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Dynamic Proteomics


NAR Molecular Biology Database Collection entry number 1293
Frenkel-Morgenstern, M.1, Cohen, A.A.1 Geva-Zatorsky, N.1 Eden, E.1 Prilusky, J.2, Issaeva, I.1, Sigal, A.3, Cohen-Saidon, C.1 Liron, Y.1 Cohen, L.1 Danon, T.1 Perzov, N.1, and Alon, U.1
1Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, 76100, Israel
2Bioinformatics Unit, Weizmann Institute of Science, Rehovot, 76100, Israel
3Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA

Database Description

The Dynamic Proteomics database is a compendium of endogenously YFP-tagged human proteins and their time-lapse microscopy movies. These movies show the protein dynamics in space and in time in individual living human cancer cells in response to an anti-cancer drug, camptothecin.
Recent advances in molecular cell biology allow tracking the levels and locations of over a thousand proteins in individual living human cancer cells over time using a library of annotated reporter cell clones (LARC). This library was created by Cohen et al. to study proteome dynamics in individual living cells of a human lung carcinoma cell-line treated with the anti-cancer drug, camptothecin [1]. Here, we report the Dynamic Proteomics database for the proteins studied by Cohen et al [1]. Each cell-line clone in the LARC library has a protein tagged with yellow fluorescent protein (eYFP or Venus), expressed from its endogenous chromosomal location and under its natural regulation [2-4]. The Dynamic Proteomics interface facilitates searches for genes of interest as well as downloads of protein fluorescent movies and alignments of protein dynamics following drug addition [1]. Each protein in the database is displayed with a detailed annotation, its cDNA sequence, fluorescent images and movies obtained by time-lapse microscopy. The protein dynamics in the database represent a quantitative trace of the tagged-protein fluorescence levels in the nucleus and cytoplasm produced by image analysis of the movies over time [1-4]. Furthermore, a sequence analysis tool provides a search and comparison of up to 50 input DNA sequences with all cDNAs in the library. The raw movies presented in the database may be useful as a benchmark for developing image analysis tools for individual-cell dynamic proteomics.

Recent Developments

Dynamic Proteomics (www.dynamicproteomics.net) currently collects 2,191 clones or 1,144 unique YFP-tagged proteins in human cells. Recent developments to the database include an addition of new search parameters (i.e. Chromosome Number and Alternative Names) with a possibility to download sequences of all clones in the Fasta format from any Search Results page. In addition, annotation of the clones and their sequences are updated on a regular basis.

Acknowledgements

We thank the Kahn Family Foundation, the Israel Science Foundation and the Horowitz Center for Complexity Science for project support.

References

1. Cohen, A.A., Geva-Zatorsky, N., Eden, E., Frenkel-Morgenstern, M., Issaeva, I., Sigal, A., Milo, R., Cohen-Saidon, C., Liron, Y., Kam, Z., Cohen, L., Danon, T., Perzov, N., and Alon, U. (2008) Dynamic Proteomics of Individual Cancer Cells in Response to a Drug. Science 322(5907), 1511-6
2. Sigal, A., Danon, T., Cohen, A., Milo, R., Geva-Zatorsky, N., Lustig, G., Liron, Y., Alon, U., and Perzov, N. (2007) Generation of a fluorescently labeled endogenous protein library in living human cells. Nat. Protoc. 2, 1515-27
3. Sigal, A., Milo, R., Cohen, A.A., Geva-Zatorsky, N., Klein, Y., Liron, Y., Rosenfeld, N., Danon, T., Perzov, N., and Alon, U. (2006) Variability and memory of protein levels in human cells. Nature 444, 643-646
4. Sigal, A., Milo, R., Cohen, A.A., Geva-Zatorsky, N., Klein, Y., Alaluf, I., Swerdlin, N., Perzov, N., Danon, T., Liron, Y., Raveh, T., Carpenter, A.E., Lahav, G., and Alon, U. (2006) Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nature Methods 3, 525-531


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