While more detailed analysis is required to address whether genes isolated in the microarray experiments are associated with the reported visual system defects, the finding that CDH1 is specifically down-regulated in the Chrnb2−/− mutant LGN is novel and intriguing.
GPX-MEA is a gene expression database that stores MIAME-compliant [ 3] microarray experiments and associated data from a variety of human and murine macrophage cell types following treatment with pathogens and immune modulators.
Tennant championed what has proven to be a vital concept in toxicogenomics: "phenotypic anchoring," or the idea that the results of microarray experiments must be associated with particular phenotypes to be of informative value.
While there are many methods by which to develop a gene list, we have designed Literature Lab to aid in the analysis of microarray experiments which frequently associate the expression of hundreds to thousands of seemingly unrelated genes with cellular behaviors, in vivo phenotypes, or disease outcomes.
Therefore, the analysis of DNA microarray experiments investigating molecular events associated with aging and with EGb 761 treatment on global gene transcription was focused on genes implicated in these processes on a limited number of rats for each group.
This method, however, does not discriminate between individual microarray experiments with or without associated biases.
Two previous studies used microarray experiments to identify genes associated with bradyzoite [ 9] and sporozoite [ 10] developmental stages of the life cycle were used to develop "tachyzoite", "bradyzoite" and "sporozoite/oocyst" gene lists.
As a result, most microarray experiments essentially act to associate known genes with new biological paradigms, and ignore much of the data.
As there is a risk of false discovery associated with microarray experiments (see above) it is important to verify data using an independent technology platform such as RTPCR.
Despite several complications associated with microarray experiments [ 8], it still provides a faster and cost-effective method for genome-wide transcriptome study than the next generation sequencing approach.
