Visualizing Protein Interactions in Corresponding Compartments

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Abstract

The visualization of networks for protein interactions is an important step to understand them. There are already many approaches for this task, but most of them do not show any information about the compartment of the cell the proteins belong to. Since the placement of proteins inside a cell is important information, because it helps to understand their interactions, this thesis proposes a method to visualize protein inside cell compartments. The objective of this project is a clear and understandable visualization of interactions between proteins and where these interactions or reactions happen inside the cell. This project uses a three-dimensional model of a cell as a base and intersects it using cutting planes. Then the intersection surface is sampled and reconstructed using Delaunay triangulation. To the mesh created by the triangulation, a force-directed algorithm is applied. This algorithm is used to scale single-cell parts in order to fit all proteins inside. This ensures that none of the cell parts get overfilled. The result is a new method that makes it possible to visualize not only protein-protein interactions but also in which compartment of the cell the proteins are located.

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BibTeX

@bachelorsthesis{rinortner_susanne-2019-vpicc,
  title =      "Visualizing Protein Interactions in Corresponding
               Compartments",
  author =     "Susanne Rinortner",
  year =       "2019",
  abstract =   "The visualization of networks for protein interactions is an
               important step to understand them. There are already many
               approaches for this task, but most of them do not show any
               information about the compartment of the cell the proteins
               belong to. Since the placement of proteins inside a cell is
               important information, because it helps to understand their
               interactions, this thesis proposes a method to visualize
               protein inside cell compartments. The objective of this
               project is a clear and understandable visualization of
               interactions between proteins and where these interactions
               or reactions happen inside the cell. This project uses a
               three-dimensional model of a cell as a base and intersects
               it using cutting planes. Then the intersection surface is
               sampled and reconstructed using Delaunay triangulation. To
               the mesh created by the triangulation, a force-directed
               algorithm is applied. This algorithm is used to scale
               single-cell parts in order to fit all proteins inside. This
               ensures that none of the cell parts get overfilled. The
               result is a new method that makes it possible to visualize
               not only protein-protein interactions but also in which
               compartment of the cell the proteins are located.",
  month =      oct,
  address =    "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria",
  school =     "Research Unit of Computer Graphics, Institute of Visual
               Computing and Human-Centered Technology, Faculty of
               Informatics, TU Wien ",
  keywords =   "Biological pathways",
  URL =        "/research/publications/2019/rinortner_susanne-2019-vpicc/",
}