Computational Analysis of Oral Cancer Gene Expression Profile and Identification of MiRNAs and their Regulatory Hub Genes

2020 ◽  
Vol 11 (3) ◽  
pp. 154
Author(s):  
Ariya S ◽  
Akhila James ◽  
Baby Joseph
Keyword(s):  
Gene Expression ◽  
Oral Cancer ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Computational Analysis ◽  
Cancer Gene ◽  
Hub Genes

scholarly journals Integrative analyses of gene expression profile reveal potential crucial roles of mitotic cell cycle and microtubule cytoskeleton in pulmonary artery hypertension

2020 ◽  
Author(s):  
Jing Luo ◽  
Zhenwei Liu ◽  
Chenlu Li ◽  
Ruochen Wang ◽  
Jinxia Fang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Mitotic Cell ◽  
Mitotic Cell Cycle ◽  
Public Database ◽  
Hub Genes ◽  
Microtubule Cytoskeleton ◽  
Integrative Analyses

Abstract Background: Pulmonary arterial hypertension (PAH) is a life-threatening condition that gets worse over time. Despite advances in the development of strategies for treating PAH, prognosis of the disease remains unsatisfactory, especially for advanced PAH. The aim of this study was to explore potential crucial genes and pathways associated with PAH based on integrative analyses of gene expression and shed light on the identification of biomarker for PAH. Results: Gene expression profile of pulmonary tissues from 27 PAH patients and 22 normal controls were downloaded from public database (GSE53408 and GSE113439). A total of 521 differentially expressed genes (DEGs), including 432 up-regulated DEGs and 89 down-regulated DEGs were identified using “limma” package in R. Functional enrichment analysis showed that these DEGs were mainly enriched in mitotic cell cycle process, mitotic cell cycle and microtubule cytoskeleton organization. Moreover, five key genes (CDK1, SMC2, SMC4, KIF23, and CENPE) were identified based on the comprehensive evaluation of protein-protein interaction (PPI) network analysis, modular analysis and cytohubba’s analysis, then further validated in another transcriptomic data set associated with PAH from public database (GSE33463). Furthermore, these hub genes were mainly enriched in promoting mitotic cell cycle process, which may be closely associated with the pathogenesis of PAH. We also found that the predicted micro-RNAs (miRNAs) targeting these hub genes were found to be enriched in TGF-β and Hippo signaling pathway. Conclusion:These findings are expected to gain a further insight into the development of PAH and provide a promising index for the detection of PAH.

scholarly journals Identification of metastasis and prognosis-associated genes for serous ovarian cancer

2020 ◽  
Vol 40 (6) ◽  
Author(s):  
Yijun Yang ◽  
Suwan Qi ◽  
Can shi ◽  
Xiao Han ◽  
Juanpeng Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Signaling Pathway ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Tumor Metastasis ◽  
Cox Regression ◽  
Serous Ovarian Cancer ◽  
Hub Genes ◽  
Blue Module

Abstract Serous ovarian cancer is one of the most fatal gynecological tumors with an extremely low 5-year survival rate. Most patients are diagnosed at an advanced stage with wide metastasis. The dysregulation of genes serves an important role in the metastasis progression of ovarian cancer. Differentially expressed genes (DEGs) between primary tumors and metastases of serous ovarian cancer were screened out in the gene expression profile of GSE73168 from Gene Expression Omnibus (GEO). Cytoscape plugin cytoHubba and weighted gene co-expression network analysis (WGCNA) were utilized to select hub genes. Univariate and multivariate Cox regression analyses were used to screen out prognosis-associated genes. Furthermore, the Oncomine validation, prognostic analysis, methylation mechanism, gene set enrichment analysis (GSEA), TIMER database analysis and administration of candidate molecular drugs were conducted for hub genes. Nine hundred and fifty-seven DEGs were identified in the gene expression profile of GSE73168. After using Cytoscape plugin cytoHubba, 83 genes were verified. In co-expression network, the blue module was most closely related to tumor metastasis. Furthermore, the genes in Cytoscape were analyzed, showing that the blue module and screened 17 genes were closely associated with tumor metastasis. Univariate and multivariate Cox regression revealed that the age, stage and STMN2 were independent prognostic factors. The Cancer Genome Atlas (TCGA) suggested that the up-regulated expression of STMN2 was related to poor prognosis of ovarian cancer. Thus, STMN2 was considered as a new key gene after expression validation, survival analysis and TIMER database validation. GSEA confirmed that STMN2 was probably involved in ECM receptor interaction, focal adhesion, TGF beta signaling pathway and MAPK signaling pathway. Furthermore, three candidate small molecule drugs for tumor metastasis (diprophylline, valinomycin and anisomycin) were screened out. The quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blot showed that STMN2 was highly expressed in ovarian cancer tissue and ovarian cancer cell lines. Further studies are needed to investigate these prognosis-associated genes for new therapy target.

scholarly journals Integrative analyses of gene expression profile reveal potential crucial roles of mitotic cell cycle and microtubule cytoskeleton in pulmonary artery hypertension

2019 ◽  
Author(s):  
Jing Luo ◽  
Zhenwei Liu ◽  
Chenlu Li ◽  
Ruochen Wang ◽  
Jinxia Fang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Mitotic Cell ◽  
Functional Enrichment ◽  
Mitotic Cell Cycle ◽  
Public Database ◽  
Hub Genes ◽  
Microtubule Cytoskeleton

Abstract Background: Pulmonary arterial hypertension (PAH) is a life-threatening condition that gets worse over time. Despite advances in the development of strategies for treating PAH, prognosis of the disease remains unsatisfactory, especially for advanced PAH. The aim of this study was to explore potential crucial genes and pathways associated with PAH that can be used as potential biomarkers for early diagnosis.Results: Gene expression profile of pulmonary tissues from 27 PAH patients and 22 normal controls were downloaded from public database (GSE53408 and GSE113439). A total of 521 differentially expressed genes (DEGs), including 432 up-regulated DEGs and 89 down-regulated DEGs were identified using “limma” package in R. Functional enrichment analysis showed that these DEGs were mainly enriched in mitotic cell cycle process, mitotic cell cycle and microtubule cytoskeleton organization. Moreover, five key genes (CDK1, SMC2, SMC4, KIF23, and CENPE) were identified based on the comprehensive evaluation of PPI analysis, modular analysis and cytohubba’s analysis, then further validated in another transcriptomic data set associated with PAH from public database (GSE33463). Furthermore, these hub genes were mainly enriched in promoting mitotic cell cycle process, which may be closely associated with the pathogenesis of PAH. We also found that the predicted miRNAs targeting these hub genes were found to be enriched in TGF-β and Hippo signaling pathway.Conclusion: These findings are expected to gain a further insight into the development of PAH and provide a promising index for the detection of PAH.

Breast cancer gene expression profile in young women who are noncarriers of BRCA1/2 mutations with and without familial history.

2010 ◽  
Vol 28 (15_suppl) ◽  
pp. 1538-1538
Author(s):  
D. M. Carraro ◽  
C. A. Moreira-Filho ◽  
P. L. Ramos ◽  
B. C. Lisboa ◽  
H. Brentani ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Young Women ◽  
Cancer Gene ◽  
Familial History ◽  
Breast Cancer Gene

scholarly journals Integration of Gene Expression Profile Data to Verify Hub Genes of Patients with Stanford A Aortic Dissection

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Weitie Wang ◽  
Tiance Wang ◽  
Yong Wang ◽  
Hulin Piao ◽  
Bo Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Aortic Dissection ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Smooth Muscle Contraction ◽  
Gene Expression Omnibus ◽  
Hub Genes ◽  
Pathogenic Genes

Thoracic aortic dissection (TAD) is a catastrophic disease worldwide, but the pathogenic genes and pathways are largely unclear. This study aims at integrating two gene expression profile datasets and verifying hub genes and pathways involved in TAD as well as exploring potential molecular mechanisms. We will combine our mRNAs expression profile (6 TAD tissues versus 6 non-TAD tissues) and GSE52093 downloaded from the Gene Expression Omnibus (GEO) database. The two mRNAs expression profiles contained 13 TAD aortic tissues and 11 non-TAD tissues. The two expression profile datasets were integrated and we found out coexpression of differentially expressed genes (DEGs) using bioinformatics methods. The gene ontology and pathway enrichment of DEGs were performed by DAVID and Kyoto Encyclopedia of Genes and Genomes online analyses, respectively. The protein-protein interaction networks of the DEGs were constructed according to the data from the STRING database. Cytohubber calculating result shows the top 10 hub genes with CDC20, AURKA, RFC4, MCM4, TYMS, MCM2, DLGAP5, FANCI, BIRC5, and POLE2. Module analysis revealed that TAD was associated with significant pathways including cell cycle, vascular smooth muscle contraction, and adrenergic signaling in cardiomyocytes. The qRT-PCR result showed that the expression levels of all the hub genes were significantly increased in OA samples (p < 0.05), and these candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of TAD.

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