Transcriptome
Expression data are available to query either by :
- accessing the GnpArray database;
- or by selecting expression data tracks (for example, expression levels) when available as annotations in the GnpGenome database (when data are available, a link can be done between the GnpGenome and GnpArray databases).
Some data are available on our public web site, while other are available only on our private web site in the frame of projects before publication.
GnpArray is the module of the INRA URGI information system dedicated to microarray data
The GnpArray database allows the storage of various expression data:
- macroarray data
- microarray data (two-colors cDNA arrays)
- very-large oligos arrays
- coming from high throughput transcriptomics platform or laboratories
The most challenging issue for GnpArray is to deliver a powerful tool to biologist, enabling to simplify the analysis of microarray data.
The database is built around the concept of gene list, as a result of the analysis of a set of hybridizations.
The textual web interface allows an exploration of the content of the database or queries on differents aspects :
- project
- experiment
- hybridization
- arrays
- gene list
- contacts
Special care have been done on the quality of the available information, according to the extracts preparation, tissues, protocols and experimental design.
The interface offers the possibility to download raw data from one experiment to perform complex analysis, and see data summary for database detail content.
On the restricted-access web site, there are more projects (Genoplante or INRA projects) on Arabidopsis, Rapeseed, Rice, Celery have already been inserted in the database.
Tools have been built in order to simplify the submissions : exchange format, automatic insertion in the database of submitted data with checking of the data.
Creation date: 28 Apr 2010
eZ PublishPublication supervisor: A-F. Adam-Blondon
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