Limits...
FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.

Mader M, Simon R, Kurtz S - J Clin Bioinforma (2014)

Bottom Line: One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events.High quality image export enables the life scientist to easily communicate their results.We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany. kurtz@zbh.uni-hamburg.de.

ABSTRACT

Background: A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events.

Results: We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. A powerful search interface and a fast visualization engine provide a highly interactive visualization for such data. High quality image export enables the life scientist to easily communicate their results. A comprehensive data administration allows to keep track of the available data sets. We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before.

Conclusions: The interactive nature of FISH Oracle 2 and the possibility to store, select and visualize large amounts of downstream processed data support life scientists in generating hypotheses. The export of high quality images supports explanatory data visualization, simplifying the communication of new biological findings. A FISH Oracle 2 demo server and the software is available at http://www.zbh.uni-hamburg.de/fishoracle.

No MeSH data available.


Related in: MedlinePlus

Genomic aberrations in EO-PCA at the 21q22 (ERG) locus. This region focuses on the fusion gene TMPRSS2:ERG[28]. In addition to the chromosome band (1) and gene annotations (2), five data tracks (dataset "Weischenfeldt" in the demo application) are displayed. Track (3) shows all SNVs including six in ERG and two in TMPRSS2. Track (4) displays inter chromosomal translocations, nine of which include ERG and three of which affect TMPRSS2. Track (5) shows several cases of interstitial deletions leading to the TMPRSS2:ERG fusion. The chromosomal ranges of TMPRSS2 and ERG overlapping with deletions are indicated by thin dotted red boxes. Track (6) shows one duplication and track (7) shows seven inversions. Tracks (5), (6) and (7) visualize generic entities, i.e. data specified by genomic coordinates only.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4230720&req=5

Figure 2: Genomic aberrations in EO-PCA at the 21q22 (ERG) locus. This region focuses on the fusion gene TMPRSS2:ERG[28]. In addition to the chromosome band (1) and gene annotations (2), five data tracks (dataset "Weischenfeldt" in the demo application) are displayed. Track (3) shows all SNVs including six in ERG and two in TMPRSS2. Track (4) displays inter chromosomal translocations, nine of which include ERG and three of which affect TMPRSS2. Track (5) shows several cases of interstitial deletions leading to the TMPRSS2:ERG fusion. The chromosomal ranges of TMPRSS2 and ERG overlapping with deletions are indicated by thin dotted red boxes. Track (6) shows one duplication and track (7) shows seven inversions. Tracks (5), (6) and (7) visualize generic entities, i.e. data specified by genomic coordinates only.

Mentions: Genomic entities (including processed data or self-defined entities) not fitting into any of the previous three categories can be visualized by generic elements, i.e. rectangles of fixed height and arbitrary length. A generic element only requires the specification of genomic coordinates, consisting of a chromosome identifier as well as a start and end position of the genomic entity, and an optional name. Examples for the use of generic elements can be found in Figure2 and Additional file1: Figure S1.


FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.

Mader M, Simon R, Kurtz S - J Clin Bioinforma (2014)

Genomic aberrations in EO-PCA at the 21q22 (ERG) locus. This region focuses on the fusion gene TMPRSS2:ERG[28]. In addition to the chromosome band (1) and gene annotations (2), five data tracks (dataset "Weischenfeldt" in the demo application) are displayed. Track (3) shows all SNVs including six in ERG and two in TMPRSS2. Track (4) displays inter chromosomal translocations, nine of which include ERG and three of which affect TMPRSS2. Track (5) shows several cases of interstitial deletions leading to the TMPRSS2:ERG fusion. The chromosomal ranges of TMPRSS2 and ERG overlapping with deletions are indicated by thin dotted red boxes. Track (6) shows one duplication and track (7) shows seven inversions. Tracks (5), (6) and (7) visualize generic entities, i.e. data specified by genomic coordinates only.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230720&req=5

Figure 2: Genomic aberrations in EO-PCA at the 21q22 (ERG) locus. This region focuses on the fusion gene TMPRSS2:ERG[28]. In addition to the chromosome band (1) and gene annotations (2), five data tracks (dataset "Weischenfeldt" in the demo application) are displayed. Track (3) shows all SNVs including six in ERG and two in TMPRSS2. Track (4) displays inter chromosomal translocations, nine of which include ERG and three of which affect TMPRSS2. Track (5) shows several cases of interstitial deletions leading to the TMPRSS2:ERG fusion. The chromosomal ranges of TMPRSS2 and ERG overlapping with deletions are indicated by thin dotted red boxes. Track (6) shows one duplication and track (7) shows seven inversions. Tracks (5), (6) and (7) visualize generic entities, i.e. data specified by genomic coordinates only.
Mentions: Genomic entities (including processed data or self-defined entities) not fitting into any of the previous three categories can be visualized by generic elements, i.e. rectangles of fixed height and arbitrary length. A generic element only requires the specification of genomic coordinates, consisting of a chromosome identifier as well as a start and end position of the genomic entity, and an optional name. Examples for the use of generic elements can be found in Figure2 and Additional file1: Figure S1.

Bottom Line: One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events.High quality image export enables the life scientist to easily communicate their results.We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany. kurtz@zbh.uni-hamburg.de.

ABSTRACT

Background: A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events.

Results: We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. A powerful search interface and a fast visualization engine provide a highly interactive visualization for such data. High quality image export enables the life scientist to easily communicate their results. A comprehensive data administration allows to keep track of the available data sets. We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before.

Conclusions: The interactive nature of FISH Oracle 2 and the possibility to store, select and visualize large amounts of downstream processed data support life scientists in generating hypotheses. The export of high quality images supports explanatory data visualization, simplifying the communication of new biological findings. A FISH Oracle 2 demo server and the software is available at http://www.zbh.uni-hamburg.de/fishoracle.

No MeSH data available.


Related in: MedlinePlus