First, we inspected the expression profiles of the Vitis vinifera stilbene synthase gene family [ 19] throughout our experimental design.
To examine which of the miRNA family members are more abundantly expressed in rice seedlings, we inspected the expression profile of known miRNAs in untreated seedlings (control library) based on their sequence frequencies.
After choosing samples in the "Sample Tree", the user could visually inspect the expression profile through a bar chart, and add mean expression for similar samples (i.e. samples in the same group) if needed.
We chose a straightforward approach of manually inspecting gene expression profiles that were generated on the basis of the original or the modified chip definition.
The expression profile of each gene can also be visually inspected in a graphical format at this site.
Inspecting the profile of differences in expression, one realizes that besides the 3,030 genes exclusively expressed in anthers, 1,455 genes have a 10-fold higher abundance in anthers than in leaves indicating strong preferential expression (Fig. 6B, inset; Supplementary Information 1).
When inspecting the metabolite profiling data, it is clear that the discussion of the results is rather superficial.
Based on all information available, we selected genes from this list and inspected their exon expression profile manually.
To this end, two independent cohorts of 140 (training set) and 78 (test set) pediatric patients with ALL/MLL+, AML/MLL+, ALL/MLL- and AML/MLL- have been inspected using gene expression profiling.
To avoid omitting profiles with a low overall expression level but with a significant peak, the filtered expression profiles were manually inspected; in the presence of a significant peak, the profile was considered to be highly expressed and added to the set.
