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.
Data was Log2 transformed and normalized using Lowess subgrid normalization in GeneTraffic Microarray Database and Analysis System (Iobion Informatics).
Data were stored and normalized in the GeneTraffic Microarray Database and Analysis System (Iobion Informatics, La Jolla, CA).
It was thus possible to link the procedure to a microarray database and analysis platform and make it freely available.
Locus identifiers were submitted to the Genevestigator Arabidopsis thaliana microarray database and analysis toolbox [ 27] at, where they were assayed against 1434 developmental and tissue-specific Arabidopsis microarray experiment results [ 35- 38].
The quantified data files were transferred to a GeneTraffic microarray database and analysis system (Iobion Informatics, Stratagene) with a complete annotation of experiments based on the current MIAME standards for microarray experiments.
This analysis has provided a set of candidate marker genes, which were further investigated to define their tumour specificity using Genevestigator V3, a web-based microarray database and analysis system [ 14].
To obtain an estimate of the relative levels of AtRaptor1A and AtRaptor1B in the signal seen in Fig. 6A, AtRaptor1A and AtRaptor1B locus IDs were used to query the Genevestigator Arabidopsis thaliana Microarray Database and Analysis Toolbox [ 27].
RETINOBASE is a microarray relational database, analysis and visualization system that allows simple yet powerful queries to retrieve information about gene expression in retina.
The processed and loess-normalized data as well as detailed experimental information according to MIAME [ 43] were stored in the in-house microarray database for further analysis [ 44].
To provide a foundation for our functional analyses, we performed an integrated analysis for our previous mRNA microarray database and IPA-predicted miRNA target analysis (Additional file 2: Table S2).
