Secondary data mining of GEO database for long non-coding RNA and Competing endogenous RNA network in keloid-prone individuals.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33203788", "kind": "science-record", "revision": 9, "content_hash": "sha256:a20a42297a0e62d5707d1b61fb9665199b24d753807e10bbe3aeee1ff13ebd95", "created_at": "2026-11-01T15:41:16Z", "updated_at": "2026-11-01T22:45:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Secondary data mining of GEO database for long non-coding RNA and Competing endogenous RNA network in keloid-prone individuals.", "doi": "10.18632/aging.104054", "pmid": "33203788", "authors": ["Yu Deng", "Yangbin Xu", "Shuqia Xu", "Yujing Zhang", "Bing Han", "Zheng Liu", "Xiangxia Liu", "Zhaowei Zhu"], "journal": "Aging", "year": 2020, "abstract": "This study aimed to identify long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) differentially expressed (DE) during keloid formation, predict DElncRNA-DEmiRNA-DEmRNA interactions, and construct a competing endogenous RNA (ceRNA) network through secondary data mining of keloid-related sequencing and microarray data in the open-source Gene Expression Omnibus (GEO) database. The GSE113621 dataset was downloaded from the GEO database, |log2FC|>1 and p<0.05 were set as screening criteria, genes expressed only in keloid-prone individuals were selected as research objects, and DEmRNAs, DElncRNAs, and DEmiRNAs before injury and 6 weeks after injury were screened. A Pearson correlation coefficient (PCC) of > 0.95 was selected as the index to predict the targeting relationships among lncRNAs, miRNAs, and mRNAs; and a network diagram was constructed using Cytoscape. The expression of 2356 lncRNAs was changed in the keloid-prone group-1306 were upregulated and 1050 were downregulated. Six lncRNAs, namely, 2 upregulated (DLEU2 and AP000317.2) and 4 downregulated (ADIRF-AS1, AC006333.2, AL137127.1 and LINC01725) lncRNAs, were expressed only in the keloid-prone group and were used to construct a ceRNA network. DLEU2 may regulate fibroblast proliferation, differentiation, and apoptosis through hsa-miR-30a-5p/hsa-miR-30b-5p. In-depth mining of GEO data indicated that lncRNAs and a ceRNA regulatory network participate in the wound healing process in keloid-prone individuals, possibly providing novel intervention targets and treatment options for keloid scars.", "claims": [{"id": "claim-method", "statement": "For differential gene expression analysis, the most recent version of DESeq2 software was used, and the thresholds for significant differential gene expression were set as follows: |log2FoldChange (FC)|>1 and FDR<0.05 [29].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33203788", "locator": "sections[13] \"Screening and statistical analysis of mRNAs differentially expressed between different groups\" paragraph 2", "quote": "For differential gene expression analysis, the most recent version of DESeq2 software was used, and the thresholds for significant differential gene expression were set as follows: |log2FoldChange (FC)|>1 and FDR<0.05 [29]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE113621 dataset was downloaded from the GEO database, |log2FC|>1 and p<0.05 were set as screening criteria, genes expressed only in keloid-prone individuals were selected as research objects, and DEmRNAs, DElncRNAs, and DEmiRNAs before injury and 6 weeks after injury were screened.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33203788", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The GSE113621 dataset was downloaded from the GEO database, |log2FC|>1 and p<0.05 were set as screening criteria, genes expressed only in keloid-prone individuals were selected as research objects, and DEmRNAs, DElncRNAs, and DEmiRNAs before injury and 6 weeks after injury were screened."}], "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:33203788"], "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:GSE113619"], "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:GSE113619"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33203788", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.104054", "sha256": 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in keloid-prone individuals were selected as research objects, and DEmRNAs, DElncRNAs, and DEmiRNAs before injury and 6 weeks after injury were screened.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE113621 dataset was downloaded from the GEO database, |log2FC|>1 and p<0.05 were set as screening criteria, genes expressed only in keloid-prone individuals were selected as research objects, and DEmRNAs, DElncRNAs, and DEmiRNAs before injury and 6 weeks after injury were screened.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3110282", "GSM3110283", "GSM3110284", "GSM3110285", "GSM3110286", "GSM3110287", "GSM3110288", "GSM3110289", "GSM3110290", "GSM3110291", "GSM3110292", "GSM3110293", "GSM3110294", "GSM3110295", "GSM3110296", "GSM3110297", "GSM3110298", "GSM3110299", "GSM3110300", "GSM3110301", "GSM3110302", "GSM3110303", "GSM3110304", "GSM3110305", "GSM3110306", "GSM3110307", 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"GO Analysis of mRNAs specifically expressed in keloid-prone individuals 6 weeks after injury.", "rows": [["", "Term ID", "Term description", "Ct.", "Adjusted p-value"], ["BP", "GO:0006936", "muscle contraction", "35", "0.001473"], ["GO:0099054", "presynapse assembly", "11", "0.001702"], ["GO:0042391", "regulation of membrane potential", "37", "0.001702"], ["GO:0099172", "presynapse organization", "11", "0.001702"], ["GO:0035270", "endocrine system development", "18", "0.001702"], ["GO:0035418", "protein localization to synapse", "12", "0.002476"], ["GO:0051952", "regulation of amine transport", "13", "0.002476"], ["GO:0071772", "response to BMP", "19", "0.003641"], ["GO:0071773", "cellular response to BMP stimulus", "19", "0.003641"], ["GO:0015837", "amine transport", "13", "0.003706"], ["CC", "GO:0097060", "synaptic membrane", "45", "2.00E-06"], ["GO:0045211", "postsynaptic membrane", "37", "4.25E-06"], ["GO:0099240", "intrinsic component of synaptic membrane", "21", "0.001069"], ["GO:0098978", "glutamatergic synapse", "34", "0.001069"], ["GO:0005858", "axonemal dynein complex", "6", "0.00128"], ["GO:0098936", "intrinsic component of postsynaptic membrane", "17", "0.001407"], ["GO:1902495", "transmembrane transporter complex", "28", "0.001456"], ["GO:0098793", "presynapse", "38", "0.001534"], ["GO:1990351", "transporter complex", "28", "0.001534"], ["GO:0034703", "cation channel complex", "21", "0.001567"], ["MF", "GO:0015267", "channel activity", "37", "0.000261"], ["GO:0022838", "substrate-specific channel activity", "35", "0.000261"], ["GO:0022803", "passive transmembrane transporter activity", "37", "0.000261"], ["GO:0015276", "ligand-gated ion channel activity", "17", "0.000513"], ["GO:0022834", "ligand-gated channel activity", "17", "0.000513"], ["GO:0005216", "ion channel activity", "33", "0.000517"], ["GO:0008509", "anion transmembrane transporter activity", "27", "0.000614"], ["GO:0005261", "cation channel activity", "27", "0.000708"], ["GO:0015077", "monovalent inorganic cation transmembrane transporter activity", "27", "0.000879"], ["GO:0046873", "metal ion transmembrane transporter activity", "32", "0.001416"]], "row_count": 31, "column_count": 5, "numeric_cells": 90, "header_rows": 0, "locator": "section[4]/table-wrap[1]#t1"}}, {"id": "asset:table:pmid:33203788:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9b7833c53f90443145cd47662b837d82b36bb51ab1ab71de30a75d7ac4ca2058", "bytes": 528, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#t2", "version": null, "note": "KEGG analysis of mRNAs specifically expressed in keloid-prone individuals 6 weeks after injury.", "structure": {"pmcid": "PMC7803517", "section_index": 5, "section_title": "KEGG enrichment analysis of mRNAs expressed only in keloid-prone individuals 6 weeks after injury", "row_count": 5, "column_count": 4}, "table": {"label": "Table 2", "caption": "KEGG analysis of mRNAs specifically expressed in keloid-prone individuals 6 weeks after injury.", "rows": [["mRNA", "Term description", "Ct.", "Adjusted p-value"], ["hsa04080", "neuroactive ligand-receptor interaction", "40", "3.42×10-6"], ["hsa05033", "nicotine addiction", "10", "0.000953"], ["hsa04020", "calcium signaling pathway", "23", "0.001322"], ["hsa04724", "glutamatergic synapse", "15", "0.010286"]], "row_count": 5, "column_count": 4, "numeric_cells": 12, "header_rows": 0, "locator": "section[5]/table-wrap[1]#t2"}}, {"id": "asset:table:pmid:33203788:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4739096390f77f3ebad41ec9654fd6fc25714063032ae9edfa2b27297c43f66c", "bytes": 1038, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#t3", "version": null, "note": "Differentially expressed lncRNAs in keloid-prone individuals 6 weeks after injury. p<0.05 indicates a statistically significant difference.", "structure": {"pmcid": "PMC7803517", "section_index": 6, "section_title": "Analysis of the lncRNA-miRNA-mRNA network present only in keloid-prone individuals after injury", "row_count": 7, "column_count": 10}, "table": {"label": "Table 3", "caption": "Differentially expressed lncRNAs in keloid-prone individuals 6 weeks after injury. p<0.05 indicates a statistically significant difference.", "rows": [["Gene Id", "Gene_Name", "KDay0", "KDay42", "log2FC", "Adjusted-P", "NDay0", "NDay42", "log2FC", "Adjusted-P"], ["ENSG00000231607", "DLEU2", "306.79", "641.38", "1.06", "1.33×10-17", "74.88", "66.26", "-0.18", "1.00"], ["ENSG00000272657", "AP000317.2", "75.61", "183.43", "1.28", "3.53×10-17", "66.42", "119.35", "0.85", "7.08×10-3"], ["ENSG00000272734", "ADIRF-AS1", "1350.45", "552.62", "-1.29", "2.46×10-29", "1251.46", "646.56", "-0.95", "1.24×10-5"], ["ENSG00000272686", "AC006333.2", "82.88", "39.50", "-1.07", "8.29×10-9", "70.48", "41.97", "-0.75", "1.46×10-2"], ["ENSG00000272084", "AL137127.1", "661.42", "240.08", "-1.46", "2.66×10-18", "407.22", "223.42", "-0.87", "7.60×10-5"], ["ENSG00000233008", "LINC01725", "257.15", "121.20", "-1.09", "1.87×10-13", "211.00", "134.79", "-0.65", "4.60×10-2"]], "row_count": 7, "column_count": 10, "numeric_cells": 60, "header_rows": 0, "locator": "section[6]/table-wrap[1]#t3"}}, {"id": "asset:table:pmid:33203788:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d916057736f1f9b396dcd23efb68d97b5aac45734e165fc66aa7b4e4cf727f15", "bytes": 556, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#t4", "version": null, "note": "Details of patients in GEO dataset SRP137071.", "structure": {"pmcid": "PMC7803517", "section_index": 11, "section_title": "Acquisition of GEO sequencing data", "row_count": 9, "column_count": 6}, "table": {"label": "Table 4", "caption": "Details of patients in GEO dataset SRP137071.", "rows": [["Keloid-prone ID", "Age (years)", "Sex", "Control ID", "Age (years)", "Sex"], ["K-1", "32", "male", "N-1", "24", "male"], ["K-2", "23", "male", "N-2", "58", "male"], ["K-3", "28", "female", "N-3", "28", "male"], ["K-4", "23", "male", "N-4", "22", "male"], ["K-5", "24", "male", "N-5", "31", "male"], ["K-6", "30", "male", "N-6", "34", "male"], ["K-7", "57", "female", "", "", ""], ["K-8", "25", "male", "", "", ""]], "row_count": 9, "column_count": 6, "numeric_cells": 28, "header_rows": 0, "locator": "section[11]/table-wrap[1]#t4"}}, {"id": "asset:table:pmid:33203788:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:48c58e13761506cd34eec30f5588cfec6cf4860d941e993e0df1716aafe8fa47", "bytes": 719, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#t5", "version": null, "note": "qPCR primer sequences of DElncRNAs specifically expressed in keloid-prone individuals.", "structure": {"pmcid": "PMC7803517", "section_index": 17, "section_title": "qPCR verification of DElncRNA expression in fibroblasts from keloid scars and normal skin", "row_count": 7, "column_count": 3}, "table": {"label": "Table 5", "caption": "qPCR primer sequences of DElncRNAs specifically expressed in keloid-prone individuals.", "rows": [["LncRNA", "Forward (5’-3’)", "Reverse (5’-3’)"], ["DLEU2", "TCC GAG AGT ATA GCG CCA CT", "ACT GCC CTT TGC TCC AAG TA"], ["ADIRF-AS1", "GCC CAC TGA ATT CCC CTG AA", "AAT CAG AGT GAC TGC CCC AC"], ["AC006333.2", "TCC AAC TTC GTA CTC TGG CC", "GCT TCG CAA AGG TGT ACG TC"], ["LINC01725", "TCC AGC TCT TCT CCC CTG AA", "GGG GGA ACT TAG AAA GGC CA"], ["AP000317.2", "AGT GGA TGG CAA GCT TCC TT", "GGA ACC CTC GTC TTT GGG AA"], 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