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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

Abundant deletions and mutations in the genomic locus of the gene APC. In addition to the chromosome band (1) and gene annotations (2), two data tracks (datasets "TCGA_COAD" and "TCGA_READ" in the demo application) are shown. Track (3) shows CNV intensity data displaying deletions at a threshold of -0.5. CNV segments are grouped by sample. Track (4) shows many SNVs, 196 of which affect the gene APC.
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Figure 4: Abundant deletions and mutations in the genomic locus of the gene APC. In addition to the chromosome band (1) and gene annotations (2), two data tracks (datasets "TCGA_COAD" and "TCGA_READ" in the demo application) are shown. Track (3) shows CNV intensity data displaying deletions at a threshold of -0.5. CNV segments are grouped by sample. Track (4) shows many SNVs, 196 of which affect the gene APC.

Mentions: Another interesting finding in this dataset was a minimally overlapping region of a deletion at the human chromosome 5q22 region, highlighting the genomic position of the APC tumor suppressor gene (Figure4). Note the high prevalence of mutations of APC (in total there are 196 SNVs in the two datasets)[43]. The APC locus is another example that a simultaneous visualization of deletion and mutation tracks in FISH Oracle 2 supports detection of "typical" tumor suppressor genes following the "second hit" sequence of inactivation[44].


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)

Abundant deletions and mutations in the genomic locus of the gene APC. In addition to the chromosome band (1) and gene annotations (2), two data tracks (datasets "TCGA_COAD" and "TCGA_READ" in the demo application) are shown. Track (3) shows CNV intensity data displaying deletions at a threshold of -0.5. CNV segments are grouped by sample. Track (4) shows many SNVs, 196 of which affect the gene APC.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Abundant deletions and mutations in the genomic locus of the gene APC. In addition to the chromosome band (1) and gene annotations (2), two data tracks (datasets "TCGA_COAD" and "TCGA_READ" in the demo application) are shown. Track (3) shows CNV intensity data displaying deletions at a threshold of -0.5. CNV segments are grouped by sample. Track (4) shows many SNVs, 196 of which affect the gene APC.
Mentions: Another interesting finding in this dataset was a minimally overlapping region of a deletion at the human chromosome 5q22 region, highlighting the genomic position of the APC tumor suppressor gene (Figure4). Note the high prevalence of mutations of APC (in total there are 196 SNVs in the two datasets)[43]. The APC locus is another example that a simultaneous visualization of deletion and mutation tracks in FISH Oracle 2 supports detection of "typical" tumor suppressor genes following the "second hit" sequence of inactivation[44].

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