The promising novel biomarkers and candidate small molecule drugs in lower‐grade glioma: Evidence from bioinformatics analysis of high‐throughput data

2019 ◽  
Vol 120 (9) ◽  
pp. 15106-15118 ◽  
Author(s):  
Bo Zhang ◽  
Qiong Wu ◽  
Ran Xu ◽  
Xinyi Hu ◽  
Yidan Sun ◽  
...  
Keyword(s):  
Small Molecule ◽  
High Throughput ◽  
Bioinformatics Analysis ◽  
Lower Grade ◽  
High Throughput Data ◽  
Small Molecule Drugs ◽  
Lower Grade Glioma ◽  
Novel Biomarkers

scholarly journals Identification of Novel Biomarkers in Hepatocellular Carcinoma by Integrated Bioinformatical Analysis and Experimental Validation

2021 ◽  
Author(s):  
Chen Liao ◽  
Lanlan Wang ◽  
Xiaoqiang Li ◽  
Jinyu Bai ◽  
Jieqiong Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Small Molecule ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Venn Diagram ◽  
Ppi Network ◽  
Qrt Pcr ◽  
Small Molecule Drugs ◽  
Novel Biomarkers

Abstract Background: Hepatocellular carcinoma (HCC) is one of the most common poorly prognosed virulent neoplasms of the digestive system. In this study, we identified novel biomarkers associated with the pathogenesis of HCC aiming to provide new diagnostic and therapeutic approaches for HCC. Methods: Gene expression profiles of GSE62232, GSE84402,GSE121248 and GSE45267 were obtained in GEO database. Differential expressed genes (DEGs) between HCC and normal samples were identified using the GEO2R tool and Venn diagram software.Database for Annotation, Visualization and Integrated Discovery (DAVID) were used to carry out enrichment analysis on gene ontology (GO) and the Kyoto Encyclopaedia of Genes and Genomes pathway (KEGG). The protein-protein interaction (PPI) network of DEGs was constructed by the Search Tool for the Retrieval of Interacting Genes (STRING) and visualized by Cytoscape. Expressions and prognostic values of hub genes were validated through Kaplan-Meier plotter, Gene Expression Profiling Interactive Analysis (GEPIA), the Human Protein Atlas Database (HPA), western blot (WB) and quantitative real-time polymerase chain reaction (qRT-PCR). Additionally, potential small molecule drugs were screened by Connectivity Map (CMAP). Results: A total of 100 overlapped DEGs were detected and results showed 23 of which were up-regulated with the rest being down-regulated. STRING screened the 70 edges and the 199 nodes in the PPI network. Survival analysis showed that aberrant mRNA expression of TOP2A, DTL, ANLN, CDKN3, BUB1B, CDK1, PBK, RRM2, RACGAP1, PRC1, NEK2, ECT2, CCNB1, HMMR, ASPM was significantly associated with a low survival rate. Results of WB and qRT-PCR showed that the expression levels of ANLN, CCNB1, DTL, RACGAP1, RRM2 and TOP2A were all increased in HCC tissues. Furthermore, CMAP predict suggest the 10 most vital small molecule drugs could reverse the progression of HCC. Conclusions: Core DEGs (ANLN, CCNB1, DTL, RACGAP1, RRM2 and TOP2A) with poor prognosis and candidate drugs for HCC treatment were identified through integrated bioinformatic analysis.This study will contribute to providing prognostic biomarker and therapeutic strategies in HCC. Background : Hepatocellular carcinoma (HCC) is one of the most common poorly prognosed virulent neoplasms of the digestive system. In this study, we identified novel biomarkers associated with the pathogenesis of HCC aiming to provide new diagnostic and therapeutic approaches for HCC. Methods : Gene expression profiles of GSE62232, GSE84402,GSE121248 and GSE45267 were obtained in GEO database. Differential expressed genes (DEGs) between HCC and normal samples were identified using the GEO2R tool and Venn diagram software.Database for Annotation, Visualization and Integrated Discovery (DAVID) were used to carry out enrichment analysis on gene ontology (GO) and the Kyoto Encyclopaedia of Genes and Genomes pathway (KEGG). The protein-protein interaction (PPI) network of DEGs was constructed by the Search Tool for the Retrieval of Interacting Genes (STRING) and visualized by Cytoscape. Expressions and prognostic values of hub genes were validated through Kaplan-Meier plotter, Gene Expression Profiling Interactive Analysis (GEPIA), the Human Protein Atlas Database (HPA), western blot (WB) and quantitative real-time polymerase chain reaction (qRT-PCR). Additionally, potential small molecule drugs were screened by Connectivity Map (CMAP). Results : A total of 100 overlapped DEGs were detected and results showed 23 of which were up-regulated with the rest being down-regulated. STRING screened the 70 edges and the 199 nodes in the PPI network. Survival analysis showed that aberrant mRNA expression of TOP2A, DTL, ANLN, CDKN3, BUB1B, CDK1, PBK, RRM2, RACGAP1, PRC1, NEK2, ECT2, CCNB1, HMMR, ASPM was significantly associated with a low survival rate. Results of WB and qRT-PCR showed that the expression levels of ANLN, CCNB1, DTL, RACGAP1, RRM2 and TOP2A were all increased in HCC tissues. Furthermore, CMAP predict suggest the 10 most vital small molecule drugs could reverse the progression of HCC. Conclusions : Core DEGs (ANLN, CCNB1, DTL, RACGAP1, RRM2 and TOP2A) with poor prognosis and candidate drugs for HCC treatment were identified through integrated bioinformatic analysis.This study will contribute to providing prognostic biomarker and therapeutic strategies in HCC.

The identification of key genes in nasopharyngeal carcinoma by bioinformatics analysis of high-throughput data

2019 ◽  
Vol 46 (3) ◽  
pp. 2829-2840 ◽  
Author(s):  
Yanshan Ge ◽  
Zhengxi He ◽  
Yanqi Xiang ◽  
Dawei Wang ◽  
Yuping Yang ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
High Throughput ◽  
Bioinformatics Analysis ◽  
High Throughput Data ◽  
Key Genes

scholarly journals Identification of novel biomarkers and candidate small-molecule drugs in cutaneous melanoma by comprehensive gene microarrays analysis

2021 ◽  
Vol 12 (5) ◽  
pp. 1307-1317
Author(s):  
Jilei Ma ◽  
Xin Cai ◽  
Li Kang ◽  
Songfeng Chen ◽  
Hongjian Liu
Keyword(s):  
Small Molecule ◽  
Cutaneous Melanoma ◽  
Small Molecule Drugs ◽  
Novel Biomarkers
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