Bioinformatics-based analysis of the lncRNA-miRNA-mRNA and TF regulatory networks reveals functional genes in esophageal squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32662828", "kind": "science-record", "revision": 8, "content_hash": "sha256:1f8efe1433a62f636fd8ac60d3b9125a55038bc8efad4bb37f0c66ed1c6ea08d", "created_at": "2026-11-01T15:41:05Z", "updated_at": "2026-11-01T22:01:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics-based analysis of the lncRNA-miRNA-mRNA and TF regulatory networks reveals functional genes in esophageal squamous cell carcinoma.", "doi": "10.1042/BSR20201727", "pmid": "32662828", "authors": ["Zhimin Ye", "Jun Fang", "Zhun Wang", "Lei Wang", "Bin Li", "Tongxin Liu", "Yuezhen Wang", "Jianfeng Hua", "FangZheng Wang", "Zhenfu Fu"], "journal": "Bioscience reports", "year": 2020, "abstract": "Esophageal squamous cell carcinoma (ESCC) is a 5-year survival rate unsatisfied malignancies. The study aimed to identify the novel diagnostic and prognostic targets for ESCC. Expression profiling (GSE89102, GSE97051, and GSE59973) data were downloaded from the GEO database. Then, differentially expressed (DE) lncRNAs, DEmiRNAs, and genes (DEGs) with P-values < 0.05, and |log2FC| ≥ 2, were identified using GEO2R. Functional enrichment analysis of miRNA-related mRNAs and lncRNA co-expressed mRNA was performed. LncRNA-miRNA-mRNA, protein-protein interaction of miRNA-related mRNAs and DEGs, co-expression, and transcription factors-hub genes network were constructed. The transcriptional data, the diagnostic and prognostic value of hub genes were estimated with ONCOMINE, receiver operating characteristic (ROC) analyses, and Kaplan-Meier plotter, respectively. Also, the expressions of hub genes were assessed through qPCR and Western blot assays. The CDK1, VEGFA, PRDM10, RUNX1, CDK6, HSP90AA1, MYC, EGR1, and SOX2 used as hub genes. And among them, PRDM10, RUNX1, and CDK6 predicted worse overall survival (OS) in ESCC patients. Our results showed that the hub genes were significantly up-regulated in ESCA primary tumor tissues and cell lines, and exhibited excellent diagnostic efficiency. These results suggest that the hub genes may server as potential targets for the diagnosis and treatment of ESCC.", "claims": [{"id": "claim-method", "statement": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool that reprocessed the raw data in a GEO series, also allowing users to evaluate the distribution of the values for the samples have been selected and viewed graphically as a box plot, was employed to identify DElncRNAs, DEmiRNAs and DEGs by comparing ESCC and normal tissue samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32662828", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), an interactive web tool that reprocessed the raw data in a GEO series, also allowing users to evaluate the distribution of the values for the samples have been selected and viewed graphically as a box plot, was employed to identify DElncRNAs, DEmiRNAs and DEGs by comparing ESCC and normal tissue samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The long non-coding RNA expression profiles (GSE89102) and two miRNA expression data (GSE97051 and GSE59973) were obtained from GEO (http://www.ncbi.nlm.nih.gov/geo/). The array data of GSE89102 consisted of five paired ESCC tissues and normal tissues based on the platform of GPL16956 (Agilent-045997 Arraystar human lncRNA microarray V3) (Agilent Technologies, Inc., Santa Clara, CA, U.S.A.), deposited by Bai et al. in Third Military Medical University [15].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32662828", "locator": "sections[3] \"Microarray data collection\" paragraph 2", "quote": "The long non-coding RNA expression profiles (GSE89102) and two miRNA expression data (GSE97051 and GSE59973) were obtained from GEO (http://www.ncbi.nlm.nih.gov/geo/). The array data of GSE89102 consisted of five paired ESCC tissues and normal tissues based on the platform of GPL16956 (Agilent-045997 Arraystar human lncRNA microarray V3) (Agilent Technologies, Inc., Santa Clara, CA, U.S.A.), deposited by Bai et al. in Third Military Medical University [15]."}], "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:32662828"], "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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"Reverse: 5′-TTTAACTCAAGCTGCCTCGC-3′"], ["PRDM10", "Forward: 5′-CATCCAGGTCAGCGAGCCTA-3′"], ["", "Reverse: 5′-CGAAGTAACCGCCTTCACCT-3′"], ["RUNX1", "Forward: 5′-GGGAGCTTGTCCTTTTCCGA-3′"], ["", "Reverse: 5′-GAGAGGCAATGGATCCCAGG-3′"], ["CDK6", "Forward: 5′-ACAGAGCACCCGAAGTCTTG-3′"], ["", "Reverse: 5′-GTATGGGTGAGACAGGGCAC-3′"], ["HSP90AA1", "Forward: 5′-CCGCCCAGAGTGCTGAATAC-3′"], ["", "Reverse: 5′-ACACCGAACTGGCCAATCAT-3′"], ["MYC", "Forward: 5′-CGTCCTCGGATTCTCTGCTC-3′"], ["", "Reverse: 5′-GCTGGTGCATTTTCGGTTGT-3′"], ["EGR1", "Forward: 5′-GCTGGTGGAGACCAGTTACC-3′"], ["", "Reverse: 5′-TCATCGCTCCTGGCAAACTT-3′"], ["SOX2", "Forward: 5′-AACCAGCGCATGGACAGTTA-3′"], ["", "Reverse: 5′-GACTTGACCACCGAACCCAT-3′"], ["GAPDH", "Forward: 5′-GGGAAACTGTGGCGTGAT-3′"], ["", "Reverse: 5′-GGGTGTCGCTGTTGAAGT-3′"]], "row_count": 21, "column_count": 2, "numeric_cells": 23, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32662828:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c96db4dc45300eae4c0c6107f51e3ee685cfd473dd377d83c39ce80648f0a659", "bytes": 922, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T2", "version": null, "note": "The overlapping genes of selected miRNAs in miRPathDB, miRWalk and Targetscan database", "structure": {"pmcid": "PMC7441485", "section_index": 16, "section_title": "Prediction of target genes and lncRNAs for DEmiRNAs", "row_count": 4, "column_count": 3}, "table": {"label": "Table 2", "caption": "The overlapping genes of selected miRNAs in miRPathDB, miRWalk and Targetscan database", "rows": [["miRNAs", "Overlapping genes", "Up/Down"], ["hsa-miR-409-3p", "MRPL35, PAQR5, AGO2, ZZZ3, SLC25A16, GAB1, TRIM5, C1QTNF1, KLF12, YTHDF3, GPR85, MSRB3, L3MBTL3, ZC3H12C, ADAMTS5, TRIM71, IPO7, NR3C2, DENND2C, MYLK, PHC3, GPR61, SCN1A, CD96, NR4A2, LGSN, TMEM242, LARP1, PAPD5, ZNF423, TNNI1, FAM229B, PRMT6", "Up"], ["hsa-miR-133b", "RAB5C", "Down"], ["hsa-miR-139-5p", "AEBP2, ANK2, ARRDC3, ATP11A, ATP2B2, ATXN1, CAMK2D, CCND2, CSRNP2, CTTNBP2NL, DPYSL5, GLCCI1, HEG1, HMGCR, IGF1R, KCND3, KIAA1549, KPNA4, MAP2, MBNL1, NME7, NRK, PDE3A, PDE4A, PGM2L1, PHF6, PIEZO1, PITPNA PMP22, PPARGC1A, PRDM10, PTPN4, RUNX1, SOCS2, STX7, STXBP5L, SYT14, TAOK1, TCF12, TET3, TMPO, TSPAN3, UHMK1, XPO4", "Down"]], "row_count": 4, "column_count": 3, "numeric_cells": 5, "header_rows": 1, "locator": "section[16]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:32662828:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:46126262a466ec60afac3609227f53e581cf096226120b4ed57520aeb83f5324", "bytes": 3236, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#T3", "version": null, "note": "The identified LncRNAs of selected miRNAs in GSE89102", "structure": {"pmcid": "PMC7441485", "section_index": 16, "section_title": "Prediction of target genes and lncRNAs for DEmiRNAs", "row_count": 39, "column_count": 7}, "table": {"label": "Table 3", "caption": "The identified LncRNAs of selected miRNAs in GSE89102", "rows": [["miRNA", "Gene Symbol", "Location", "adj.P.Val", "P-value", "logFC", "Down/Up"], ["hsa-miR-409-3P", "RP11-1437A8.4", "chr16:33203773-33206462", "7.87E-03", "2.18E-03", "-6.478", "Down"], ["", "RP11-586K12.10", "chr16:32663925-32666533", "0.00973", "0.00288", "-5.318", "Down"], ["", "XLOC_013268", "chr19", "0.000213", "0.000018", "-2.054", "Down"], ["", "LINC00299", "chr2:8007771-8324630", "0.000766", "0.000103", "-2.449", "Down"], ["", "RP11-308D13.3", "chr4:139618136-139623232", "1.72E-02", "5.99E-03", "-3.135", "Down"], ["", "XLOC_004270", "chr5", "0.00114", "0.000174", "-2.928", "Down"], ["", "RMST", "chr12:97431653-97565015", "0.00798", "0.00223", "-2.177", "Down"], ["", "UCA1", "chr19:15828961-15836320", "3.74E-03", "8.36E-04", "-2.092", "Down"], ["", "RP11-214L13.1", "chr18:55881688-55920199", "3.93E-05", "1.71E-06", "-2.101", "Down"], ["", "LINC00475", "chr9:92141467-92160114", "4.25E-04", "4.60E-05", "-2.394", "Down"], ["", "TMEM161B-AS1", "chr5:88269024-88436674", "1.91E-03", "3.49E-04", "-3.055", "Down"], ["", "XLOC_013708", "chr20", "2.55E-03", "5.04E-04", "-2.049", "Down"], ["", "CLDN10-AS1", "chr13:95479444-95533910", "5.34E-04", "6.24E-05", "-3.687", "Down"], ["", "AC104777.3", "chr2:150566134-150568080", "3.80E-03", "8.53E-04", "-2.072", "Down"], ["hsa-miR-133b", "RP11-363G2.4", "chr13:22851773-22854138", "2.97E-07", "7.87E-10", "2.287", "Up"], ["", "THAP9-AS1", "chr4:82893009-82900960", "1.09E-05", "2.70E-07", "2.988", "Up"], ["", "RP11-385J1.2", "chr3:178526505-178860352", "6.10E-03", "1.57E-03", "3.327", "Up"], ["", "AC096559.1", "chr2:12576038-12642912", "2.98E-03", "6.22E-04", "2.993", "Up"], ["", "RP11-562F9.2", "chr4:92268767-92277075", "1.15E-04", "7.80E-06", "2.746", "Up"], ["", "SOX2-OT", "chr3:180989783-181699883", "6.71E-03", "1.78E-03", "2.424", "Up"], ["", "RP11-70C1.1", "chr3:42770612-42773635", "1.30E-02", "4.20E-03", "2.096", "Up"], ["", "DNM3OS", "chr1:172136531-172144794", "7.19E-03", "1.94E-03", "2.787", "Up"], ["", "RP11-657O9.1", "chr3:135356067-135439829", "1.85E-05", "5.72E-07", "3.346", "Up"], ["", "RP11-366F6.2", "chrX:151904431-151911455", "2.08E-06", "1.98E-08", "6.928", "Up"], ["", "LINC00467", "chr1:211382803-211435333", "3.39E-03", "7.38E-04", "2.245", "Up"], ["", "CTB-89H12.4", "chr5:149494314-149504670", "5.13E-03", "1.26E-03", "2.999", "Up"], ["", "RP11-392P7.6", "chr12:12927726-12980307", "6.86E-03", "1.83E-03", "2.121", "Up"], ["", "XLOC_014080", "chr21", "2.40E-04", "2.14E-05", "3.045", "Up"], ["", "RP11-160O5.1", "chr17:65100812-65111058", "1.30E-04", "9.18E-06", "2.078", "Up"], ["hsa-miR-139-5p", "MAST4-IT1", "chr5:66662331-66662988", "0.0000001", "2.23E-10", "3.046", "Up"], ["", 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