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PROTICdb: a plant 2-D PAGE database

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PROTICdb: a plant 2-D PAGE database

Project team

Olivier Langella, Pierre Montalent, Guy Decoux, Thierry Balliau, Michel Zivy & Johann Joets

Project previous members

Thomas Leboucher, Gwenn Houel, Luc Moreau, Luc Negroni, Delphine Vincent, Johan Bordeau, Hélène Denos

Project collaborators

Hélène Ferry-Dumazet, Antoine de Daruvar (CBIB, Bordeaux, France), Céline Lalanne, Christophe Plomion (INRA, BIOGECO, Cestas, France)


PROTICdb is a web-based application mainly designed to store and analyse plant proteome data obtained by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry (MS). The objectives of PROTICdb are twofold: 1/ to store, track and query information related to a proteomic experiment, i.e. from tissue sampling to protein identification via the quantitative measurement of protein accumulation by image analysis, 2/ to integrate information from the user own expertise or other sources into a knowledge base, and support the interpretation of the data (e.g. function, post-translational modification, allelic variant determination...). The insertion of data into the relational database of PROTICdb is achieved either by direct upload of output of widely used image analysis and MS identification or by filling web forms. 2-D PAGE annotated maps can be displayed, queried and compared through a graphical interface. Links to external databases are available. Quantitative data can be easily exported into a tabulated format for statistical analyses. PROTICdb is based on the Oracle or the PostgreSQL DataBase Management System (DBMS).

News

PROTICdb 1.2 is now available.
This new version includes an advanced query builder tool. It is now possible to search for protein, sample, gel, ... according to a large number of criteria. A flash tutorial is provided, describing the main functionalities of this new tool.
The gel browser was improved (faster gel image loading).
Poster
The 7th Sienna Meeting from Genome to Proteome 2006 poster is available here.

PROTICdb demo

Visit the local PROTICdb database.

 

PROTICdb availability

The PROTICdb package (empty database) is available for free here.

 

Support

please contact us at Cette adresse email est protégée contre les robots des spammeurs, vous devez activer Javascript pour la voir. (without 'nospam' !)

 

Reference

Ferry-Dumazet H, Houel G, Montalent P, Moreau L, Langella O, Negroni L, Vincent D, Lalanne C, de Daruvar A, Plomion C, Zivy M, Joets J. PROTICdb: a web-based application to store, track, query, and compare plant proteome data. Proteomics. (2005) May;5(8):2069-81