Accordingly, this system can be adopted to analyze co-regulation in microarray gene expression databases, such as AtGenExpress [ 48] and Genevestigator [ 49].
The proposed system can be applied to analyze co-regulation in microarray gene-expression databases such as COXPRESdb [ 40] and Genevestigator [ 41].
In silico microarray-based co-expression databases such as ATTED-II [ 15] and CressExpress [ 16] are powerful tools for elucidating metabolic networks in Arabidopsis.
This is made possible thanks to the recent publications of several large microarray datasets in gene expression databases, such as the Gene Expression Omnibus (GEO, Barrett et al., 2005) An important outcome of the analysis is that, in spite of the large number of samples, there is no statistical evidence that complex methods outperform the simplest BC prognostication techniques.
Contact: [email protected] The most common approach for searching in microarray databases is based on metadata such as annotations and descriptions of the arrays and genes (Zhu et al., 2008).
Currently, data from thousands of studies on all of the major microarray platforms are publicly available in databases such as ArrayExpress [ 8] and Gene Expression Omnibus (GEO) [ 9].
The presence of a large number of probe sets on the MOE430 2.0 GeneChip that detect antisense transcripts for an mRNA that is probed by a complementary probe set [see Additional file 3] makes it possible to analyze the regulation of SAS transcript pairs by using the large number of Affymetrix microarray data sets deposited in public databases such as Gene Expression Omnibus (GEO) or ArrayExpress.
Additionally to the repositories storing microarray data such as ArrayExpress and GEO (3), more specialized databases have become available; for example, databases such as MDB (57) and M3D (58) collected microarray data and uniformly pre-processed it, but do not provide data analysis and integration.
The microarray data from many experiments are uploaded to public databases such as GEO (Gene Expression Omnibus) [38], for other scientists to use in their research.
To gain insight into their probable role in both biotic and abiotic stress response, we analyzed the expression of histone chaperones under such stress conditions using publicly available microarray databases.
