Background: Copy number alterations (CNAs) are genetic changes commonly found in cancer that involve different regions of the genome and impact cancer progression by affecting gene expression and genomic stability. Computational techniques can analyze copy number data obtained from high-throughput sequencing platforms, and various tools visualize and analyze CNAs in cancer genomes, providing insights into genetic mechanisms driving cancer development and progression. However, tools for visualizing copy number data in cancer research have some limitations. In fact, they can be complex to use and require expertise in bioinformatics or computational biology. While copy number data analysis and visualization provide insights into cancer biology, interpreting results can be challenging, and there may be multiple explanations for observed patterns of copy number alterations. Results: We created Control-FREEC Viewer, a tool that facilitates effective visualization and exploration of copy number data. With Control-FREEC Viewer, experimental data can be easily loaded by the user. After choosing the reference genome, copy number data are displayed in whole genome or single chromosome view. Gain or loss on a specific gene can be found and visualized on each chromosome. Analysis parameters for subsequent sessions can be stored and images can be exported in raster and vector formats. Conclusions: Control-FREEC Viewer enables users to import and visualize data analyzed by the Control-FREEC tool, as well as by other tools sharing a similar tabular output, providing a comprehensive and intuitive graphical user interface for data visualization.

Crippa, V., Fina, E., Ramazzotti, D., Piazza, R. (2024). Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data. BMC BIOINFORMATICS, 25(1) [10.1186/s12859-024-05694-w].

Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data

Crippa V.
Primo
;
Ramazzotti D.
Penultimo
;
Piazza R.
Ultimo
2024

Abstract

Background: Copy number alterations (CNAs) are genetic changes commonly found in cancer that involve different regions of the genome and impact cancer progression by affecting gene expression and genomic stability. Computational techniques can analyze copy number data obtained from high-throughput sequencing platforms, and various tools visualize and analyze CNAs in cancer genomes, providing insights into genetic mechanisms driving cancer development and progression. However, tools for visualizing copy number data in cancer research have some limitations. In fact, they can be complex to use and require expertise in bioinformatics or computational biology. While copy number data analysis and visualization provide insights into cancer biology, interpreting results can be challenging, and there may be multiple explanations for observed patterns of copy number alterations. Results: We created Control-FREEC Viewer, a tool that facilitates effective visualization and exploration of copy number data. With Control-FREEC Viewer, experimental data can be easily loaded by the user. After choosing the reference genome, copy number data are displayed in whole genome or single chromosome view. Gain or loss on a specific gene can be found and visualized on each chromosome. Analysis parameters for subsequent sessions can be stored and images can be exported in raster and vector formats. Conclusions: Control-FREEC Viewer enables users to import and visualize data analyzed by the Control-FREEC tool, as well as by other tools sharing a similar tabular output, providing a comprehensive and intuitive graphical user interface for data visualization.
Articolo in rivista - Articolo scientifico
Copy number variation; Data exploration; Data visualization;
English
14-feb-2024
2024
25
1
72
open
Crippa, V., Fina, E., Ramazzotti, D., Piazza, R. (2024). Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data. BMC BIOINFORMATICS, 25(1) [10.1186/s12859-024-05694-w].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/459878
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