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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 EO-PCA at the 12q24 locus. Genomic aberrations in EO-PCA at the 12q24 locus. This region focuses on the androgen-receptor interacting gene NCOR2. In addition to the chromosome band (1) and gene annotations (2), three data tracks (datasets "TCGA_COAD" and "TCGA _READ" in the demo application) are shown. Track (3) shows all SNVs, two of which target NCOR2. Track (4) shows two translocations, one of which leads to a gene fusion of PDE4D and NCOR2. Track (5) shows one deletion (generic features) covering NCOR2. The insert in the red box magnifies a part of the NCOR2 gene, including SNVs and two translocations.
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Figure 3: Genomic aberrations in EO-PCA at the 12q24 locus. Genomic aberrations in EO-PCA at the 12q24 locus. This region focuses on the androgen-receptor interacting gene NCOR2. In addition to the chromosome band (1) and gene annotations (2), three data tracks (datasets "TCGA_COAD" and "TCGA _READ" in the demo application) are shown. Track (3) shows all SNVs, two of which target NCOR2. Track (4) shows two translocations, one of which leads to a gene fusion of PDE4D and NCOR2. Track (5) shows one deletion (generic features) covering NCOR2. The insert in the red box magnifies a part of the NCOR2 gene, including SNVs and two translocations.

Mentions: Figure3 exemplifies how FISH Oracle 2 facilitates the identification of genes that are recurrently affected by genomic alterations of different types. The nuclear receptor corepressor 2 (NCOR2) gene has five alterations in the 11 EO-PCA cases. These include a large deletion accompanied by a disruptive translocation in case EO-PCA06, resulting in complete inactivation of NCOR2. Given the functional involvement of NCOR2 in chromatin remodeling and AR-dependent transcription control[40,41], this finding already qualifies NCOR2 as an interesting candidate for further investigations. The presence of mutations in two additional tumors (track 3) as well as another case of translocation (track 4), further supports the hypothesis that the NCOR2 gene is relevant for prostate cancer biology. Note that some alterations (i.e. translocations and the 3 ′-mutation of NCOR2) seem to be located very closely together when viewed at a high zoom level. However, the flexible zooming capabilities of FISH Oracle 2 quickly reveals that these events are actually not co-localized.


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 12q24 locus. Genomic aberrations in EO-PCA at the 12q24 locus. This region focuses on the androgen-receptor interacting gene NCOR2. In addition to the chromosome band (1) and gene annotations (2), three data tracks (datasets "TCGA_COAD" and "TCGA _READ" in the demo application) are shown. Track (3) shows all SNVs, two of which target NCOR2. Track (4) shows two translocations, one of which leads to a gene fusion of PDE4D and NCOR2. Track (5) shows one deletion (generic features) covering NCOR2. The insert in the red box magnifies a part of the NCOR2 gene, including SNVs and two translocations.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Genomic aberrations in EO-PCA at the 12q24 locus. Genomic aberrations in EO-PCA at the 12q24 locus. This region focuses on the androgen-receptor interacting gene NCOR2. In addition to the chromosome band (1) and gene annotations (2), three data tracks (datasets "TCGA_COAD" and "TCGA _READ" in the demo application) are shown. Track (3) shows all SNVs, two of which target NCOR2. Track (4) shows two translocations, one of which leads to a gene fusion of PDE4D and NCOR2. Track (5) shows one deletion (generic features) covering NCOR2. The insert in the red box magnifies a part of the NCOR2 gene, including SNVs and two translocations.
Mentions: Figure3 exemplifies how FISH Oracle 2 facilitates the identification of genes that are recurrently affected by genomic alterations of different types. The nuclear receptor corepressor 2 (NCOR2) gene has five alterations in the 11 EO-PCA cases. These include a large deletion accompanied by a disruptive translocation in case EO-PCA06, resulting in complete inactivation of NCOR2. Given the functional involvement of NCOR2 in chromatin remodeling and AR-dependent transcription control[40,41], this finding already qualifies NCOR2 as an interesting candidate for further investigations. The presence of mutations in two additional tumors (track 3) as well as another case of translocation (track 4), further supports the hypothesis that the NCOR2 gene is relevant for prostate cancer biology. Note that some alterations (i.e. translocations and the 3 ′-mutation of NCOR2) seem to be located very closely together when viewed at a high zoom level. However, the flexible zooming capabilities of FISH Oracle 2 quickly reveals that these events are actually not co-localized.

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