Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 15488149

Caryoscope: an Open Source Java application for viewing microarray data in a genomic context.

Ihab A B Awad·Christian A Rees·Tina Hernandez-Boussard·Catherine A Ball·Gavin Sherlock
View original source ↗Export metadata ↓

Abstract

BACKGROUND: Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context. RESULTS: We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files), as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript. CONCLUSION: Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context.

Explore related subjects

Chromosome MappingComputational BiologyComputer GraphicsGenomeMicroarray AnalysisNucleic Acid HybridizationProgramming LanguagesSoftwareSoftware DesignComparative StudyJournal ArticleResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ihab A B Awad, Christian A Rees, Tina Hernandez-Boussard, Catherine A Ball, Gavin Sherlock. 2004-10-15. Caryoscope: an Open Source Java application for viewing microarray data in a genomic context.. https://doi.org/10.1186/1471-2105-5-151

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Mitotic karyotyping and FISH mapping of the gender-specific locus indicate an advanced XY system in Hippophae rhamnoides.

Hippophae rhamnoides ssp. turkestanica, a subdioecious plant inhabiting the cold desert of the Indian Himalaya, has gained immense recognition for its nutritional and medicinal values. In recent years, the plant species has proven to be a suitable system to understand the evolution of dioecy. Despite its biological significance, the cytogenetics of this dioecious plant is unclear due to various conflicting accounts of its X-Y chromosome system, particularly the length of Y-chromosome. In this study, we resolved these ambiguities through comprehensive cytogenetic analyses across diverse western Himalayan populations. Using morphometric analysis and fluorescence in situ hybridization (FISH) with a gender-specific marker (HRMSSR), we confirmed homomorphic XX chromosomes in females and heteromorphic sex-chromosomes in males with a notably smaller Y-chromosome. The investigation also revealed a predominant somatic chromosome number of 2n = 24, although minor deviations (2n = 18, 20, 22) appeared at the seed level. These findings highlight an evolutionarily advanced sex-chromosome system. This first detailed cytogenetic investigation of Himalayan Seabuckthorn provides critical insights into the chromosomal architecture, laying a crucial foundation for future evolutionary, genomic, and conservation studies in the species.

Chromosome Mapping↗
PubMed2006

Molecular basis of human dentin diseases.

In recent years, substantial progress has been made regarding the molecular etiology of human structural tooth diseases that alter dentin matrix formation. These diseases have been classified into two major groups with subtypes: dentin dysplasia (DD) types I and II and dentinogenesis imperfecta (DGI) types I-III. Genetic linkage studies have identified the critical loci for DD-II, DGI-II, and DGI-II to human chromosome 4q21. Located within the common disease loci for these diseases is cluster of dentin/bone genes that includes osteopontin (OPN), bone sialoprotein (BSP), matrix extracellular phosphoglycoprotein (MEPE), dentin matrix protein 1 (DMP1), and dentin sialophosphoprotein (DSPP). To date, only mutations within dentin sialophosphoprotein have been associated with the pathogenesis of dentin diseases including DGI types-II and -III and DD-II. In this article, we overview the recent literature related to these dentin genetic diseases, their clinical features, and molecular pathogenesis.

Chromosome Mapping↗
PubMed2006

Mitochondrial microsatellite instability of colorectal cancer stroma.

Mitochondrial microsatellite instability (mtMSI) and mutations of mitochondrial DNA has been reported in cancer epithelia of carcinomas. However, mtMSI in cancer stroma has not yet been identified in human cancers. In this study, we attempted to determine if mtMSI occurs in the cancer stroma of sporadic colorectal cancers, and if the stromal mtMSI has any correlations with stromal nuclear MSI (nMSI) and cancer epithelial mtMSI. Nine microsatellite sequences within the D-loop and 5 coding genes for mtMSI, and 9 microsatellites for nMSI were analyzed in the microdissected cancer epithelia and adjacent stromas of 48 sporadic colorectal cancers. Overall, 23 somatic mitochondrial DNA alterations were detected in 15 cancer epithelia (31.2%) and 5 stromas (10.4%). The mutations consisted of 19 D-loop mtMSI alterations, and 1 missense and 3 framshift mutations of repeat sequences within the coding genes. All of the 5 stromal genetic alterations showed D-loop mtMSI. In regards to other MSI status, the stromal mtMSI had no association with stromal nMSI or epithelial mtMSI, either. These findings indicate that in addition to the cancer epithelia the cancer stroma harbor mtMSI, and suggest a possible role of stromal mtMSI in the pathogenesis of colorectal cancers. Furthermore, the data suggest that stromal mtMSI may occur independently of stromal nMSI and epithelial mtMSI in sporadic colorectal cancers.

Chromosome Mapping↗