dc.contributor.author
Tebel, Katrin
dc.contributor.author
Boldt, Vivien
dc.contributor.author
Steininger, Anne
dc.contributor.author
Port, Matthias
dc.contributor.author
Ebert, Grit
dc.contributor.author
Ullmann, Reinhard
dc.date.accessioned
2018-06-08T11:06:44Z
dc.date.available
2017-03-03T11:34:47.660Z
dc.identifier.uri
https://refubium.fu-berlin.de/handle/fub188/21634
dc.identifier.uri
http://dx.doi.org/10.17169/refubium-24922
dc.description.abstract
Background The analysis of DNA copy number variants (CNV) has increasing
impact in the field of genetic diagnostics and research. However, the
interpretation of CNV data derived from high resolution array CGH or NGS
platforms is complicated by the considerable variability of the human genome.
Therefore, tools for multidimensional data analysis and comparison of patient
cohorts are needed to assist in the discrimination of clinically relevant CNVs
from others. Results We developed GenomeCAT, a standalone Java application for
the analysis and integrative visualization of CNVs. GenomeCAT is composed of
three modules dedicated to the inspection of single cases, comparative
analysis of multidimensional data and group comparisons aiming at the
identification of recurrent aberrations in patients sharing the same
phenotype, respectively. Its flexible import options ease the comparative
analysis of own results derived from microarray or NGS platforms with data
from literature or public depositories. Multidimensional data obtained from
different experiment types can be merged into a common data matrix to enable
common visualization and analysis. All results are stored in the integrated
MySQL database, but can also be exported as tab delimited files for further
statistical calculations in external programs. Conclusions GenomeCAT offers a
broad spectrum of visualization and analysis tools that assist in the
evaluation of CNVs in the context of other experiment data and annotations.
The use of GenomeCAT does not require any specialized computer skills. The
various R packages implemented for data analysis are fully integrated into
GenomeCATs graphical user interface and the installation process is supported
by a wizard. The flexibility in terms of data import and export in combination
with the ability to create a common data matrix makes the program also well
suited as an interface between genomic data from heterogeneous sources and
external software tools. Due to the modular architecture the functionality of
GenomeCAT can be easily extended by further R packages or customized plug-ins
to meet future requirements.
en
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
DNA copy number variants
dc.subject
Integrative visualization
dc.subject.ddc
500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie
dc.type
Wissenschaftlicher Artikel
dcterms.bibliographicCitation
BMC Bioinformatics. - 18 (2017), Artikel Nr. 19
dc.title.subtitle
a versatile tool for the analysis and integrative visualization of DNA copy
number variants
dcterms.bibliographicCitation.doi
10.1186/s12859-016-1430-x
dcterms.bibliographicCitation.url
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1430-x
refubium.affiliation
Biologie, Chemie, Pharmazie
de
refubium.mycore.fudocsId
FUDOCS_document_000000026536
refubium.note.author
Der Artikel wurde in einer reinen Open-Access-Zeitschrift publiziert.
refubium.resourceType.isindependentpub
no
refubium.mycore.derivateId
FUDOCS_derivate_000000007836
dcterms.accessRights.openaire
open access