Screening the Significant Hub Genes by Comparing Tumor Cells, Normoxic and Hypoxic Glioblastoma Stem-like Cell Lines Using Co-Expression Analysis in Glioblastoma

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dc.authoridKazmi, Imran/0000-0003-1881-5219
dc.authoridKazmi, Imran/0000-0003-1881-5219
dc.authoridGüven, Emine/0000-0001-9324-0879
dc.authoridAfzal, Muhammad/0000-0003-2570-3223
dc.authorwosidKazmi, Imran/GRJ-9647-2022
dc.authorwosidKazmi, Imran/AAO-3922-2020
dc.authorwosidKazmi, Imran/GSD-2298-2022
dc.contributor.authorGüven, Emine
dc.contributor.authorAfzal, Muhammad
dc.contributor.authorKazmi, Imran
dc.date.accessioned2023-07-26T11:57:19Z
dc.date.available2023-07-26T11:57:19Z
dc.date.issued2022
dc.departmentDÜ, Mühendislik Fakültesi, Biyomedikal Mühendisliği Bölümüen_US
dc.description.abstractGlioblastoma multiforme (GBM) is categorized by rapid malignant cellular growth in the central nervous system (CNS) tumors. It is one of the most prevailing primary brain tumors, particularly in human male adults. Even though the combination therapy comprises surgery, chemotherapy, and adjuvant therapies, the survival rate is on average 14.6 months. Glioma stem cells (GSCs) have key roles in tumorigenesis, progression, and counteracting chemotherapy and radiotherapy. In our study, firstly, the gene expression dataset GSE45117 was retrieved and differentially expressed genes (DEGs) were spotted. The co-expression network analysis was employed on DEGs to find the significant modules. The most significant module resulting from co-expression analysis was the turquoise module. The turquoise module related to the tumor cells, hypoxia, normoxic treatments of glioblastoma tumor (GBT), and GSCs were screened. Sixty-one common genes in the turquoise module were selected generated through the co-expression analysis and protein-protein interaction (PPI) network. Moreover, the GO and KEGG pathway enrichment results were studied. Twenty common hub genes were screened by the NetworkAnalyst web instrument constructed on the PPI network through the STRING database. After survival analysis via the Kaplan-Meier (KM) plotter from The Cancer Genome Atlas (TCGA) database, we identified the five most significant hub genes strongly related to the progression of GBM. We further observed these five most significant hub genes also up-regulated in another GBM gene expression dataset. The protein-protein interaction (PPI) network of the turquoise module genes was constructed and a KEGG pathway enrichments study of the turquoise module genes was performed. The VEGF signaling pathway was emphasized because of the strong link with GBM. A gene-disease association network was further constructed to demonstrate the information of the progression of GBM and other related brain neoplasms. All hub genes assessed through this study would be potential markers for the prognosis and diagnosis of GBM.en_US
dc.description.sponsorshipDeanship of Scientific Research, Jouf University, Saudi Arabia [DSR-2021-01-0316]en_US
dc.description.sponsorshipThis work was funded by Deanship of Scientific Research, Jouf University, Saudi Arabia under the grant number (DSR-2021-01-0316).en_US
dc.identifier.doi10.3390/genes13030518
dc.identifier.issn2073-4425
dc.identifier.issue3en_US
dc.identifier.pmid35328072en_US
dc.identifier.scopus2-s2.0-85127061953en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.urihttps://doi.org/10.3390/genes13030518
dc.identifier.urihttps://hdl.handle.net/20.500.12684/13128
dc.identifier.volume13en_US
dc.identifier.wosWOS:000775336100001en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakPubMeden_US
dc.indekslendigikaynakScopusen_US
dc.institutionauthorGüven, Emine
dc.language.isoenen_US
dc.publisherMdpien_US
dc.relation.ispartofGenesen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.snmz$2023V1Guncelleme$en_US
dc.subjectBiomarker; Differentially Expressed Genes; Co-Expression; Vegf Signaling Pathway; Gene Ontology Pathway Enrichment; Glioblastoma Multiformeen_US
dc.subjectExpression Omnibus; Up-Regulation; Glioma; Multiforme; Survival; Pathway; Vegfen_US
dc.titleScreening the Significant Hub Genes by Comparing Tumor Cells, Normoxic and Hypoxic Glioblastoma Stem-like Cell Lines Using Co-Expression Analysis in Glioblastomaen_US
dc.typeArticleen_US

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