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

Frenkel-Morgenstern, Milana and Cohen, Ariel A. and Geva-Zatorsky, Naama and Eden, Eran and Prilusky, Jaime and Issaeva, Irina and Sigal, Alex and Cohen-Saidon, Cellina and Liron, Yuvalal and Cohen, Lydia and Danon, Tamar and Perzov, Natalie and Alon, Uri (2010) Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. Nucleic Acids Research, 38 . D508-D512 . ISSN 0305-1048. http://resolver.caltech.edu/CaltechAUTHORS:20100514-095126619

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Abstract

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/.


Item Type:Article
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URLURL TypeDescription
http://dx.doi.org/10.1093/nar/gkp808 DOIUNSPECIFIED
http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D508PublisherUNSPECIFIED
Additional Information:© 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. Received August 15, 2009; Revised December 10, 2009; Accepted September 12, 2009. The authors thank the Kahn Family Foundation and the Israel Science Foundation for the project support. M.F.M. and E.E. are supported by the Horowitz Center for Complexity Science. The authors also thank Pierre Choukroun and Michael Green for the UNIX system administration; Malka Cymbalista and Shlomit Afgin for a technical help in the website and database construction. Funding for open access charge: The Kahn Family Foundation and the Israel Science Foundation.
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Kahn Family Foundation UNSPECIFIED
Israel Science Foundation UNSPECIFIED
Horowitz Center for Complexity Science UNSPECIFIED
Record Number:CaltechAUTHORS:20100514-095126619
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20100514-095126619
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:18306
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:24 May 2010 02:53
Last Modified:26 Dec 2012 12:02

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