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Rhodes, D. R. et al. ONCOMINE: a cancer microarray database and integrated data-mining platform.
Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D et al. ONCOMINE: a cancer microarray database and integrated data-mining platform.
To better exploit the increasing amount of data available from genomic sequencing, microarray database and RNAseq, time-efficient methods for identification and validation of candidate genes are needed.
The expression data for AtNCX4 (At1g55720) was not available in the microarray database and hence could not be included in expression analysis under different stresses.
Data was Log2 transformed and normalized using Lowess subgrid normalization in GeneTraffic Microarray Database and Analysis System (Iobion Informatics).
Data was uploaded to the GeneTraffic Bioinformatics server with GeneTraffic microarray database and analysis software (Stratagene/Agilent Technologies, La Jolla, CA) for raw image analysis, filtering and processing.
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As a matter of fact, this method can be used to retrieve data from public microarray databases and perform comparisons at the pathway level.
Thus, we propose to store PSs as an additional experimental annotation in the microarray databases and implement methods using pathway signatures to query experiments in public databases and concurrent analyses of subsets of experiments.
PS generated using sBEFs can be useful as "barcodes" to classify experiments in microarray databases and clustering of sBEFs can be a useful way to query experiments in databases according to their similarity at a pathway level.
Relationships between MYBBP1A expression levels and breast cancer progression were examined using patient microarray databases and tissue microarrays.
Issues of experimental reproducibility have become increasingly important with the advent of microarray databases and repositories (e.g. ArrayExpress [ 1], GEO [ 3]), given the potential they offer for cross-experimental comparison and data mining.
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