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pmid:34012270
Epigenetic Study of Esophageal Carcinoma Based on Methylation, Gene Integration and Weighted Correlation Network Analysis.
Yanzhao Xu · Na Wang · Rongfeng Liu · Huilai Lv · Zhenhua Li · Fan Zhang · Chunyue Gai · Ziqiang Tian
OncoTargets and therapy · 2021 doi:10.2147/OTT.S298620
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Experiment
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34012270", "kind": "science-record", "revision": 8, "content_hash": "sha256:3e408c702961fcdea3af7a22c5baf6a28999f2213c806a0e41c1f1e197f92c94", "created_at": "2026-11-01T15:41:36Z", "updated_at": "2026-11-01T22:46:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Epigenetic Study of Esophageal Carcinoma Based on Methylation, Gene Integration and Weighted Correlation Network Analysis.", "doi": "10.2147/OTT.S298620", "pmid": "34012270", "authors": ["Yanzhao Xu", "Na Wang", "Rongfeng Liu", "Huilai Lv", "Zhenhua Li", "Fan Zhang", "Chunyue Gai", "Ziqiang Tian"], "journal": "OncoTargets and therapy", "year": 2021, "abstract": "PURPOSE: Esophageal carcinoma is a common and highly metastatic malignant tumor of the digestive tract. The aim of the present study was to identify potential molecular markers of esophageal carcinoma that may help its diagnosis and treatment.\nMATERIALS AND METHODS: First, mRNA and DNA methylation data were downloaded from The Cancer Genome Atlas (TCGA) database for the identification of differentially expressed genes (DEGs) and DNA methylation analysis. Secondly, Weighted Gene Co-Expression Network Analysis (WGCNA) was used to identify important modules and hub genes. In addition, correlation analysis between DNA methylation genes and DEGs was performed. Thirdly, the GSE45670 dataset was used to validate the expression of the diagnostic and survival ability analysis of genes in TCGA data. Finally, reverse transcription-quantitative PCR and immunohistochemical analysis of genes were performed.\nRESULTS: A total of 2408 DEGs and 5134 differentially methylated sites were obtained. In the WGCNA analysis, the royal blue module was found to be the optimal module. In addition, hub genes in the module, including ESRRG, MFSD4, CCKBR, ATP4B, ESRRB, ATP4A, CCKAR and B3GAT1, were also differentially methylated genes and DEGs. It was found that CCKAR, MFSD4 and ESRRG may be diagnostic gene biomarkers for esophageal carcinoma. In addition, the high expression of MFSD4 was significantly correlated with patient survival. Immunohistochemistry analysis results showed that the gene expression levels of ATP4B, B3GAT1, CCKBR and ESRRG were decreased in esophageal carcinoma tissues, which was in line with the bioinformatics results.\nCONCLUSION: Therefore, these identified molecular markers may be helpful in the diagnosis and treatment of esophageal carcinoma.", "claims": [{"id": "claim-method", "statement": "The differentially expressed genes (DEGs) were screened out using the R-Bioconductor package DESeq.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34012270", "locator": "sections[4] \"Differential Analysis of Genes and DNA Methylation\" paragraph 2", "quote": "The differentially expressed genes (DEGs) were screened out using the R-Bioconductor package DESeq."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34012270", "locator": "sections[23] \"Data Sharing State\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published 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:34012270"], "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:GSE45670"], "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:GSE45670"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34012270", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S298620", "sha256": 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"access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1111662", "GSM1111663", "GSM1111664", "GSM1111665", "GSM1111666", "GSM1111667", "GSM1111668", "GSM1111669", "GSM1111670", "GSM1111671", "GSM1111672", "GSM1111673", "GSM1111674", "GSM1111675", "GSM1111676", "GSM1111677", "GSM1111678", "GSM1111679", "GSM1111680", "GSM1111681", "GSM1111682", "GSM1111683", "GSM1111684", "GSM1111685", "GSM1111686", "GSM1111687", "GSM1111688", "GSM1111689", "GSM1111690", "GSM1111691", "GSM1111692", "GSM1111693", "GSM1111694", "GSM1111695", "GSM1111696", "GSM1111697", "GSM1111698", "GSM1111699"], "sample_count": 38, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from esophageal squamous cell carcinomas and normal esophageal epithelia", 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Hub Genes in the Royal Blue Module", "rows": [["Hubs", "Module", "Coefficient", "P value"], ["KCNE2", "Royalblue", "0.968426", "2.34996E-13"], ["ESRRG", "Royalblue", "0.968071", "2.59365E-16"], ["MFSD4", "Royalblue", "0.956811", "2.35772E-15"], ["CCKBR", "Royalblue", "0.950419", "1.07104E-10"], ["ATP4B", "Royalblue", "0.944469", "2.41009E-17"], ["SIGLEC11", "Royalblue", "0.944115", "7.91562E-23"], ["ESRRB", "Royalblue", "0.93753", "7.82567E-21"], ["ATP4A", "Royalblue", "0.936846", "4.9997E-18"], ["CCKAR", "Royalblue", "0.911212", "2.05779E-08"], ["B3GAT1", "Royalblue", "0.910831", "1.56673E-15"]], "row_count": 11, "column_count": 4, "numeric_cells": 21, "header_rows": 1, "locator": "section[14]/table-wrap[3]#t0004"}}, {"id": "asset:table:pmid:34012270:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3d7ebd92ed33e2eef15df5a8e6cb93da0c73f3c2c1bdf3f19f7d051a7b417d12", "bytes": 2912, "access": "open", "state": 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["HOXD10", "cg06005169", "0.590076", "3.87E-17"], ["HOXD9", "cg13158481", "0.51537", "6.42E-13"], ["HYAL1", "cg06360465", "−0.567", "7.59E-16"], ["HYAL1", "cg10580282", "−0.50645", "1.84E-12"], ["HYAL1", "cg12930727", "−0.65804", "1.85E-22"], ["HYAL1", "cg14943722", "−0.56014", "1.99E-15"], ["IGFBP2", "cg23059946", "−0.55095", "7.00E-15"], ["IQGAP2", "cg08356262", "−0.64251", "3.58E-21"], ["KALRN", "cg21425296", "−0.58269", "7.69E-17"], ["KCNQ1", "cg02180189", "−0.54064", "2.74E-14"], ["LRRC2", "cg10031651", "−0.52858", "1.28E-13"], ["MAPK12", "cg13963658", "0.562568", "1.42E-15"], ["ME3", "cg02493602", "−0.69321", "1.13E-25"], ["ME3", "cg14883291", "−0.69388", "9.67E-26"], ["ME3", "cg15698545", "−0.70097", "1.90E-26"], ["MECOM", "cg00024967", "−0.63607", "1.16E-20"], ["MECOM", "cg00988247", "−0.58743", "3.76E-17"], ["MECOM", "cg01277372", "−0.57962", "1.22E-16"], ["MECOM", "cg03679456", "−0.59565", "1.06E-17"], ["MECOM", "cg06201393", "−0.52954", "1.13E-13"], ["MECOM", "cg20096204", 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"section_index": 16, "section_title": "Correlation Analysis of DNA Methylation Genes and DEGs", "row_count": 10, "column_count": 5}, "table": {"label": "Table 6", "caption": "Enrichment of Differentially Methylated and DEGs in Modules", "rows": [["Module", "Odds Ratio", "95% CI_Lower", "95% CI_Upper", "P value"], ["Royalblue", "18.01649", "8.445462", "35.03891", "1.97E-10"], ["Violet", "0", "0", "7.914082", "1"], ["Diumpurple3", "0", "0", "Inf", "1"], ["Darkolivegreen", "0", "0", "8.075999", "1"], ["Yellow", "0", "0", "0.510528", "0.001837"], ["Darkturquoise", "0", "0", "5.941329", "1"], ["Turquoise", "0.147352", "0.017565", "0.549924", "0.000464"], ["Darkred", "0", "0", "5.12711", "1"], ["Grey", "0.985924", "0.383056", "2.134444", "1"]], "row_count": 10, "column_count": 5, "numeric_cells": 37, "header_rows": 1, "locator": "section[16]/table-wrap[2]#t0006"}}, {"id": "asset:table:pmid:34012270:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c7abe99db9743b838617b588a1a5cb777cd6d491ed38ce0441f044bb19522cb5", "bytes": 1377, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#t0007", "version": null, "note": "Clinical Information of Patients and Normal Controls in the RT-qPCR", "structure": {"pmcid": "PMC8128498", "section_index": 18, "section_title": "RT-qPCR Verification", "row_count": 7, "column_count": 16}, "table": {"label": "Table 7", "caption": "Clinical Information of Patients and Normal Controls in the RT-qPCR", "rows": [["Number", "Gender", "Age", "BMI", "Symptom", "Tumor Location", "Pathological Type", "Clinical Stages", "Onset Time (Day)", "Smoking History", "Drinking History", "Family History of Cancer", "Other Tumors", "First Diagnosed", "Radiotherapy and Chemotherapy", "Medication History (Within 1 Month)"], ["1", "Male", "62", "19.8", "Dysphagia", "From the incisors 29–34cm", "Squamous carcinoma", "IIIA", "180", "Yes", "Yes", "No", "No", "Yes", "No", "No"], ["2", "Male", "76", "29", "Swallowing discomfort", "From the incisors 25–30cm", "Squamous carcinoma", "IIA", "35", "No", "Occasional", "No", "No", "Yes", "No", "No"], ["3", "Male", "56", "25.4", "Dysphagia", "From the incisors 33–36cm", "Squamous carcinoma", "IIIA", "30", "Yes", "Occasional", "No", "No", "Yes", "No", "No"], ["4", "Male", "65", "23.6", "Dysphagia", "From the incisors 26cm", "Squamous carcinoma", "IIA", "90", "Yes", "Occasional", "No", "No", "Yes", "No", "No"], ["5", "Female", "63", "28.4", "Dysphagia", "From the incisors 29–36cm", "Squamous carcinoma", "I", "15", "No", "No", "No", "No", "Yes", "No", "No"], ["6", "Female", "72", "17.8", "Dysphagia", "From the incisors 20–25cm", "Squamous carcinoma", "IIIB", "150", "No", "No", "No", "Early cardia adenocarcinoma", "Yes", "No", "No"]], "row_count": 7, "column_count": 16, "numeric_cells": 31, "header_rows": 1, "locator": "section[18]/table-wrap[1]#t0007"}}, {"id": 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["GPR155-R", "5-GCCACCAAATAAATGTACTGGA-3"], ["ESRRB-F", "5-GCAGCCCTGAACACCCATT-3"], ["ESRRB-R", "5-AAGGGCGTGGATTGGGGAT-3"], ["ESRRG-F", "5-GCCCTGCCACGAATGAATGT-3"], ["ESRRG-R", "5-TGGGCTGTTCTCCGCATCT-3"], ["CCKAR-F", "5-GTGATCCGCATGCTCATCGT-3"], ["CCKAR-R", "5-TGACGCAGGAGGAGGTGTAG-3"], ["MMP11-F", "5-CCCTGTGAAGGTGAAGGCTC-3"], ["MMP11-R", "5-GATGGCCATGGGTCTCTAGC-3"], ["TPX2-F", "5-ATGGAACTGGAGGGCTTTTTC-3"], ["TPX2-R", "5-TGTTGTCAACTGGTTTCAAAGGT-3"], ["BIRC5-F", "5-AGGACCACCGCATCTCTACAT-3"], ["BIRC5-R", "5-AAGTCTGGCTCGTTCTCAGTG-3"], ["NUF2-F", "5-TGCCTGCCTTCATGTCAGT-3"], ["NUF2-R", "5-GGTCCTCCAAGTTCAGGCTC-3"], ["ANO1-F", "5-GAGAGATCGGTTCCCAGCCT-3"], ["ANO1-R", "5-TGTGACTGTGACCCGGATGT-3"]], "row_count": 23, "column_count": 2, "numeric_cells": 27, "header_rows": 1, "locator": "section[18]/table-wrap[2]#t0008"}}], "gaps": ["asset:data:geo:GSE45670 not downloaded", "asset:data:geo:GSE45670 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The differentially expressed genes (DEGs) were screened out using the R-Bioconductor package DESeq."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], 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