Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number aberrations and gene–loci expression

DNA copy number aberrations (CNAs) are genetic alterations common in cancer cells. Their transcriptional consequences are still poorly understood. Based on the fact that DNA copy number (CN) is highly correlated with the genomic position, we have applied a segmentation algorithm to gene expression (...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2011-02, Vol.97 (2), p.86-93
Main Authors: Ortiz-Estevez, M., De Las Rivas, J., Fontanillo, C., Rubio, A.
Format: Article
Language:English
Subjects:
algorithms
Biological and medical sciences
Chromosome Aberrations
Copy number
data collection
Diverse techniques
DNA
DNA Copy Number Variations - genetics
Fundamental and applied biological sciences. Psychology
Gene expression
Gene Expression Profiling - methods
genes
Genes. Genome
Genetics of eukaryotes. Biological and molecular evolution
Genome
Humans
loci
microarray technology
Microarrays
Molecular and cellular biology
Molecular genetics
Neoplasms - genetics
Oligonucleotide Array Sequence Analysis - methods
Segmentation
transcription (genetics)
transcriptomics
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Summary:DNA copy number aberrations (CNAs) are genetic alterations common in cancer cells. Their transcriptional consequences are still poorly understood. Based on the fact that DNA copy number (CN) is highly correlated with the genomic position, we have applied a segmentation algorithm to gene expression (GE) to explore its relation with CN. We have found a strong correlation between segmented CN (sCN) and segmented GE (sGE), corroborating that CNAs have clear effects on genome-wide expression. We have found out that most of the recurrent regions of sGE are common to those obtained from sCN analysis. Results for two cancer datasets confirm the known targets of aberrations and provide new candidates to study. The suggested methodology allows to find recurrent aberrations specific to sGE, revealing loci where the expression of the genes is independent from their CNs. R code and additional files are available as supplementary material.
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2010.10.008