Guang-Jie Jiang1, Yan-Hua Chen, Wei Guo, Hang Zhang, Lin Zou. 1. Center for Clinical Molecular Medicine, Children's Hospital of Chongqing Medical University/Ministry of Education Key Laboratory of Child Development and Disorders/Key Laboratory of Pediatrics in Chongqing/Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China. E-mail: 306118416@qq.com.
Abstract
OBJECTIVE: To explore the key genes in T-cell acute lymphoblastic leukemia (T-ALL) using bioinformatics method to better understand the pathogenic mechanisms of T-ALL. METHODS: The gene expression profiles of GSE14317 were obtained from Gene Expression Omnibus database. The differentially expressed genes (DEGs) in T-ALL were analyzed using R package Limma. The online analysis tool DAVID was used to perform the functional and pathway enrichment analysis. The protein-protein interaction network was constructed by STRING and visualized by Cytoscape. Based on the JASPAR database, the transcription factors (TFs) of the hub genes were obtained. RT-PCR was used to test the mRNA expression level of the key genes. RESULTS: A total of 1443 DEGs were identified, including 800 up-regulated genes and 643 down-regulated genes. These DEGs were significantly enriched in the cell cycle, hematopoietic cell lineage, cytokine-cytokine receptor interaction and T cell receptor signaling pathway. The top 10 hub genes identified from the PPI networks included CDK1, PIK3R1, CCNB1, CCNA2, CDC20, JUN, GNG11, PLK1, PCNA and CCNB2, which were enriched in chemokine signaling pathway, ubiquition mediated proteolysis and cell cycle. In the TF-target gene network, 42 differentially expressed TFs were identified, among which ELF5, HIC2 and MEISI had binding sites with 9 of the candidate hub genes. RT-PCR showed that the mRNA expression level of all the candidate hub genes except for GNG11 were consistent with the gene expression profiles. CONCLUSION: The hub genes CDK1, PIK3R1, CCNB1, CCNA2, CDC20, JUN, PLK1, PCNA, CCNB2, ELF5, HIC2 and MEISI participate in the occurrence of T-ALL. Our finding provides new insights into the pathogenesis of T-ALL.
OBJECTIVE: To explore the key genes in T-cell acute lymphoblastic leukemia (T-ALL) using bioinformatics method to better understand the pathogenic mechanisms of T-ALL. METHODS: The gene expression profiles of GSE14317 were obtained from Gene Expression Omnibus database. The differentially expressed genes (DEGs) in T-ALL were analyzed using R package Limma. The online analysis tool DAVID was used to perform the functional and pathway enrichment analysis. The protein-protein interaction network was constructed by STRING and visualized by Cytoscape. Based on the JASPAR database, the transcription factors (TFs) of the hub genes were obtained. RT-PCR was used to test the mRNA expression level of the key genes. RESULTS: A total of 1443 DEGs were identified, including 800 up-regulated genes and 643 down-regulated genes. These DEGs were significantly enriched in the cell cycle, hematopoietic cell lineage, cytokine-cytokine receptor interaction and T cell receptor signaling pathway. The top 10 hub genes identified from the PPI networks included CDK1, PIK3R1, CCNB1, CCNA2, CDC20, JUN, GNG11, PLK1, PCNA and CCNB2, which were enriched in chemokine signaling pathway, ubiquition mediated proteolysis and cell cycle. In the TF-target gene network, 42 differentially expressed TFs were identified, among which ELF5, HIC2 and MEISI had binding sites with 9 of the candidate hub genes. RT-PCR showed that the mRNA expression level of all the candidate hub genes except for GNG11 were consistent with the gene expression profiles. CONCLUSION: The hub genes CDK1, PIK3R1, CCNB1, CCNA2, CDC20, JUN, PLK1, PCNA, CCNB2, ELF5, HIC2 and MEISI participate in the occurrence of T-ALL. Our finding provides new insights into the pathogenesis of T-ALL.
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