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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

Genomic aberrations in colon and rectal tumors at the 22q12 locus. This region focuses on the frequently translocated gene TTC28. In addition to the chromosome band (1) and gene annotations (2), four data tracks (datasets "TCGA_COAD" and "TCGA_READ" in the demo application) are shown. Track (3) and (4) show CNV intensities in form of deletions (3) and amplifications (4) at a threshold of -0.5 and 0.5 respectively. Track (5) shows SNVs and track (6) shows translocations. The gene TTC28 is affected by six translocations all of which result in a gene fusion.
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Figure 5: Genomic aberrations in colon and rectal tumors at the 22q12 locus. This region focuses on the frequently translocated gene TTC28. In addition to the chromosome band (1) and gene annotations (2), four data tracks (datasets "TCGA_COAD" and "TCGA_READ" in the demo application) are shown. Track (3) and (4) show CNV intensities in form of deletions (3) and amplifications (4) at a threshold of -0.5 and 0.5 respectively. Track (5) shows SNVs and track (6) shows translocations. The gene TTC28 is affected by six translocations all of which result in a gene fusion.

Mentions: Figure5 indicates the presence of biallelic hits in the human chromosome 22q12 locus, which includes the gene TTC28. A comparison of the case IDs reveals that in five of six cases with a translocation, also a deletion is present, resulting in complete inactivation of TTC28. Interestingly, no mutations of TTC28 were found in this study, further supporting the hypothesis that a combination of deletion and breakage may be an important – and probably alternative – mechanism for complete gene inactivation in neoplasia. This is the first report suggesting a biallelic inactivation of TTC28 in colon and rectal cancer, thus complementing recent findings of[43], describing TTC28 as frequently hit by translocations. The combination of tracks displaying SNVs and translocations massively facilitates the identification of areas in the genome harboring potentially interesting candidate genes. With the increasing application of the mate pair sequencing technique, it is likely that a multitude of novel translocations will be detected, some of which might represent a common second hit in areas with large deletions.


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 colon and rectal tumors at the 22q12 locus. This region focuses on the frequently translocated gene TTC28. In addition to the chromosome band (1) and gene annotations (2), four data tracks (datasets "TCGA_COAD" and "TCGA_READ" in the demo application) are shown. Track (3) and (4) show CNV intensities in form of deletions (3) and amplifications (4) at a threshold of -0.5 and 0.5 respectively. Track (5) shows SNVs and track (6) shows translocations. The gene TTC28 is affected by six translocations all of which result in a gene fusion.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Genomic aberrations in colon and rectal tumors at the 22q12 locus. This region focuses on the frequently translocated gene TTC28. In addition to the chromosome band (1) and gene annotations (2), four data tracks (datasets "TCGA_COAD" and "TCGA_READ" in the demo application) are shown. Track (3) and (4) show CNV intensities in form of deletions (3) and amplifications (4) at a threshold of -0.5 and 0.5 respectively. Track (5) shows SNVs and track (6) shows translocations. The gene TTC28 is affected by six translocations all of which result in a gene fusion.
Mentions: Figure5 indicates the presence of biallelic hits in the human chromosome 22q12 locus, which includes the gene TTC28. A comparison of the case IDs reveals that in five of six cases with a translocation, also a deletion is present, resulting in complete inactivation of TTC28. Interestingly, no mutations of TTC28 were found in this study, further supporting the hypothesis that a combination of deletion and breakage may be an important – and probably alternative – mechanism for complete gene inactivation in neoplasia. This is the first report suggesting a biallelic inactivation of TTC28 in colon and rectal cancer, thus complementing recent findings of[43], describing TTC28 as frequently hit by translocations. The combination of tracks displaying SNVs and translocations massively facilitates the identification of areas in the genome harboring potentially interesting candidate genes. With the increasing application of the mate pair sequencing technique, it is likely that a multitude of novel translocations will be detected, some of which might represent a common second hit in areas with large deletions.

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