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The LIFEdb functional genomics resource

© dkfz.de

Based on the ORF-collection of the division Molecular Genome Analysis and the international ORFeome collaboration (ORFeome Tools), we generate tools for the expression of encoded proteins. These are systematically exploited to determine the subcellular localization of these proteins.

We have implemented the LIFEdb infostructure to disseminate information on the ORFeome resource (e.g., clone quality metrics) and on the utilization of this resource towards a functional annotation of encoded proteins (genes, subcellular localization data). The concept was originally described in Simpson (2000).

This project is a collaboration with the EMBL-Heidelberg (Pepperkok Team) and the UCD Dublin (Simpson Group). Data presented has been published e.g., in Simpson (2012), Laketa (2007), Neubrand (2005), Starkuviene (2004), Simpson (2001), Pepperkok (2001). LIFEdb has been described in Mehrle (2006), Bannasch (2004).

Database

The data is available here. The table provides several sort options as well as a number of links.

  • GeneSymbol -> ENTREZ Gene symbol of the respective genes
  • ParentCloneID -> information of the respective proteins (e.g., GO-term) - under construction
  • EntryCloneID -> information on the quality and availability of clones through the ORFeome Collaboration - under construction
  • NCBI -> link to sequence in EMBL/GenBank/DDBJ database
  • UCSC -> link to mapping position in the UCSC genome browser
  • ProteinLocalization -> experimentally determined localization of encoded proteins
  • ImageFile -> link to higher resolution microscopic images of GFP-tagged fusion proteins (N- and C-terminal tagging)

(The presentation of data has been realized by Oliver Heil)

Controls

In order to evaluate potential effects of GFP on the localization of fusion proteins we performed two types of assays.

1. We analyzed the sub-cellular localization of several fusion proteins in Vero (monkey kidney) and HeLa (human cervix carcinoma) cells (-> Cell Line Control). In every case the results obtained with the two cell lines were identical, demonstrating that the sub-cellular localization in most cases will be independent on the cell line used in the analysis. Nevertheless, we will use cell lines of different origin (e.g. hepatocytes, neuronal cells) for future experiments.

2. We analyzed the sub-cellular localization of several known proteins with predicted or known localization (-> Known Protein Control). In most cases, the localization was verified - independent of the GFP fusion part.

We conclude that the sub-cellular localization of the proteins is mostly not affected by the GFP fusion part. Since the relative orientation of the two fusion parts (ORF vs. GFP) in many cases does impact localization we always determine the localization of N- and C-terminal fusions (GFP-ORF and ORF-GFP).

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