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Searching the lists of differentially expressed genes from twelve honey bee brain microarray experiments published to date (see Methods), revealed that the only condition that affects more than half of these genes (DJ-1, SUMO-1, UBC7) is manganese treatment [25] (Table 2).
We compiled data from four microarray experiments published between 2001 and 2005 [ 22- 26, 26] that compared gene expression in infected and naïve D. melanogaster and characterized genes as up-regulated or down-regulated.
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Just over half of the studies fulfilled the MIAMI criteria (Minimum Information About Microarray Experiment, published guidelines on the design, conducting, analysis and reporting of the microarray experiments) [ 7].
Finally, the list of differentially expressed genes generated from analysis of the RNA-seq data was compared to results from a comparable microarray experiment published by our group [ 20].
To this end, biannual updates of the database will be conducted when new microarray experiments are published or sufficient arrays from other platforms becomes available for GCA.
Details of microarray experiment were published previously [ 10].
Data for the four biological replicates of each of B. napus 1 and B. napus 2 was obtained from the Agilent 60-mer oligonucleotide microarray experiment already published by Trick et al.[ 41] and available from the GEO repository, accession number GSE15915.
The HESI experiments, published in the March 2004 toxicogenomics issue of EHP, showed the patterns of gene expression detected in microarray experiments can give insight into biologic mechanisms, and can even distinguish between damage found in different cell types.
Sequences derived from the microarray experiments and the published flower-related genes were used to design primers.
PubLiME (Published Lists of Microarray Experiments) is a repository of published cancer related gene expression signatures (http://bio.ifom-ieo-campus.it/Publime).it/Publime
Six of the ten targets have data from the University of Michigan PRC showing that they were differentially expressed in published microarray experiments.
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