Visualization-based discovery and analysis of genomic aberrations in microarray data.
BACKGROUND
Chromosomal copy number changes (aneuploidies) play a key role in cancer progression and molecular evolution. These copy number changes can be studied using microarray-based comparative genomic hybridization (array CGH) or gene expression microarrays. However, accurate identification of amplified or deleted regions requires a combination of visual and computational analysis of these microarray data.


RESULTS
We have developed ChARMView, a visualization and analysis system for guided discovery of chromosomal abnormalities from microarray data. Our system facilitates manual or automated discovery of aneuploidies through dynamic visualization and integrated statistical analysis. ChARMView can be used with array CGH and gene expression microarray data, and multiple experiments can be viewed and analyzed simultaneously.


CONCLUSIONS
ChARMView is an effective and accurate visualization and analysis system for recognizing even small aneuploidies or subtle expression biases, identifying recurring aberrations in sets of experiments, and pinpointing functionally relevant copy number changes. ChARMView is freely available under the GNU GPL at http://function.princeton.edu/ChARMView.
Myers
Chad L
CL
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ 08544, USA. clmyers@princeton.edu
Chen
Xing
X
Troyanskaya
Olga G
OG
D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics; D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D005784:Gene Amplification; D018628:Gene Dosage; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D015894:Genome, Human; D006801:Humans; D020407:Internet; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated; D010641:Phenotype; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface