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CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform.

Gagnot S, Tamby JP, Martin-Magniette ML, Bitton F, Taconnat L, Balzergue S, Aubourg S, Renou JP, Lecharny A, Brunaud V - Nucleic Acids Res. (2007)

Bottom Line: CATdb contains the results of 53 projects including 1724 hybridized samples distributed between 13 different organs, 49 different developmental conditions, 45 mutants and 63 environmental conditions.All the data contained in CATdb can be downloaded from the web site and subsets of data can be sorted out and displayed either by keywords, by experiments, genes or lists of genes up to 100.CATdb gives an easy access to the complete description of experiments with a picture of the experiment design.

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche en Génomique Végétale (URGV)-UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France.

ABSTRACT
CATdb is a free resource available at http://urgv.evry.inra.fr/CATdb that provides public access to a large collection of transcriptome data for Arabidopsis thaliana produced by a single Complete Arabidopsis Transcriptome Micro Array (CATMA) platform. CATMA probes consist of gene-specific sequence tags (GSTs) of 150-500 bp. The v2 version of CATMA contains 24 576 GST probes representing most of the predicted A. thaliana genes, and 615 probes tiling the chloroplastic and mitochondrial genomes. Data in CATdb are entirely processed with the same standardized protocol, from microarray printing to data analyses. CATdb contains the results of 53 projects including 1724 hybridized samples distributed between 13 different organs, 49 different developmental conditions, 45 mutants and 63 environmental conditions. All the data contained in CATdb can be downloaded from the web site and subsets of data can be sorted out and displayed either by keywords, by experiments, genes or lists of genes up to 100. CATdb gives an easy access to the complete description of experiments with a picture of the experiment design.

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Related in: MedlinePlus

Results of a query of CATdb with a list of gene identifiers. From the left to the right, columns are the probe name, the corresponding gene name, the differential expression log2-ratio in all the different projects contained in CATdb. The differential expression is colour coded in green, red or black corresponding to the levels of log2-ratio in each swap analysed, and in grey for missing values. The correspondence between the colours and the log2-ratio values is given in a bar above the table. By rolling over a cell of the table, as shown by the arrows, one may display more information about either the projects, dye-swaps or expression values, depending on the selected cell.
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Figure 3: Results of a query of CATdb with a list of gene identifiers. From the left to the right, columns are the probe name, the corresponding gene name, the differential expression log2-ratio in all the different projects contained in CATdb. The differential expression is colour coded in green, red or black corresponding to the levels of log2-ratio in each swap analysed, and in grey for missing values. The correspondence between the colours and the log2-ratio values is given in a bar above the table. By rolling over a cell of the table, as shown by the arrows, one may display more information about either the projects, dye-swaps or expression values, depending on the selected cell.

Mentions: CATdb is a free web resource available at the following address: http://urgv.evry.inra.fr/CATdb. There are four different possibilities to select a subset of data. First, a list of all the available projects is displayed by default. A limited list may be obtained by querying the database by keywords. These keywords are searched for in both the description of the projects, i.e. coordinator name, experiment type, environmental or treatment factor, mutant name and the description of the samples, i.e. plant species, organs, treatments and type of arrays. Second, an experiment name may be selected in the project table giving access to the entire description of the corresponding experiment including a picture of the experiment design (Figure 1A). The swap column gives access to all the results of hybridizations organized by dye-swap for the selected experiment. Normalized log2 intensities, log2-ratios and Bonferroni P-values are given for each probe (Figure 1B). As this table is rather large, only the probes with statistically significant differential expression for a dye-swap are displayed on the screen. Nevertheless, the complete table may be downloaded as a tabulated text file. Third, from either a gene or a probe accession, one may obtain signal intensities and Bonferroni P-value for all the dye-swaps processed in all the projects (Figure 2). Furthermore, data may be sorted by project, organ or any statistics. For each probe, the associated features, i.e. sequence, quality of PCR results and if applicable, the tagged gene with functional annotation, are given. Fourth, from a list of genes or probe accessions, one obtains a table containing, for each selected probe, the log2-ratios for all the projects (Figure 3). The coloured display of the differential expression allows the comparison of the data for a list of up to 100 genes.Figure 1.


CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform.

Gagnot S, Tamby JP, Martin-Magniette ML, Bitton F, Taconnat L, Balzergue S, Aubourg S, Renou JP, Lecharny A, Brunaud V - Nucleic Acids Res. (2007)

Results of a query of CATdb with a list of gene identifiers. From the left to the right, columns are the probe name, the corresponding gene name, the differential expression log2-ratio in all the different projects contained in CATdb. The differential expression is colour coded in green, red or black corresponding to the levels of log2-ratio in each swap analysed, and in grey for missing values. The correspondence between the colours and the log2-ratio values is given in a bar above the table. By rolling over a cell of the table, as shown by the arrows, one may display more information about either the projects, dye-swaps or expression values, depending on the selected cell.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238931&req=5

Figure 3: Results of a query of CATdb with a list of gene identifiers. From the left to the right, columns are the probe name, the corresponding gene name, the differential expression log2-ratio in all the different projects contained in CATdb. The differential expression is colour coded in green, red or black corresponding to the levels of log2-ratio in each swap analysed, and in grey for missing values. The correspondence between the colours and the log2-ratio values is given in a bar above the table. By rolling over a cell of the table, as shown by the arrows, one may display more information about either the projects, dye-swaps or expression values, depending on the selected cell.
Mentions: CATdb is a free web resource available at the following address: http://urgv.evry.inra.fr/CATdb. There are four different possibilities to select a subset of data. First, a list of all the available projects is displayed by default. A limited list may be obtained by querying the database by keywords. These keywords are searched for in both the description of the projects, i.e. coordinator name, experiment type, environmental or treatment factor, mutant name and the description of the samples, i.e. plant species, organs, treatments and type of arrays. Second, an experiment name may be selected in the project table giving access to the entire description of the corresponding experiment including a picture of the experiment design (Figure 1A). The swap column gives access to all the results of hybridizations organized by dye-swap for the selected experiment. Normalized log2 intensities, log2-ratios and Bonferroni P-values are given for each probe (Figure 1B). As this table is rather large, only the probes with statistically significant differential expression for a dye-swap are displayed on the screen. Nevertheless, the complete table may be downloaded as a tabulated text file. Third, from either a gene or a probe accession, one may obtain signal intensities and Bonferroni P-value for all the dye-swaps processed in all the projects (Figure 2). Furthermore, data may be sorted by project, organ or any statistics. For each probe, the associated features, i.e. sequence, quality of PCR results and if applicable, the tagged gene with functional annotation, are given. Fourth, from a list of genes or probe accessions, one obtains a table containing, for each selected probe, the log2-ratios for all the projects (Figure 3). The coloured display of the differential expression allows the comparison of the data for a list of up to 100 genes.Figure 1.

Bottom Line: CATdb contains the results of 53 projects including 1724 hybridized samples distributed between 13 different organs, 49 different developmental conditions, 45 mutants and 63 environmental conditions.All the data contained in CATdb can be downloaded from the web site and subsets of data can be sorted out and displayed either by keywords, by experiments, genes or lists of genes up to 100.CATdb gives an easy access to the complete description of experiments with a picture of the experiment design.

View Article: PubMed Central - PubMed

Affiliation: Unité de Recherche en Génomique Végétale (URGV)-UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France.

ABSTRACT
CATdb is a free resource available at http://urgv.evry.inra.fr/CATdb that provides public access to a large collection of transcriptome data for Arabidopsis thaliana produced by a single Complete Arabidopsis Transcriptome Micro Array (CATMA) platform. CATMA probes consist of gene-specific sequence tags (GSTs) of 150-500 bp. The v2 version of CATMA contains 24 576 GST probes representing most of the predicted A. thaliana genes, and 615 probes tiling the chloroplastic and mitochondrial genomes. Data in CATdb are entirely processed with the same standardized protocol, from microarray printing to data analyses. CATdb contains the results of 53 projects including 1724 hybridized samples distributed between 13 different organs, 49 different developmental conditions, 45 mutants and 63 environmental conditions. All the data contained in CATdb can be downloaded from the web site and subsets of data can be sorted out and displayed either by keywords, by experiments, genes or lists of genes up to 100. CATdb gives an easy access to the complete description of experiments with a picture of the experiment design.

Show MeSH
Related in: MedlinePlus