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The data presented here can serve as a starting point for further biomarker discovery, since the gene expression repository can be used for identifying muscle specific biomarkers that are unique or common for different types of muscles.
All data sets except for E-MTAB-874 (the raw data generated by PMI Research and Development and analyzed for this manuscript prior to their deposition in a public gene expression repository) were downloaded from Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/gds).nih.gov/gds
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The method synergizes with large-scale efforts to systematically extract differentially expressed genes in many different conditions represented in current microarray gene expression repositories, such as Oncomine [26] and GeneChaser [27].
The S-MAP approach synergizes with large-scale efforts to systematically extract differentially expressed genes in many different conditions represented in current microarray gene expression repositories, such as Oncomine [26] and GeneChaser [27].
It should be stressed, however, that the absence of a validated probe for eggplant may also indicate that the expression of this gene is Torvum-specific; alternatively, the gene may be expressed at very low levels in eggplant causing its absence in expression repositories.
Indeed, large-scale microarray experiments have recently been used to construct such powerful expression repositories [ 5- 8].
The availability of public gene expression repositories has opened up a new realm of possibilities especially for microarray data analysis.
Microarray studies fulfilling these biological criteria were collated from a survey of five major gene expression repositories (GEO [ 4], ArrayExpress [ 5], SMD[ 8], RAD [ 9] and CIBEX [ 10]).
URSA can be used to automatically annotate samples in public gene expression repositories where most samples are currently lacking tissue/cell-type-specific information.
As gene expression repositories grow, finding the experimental context in which a pathway is coregulated will be a key step in identifying previously unknown genes in a pathway.
The availability of public gene expression repositories, such as GEO [ 1] and ArrayExpress [ 2] has opened up new challenges on microarray data analyses, especially in the field of data integration and meta-analysis [ 3- 6].
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