scholarly journals Integrated Analysis of DNA Copy Number Changes and Gene Expression Identifies Key Genes in Gastric Cancer

2020 ◽  
Vol 27 (6) ◽  
pp. 877-887 ◽  
Author(s):  
Ye Feng ◽  
Chunyu Shi ◽  
Dayu Wang ◽  
Xuefeng Wang ◽  
Zhi Chen
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Copy Number ◽  
Integrated Analysis ◽  
Dna Copy Number ◽  
Key Genes ◽  
Copy Number Changes

scholarly journals DNA copy number changes in young gastric cancer patients with special reference to chromosome 19

2003 ◽  
Vol 88 (12) ◽  
pp. 1914-1919 ◽  
Author(s):  
A Varis ◽  
B van Rees ◽  
M Weterman ◽  
A Ristimäki ◽  
J Offerhaus ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Special Reference ◽  
Cancer Patients ◽  
Copy Number ◽  
Chromosome 19 ◽  
Dna Copy Number ◽  
Copy Number Changes ◽  
Gastric Cancer Patients

scholarly journals Genes with Relevance for Early to Late Progression of Colon Carcinoma Based on Combined Genomic and Transcriptomic Information from the Same Patients

2010 ◽  
Vol 9 ◽  
pp. CIN.S4545 ◽  
Author(s):  
Kristina K. Lagerstedt ◽  
Erik Kristiansson ◽  
Christina Lönnroth ◽  
Marianne Andersson ◽  
Britt-Marie IresjÖ ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colon Cancer ◽  
Tumor Progression ◽  
Cancer Progression ◽  
Copy Number ◽  
Dna Copy Number ◽  
Colon Cancer Progression ◽  
Dna Alterations ◽  
Copy Number Changes ◽  
Dukes C

Background Genetic and epigenetic alterations in colorectal cancer are numerous. However, it is difficult to judge whether such changes are primary or secondary to the appearance and progression of tumors. Therefore, the aim of the present study was to identify altered DNA regions with significant covariation to transcription alterations along colon cancer progression. Methods Tumor and normal colon tissue were obtained at primary operations from 24 patients selected by chance. DNA, RNA and microRNAs were extracted from the same biopsy material in all individuals and analyzed by oligo-nucleotide array-based comparative genomic hybridization (CGH), mRNA- and microRNA oligo-arrays. Statistical analyses were performed to assess statistical interactions (correlations, co-variations) between DNA copy number changes and significant alterations in gene and microRNA expression using appropriate parametric and non-parametric statistics. Results Main DNA alterations were located on chromosome 7, 8, 13 and 20. Tumor DNA copy number gain increased with tumor progression, significantly related to increased gene expression. Copy number loss was not observed in Dukes A tumors. There was no significant relationship between expressed genes and tumor progression across Dukes A–D tumors; and no relationship between tumor stage and the number of microRNAs with significantly altered expression. Interaction analyses identified overall 41 genes, which discriminated early Dukes A plus B tumors from late Dukes C plus D tumor; 28 of these genes remained with correlations between genomic and transcriptomic alterations in Dukes C plus D tumors and 17 in Dukes D. One microRNA (microR-663) showed interactions with DNA alterations in all Dukes A-D tumors. Conclusions Our modeling confirms that colon cancer progression is related to genomic instability and altered gene expression. However, early invasive tumor growth seemed rather related to transcriptomic alterations, where changes in microRNA may be an early phenomenon, and less to DNA copy number changes.

scholarly journals Identification of genes with correlated patterns of variations in DNA copy number and gene expression level in gastric cancer

Genomics ◽  
2007 ◽  
Vol 89 (4) ◽  
pp. 451-459 ◽  
Author(s):  
Sanghwa Yang ◽  
Hei-Cheul Jeung ◽  
Ha Jin Jeong ◽  
Yeon Ho Choi ◽  
Ji Eun Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Copy Number ◽  
Gene Expression Level ◽  
Expression Level ◽  
Dna Copy Number ◽  
Correlated Patterns

scholarly journals An Integrated Approach for RNA-seq Data Normalization

2016 ◽  
Vol 15 ◽  
pp. CIN.S39781 ◽  
Author(s):  
Shengping Yang ◽  
Donald E. Mercante ◽  
Kun Zhang ◽  
Zhide Fang
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Copy Number ◽  
Differentially Expressed Gene ◽  
Integrated Approach ◽  
Gene Profiling ◽  
Data Normalization ◽  
Rna Seq ◽  
Dna Copy Number ◽  
Copy Number Changes

Background DNA copy number alteration is common in many cancers. Studies have shown that insertion or deletion of DNA sequences can directly alter gene expression, and significant correlation exists between DNA copy number and gene expression. Data normalization is a critical step in the analysis of gene expression generated by RNA-seq technology. Successful normalization reduces/removes unwanted nonbiological variations in the data, while keeping meaningful information intact. However, as far as we know, no attempt has been made to adjust for the variation due to DNA copy number changes in RNA-seq data normalization. Results In this article, we propose an integrated approach for RNA-seq data normalization. Comparisons show that the proposed normalization can improve power for downstream differentially expressed gene detection and generate more biologically meaningful results in gene profiling. In addition, our findings show that due to the effects of copy number changes, some housekeeping genes are not always suitable internal controls for studying gene expression. Conclusions Using information from DNA copy number, integrated approach is successful in reducing noises due to both biological and nonbiological causes in RNA-seq data, thus increasing the accuracy of gene profiling.

scholarly journals Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma

2012 ◽  
Vol 44 (6) ◽  
pp. 694-698 ◽  
Author(s):  
Cécile Guichard ◽  
Giuliana Amaddeo ◽  
Sandrine Imbeaud ◽  
Yannick Ladeiro ◽  
Laura Pelletier ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Somatic Mutations ◽  
Integrated Analysis ◽  
Key Genes ◽  
Copy Number Changes
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