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Nucleic Acids Research Advance Access published online on October 9, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp808
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells

Milana Frenkel-Morgenstern1,*, Ariel A. Cohen1, Naama Geva-Zatorsky1, Eran Eden1, Jaime Prilusky2, Irina Issaeva1, Alex Sigal3, Cellina Cohen-Saidon1, Yuvalal Liron, Lydia Cohen1, Tamar Danon1, Natalie Perzov1 and Uri Alon1

1Molecular Cell Biology Department, 2Bioinformatics Unit, Weizmann Institute of Science, Rehovot, 76100, Israel and 3Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA

*To whom correspondence should be addressed. Tel: +972523450459; Fax: +34912246976; Email: milana.frenkel{at}weizmann.ac.il

Received August 15, 2009. Revised December 10, 2009. Accepted September 12, 2009.

Recent advances allow tracking the levels and locations of a thousand proteins in individual living human cells over time using a library of annotated reporter cell clones (LARC). This library was created by Cohen et al. to study the proteome dynamics of a human lung carcinoma cell-line treated with an anti-cancer drug. Here, we report the Dynamic Proteomics database for the proteins studied by Cohen et al. Each cell-line clone in LARC has a protein tagged with yellow fluorescent protein, expressed from its endogenous chromosomal location, under its natural regulation. The Dynamic Proteomics interface facilitates searches for genes of interest, downloads of protein fluorescent movies and alignments of dynamics following drug addition. Each protein in the database is displayed with its annotation, cDNA sequence, fluorescent images and movies obtained by the time-lapse microscopy. The protein dynamics in the database represents a quantitative trace of the protein fluorescence levels in nucleus and cytoplasm produced by image analysis of movies over time. Furthermore, a sequence analysis provides a search and comparison of up to 50 input DNA sequences with all cDNAs in the library. The raw movies may be useful as a benchmark for developing image analysis tools for individual-cell dynamic-proteomics. The database is available at http://www.dynamicproteomics.net/.

Present address: Milana Frenkel-Morgenstern, CNIO, C/Melchor Fernandez Almagro, 3, Madrid, E-28029 Spain.


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