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

Bjorn Sommer, Benjamin Kormeier, Pavel Sergeevich Demenkov, Patrizio Arrigo, Klaus Hippe, Ozgur Ates, Alexey Vladimirovich Kochetov, Vladimir Aleksandrovich Ivanisenko, Nikolay Aleksandrovich Kolchanov, Ralf Hofestadt

Research output: Contribution to journalArticleResearchpeer-review

10 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)1 - 18
Number of pages18
JournalJournal of Bioinformatics and Computational Biology
Volume11
Issue number1
DOIs
Publication statusPublished - 2013
Externally publishedYes

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