Identification of differentially expressed key genes between glioblastoma and low-grade glioma by bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30867991", "kind": "science-record", "revision": 7, "content_hash": "sha256:6163401f022c7a19cd28999b8d89abf4965c315e96a215f7cda773899e057d94", "created_at": "2026-11-01T15:40:43Z", "updated_at": "2026-11-01T22:00:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of differentially expressed key genes between glioblastoma and low-grade glioma by bioinformatics analysis.", "doi": "10.7717/peerj.6560", "pmid": "30867991", "authors": ["Yang Xu", "Rongxin Geng", "Fan'en Yuan", "Qian Sun", "Baohui Liu", "Qianxue Chen"], "journal": "PeerJ", "year": 2019, "abstract": "Gliomas are a very diverse group of brain tumors that are most commonly primary tumor and difficult to cure in central nervous system. It's necessary to distinguish low-grade tumors from high-grade tumors by understanding the molecular basis of different grades of glioma, which is an important step in defining new biomarkers and therapeutic strategies. We have chosen the gene expression profile GSE52009 from gene expression omnibus (GEO) database to detect important differential genes. GSE52009 contains 120 samples, including 60 WHO II samples and 24 WHO IV samples that were selected in our analysis. We used the GEO2R tool to pick out differently expressed genes (DEGs) between low-grade glioma and high-grade glioma, and then we used the database for annotation, visualization and integrated discovery to perform gene ontology analysis and Kyoto encyclopedia of gene and genome pathway analysis. Furthermore, we used the Cytoscape search tool for the retrieval of interacting genes with molecular complex detection plug-in applied to achieve the visualization of protein-protein interaction (PPI). We selected 15 hub genes with higher degrees of connectivity, including tissue inhibitors metalloproteinases-1 and serum amyloid A1; additionally, we used GSE53733 containing 70 glioblastoma samples to conduct Gene Set Enrichment Analysis. In conclusion, our bioinformatics analysis showed that DEGs and hub genes may be defined as new biomarkers for diagnosis and for guiding the therapeutic strategies of glioblastoma.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes between low-grade glioma and high-grade glioma was detected by GEO2R, which was an online analysis tool based on R language (Davis & Meltzer, 2007).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30867991", "locator": "sections[4] \"Screen genes of differential expression\" paragraph 2", "quote": "Differentially expressed genes between low-grade glioma and high-grade glioma was detected by GEO2R, which was an online analysis tool based on R language (Davis & Meltzer, 2007)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nData is available at NCBI GEO, accession numbers: GSE52009, GSE4290, GSE53733.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30867991", "locator": "sections[32] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nData is available at NCBI GEO, accession numbers: GSE52009, GSE4290, GSE53733."}], "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:30867991"], "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:GSE4290"], "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:GSE4290"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30867991", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.6560", "sha256": 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GSE53733.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nData is available at NCBI GEO, accession numbers: GSE52009, GSE4290, GSE53733.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM97793", "GSM97794", "GSM97795", "GSM97796", "GSM97797", "GSM97798", "GSM97799", "GSM97800", "GSM97801", "GSM97802", "GSM97803", "GSM97804", "GSM97805", "GSM97806", "GSM97807", "GSM97808", "GSM97809", "GSM97810", "GSM97811", "GSM97812", "GSM97813", "GSM97814", "GSM97815", "GSM97816", "GSM97817", "GSM97818", "GSM97819", "GSM97820", "GSM97821", "GSM97822", "GSM97823", "GSM97824", "GSM97825", "GSM97826", "GSM97827", "GSM97828", "GSM97829", "GSM97830", "GSM97831", "GSM97832", "GSM97833", "GSM97834", "GSM97835", "GSM97836", "GSM97837", "GSM97838", "GSM97839", "GSM97840", "GSM97841", "GSM97842", "GSM97843", "GSM97844", "GSM97845", "GSM97846", 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"uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52009", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE52009", "version": null, "note": "The following information was supplied regarding data availability:\nData is available at NCBI GEO, accession numbers: GSE52009, GSE4290, GSE53733.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nData is available at NCBI GEO, accession numbers: GSE52009, GSE4290, GSE53733.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1257398", "GSM1257399", "GSM1257400", "GSM1257401", "GSM1257402", "GSM1257403", "GSM1257404", "GSM1257405", "GSM1257406", "GSM1257407", "GSM1257408", "GSM1257409", "GSM1257410", "GSM1257411", "GSM1257412", "GSM1257413", "GSM1257414", "GSM1257415", "GSM1257416", 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["ANXA1", "6", "6.32E-08"], ["CDCA2", "6", "6.42E-09"], ["PLAT", "5", "2.64E-08"], ["PARPBP", "5", "6.34E-15"], ["TIMP1", "4", "2.06E-06"], ["SAA1", "4", "2.40E-06"]], "row_count": 16, "column_count": 3, "numeric_cells": 31, "header_rows": 1, "locator": "section[12]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:30867991:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3f482ba97ca6a42f592c0f81e350107c6efa815adda8f73e7f370bf5ad2a9426", "bytes": 2942, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#table-2", "version": null, "note": "Gene ontology analysis of differentially expressed genes associated with LGG and HGG.", "structure": {"pmcid": "PMC6409090", "section_index": 13, "section_title": "GO function and KEGG pathway enrichment analysis", "row_count": 29, "column_count": 7}, "table": {"label": "Table 2", "caption": "Gene ontology analysis of differentially expressed genes associated with LGG and HGG.", "rows": [["Expression", "Category", "Term", "Count", "%", "P-value", "FDR"], ["Upregulated", "GOTERM_BP_FAT", "GO:0016477—cell migration", "13", "22.80702", "3.95E-05", "0.067618"], ["GOTERM_BP_FAT", "GO:0050900—leukocyte migration", "8", "14.03509", "5.28E-05", "0.090452"], ["GOTERM_BP_FAT", "GO:0040011—locomotion", "14", "24.5614", "1.09E-04", "0.185762"], ["GOTERM_BP_FAT", "GO:0051674—localization of cell", "13", "22.80702", "1.22E-04", "0.208673"], ["GOTERM_BP_FAT", "GO:0048870—cell motility", "13", "22.80702", "1.22E-04", "0.208673"], ["GOTERM_MF_FAT", "GO:0019838—growth factor binding", "4", "7.017544", "0.004366", "5.428929"], ["GOTERM_MF_FAT", "GO:0019834—phospholipase A2 inhibitor activity", "2", "3.508772", "0.010298", "12.37092"], ["GOTERM_MF_FAT", "GO:0005102—receptor binding", "10", "17.54386", "0.010815", "12.95228"], ["GOTERM_MF_FAT", "GO:0005201—extracellular matrix structural constituent", "3", "5.263158", "0.018986", "21.69308"], ["GOTERM_MF_FAT", "GO:0005125—cytokine activity", "4", "7.017544", "0.019477", "22.19193"], ["GOTERM_CC_FAT", "GO:0005615—extracellular space", "16", "28.07018", "3.09E-06", "0.003877"], ["GOTERM_CC_FAT", "GO:0005578—proteinaceous extracellular matrix", "7", "12.2807", "4.24E-04", "0.531176"], ["GOTERM_CC_FAT", "GO:0031012—extracellular matrix", "8", "14.03509", "5.41E-04", "0.676623"], ["GOTERM_CC_FAT", "GO:0060205—cytoplasmic membrane-bounded vesicle lumen", "4", "7.017544", "0.002985", "3.680925"], ["GOTERM_CC_FAT", "GO:0031983—vesicle lumen", "4", "7.017544", "0.003066", "3.779192"], ["Downregulated", "GOTERM_BP_FAT", "GO:0007399—nervous system development", "15", "31.91489", "3.29E-04", "0.533895"], ["GOTERM_BP_FAT", "GO:0007420—brain development", "7", "14.89362", "0.00548", "8.553316"], ["GOTERM_BP_FAT", "GO:0060322—head development", "7", "14.89362", "0.007003", "10.80691"], ["GOTERM_BP_FAT", "GO:0031344—regulation of cell projection organization", "6", "12.76596", "0.011466", "17.11031"], ["GOTERM_BP_FAT", "GO:0007417—central nervous system development", "7", "14.89362", "0.019918", "27.91963"], ["GOTERM_MF_FAT", "GO:0005509—calcium ion binding", "6", "12.76596", "0.021579", "24.70502"], ["GOTERM_MF_FAT", "GO:0019911—structural constituent of myelin sheath", "2", "4.255319", "0.02239", "25.5132"], ["GOTERM_MF_FAT", "GO:0032403—protein complex binding", "5", "10.6383", "0.092825", "71.83703"], ["GOTERM_CC_FAT", "GO:0097458—neuron part", "15", "31.91489", "6.61E-06", "0.007993"], ["GOTERM_CC_FAT", "GO:0045202—synapse", "9", "19.14894", "8.96E-04", "1.078808"], ["GOTERM_CC_FAT", "GO:0043005—neuron projection", "9", "19.14894", "0.00424", "5.011629"], ["GOTERM_CC_FAT", "GO:0033269—internode region of axon", "2", "4.255319", "0.01097", "12.49482"], ["GOTERM_CC_FAT", "GO:0043209—myelin sheath", "4", "8.510638", "0.01206", "13.65505"]], "row_count": 29, "column_count": 7, "numeric_cells": 140, "header_rows": 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