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pmid:29962817
Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma.
Liang Sang · Xue-Mei Wang · Dong-Yang Xu · Wen-Jing Zhao
World journal of gastroenterology · 2018 doi:10.3748/wjg.v24.i24.2605
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Complete file
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We analyzed the differentially methylated genes and differentially expressed genes online using GEO2R. Functional and enrichment analyses of MDEGs were conducted using the DAVID database. A protein-protein interaction (PPI) network was performed by STRING and then visualized in Cytoscape. Hub genes were ranked by cytoHubba, and a module analysis of the PPI network was conducted by MCODE in Cytoscape software.\nRESULTS: In total, we categorized 266 genes as hypermethylated, lowly expressed genes (Hyper-LGs) referring to endogenous and hormone stimulus, cell surface receptor linked signal transduction and behavior. In addition, 161 genes were labelled as hypomethylated, highly expressed genes (Hypo-HGs) referring to DNA replication and metabolic process, cell cycle and division. Pathway analysis illustrated that Hyper-LGs were enriched in cancer, Wnt, and chemokine signalling pathways, while Hypo-HGs were related to cell cycle and steroid hormone biosynthesis pathways. Based on PPI networks, PTGS2, PIK3CD, CXCL1, ESR1, and MMP2 were identified as hub genes for Hyper-LGs, and CDC45, DTL, AURKB, CDKN3, MCM2, and MCM10 were hub genes for Hypo-HGs by combining six ranked methods of cytoHubba.\nCONCLUSION: In the study, we disclose numerous novel genetic and epigenetic regulations and offer a vital molecular groundwork to understand the pathogenesis of HCC. Hub genes, including PTGS2, PIK3CD, CXCL1, ESR1, MMP2, CDC45, DTL, AURKB, CDKN3, MCM2, and MCM10, can be used as biomarkers based on aberrant methylation for the accurate diagnosis and treatment of HCC.", "claims": [{"id": "claim-method", "statement": "We used an online tool, GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), to analyze the differential expression by comparing two groups of samples across setup conditions in a GEO series.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29962817", "locator": "sections[5] \"Data processing\" paragraph 2", "quote": "We used an online tool, GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), to analyze the differential expression by comparing two groups of samples across setup conditions in a GEO series."}], "state": "complete"}, {"id": "claim-data-access", "statement": "One gene expression profiling dataset, GSE25097, and another gene methylation dataset, GSE57956, were downloaded from Gene Expression Omnibus (GEO, www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29962817", "locator": "sections[4] \"Microarray data\" paragraph 2", "quote": "One gene expression profiling dataset, GSE25097, and another gene methylation dataset, GSE57956, were downloaded from Gene Expression Omnibus (GEO, www.ncbi.nlm.nih.gov/geo/)."}], "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:29962817"], "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. 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"11", "4.15", "1.72E-04"], ["", "GOTERM_MF_FAT", "GO:0030247~polysaccharide binding", "11", "4.15", "1.72E-04"], ["", "GOTERM_MF_FAT", "GO:0004713~protein tyrosine kinase activity", "11", "4.15", "3.15E-04"], ["", "", "", "", "", ""], ["Hypo-HGs", "GOTERM_BP_FAT", "GO:0006260~DNA replication", "10", "6.25", "6.22E-05"], ["", "GOTERM_BP_FAT", "GO:0051301~cell division", "12", "7.50", "8.37E-05"], ["", "GOTERM_BP_FAT", "GO:0051276~chromosome organization", "15", "9.38", "1.41E-04"], ["", "GOTERM_BP_FAT", "GO:0006259~DNA metabolic process", "15", "9.38", "2.19E-04"], ["", "GOTERM_BP_FAT", "GO:0007049~cell cycle", "19", "11.88", "2.44E-04"], ["", "GOTERM_CC_FAT", "GO:0005694~chromosome", "14", "8.75", "3.77E-04"], ["", "GOTERM_CC_FAT", "GO:0044427~chromosomal part", "12", "7.50", "1.01E-03"], ["", "GOTERM_CC_FAT", "GO:0000793~condensed chromosome", "7", "4.38", "1.34E-03"], ["", "GOTERM_CC_FAT", "GO:0000785~chromatin", "8", "5.00", "2.77E-03"], ["", "GOTERM_CC_FAT", 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"section[11]/table-wrap[1]#T2", "version": null, "note": "KEGG pathway analysis of methylated-differentially expressed genes related with hepatocellular carcinoma", "structure": {"pmcid": "PMC6021769", "section_index": 11, "section_title": "KEGG pathway analysis", "row_count": 8, "column_count": 7}, "table": {"label": "Table 2", "caption": "KEGG pathway analysis of methylated-differentially expressed genes related with hepatocellular carcinoma", "rows": [["Category", "Term", "Count", "%", "P value", "Gene"], ["Hyper-LGs", "KEGG_PATHWAY", "hsa04610:Complement and coagulation cascades", "7", "2.64", "6.62E-03", "C7, CR1, CD55, THBD, MASP1, SERPINE1, PLAUR"], ["", "KEGG_PATHWAY", "hsa05414:Dilated cardiomyopathy", "7", "2.64", "2.50E-02", "LAMA2, ITGA9, ADCY1, ADRB1, ITGB8, ADCY5, TGFB3"], ["", "KEGG_PATHWAY", "hsa05200:Pathways in cancer", "15", "5.66", "2.94E-02", "FGFR2, PTGS2, FLT3, PIK3CD, FZD1, TGFB3, MMP2, WNT2, LAMA2, RAC2, NKX3-1, LAMC2, WNT11, HHIP, GSTP1"], ["", "KEGG_PATHWAY", "hsa04310:Wnt signaling pathway", "9", "3.40", "3.16E-02", "WNT2, SFRP5, NKD2, RAC2, PRICKLE1, SFRP1, FZD1, WNT11, FOSL1"], ["", "KEGG_PATHWAY", "hsa04062:Chemokine signaling pathway", "10", "3.77", "3.97E-02", "CXCL1, ADCY1, DOCK2, CCL23, RAC2, TIAM1, ADCY5, PIK3CD, CCL19, CXCL6"], ["Hypo-HGs", "KEGG_PATHWAY", "hsa04110:Cell cycle", "7", "4.38", "2.32E-03", "CCNE2, E2F2, PRKDC, CDC20, MCM2, SFN, PTTG1"], ["", "KEGG_PATHWAY", "hsa00140:Steroid hormone biosynthesis", "3", "1.88", "9.07E-02", "CYP17A1, CYP7A1, UGT2B11"]], "row_count": 8, "column_count": 7, "numeric_cells": 34, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:29962817:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9c05af79f86a0ac35cb9d9aaa6153c671d6951a23e6643ff5a82abe117aae344", "bytes": 829, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T3", "version": null, "note": "Hub genes for hypermethylated, lowly expressed genes ranked in cytoHubba", "structure": {"pmcid": "PMC6021769", "section_index": 12, "section_title": "PPI network construction and cytoHubba analysis", "row_count": 12, "column_count": 7}, "table": {"label": "Table 3", "caption": "Hub genes for hypermethylated, lowly expressed genes ranked in cytoHubba", "rows": [["Catelogy", "Rank methods in cytoHubba"], ["MNC", "Degree", "EPC", "Closeness", "Radiality", "Stress"], ["Gene symbol top 10", "PTGS2", "ADCY5", "PTGS2", "PIK3CD", "PIK3CD", "PTGS2"], ["PIK3CD", "MMP2", "PIK3CD", "PTGS2", "PTGS2", "PIK3CD"], ["ADCY5", "PTGS2", "MMP2", "MMP2", "MMP2", "MMP2"], ["ADCY1", "PIK3CD", "ADCY5", "ESR1", "ESR1", "PRKG1"], ["CXCL1", "PRKG1", "ADCY1", "PRKG1", "TLR2", "ESR1"], ["ESR1", "ADCY1", "ESR1", "TLR2", "SERPINE1", "FYN"], ["MMP2", "ESR1", "CXCL1", "FYN", "PRKG1", "RAC2"], ["FYN", "FYN", "TLR2", "CXCL1", "SNAI1", "SERPINE1"], ["TLR2", "CXCL1", "CALCA", "SERPINE1", "CRP", "CXCL1"], ["SERPINE1", "TLR2", "PTGER2", "ADCY5", "CXCL1", "ADCY5"]], "row_count": 12, "column_count": 7, "numeric_cells": 1, "header_rows": 2, "locator": "section[12]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:29962817:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d358c1d731b8728696a9dc8f50eb5c5a095a75151e5e8b35f99e810f3e9e49a", "bytes": 821, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#T4", "version": null, "note": "Hub genes for hypomethylated, highly expressed genes ranked in cytoHubba", "structure": {"pmcid": "PMC6021769", "section_index": 12, "section_title": "PPI network construction and cytoHubba analysis", "row_count": 12, "column_count": 7}, "table": {"label": "Table 4", "caption": "Hub genes for hypomethylated, highly expressed genes ranked in cytoHubba", "rows": [["Catelogy", "Rank methods in cytoHubba"], ["MCC", "MNC", "Degree", "EPC", "Closeness", "Radiality"], ["Gene symbol top 10", "CDC45", "CDC45", "CDC45", "CDC45", "CDKN3", "CDKN3"], ["DTL", "AURKB", "AURKB", "AURKB", "CDC45", "PRKDC"], ["RACGAP1", "DTL", "CDKN3", "CDKN3", "AURKB", "CDC45"], ["AURKB", "RACGAP1", "DTL", "DTL", "PTTG1", "PTTG1"], ["CDC20", "CDC20", "RACGAP1", "RACGAP1", "DTL", "MCM10"], ["CDKN3", "CDKN3", "CDC20", "CDC20", "MCM2", "BRCA1"], ["RRM2", "MCM2", "MCM2", "MCM2", "MCM10", "PI3"], ["MCM2", "PTTG1", "PTTG1", "PTTG1", "RACGAP1", "AURKB"], ["MCM10", "RRM2", "RRM2", "RRM2", "CDC20", "MCM2"], ["MKI67", "MCM10", "MCM10", "MCM10", "RRM2", "DTL"]], "row_count": 12, "column_count": 7, "numeric_cells": 19, "header_rows": 2, "locator": "section[12]/table-wrap[2]#T4"}}, {"id": "asset:table:pmid:29962817:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fee801fcebe6cdf53655765c94a2398020d3ed2d6500748e1b199a2dc318d91d", "bytes": 1843, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T5", "version": null, "note": "Modules analysis of the protein–protein interaction network", "structure": {"pmcid": "PMC6021769", "section_index": 13, "section_title": "Module analysis", "row_count": 22, "column_count": 6}, "table": {"label": "Table 5", "caption": "Modules analysis of the protein–protein interaction network", "rows": [["Category", "Module", "Score", "Nodes", "Enrichment and pathway description", "Genes"], ["Hyper-LGs", "1", "10.00", "10", "GO.0005886: plasma membrane", "ADRB1, VIPR1, PTGDR, SCTR, CALCA, GPR83, ADCY1, ADCY5, PTGER2, PTGER4"], ["GO.0007187: G-protein coupled receptor signaling pathway"], ["GO.0004016: adenylate cyclase activity"], ["has04080: Neuroactive ligand-receptor interaction"], ["2", "6.00", "6", "GO.0051953: negative regulation of amine transport", "CCL19, ADRA2B, P2RY12, CXCL6, NPY5R, CXCL1"], ["GO.0008009: chemokine activity"], ["has04062: Chemokine signaling pathway"], ["3", "5.68", "20", "GO.0005886: plasma membrane", "OXT, SERPINE1, EDNRB, PTGS2, ADRA1A, IL18, CRP, SOCS3, EFNB3, MMP2, EPHB1, TIAM1, EFNA5, TBXA2R, EPHA2, TLR2, SNAI1, FYN, GNA14, PROK2"], ["GO.0005003: ephrin receptor activity"], ["GO.0051240: positive regulation of multicellular organismal process"], ["hsa04360: Axon guidance"], ["4", "4.50", "5", "GO.0005605: basal lamina", "ITGA9, ITGB8, COL6A2, LAMC2, LAMA2"], ["GO.0030198: extracellular matrix organization"], ["hsa04512: ECM-receptor interaction"], ["Hypo-HGs", "1", "17.56", "19", "GO.0022402: cell cycle process", "CDCA5, KIF14, BRCA1, CENPF, RACGAP1, NEK2, CDKN3, DTL, MCM2, MCM10, CDC45, PTTG1, ANLN, CDC20, RRM2, AURKB, MKI67, STIL, CCNE2"], ["GO.0015630: microtubule cytoskeleton"], ["GO.0003688: DNA replication origin binding"], ["hsa04110: Cell cycle"], ["2", "5.00", "5", "GO.0007188: adenylate cyclase-modulating G-protein coupled receptor signaling pathway", "CNR1, CCL20, ADCY6, HTR1D, CCL25"], ["hsa04062: Chemokine signaling pathway"], ["3", "4.50", "5", "GO.0005615: extracellular space", "REN, PLA2G1B, TIMP1, MMP9, VWF"]], "row_count": 22, "column_count": 6, "numeric_cells": 47, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T5"}}], "gaps": ["asset:data:geo:GSE25097 not downloaded", "asset:data:geo:GSE25097 licence not read", "asset:data:geo:GSE57956 not downloaded", "asset:data:geo:GSE57956 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R differential expression and methylation analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used an online tool, GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), to analyze the differential expression by comparing two groups of samples across setup conditions in a GEO series."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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"}], 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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": ["GSE25097", "GSE57956"], "resolved_accessions": ["GSE25097", "GSE57956"], "statements": ["One gene expression profiling dataset, GSE25097, and another gene methylation dataset, GSE57956, were downloaded from Gene Expression Omnibus (GEO, www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE25097, GSE57956 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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