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. 2006 Jan 1;34(Database issue):D415-8.
doi: 10.1093/nar/gkj139.

The LIFEdb database in 2006

Alexander Mehrle  1 , Heiko Rosenfelder, Ingo Schupp, Coral del Val, Dorit Arlt, Florian Hahne, Stephanie Bechtel, Jeremy Simpson, Oliver Hofmann, Winston Hide, Karl-Heinz Glatting, Wolfgang Huber, Rainer Pepperkok, Annemarie Poustka, Stefan Wiemann
Affiliations

Affiliation

  • 1 Division Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany. a.mehrle@dkfz.de

The LIFEdb database in 2006

Alexander Mehrle et al. Nucleic Acids Res. .
. 2006 Jan 1;34(Database issue):D415-8.
doi: 10.1093/nar/gkj139.

Authors

Alexander Mehrle  1 , Heiko Rosenfelder, Ingo Schupp, Coral del Val, Dorit Arlt, Florian Hahne, Stephanie Bechtel, Jeremy Simpson, Oliver Hofmann, Winston Hide, Karl-Heinz Glatting, Wolfgang Huber, Rainer Pepperkok, Annemarie Poustka, Stefan Wiemann

Affiliation

  • 1 Division Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany. a.mehrle@dkfz.de

Abstract

LIFEdb (http://www.LIFEdb.de) integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an updated user interface with enhanced query capabilities, (ii) a configurable output table and the option to download search results in XML, (iii) the integration of data from cell-based screening assays addressing the influence of protein-overexpression on cell proliferation and (iv) the display of the relative expression ('Electronic Northern') of the genes under investigation using curated gene expression ontology information. LIFEdb enables researchers to systematically select and characterize genes and proteins of interest, and presents data and information via its user-friendly web-based interface.

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Figures

Figure 1

Figure 1

The new LIFEdb web-interface. Users…

Figure 1

The new LIFEdb web-interface. Users can choose between several search forms and are…

Figure 1
The new LIFEdb web-interface. Users can choose between several search forms and are able to customize the output to display features of interest (left). All search results can be downloaded in XML (right).
Figure 2

Figure 2

Presentation of new data in…

Figure 2

Presentation of new data in LIFEdb. ‘Electronic Northern’ data are shown color-coded indicating…

Figure 2
Presentation of new data in LIFEdb. ‘Electronic Northern’ data are shown color-coded indicating the relative over-representation (red) or under-representation (blue) of the displayed genes in several tissues. Details are shown by moving the mouse over the respective tissue (left). Results of S-Phase assays are shown in a separate column with an extra window ploting the Z-scores of the single experiments for each protein (right) and the statistical significance of the result (P-value).
See this image and copyright information in PMC

References

    1. Bannasch D., Mehrle A., Glatting K.H., Pepperkok R., Poustka A., Wiemann S. LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system. Nucleic Acids Res. 2004;32:D505–D508. - PMC - PubMed
    1. Wiemann S., Arlt D., Huber W., Wellenreuther R., Schleeger S., Mehrle A., Bechtel S., Sauermann M., Korf U., Pepperkok R., et al. From ORFeome to biology: a functional genomics pipeline. Genome Res. 2004;14:2136–2144. - PMC - PubMed
    1. del Val C., Mehrle A., Falkenhahn M., Seiler M., Glatting K.H., Poustka A., Suhai S., Wiemann S. High-throughput protein analysis integrating bioinformatics and experimental assays. Nucleic Acids Res. 2004;32:742–748. - PMC - PubMed
    1. Simpson J.C., Wellenreuther R., Poustka A., Pepperkok R., Wiemann S. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep. 2000;1:287–292. - PMC - PubMed
    1. Arlt D., Huber W., Schmidt C., Liebel U., Rosenfelder H., Bechtel S., Mehrle A., Bannasch D., Schupp I., Seiler M., et al. Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle. Cancer Res. 2005;65:7733–7742. - PubMed

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