scholarly journals DNA Copy-Number Alterations Underlie Gene Expression Differences between Microsatellite Stable and Unstable Colorectal Cancers

2008 ◽  
Vol 14 (24) ◽  
pp. 8061-8069 ◽  
Author(s):  
R. N. Jorissen ◽  
L. Lipton ◽  
P. Gibbs ◽  
M. Chapman ◽  
J. Desai ◽  
...  
2016 ◽  
Vol 39 (6) ◽  
pp. 545-558 ◽  
Author(s):  
Elisabetta Bigagli ◽  
Carlotta De Filippo ◽  
Cinzia Castagnini ◽  
Simona Toti ◽  
Francesco Acquadro ◽  
...  

2008 ◽  
Vol 216 (4) ◽  
pp. 471-482 ◽  
Author(s):  
Y Tsukamoto ◽  
T Uchida ◽  
S Karnan ◽  
T Noguchi ◽  
LT Nguyen ◽  
...  

2014 ◽  
Vol 13s7 ◽  
pp. CIN.S16353
Author(s):  
Lie Xiong ◽  
Pei-Fen Kuan ◽  
Jianan Tian ◽  
Sunduz Keles ◽  
Sijian Wang

In this paper, we propose a novel multivariate component-wise boosting method for fitting multivariate response regression models under the high-dimension, low sample size setting. Our method is motivated by modeling the association among different biological molecules based on multiple types of high-dimensional genomic data. Particularly, we are interested in two applications: studying the influence of DNA copy number alterations on RNA transcript levels and investigating the association between DNA methylation and gene expression. For this purpose, we model the dependence of the RNA expression levels on DNA copy number alterations and the dependence of gene expression on DNA methylation through multivariate regression models and utilize boosting-type method to handle the high dimensionality as well as model the possible nonlinear associations. The performance of the proposed method is demonstrated through simulation studies. Finally, our multivariate boosting method is applied to two breast cancer studies.


2012 ◽  
Vol 32 (1) ◽  
pp. 5-9 ◽  
Author(s):  
Bing-ji WEN ◽  
Wen-ming CONG ◽  
Ai-zhong WANG ◽  
Song-qin HE ◽  
Hong-mei JIANG ◽  
...  

Medicina ◽  
2021 ◽  
Vol 57 (5) ◽  
pp. 502
Author(s):  
Georgiana Gug ◽  
Caius Solovan

Background and Objectives: Mycosis fungoides (MF) and large plaque parapsoriasis (LPP) evolution provide intriguing data and are the cause of numerous debates. The diagnosis of MF and LPP is associated with confusion and imprecise definition. Copy number alterations (CNAs) may play an essential role in the genesis of cancer out of genes expression dysregulation. Objectives: Due to the heterogeneity of MF and LPP and the scarcity of the cases, there are an exceedingly small number of studies that have identified molecular changes in these pathologies. We aim to identify and compare DNA copy number alterations and gene expression changes between MF and LPP to highlight the similarities and the differences between these pathologies. Materials and Methods: The patients were prospectively selected from University Clinic of Dermatology and Venereology Timișoara, Romania. From fresh frozen skin biopsies, we extracted DNA using single nucleotide polymorphism (SNP) data. The use of SNP array for copy number profiling is a promising approach for genome-wide analysis. Results: After reviewing each group, we observed that the histograms generated for chromosome 1–22 were remarkably similar and had a lot of CNAs in common, but also significant differences were seen. Conclusions: This study took a step forward in finding out the differences and similarities between MF and LPP, for a more specific and implicitly correct approach of the case. The similarity between these two pathologies in terms of CNAs is striking, emphasizing once again the difficulty of approaching and differentiating them.


2010 ◽  
Vol 35 (7) ◽  
pp. 1172-1183.e7 ◽  
Author(s):  
Barbara B. Shih ◽  
May Tassabehji ◽  
James S. Watson ◽  
Angus D. McGrouther ◽  
Ardeshir Bayat

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