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 ...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.Diferentially expressed gencs(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 identifed,including 413 down-regulated and 105 up-regulated gencs.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.F our 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 identifed DEGs,hub genes and pathways associated with PTCL by bioinformatic analysis.Results provide a basis for further study on the pathogenesis of PTCL.展开更多
Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding, transporting and metabolism have aroused much intere...Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding, transporting and metabolism have aroused much interest. To facilitate the study on this topic, we constructed two databases （DCCP and DICP） containing the known copper- and iron-chelating proteins~ which are freely available from the website http：//sdbi.sdut.edu.cn/en. Users can conveniently search and browse all of the entries in the databases. Based on the two databases, bioinformatic analyses were performed, which provided some novel insights into metalloproteins.展开更多
基金The study was supported by grants from the National Natural Science Foundation of China(No.81660036)the Project of the Bingtuan Science and Technology(No.2019DB012).
文摘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.Diferentially expressed gencs(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 identifed,including 413 down-regulated and 105 up-regulated gencs.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.F our 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 identifed DEGs,hub genes and pathways associated with PTCL by bioinformatic analysis.Results provide a basis for further study on the pathogenesis of PTCL.
基金This work was supported by the National Basic Research Program of China(2003CB114400)the National Natural Science Foundation of China(Grant No.30100035).
文摘Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding, transporting and metabolism have aroused much interest. To facilitate the study on this topic, we constructed two databases （DCCP and DICP） containing the known copper- and iron-chelating proteins~ which are freely available from the website http：//sdbi.sdut.edu.cn/en. Users can conveniently search and browse all of the entries in the databases. Based on the two databases, bioinformatic analyses were performed, which provided some novel insights into metalloproteins.
