Non-negative matrix factorization and differential expression analyses identify hub genes linked to progression and prognosis of glioblastoma multiforme

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dc.authoridKazmi, Imran/0000-0003-1881-5219
dc.authoridKazmi, Imran/0000-0003-1881-5219
dc.authorwosidKazmi, Imran/GRJ-9647-2022
dc.authorwosidKazmi, Imran/GSD-2298-2022
dc.authorwosidKazmi, Imran/AAO-3922-2020
dc.contributor.authorAkçay, Sevinç
dc.contributor.authorGüven, Emine
dc.contributor.authorAfzal, Muhammad
dc.contributor.authorKazmi, Imran
dc.date.accessioned2023-07-26T11:54:28Z
dc.date.available2023-07-26T11:54:28Z
dc.date.issued2022
dc.departmentDÜ, Mühendislik Fakültesi, Biyomedikal Mühendisliği Bölümüen_US
dc.description.abstractOne of the most prevailing primary brain tumors in adult human male is glioblastoma multiforme (GBM), which is categorized by rapid cellular growth. Even though the combination therapy comprises surgery, chemotherapy, and adjuvant therapies, the survival rate, on average, is 14.6 months. Glioma stem cells (GSCs) have key roles in tumorigenesis, progression, and defiance against chemotherapy and radiotherapy. In our study, firstly, the gene expression dataset GSE124145 was retrieved; the non-negative matrix factorization (NMF) method was applied on GBM dataset, and differentially expressed genes analysis (DEGs) was performed. After which, overlapping genes between metagenes and DEGs were detected to examine the Gene Ontology (GO) categories in the biological process (BP) in the stemness of GBM. The common hub genes were used to construct protein-protein interaction (PPI) network and further GO, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was utilized to pinpoint the real hub genes. The analysis of hub genes particular for the same GO categories demonstrated that specific hub genes triggered distinct features of the same biological processes. After utilizing GSE124145 and The Cancer Genome Atlas (TCGA) dataset for survival analysis, we screened five real hub genes: GUCA1A, RFC2, GNG11, MMP19, and NRG1, which are strongly associated with the progression and prognosis of GBM. The DEGs analysis revealed that all real hub genes were overexpressed in GBM and TCGA datasets, which further validates our results. The constructed study of PPI, GO, and KEGG pathway on common hub genes was performed. Finally, the KEGG pathways performed on the top 15 candidate hub genes (including six real hub genes) of the PPI network in the GBM gene expression dataset study found mitogen-activated protein kinase (Mapk) signaling pathway to be the most significant pathway. The rest of the hub genes reviewed throughout the analysis might be favorable targets for diagnosing and treating GBM and lower-grade gliomas.en_US
dc.description.sponsorshipDeanship of Scientific Research Jouf University, Saudi Arabia [DSR-2021-01-0315]en_US
dc.description.sponsorshipThis work was funded by the Deanship of Scientific Research Jouf University, Saudi Arabia under the grant number (DSR-2021-01-0315) .en_US
dc.identifier.doi10.1016/j.gene.2022.146395
dc.identifier.issn0378-1119
dc.identifier.issn1879-0038
dc.identifier.pmid35283227en_US
dc.identifier.scopus2-s2.0-85126625848en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.urihttps://doi.org/10.1016/j.gene.2022.146395
dc.identifier.urihttps://hdl.handle.net/20.500.12684/12843
dc.identifier.volume824en_US
dc.identifier.wosWOS:000795525000003en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakPubMeden_US
dc.indekslendigikaynakScopusen_US
dc.institutionauthorGüven, Emine
dc.language.isoenen_US
dc.publisherElsevieren_US
dc.relation.ispartofGeneen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.snmz$2023V1Guncelleme$en_US
dc.subjectGlioblastoma Multiforme (Gbm); Non-Negative Matrix Factorization (Nmf); Metagenes; Glioblastoma Stem Cells (Gscs); Differentially Expressed Genes (Degs)en_US
dc.subjectStem-Cells; Receptors; Promotes; Database; Mapken_US
dc.titleNon-negative matrix factorization and differential expression analyses identify hub genes linked to progression and prognosis of glioblastoma multiformeen_US
dc.typeArticleen_US

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