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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

Main window of FISH Oracle 2. Main window of FISH Oracle 2 focusing on the 10q23 locus which includes the tumor suppressor gene PTEN. Part (1) shows the search menu, which, in the displayed case, is used for searching a gene by its name. Part (2) consists of the toolbar showing different navigation and configuration options. Part (3) consists of the visualization area with the chromosome band below the genomic scale and four further tracks, one for Ensembl genes (in this case genes corresponding to Ensembl version 75 are displayed, indicated by the caption of the tab), one for CNVs (deletions in our case), one for SNVs and one for translocations, all displayed in default colors. All CNVs with a segment intensity value of less than -0.5 are shown. The SNV track displays several genes containing between one and seven SNVs followed by seven translocations in the next track. Each track shows a different data set (here obtained by microarrays and NGS), but all data refer to prostate cancer tissue samples. The most frequently occurring copy number changes form a minimal common region including the gene PTEN. Furthermore, PTEN is associated with seven SNVs in one dataset and three translocations in eleven samples of EO-PCA. The characteristic minimal common region derived from three different kinds of genomic events highlight the gene PTEN.
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Figure 1: Main window of FISH Oracle 2. Main window of FISH Oracle 2 focusing on the 10q23 locus which includes the tumor suppressor gene PTEN. Part (1) shows the search menu, which, in the displayed case, is used for searching a gene by its name. Part (2) consists of the toolbar showing different navigation and configuration options. Part (3) consists of the visualization area with the chromosome band below the genomic scale and four further tracks, one for Ensembl genes (in this case genes corresponding to Ensembl version 75 are displayed, indicated by the caption of the tab), one for CNVs (deletions in our case), one for SNVs and one for translocations, all displayed in default colors. All CNVs with a segment intensity value of less than -0.5 are shown. The SNV track displays several genes containing between one and seven SNVs followed by seven translocations in the next track. Each track shows a different data set (here obtained by microarrays and NGS), but all data refer to prostate cancer tissue samples. The most frequently occurring copy number changes form a minimal common region including the gene PTEN. Furthermore, PTEN is associated with seven SNVs in one dataset and three translocations in eleven samples of EO-PCA. The characteristic minimal common region derived from three different kinds of genomic events highlight the gene PTEN.

Mentions: FISH Oracle 2 allows users to query the FISH Oracle database in a variety of ways. It enables an interactive visual data exploration of large amounts of different kinds of genomic data in the context of genome annotations offering a chromosomal resolution ranging from a few base pairs to whole chromosome view. Several easily configurable filters can be applied to select data with specific attributes, which are specified in the search menu on the left side of the main window of FISH Oracle 2 (Figure1). The selected data is displayed in the main window using one of the following four visualization elements, each of which has an optional caption providing additional information about the displayed genomic entity.


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)

Main window of FISH Oracle 2. Main window of FISH Oracle 2 focusing on the 10q23 locus which includes the tumor suppressor gene PTEN. Part (1) shows the search menu, which, in the displayed case, is used for searching a gene by its name. Part (2) consists of the toolbar showing different navigation and configuration options. Part (3) consists of the visualization area with the chromosome band below the genomic scale and four further tracks, one for Ensembl genes (in this case genes corresponding to Ensembl version 75 are displayed, indicated by the caption of the tab), one for CNVs (deletions in our case), one for SNVs and one for translocations, all displayed in default colors. All CNVs with a segment intensity value of less than -0.5 are shown. The SNV track displays several genes containing between one and seven SNVs followed by seven translocations in the next track. Each track shows a different data set (here obtained by microarrays and NGS), but all data refer to prostate cancer tissue samples. The most frequently occurring copy number changes form a minimal common region including the gene PTEN. Furthermore, PTEN is associated with seven SNVs in one dataset and three translocations in eleven samples of EO-PCA. The characteristic minimal common region derived from three different kinds of genomic events highlight the gene PTEN.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Main window of FISH Oracle 2. Main window of FISH Oracle 2 focusing on the 10q23 locus which includes the tumor suppressor gene PTEN. Part (1) shows the search menu, which, in the displayed case, is used for searching a gene by its name. Part (2) consists of the toolbar showing different navigation and configuration options. Part (3) consists of the visualization area with the chromosome band below the genomic scale and four further tracks, one for Ensembl genes (in this case genes corresponding to Ensembl version 75 are displayed, indicated by the caption of the tab), one for CNVs (deletions in our case), one for SNVs and one for translocations, all displayed in default colors. All CNVs with a segment intensity value of less than -0.5 are shown. The SNV track displays several genes containing between one and seven SNVs followed by seven translocations in the next track. Each track shows a different data set (here obtained by microarrays and NGS), but all data refer to prostate cancer tissue samples. The most frequently occurring copy number changes form a minimal common region including the gene PTEN. Furthermore, PTEN is associated with seven SNVs in one dataset and three translocations in eleven samples of EO-PCA. The characteristic minimal common region derived from three different kinds of genomic events highlight the gene PTEN.
Mentions: FISH Oracle 2 allows users to query the FISH Oracle database in a variety of ways. It enables an interactive visual data exploration of large amounts of different kinds of genomic data in the context of genome annotations offering a chromosomal resolution ranging from a few base pairs to whole chromosome view. Several easily configurable filters can be applied to select data with specific attributes, which are specified in the search menu on the left side of the main window of FISH Oracle 2 (Figure1). The selected data is displayed in the main window using one of the following four visualization elements, each of which has an optional caption providing additional information about the displayed genomic entity.

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