Analysis and visualization of multidimensional cancer genomics data
Cancer is a complex disease caused by somatic alterations of the genome and epigenome in tumor cells. Increased investments and cheaper access to various technologies have built momentum for the generation of cancer genomics data. The availability of such large datasets offers many new possibilities...
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| Format: | Doctoral thesis |
| Status: | Published version |
| Publication date: | 2014 |
| Country: | España |
| Institution: | CBUC, CESCA |
| Repository: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/301436 |
| Online Access: | http://hdl.handle.net/10803/301436 |
| Access Level: | Open access |
| Keyword: | Cancer Càncer Genomics Genòmica Data visualization Visualització de dades Machine learning Aprenentatge automàtic Data integration Integració de dades 616 |
| Summary: | Cancer is a complex disease caused by somatic alterations of the genome and epigenome in tumor cells. Increased investments and cheaper access to various technologies have built momentum for the generation of cancer genomics data. The availability of such large datasets offers many new possibilities to gain insight into cancer molecular properties. Within this scope I present two methods that exploit the broad availability of cancer genomic data: OncodriveROLE, an approach to classify mutational cancer driver genes into activating and loss of function mode of actions and MutEx, a statistical measure to assess the trend of the somatic alterations in a set of genes to be mutually exclusive across tumor samples. Nevertheless, the unprecedented dimension of the available data raises new complications for its accessibility and exploration which we try to solve with new visualization solutions: i) Gitools interactive heatmaps with prepared large scale cancer genomics datasets ready to be explored, ii) jHeatmap, an interactive heatmap browser for the web capable of displaying multidimensional cancer genomics data and designed for its inclusion into web portals, and iii) SVGMap, a web server to project data onto customized SVG figures useful for mapping experimental measurements onto the model. |
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