With regard to the initiation of shoot formation, the most characterized gene reported is ESR1, which confers, when overexpressed, cytokinin-independent shoot formation in Arabidopsis root explants [ 18].
Lettuce downy mildew is one of the most characterized gene-for-gene plant−pathogen interactions; more than 25 genes for resistance to downy mildew (Dm) have been identified, most of which are dominant genes that confer resistance in a gene-for-gene manner (Crute and Johnson 1976; Farrara et al. 1987; Ilott et al. 1989; Michelmore et al. 2009).
Indeed, the epichloid biosynthetic gene clusters show a level of complexity somewhat higher than that of most characterized gene clusters in other fungi, with "mini-clusters" of genes and MITEs separated by nested autonomous retrotransposons and DNA transposons (Young et al. 2006; Fleetwood 2007).
This is in sharp contrast to microarray analysis, where expression profile and scope of analysis is predetermined by target design typically employing a limited number of the most commonly characterized genes [17].
While the expression of these and other genes clearly distinguish HVC and Shelf, most currently characterized genes do not differentiate molecularly the Shelf from the rest of the nidopallium, indicating that the properties of the Shelf resemble closely those of this general pallial subdivision.
This gene is tightly co-expressed with C4H and most other characterized genes involved in the general phenylpropanoid pathway (Additional File 4).
We expect these novel genes to be of functional significance since new genes tend to display accelerated sequence and structural changes towards neo-functionalization [ 1], and most newly characterized genes from other species have been shown to be characteristically functional [ 35, 56].
Moreover, most of the characterized genes showed similar expression patterns to that already described in the literature, which strengthens the reliability of the data obtained by using microarrays [ 33]Expression levels of four MADS-box genes (OsMADS18, 22, 26 and 27) were up regulated by more than two folds in response to cold and dehydration stress treatments.
This suggests either a characterization or mutational bias (characterized genes, most of which have been identified through mutant alleles, are significantly longer in both ORF and UIR than uncharacterized genes, data not shown), or, more likely in our view, genuine enrichment for mutant phenotypes.
Manohar et al. proposed that overexpression of MYCN, the most widely characterized gene associated with poor outcome of neuroblastoma, resulted in increased drug resistance and expression of MRP1, suggesting that MRP1 may be a MYCN target gene involved in the drug-resistance phenotype of neuroblastoma [ 16].
