Identification of Hub Genes and Key Pathways Associated with Peripheral T-cell Lymphoma
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40(5):1-15,2020
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Identification of Hub Genes and Key Pathways Associated with Peripheral T-cell Lymphoma* Hai-xia GAO1, 2, 3† , Meng-bo WANG4†, Si-jing LI1, 2, Jing NIU1, 2, Jing XUE1, 2, Jun LI4, Xin-xia LI1# Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China 2 Xinjiang Medical University, Urumqi 830011, China 3 Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, China 4 Department of Ultrasound, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, China 1
Huazhong University of Science and Technology 2020
Summary: Peripheral T-cell lymphoma (PTCL) is a very aggressive and heterogeneous hematological malignancy and has no effective targeted therapy. The molecular pathogenesis of PTCL remains unknown. In this study, we chose the gene expression profile of GSE6338 from the Gene Expression Omnibus (GEO) database to identify hub genes and key pathways and explore possible molecular pathogenesis of PTCL by bioinformatic analysis. Differentially expressed genes (DEGs) between PTCL and normal T cells were selected using GEO2R tool. Gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis were performed using Database for Annotation, Visualization and Integrated Discovery (DAVID). Moreover, the Search Tool for the Retrieval of Interacting Genes (STRING) and Molecular Complex Detection (MCODE) were utilized to construct protein-protein interaction (PPI) network and perform module analysis of these DEGs. A total of 518 DEGs were identified, including 413 down-regulated and 105 up-regulated genes. The down-regulated genes were enriched in osteoclast differentiation, Chagas disease and mitogen-activated protein kinase (MAPK) signaling pathway. The up-regulated genes were mainly associated with extracellular matrix (ECM)-receptor interaction, focal adhesion and pertussis. Four important modules were detected from the PPI network by using MCODE software. Fifteen hub genes with a high degree of connectivity were selected. Our study identified DEGs, hub genes and pathways associated with PTCL by bioinformatic analysis. Results provide a basis for further study on the pathogenesis of PTCL. Key words: peripheral T-cell lymphomas; bioinformatic analysis; protein-protein interaction; hub genes; pathways
Peripheral T-cell lymphoma (PTCL) is a very aggressive and heterogeneous hematological malignancy[1, 2]. The molecular pathogenesis of PTCL remains unknown. Therefore, searching for effective therapies that could improve the outcome of patients with PTCL remains challenging[3]. The limited knowledge of this disease could be due to several factors, such as heterogeneity of its subtypes and few available representative cell lines or mouse models. The majority of available cell lines cover very few PTCL subtypes and are mostly derived from cutaneous Hai-xia GAO, E-mail: [email protected]; Men
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