The majority of the 17 confirmed NMD targets (defined as UPF1 and translation-dependent) have not been previously identified by microarray studies of UPF1 dependent gene expression in mammals [ 15, 29- 32, 51, 69], indicating the complementarity of proteomic and transcriptomic analyses.
A large number of BR-regulated genes have been identified by microarray studies; most of the known BR-regulated genes are associated with plant growth and development, such as cell wall modification, cytoskeleton formation, and hormone synthesis [ 4].
The suitability of this strategy is underscored by a recent microarray study of transporters in the mouse intestine [ 51].
We can also determine the kinetics of transcription by combining the DNA microarray study of nascent mRNAs with that of existing mRNAs.
1) Molecular apocrine-genes: Top ranking genes in molecular apocrine-signature, based on their fold-change for gene expression, were extracted from a meta-analysis microarray study of 186 ER- breast tumors by Teschendorff et al. and an expression microarray study of ER- cell lines by Doane et al. [ 4, 5].
Those observations have been supported in recent years by microarray studies showing elevated expression of a broad spectrum of IFN-inducible genes in peripheral blood cells of many lupus patients (the 'IFN signature').
The procell death gene BNIP3 has been identified by microarray studies as a target of SIM2s repression.
While tumor subtypes still segregate primarily by expression of estrogen receptor (ER), p53, and ErbB2, the 'intrinsic' genetic signatures as defined by microarray studies are more informative classifiers of tumor subtypes.
Many new bioinformatics approaches are being developed to support the analysis of the large amount of data generated by microarray studies.
An example of this particular context would be in the evaluation of regulons elucidated by microarray studies, where both related and unrelated target genes may be part of a downstream battery of genes under the control of a particular transcription factor.
