scholarly journals Integrated analysis of DNA methylation and mRNA expression profiles to identify key genes involved in the regrowth of clinically non-functioning pituitary adenoma

Aging ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 2408-2427 ◽  
Author(s):  
Sen Cheng ◽  
Chuzhong Li ◽  
Weiyan Xie ◽  
Yazhou Miao ◽  
Jing Guo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Pituitary Adenoma ◽  
Mrna Expression ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Key Genes

scholarly journals Integrated Analysis of DNA Methylation and mRNA Expression Profiles Data to Identify Key Genes in Lung Adenocarcinoma

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Xiang Jin ◽  
Xingang Liu ◽  
Xiaodan Li ◽  
Yinghui Guan
Keyword(s):  
Dna Methylation ◽  
Lung Adenocarcinoma ◽  
Mrna Expression ◽  
Early Stage ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Integrated Analysis ◽  
Tissue Samples ◽  
Ppi Networks ◽  
Key Genes

Introduction. Lung adenocarcinoma (LAC) is the most frequent type of lung cancer and has a high metastatic rate at an early stage. This study is aimed at identifying LAC-associated genes.Materials and Methods. GSE62950 downloaded from Gene Expression Omnibus included a DNA methylation dataset and an mRNA expression profiles dataset, both of which included 28 LAC tissue samples and 28 adjacent normal tissue samples. The differentially expressed genes (DEGs) were screened by Limma package in R, and their functions were predicted by enrichment analysis using TargetMine online tool. Then, protein-protein interaction (PPI) network was constructed using STRING and Cytoscape. Finally, LAC-associated methylation sites were identified by CpGassoc package in R and mapped to the DEGs to obtain LAC-associated DEGs.Results. Total 913 DEGs were identified in LAC tissues. In the PPI networks,MAD2L1,AURKB,CCNB2,CDC20,andWNT3Ahad higher degrees, and the first four genes might be involved in LAC through interaction. Total 8856 LAC-associated methylation sites were identified and mapped to the DEGs. And there were 29 LAC-associated methylation sites located in 27 DEGs (e.g.,SH3GL2,BAI3,CDH13,JAM2,MT1A,LHX6,andIGFBP3).Conclusions. These key genes might play a role in pathogenesis of LAC.

scholarly journals Identification of key genes in invasive clinically non-functioning pituitary adenoma by integrating analysis of DNA methylation and mRNA expression profiles

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Sen Cheng ◽  
Weiyan Xie ◽  
Yazhou Miao ◽  
Jing Guo ◽  
Jichao Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Pituitary Adenoma ◽  
Candidate Genes ◽  
Tumor Invasion ◽  
Expression Profiles ◽  
Methylation Status ◽  
Rt Pcr ◽  
Expression Levels ◽  
Key Genes

Abstract Background Tumor surrounding the internal carotid artery or invading to the cavernous sinus is an important characteristic of invasive pituitary adenoma, and a pivotal factor of tumor residue and regrowth. Without specific changes in serum hormone related to the adenohypophyseal cell of origin, clinically non-functioning pituitary adenoma is more likely to be diagnosed at invasive stages compared with functioning pituitary adenoma. The underlying mechanism of tumor invasion remains unknown. In this study, we aimed to identify key genes in tumor invasion by integrating analyses of DNA methylation and gene expression profiles. Method Genome-wide DNA methylation and mRNA microarray analysis were performed for tumor samples from 68 patients at the Beijing Tiantan Hospital. Differentially expressed genes and methylated probes were identified based on an invasive vs non-invasive grouping. Differentially methylated probes in the promoter region of targeted genes were assessed. Pearson correlation analysis was used to identify genes with a strong association between DNA methylation status and expression levels. Pyrosequencing and RT-PCR were used to validate the methylation status and expression levels of candidate genes, respectively. Results A total of 8842 differentially methylated probes, located on 4582 genes, and 661 differentially expressed genes were identified. Both promoter methylation and expression alterations were observed for 115 genes with 58 genes showing a negative correlation between DNA methylation status and expression level. Nineteen genes that exhibited notably negative correlations between DNA methylation and gene expression levels, are involved in various gene ontologies and pathways, or played an important role in different diseases, were regarded as candidate genes. We found an increased methylation with a decreased expression of PHYHD1, LTBR, C22orf42, PRR5, ANKDD1A, RAB13, CAMKV, KIFC3, WNT4 and STAT6, and a decreased methylation with an increased expression of MYBPHL. The methylation status and expression levels of these genes were validated by pyrosequencing and RT-PCR. Conclusions The DNA methylation and expression levels of PHYHD1, LTBR, MYBPHL, C22orf42, PRR5, ANKDD1A, RAB13, CAMKV, KIFC3, WNT4 and STAT6 are associated with tumor invasion, and these genes may become the potential genes for targeted therapy.

Integrated analysis of non-coding RNA and mRNA expression profiles of 2 pig breeds differing in muscle traits

2017 ◽  
Vol 95 (3) ◽  
pp. 1092 ◽  
Author(s):  
J. Sun ◽  
M. Xie ◽  
Z. Huang ◽  
H. Li ◽  
T. chen ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Pig Breeds ◽  
Non Coding Rna

scholarly journals Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Wenjing Tao ◽  
Lina Sun ◽  
Hongjuan Shi ◽  
Yunying Cheng ◽  
Dongneng Jiang ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Early Stage ◽  
Expression Profiles ◽  
Sex Differentiation ◽  
Integrated Analysis

scholarly journals Integrated analysis of microRNA and mRNA expression profiles in abdominal adipose tissues in chickens

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
H. Y. Huang ◽  
R. R. Liu ◽  
G. P. Zhao ◽  
Q.H. Li ◽  
M. Q. Zheng ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Adipose Tissues

scholarly journals Integrated analysis of microRNA and mRNA expression profiles in splenomegaly induced by non-cirrhotic portal hypertension in rats

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Junji Saruwatari ◽  
Chao Dong ◽  
Teruo Utsumi ◽  
Masatake Tanaka ◽  
Matthew McConnell ◽  
...  
Keyword(s):  
Portal Hypertension ◽  
Mrna Expression ◽  
Expression Profiles ◽  
Integrated Analysis

Integrated Analysis of MicroRNA and mRNA Expression Profiles in Rheumatoid Arthritis Synovial Monocytes

2011 ◽  
Vol 18 (4) ◽  
pp. 253 ◽  
Author(s):  
Jong Dae Ji ◽  
Tae-Hwan Kim ◽  
Bitnara Lee ◽  
Kyung-Sun Na ◽  
Sung Jae Choi ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Mrna Expression ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Synovial Monocytes
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