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Subcellular localization charts : a new visual methodology for the semi-automatic localization of protein-related data sets

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2013

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Kormeier, Benjamin
Demenkov, Pavel S.
Arrigo, Patrizio
Hippe, Klaus
Ates, Özgür
Kochetov, Alexey V.
Ivanisenko, Vladimir A.
Kolchanov, Nikolay A.
Hofestädt, Ralf

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https://doi.org/10.1142/S0219720013400052
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Journal of bioinformatics and computational biology. 2013, 11(1), 1340005. ISSN 0219-7200. eISSN 1757-6334. Available under: doi: 10.1142/S0219720013400052

Zusammenfassung

The CELLmicrocosmos PathwayIntegration (CmPI) was developed to support and visualize the subcellular localization prediction of protein-related data such as protein-interaction networks. From the start it was possible to manually analyze the localizations by using an interactive table. It was, however, quite complicated to compare and analyze the different localization results derived from data integration as well as text-mining-based databases. The current software release provides a new interactive visual workflow, the Subcellular Localization Charts. As an application case, a MUPP1-related protein-protein interaction network is localized and semi-automatically analyzed. It will be shown that the workflow was dramatically improved and simplified. In addition, it is now possible to use custom protein-related data by using the SBML format and get a view of predicted protein localizations mapped onto a virtual cell model.

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004 Informatik

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Subcellular Localization Charts, 3D visualization, dilated cardiomyopathy, virtual cell

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ISO 690SOMMER, Björn, Benjamin KORMEIER, Pavel S. DEMENKOV, Patrizio ARRIGO, Klaus HIPPE, Özgür ATES, Alexey V. KOCHETOV, Vladimir A. IVANISENKO, Nikolay A. KOLCHANOV, Ralf HOFESTÄDT, 2013. Subcellular localization charts : a new visual methodology for the semi-automatic localization of protein-related data sets. In: Journal of bioinformatics and computational biology. 2013, 11(1), 1340005. ISSN 0219-7200. eISSN 1757-6334. Available under: doi: 10.1142/S0219720013400052
BibTex
@article{Sommer2013-02Subce-44743,
  year={2013},
  doi={10.1142/S0219720013400052},
  title={Subcellular localization charts : a new visual methodology for the semi-automatic localization of protein-related data sets},
  number={1},
  volume={11},
  issn={0219-7200},
  journal={Journal of bioinformatics and computational biology},
  author={Sommer, Björn and Kormeier, Benjamin and Demenkov, Pavel S. and Arrigo, Patrizio and Hippe, Klaus and Ates, Özgür and Kochetov, Alexey V. and Ivanisenko, Vladimir A. and Kolchanov, Nikolay A. and Hofestädt, Ralf},
  note={Article Number: 1340005}
}
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