYNJ2, SHMT2, EIF4A1, USP7, CHEK1, EEF2"], ["Closeness", "AKT1, PRDM10, ACACA, GNB1, CCND1 , CTBP1, GNG7, DICER1, CREBBP, ADCY7, GNB2, PXN, IGF1R, PPP3CA, HSP90AB1, LEF1, EIF4A1, PDPK1, ITPR3, RPTOR, EHMT2, CHEK1, ACTG1, POLR2D, YWHAG, TCF7L2, EEF2, FASN , EPHB2, POLR3A"], ["Radiality", "AKT1, PRDM10 , ACACA, CCND1, CTBP1, DICER1, CREBBP, PPP3CA, IGF1R, GNB1, ADCY7, LEF1, PXN, EIF4A1, GNB2, HSP90AB1, GNG7, RPTOR, ITPR3, YWHAG, PDPK1, CHEK1, EHMT2, ACTG1, CASP8, TJP1, FASN , TSC2, EPHB2, TCF7L2"], ["Stress", "AKT1, PRDM10 , ACACA, GNB1, DICER1, CTBP1, ADCY7, GNG7, HSP90AB1, CREBBP, ACTG1, GNB2, POLR2D, PPP3CA, PXN, CBLB, EEF2, CCND1 , EHMT2, BGN, TCF7L2, UBE4A, ATP5B, IGF1R, SYNJ2, POLR3A, FASN , SHMT2, EIF4A1, CHEK1"], ["Hypermethylated with low expression", "Betweenness", "CTNNB1, DPYD, FGF2, VCAM1, PTEN, KIT, CFTR, RHOB, DCN, KDR, DMD, ANXA2, PRKCB , PRKG2, DES, FLNA , FST, KAT2B, PIK3R1, ITGA1, FOXO1, TPM1, PDE4D, ACSS3, CCK, KITLG, NT5E, CUL1, GATA3, HOPX"], ["Closeness", "CTNNB1, FGF2, PTEN, KIT, VCAM1, KDR, PIK3R1, FOXO1, KITLG, DPYD, PROM1, CDKN1B, RHOB, LEPR, GJA1, PRKCB , KAT2B, ANXA2, DCN, SNAI2, DES, FGFR2, ITGA1, CUL1, FLNA , NT5E, CFTR, CCK, ANGPT1, PRKG2"], ["Degree", "CTNNB1, FGF2, PTEN,KIT, VCAM1, KDR, KITLG, PIK3R1, KAT2B, CUL1, DPYD, RHOB, FOXO1, FLNA , CDKN1B, DES, DCN, PRKCB, ITGA1, DMD, CCK, CFTR, ANXA2, PROM1, UBE3A, TPM1, PRKG2, NT5E, LEPR, FGFR2"], ["Eccentricity", "VCAM1, ANXA2, KIT, FGF2, KDR, PIK3R1, DMD, GJA1, PRKCB, PRKG2, TMOD1, ITGA1, COCH, CCK, AVPR1A, MTUS1, EDNRA, MYOF, FLNA, CFTR, CXCL1, LPAR1, ANXA6, GSN, PDE4D, NT5E, COL4A6, HLA-F, TRIM29, DAB1"], ["Edge percolated component (EPC)", "FGF2, CTNNB1, KIT, PTEN, KDR, VCAM1, KITLG, PIK3R1, PROM1, CDKN1B, FOXO1, CUL1, KAT2B, ITGA1, FGFR2, ANGPT1, GJA1, DES, SNAI2, RHOB, UBE3A, FLNA, PRKCB , CCK, LEPR, CUL2, NT5E, TNS1, DCN, ANXA2"]], "row_count": 11, "column_count": 3, "numeric_cells": 7, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:30872976:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3133802c705078e3ee3e52b68b7c15b966d9517be2f5f7fc2b77a018923eaaab", "bytes": 2926, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab4", "version": null, "note": "Module analysis of the protein–protein interaction network", "structure": {"pmcid": "PMC6402097", "section_index": 14, "section_title": "Module analysis", "row_count": 11, "column_count": 6}, "table": {"label": "Table 4", "caption": "Module analysis of the protein–protein interaction network", "rows": [["Category", "Module", "Score", "Nodes", "Enrichment and pathway description", "Genes"], ["Hypomethylated with high expression", "1", "12.00", "12", "GO:0016874—ligase activityGO:0004842—ubiquitin protein transferase activityGO:0000209—protein polyubiquitinationhsa04120: ubiquitin-mediated proteolysisGO:0071377—cellular response to glucagon stimulus", "TRIM36, HERC3, NEDD4L, UBE4A, CBLB, SH3RF1, ASB13, MYLIP, RNF220, UBA1, UBE2H, RBBP6"], ["2", "10.00", "10", "GO:0007186—G-protein-coupled receptor signalling pathwayGO:0007193—adenylate cyclase-inhibiting G-protein-coupled receptor signalling pathwayhsa04727: GABAergic synapse", "ADCY7, GNB1, GNB2, GNG7, ADCY1, DRD3, HTR1E, SST, RLN3, ADRA2A"], ["3", "8.889", "10", "GO:0005634—nucleusGO:0005515—protein bindingGO:0006260—DNA replicationhsa04110: cell cycle", "CENPF, E2F8, TK1, HJURP, MCM3, ZWINT, MELK, CDKN3, EXO1, CHEK1"], ["4", "7.00", "7", "GO:0030669—clathrin-coated endocytic vesicle membraneGO:0060071—Wnt signalling pathway, planar cell polarity pathwayGO:0035615—clathrin adaptor activityhsa04144: endocytosis", "FZD4, REPS2, ADRB2, SYNJ2, AP2M1, AP2A2, AAK1"], ["5", "5.20", "16", "GO:0006383—transcription from RNA polymerase III promoterGO:0003899—DNA-directed RNA polymerase activityGO:0032481—positive regulation of type I interferon productionhsa00230: purine metabolism", "POLR2D, GUCY2F, TCF7L2, POLR1D, EEF2, POLR3H, GUCY1A3, SNAPC4, TCEANC, JUP, WNT7B, CTBP1, DVL3, BRF1, CREBBP, POLR3A"], ["6", "3.444", "19", "GO:0001649—osteoblast differentiationGO:0030206—chondroitin sulfateGO:0005515—protein bindinghsa05222: focal adhesion", "FHIT, COL4A1, DROSHA, NUMA1, DDX21, CMKLR1, COL3A1, DICER1, B3GALT6, OXA1L, MEF2D, FUS, DNMT3B, ARFIP2, VCAN, THBS2, CCND1, XYLT1, AKT1"], ["7", "3.143", "8", "GO:0009058—biosynthetic processGO:0005759—mitochondrial matrixGO:0030170—pyridoxal phosphate bindinghsa01230: biosynthesis of amino acids", "GPT2, FASN, GOT2, RPTOR, ATP5B, TSC2, PRDM10, SHMT2"], ["Hypermethylated with low expression", "1", "6.00", "13", "GO:0016032—viral processGO:0048015—phosphatidylinositol-mediated signallingGO:0061630—ubiquitin protein ligase activityhsa05200: pathways in cancer", "CUL2, PIK3R1, UBE3A, PTEN, PROM1, FBXL3, KITLG, KIT, KLHL2, FBXO17, CUL1, VCAM1, UBE2V2"], ["2", "3.667", "7", "GO:0007202—activation of phospholipase C activityGO:0010595—positive regulation of endothelial cell migrationGO:0008284—positive regulation of cell proliferation", "ANGPT1, FGF2, LPAR1, EDNRA, KDR, AVPR1A, CCK"], ["3", "3.333", "7", "hsa04015: Rap1 signalling pathwayGO:0045944—positive regulation of transcription from RNAPolymerase II promoterGO:0005654—nucleoplasm", "HLA-F, IRF2, PPARGC1A, TRIM29, CDK8, CEBPB, KAT2B"]], "row_count": 11, "column_count": 6, "numeric_cells": 45, "header_rows": 1, "locator": "section[14]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:30872976:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:20f04455a16ad8a87199fd7d4d2f9bdc487182bfe08a2641e24830e2c867dbad", "bytes": 710, "access": "open", "state": "verified", "reader": 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE29079", "GSE76938"], "resolved_accessions": ["GSE29079", "GSE76938"], "statements": ["The authors declare that the data supporting the findings of this study are available within the article."], "basis": "The paper names GSE29079, GSE76938 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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