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Interestingly, a statistically significant proportion of genes shown to be differentially expressed mapped to chromosomes described to be recurrently altered in NBTs, chromosomes 1 and 17 [ 17].
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The expressed activities mapped to KEGG pathways were analyzed to identify metabolic activities that are uniquely expressed only in aspen or L. bicolor.
In WED-immunized zebrafish liver, 21 differentially expressed genes mapped to various TLR pathways, including the TLR5, TLR8, TLR18 and TLR21 subcategories, which are not only expressed on the outer membrane of immune cells but also on endosome-lysosome membranes.
In looking at differentially expressed genes mapped to canonical pathways (Table 3), we noted that the overlap between results of the non-parametric method and SAM was much higher (∼70% as opposed to 45 55% in Figure 5).
€Number of differentially expressed sequences mapped to a given signalling pathway.
Several of the differentially expressed genes mapped to the polyamine biosynthetic and associated metabolic pathways.
These 22,144 differentially expressed tags mapped to 3,027 unigenes using SeqMap [ 30].
In addition to gene24414, only 3 other genes among the 617 differentially expressed genes mapped to the γ-decalactone content locus.
A statistically significant portion of the differentially expressed genes mapped to chromosome 1, (16.7% P < 0.0001); chromosomal regions 1p36-p34, 1p21-p13 and 1q21.2-q42; a majority (90%) showed higher expression in stage 4s NB.
For all expressed genes mapped to nearby enhancers, the Pearson correlation coefficient was calculated between the H3K27ac and p63 ChIP-seq read counts at the associated enhancers (normalized for per-sample total read count) and the gene body RNAPII RPKM score across the four differentiation stages.
There were 12 transcripts exclusively expressed in cases (mapped to 12 unique genes) and 8 transcripts exclusively expressed in controls (mapped to 8 unique genes) (Table S2).
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