Pathway visualization - BA, Internship - Kuster Lab
Title: Overlaying information on pathway diagrams
Type: [ BA, internship ]
Category: [ UI ]
Programming language: [ JavaScript ]
Language: [ English ]
Prior experience: [ basic programming skills required, basic understanding of pathways is a plus ]
Complexity/Risk: [ medium ]
Contact person: Julian Müller
Brief background description: Results from shotgun proteomics experiments are typically given as lists of peptides and/or proteins. However, these lists are hard to interpret for biologists, as they are used to reason about biological processes in terms of biological pathways. Resources with information about pathways are available, but it is not trivial how one would project data from a specific project onto these 2D graph representations.
Brief description of the project: As part of a project investigating drug response data on cancer cell lines (TOPAS), we are developing an analysis platform that our researchers can use to easily browse the data coming out from these experiments. One particular visualization we would benefit greatly from is to see how the proteins in pathways react to different drug treatments. In this project, you will explore the different options of creating such visualizations, based on a graph representation of the pathway and a list of drug responses from our experiments. Ideally, we would use existing pathway diagrams from KEGG (https://www.genome.jp/kegg/) or Reactome (https://reactome.org/) and overlay our information. To ensure easy integration with other platforms, we will use the javascript platform VueJS.
Expected result: A VueJS component that can overlay different types of data on top of a pathway diagram which will be extremely useful for our researchers in the TOPAS project and potentially for users of ProteomicsDB as well.
Literature:
- Zhang, Jitao David, and Stefan Wiemann. "KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor." Bioinformatics 25.11 (2009): 1470-1471.
- Klukas, Christian, and Falk Schreiber. "Dynamic exploration and editing of KEGG pathway diagrams." Bioinformatics 23.3 (2007): 344-350.
- Croft, David, et al. "The Reactome pathway knowledgebase." Nucleic acids research 42.D1 (2014): D472-D477.
- Mlecnik, Bernhard, et al. "PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways." Nucleic acids research 33.suppl_2 (2005): W633-W637.
- Villaveces, Jose M., Rafael C. Jimenez, and Bianca H. Habermann. "KEGGViewer, a BioJS component to visualize KEGG Pathways." F1000Research 3 (2014).
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