In order to control the hybridization step, the raw data were evaluated for their accuracy based on intensity and expression box plots, MA plots and spike-in controls.
A variety of other tools can be used to characterize variants, including analysis of protein-DNA interactions and reporter gene expression (Box 1).
Expression box plots across the nineteen tissues having at least one promoter specific to brain, is shown in Figure 3E and 3F for human GRIA2 and mouse Gria1 genes, respectively.
Although these patient-derived cells recapitulate some molecular features of the disease, including the epigenetic silencing of FXN expression (Box 2), they do not develop spontaneous phenotypic characteristics of FRDA (Rotig et al., 1997; Sturm et al., 2005).
To assess the similarity of our Ward's clusters with Kapatai's subgroups, expression box plots of 5 cell cycle markers (E2F1, E2F2, E2F3, PCNA, CCNE1), 5 rod photoreceptor markers (RHO, CNGB1, ROM1, PDE6G, CNGA1) and 5 cone photoreceptor markers (PDE6C, PDE6H, GNAT2, OPN1SW, ARR3) were made (Fig. 1C) (Sharon et al., 2002).
(D) Expression box plots for McEvoy groups 1 4 of 5 cell cycle markers (E2F1, E2F2, E2F3, CCNE1, PCNA, top row), 5 rod photoreceptor markers (RHO, SAG, CNGB1, PDE6G, CNGA1, 2nd row), 5 cone photoreceptor markers (PDE6C, PDE6H, GNAT2, OPN1SW, ARR3, 3rd row), and 5 immune cell markers (CD2, CD4, CD33, CD34, CD14, bottom row).
Lines signify median expression; boxes extend to 25 and 75 percentiles while whiskers extend to the 1.5*IQR.
Box-whisker parameters: horizontal bar indicates median expression, the box indicates interquartile range; whiskers represent the range.
The independently transcribed strategy dominates in the expression of box H/ACA snoRNA genes, whereas most of the box C/D snoRNA genes are intron-encoded.
(A ) Schematic of a worm depicting the region imaged for axonal expression (pink box ).
The p-value was utilized to rank genes in expression clusters (Box F).
